Citrus Sinensis ID: 005860

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670---
Protein Sequence
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLRYT
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccEEEEEEccccccHHHHHHHHHccHHHHcccccEEEEEEcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccEEEEEEccccccccccHHHHHHHHcccccccEEEEEcccHHHHHHcccccEEEccccccccccccccHHHHHHHHHHHcccccHHHHHHHHccccccccccccccHHHHHccccccccHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccccccccccccEEEEEEcHHHHHHHHHHHHccEEEEEEccccccccccccccccEEEEEEEcccccccccccccccccEEEEEccccccccHHHHHHHHHcccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccEEEEcccccccccccccccccccccccEEEcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHcHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHccccccccccEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEcccHHHHHHHHHHHccccccccccEEEEEEEccccccHHHHHHHHHccHHHHHHccEEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHHHHHccccccEEEEEEccHHHHHHHccccccccccccHcccccccHHHHHHHHHHHHHccccHHHHHHHHHcHHHccccccccccHHHHEcHccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEHHHHHHHHHHHHcccEEEEEEcccccccccccccccccEEEEEEEcccccccHHHHHHcccccEEEcccccccccccccHHHHHHHcccEEEEEEcccccccccccHHHccccHHcHHHHHEEEccccccccccHHHHHHHHHHEEEccccHHHHHccHHHHcccccEEEEccccccccccccccccHHHccccEEEEcccccccHHHHHHHHccccc
Coil and Loop (DISEMBL)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGvdalvpqrkvcsflpaascfgfsqtfQRRDIAVKIKAINgklddiakqkdmynfnvirstenseriqstslidvseirgrdeeksslksKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFayndsdvfeYFDKRMwvcvsdpfDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDmwtddyskwepfhyclkngvrgskILVTTRKETVARMMESIHVISIKElseqecwckglpLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPlllsyndlppmiKRCFQYYELIKLWMaqdyimpegNKELEIIGEEYFDYLAMRSFFQEFfkdnegvvvrCKMHDIVHDFAQFLtkneciaievdddeeplsLINTYQEKLRHSMLVLgyeasfpisiFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMntwdvnstNKILKGIEKLIHLRYLRLvglgteelpETCCELLNLQVLEIeqctslkrlplgigklvnlrhltyddsclefIPKGIQRLTNLRTLSEFVVVrggskyggkacnleglryt
Flexible Loop (DISEMBL)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAingklddiakqkdmYNFNVirstenseriqstslidvseirgrdeeksslkskllCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHyclkngvrgskiLVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATlmntwdvnstnKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEfvvvrggskyggkacnleglryt
Low Complexity Region (SEG)
MVDAIVSPlleqlisisleeAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDeeksslkskllcesseeiindiqiitiVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGlgteelpetccellNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLRYT
Disordered region (IsUnstruct)
****IVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIR*********************************LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLE*****
Disordered Region (DISOPRED)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARL**********************ASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDM************************EIRGRDEEKSSLKSK***********DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALE***********LLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR**
Disordered Region (DISEMBL)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEI*************LLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLRYT
Disordered Region (DISPRO)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFN***************LIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEG****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLRYT
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	673	2.2.26 [Sep-21-2011]
Q7XA40	992	Putative disease resistan	N/A	no	0.895	0.607	0.322	2e-90
Q7XBQ9	970	Disease resistance protei	N/A	no	0.891	0.618	0.315	7e-89
Q7XA39	988	Putative disease resistan	N/A	no	0.894	0.609	0.311	2e-86
Q7XA42	979	Putative disease resistan	N/A	no	0.893	0.613	0.304	2e-84
Q9LRR4	1054	Putative disease resistan	yes	no	0.933	0.595	0.304	6e-80
Q9LRR5	1424	Putative disease resistan	no	no	0.869	0.410	0.303	1e-69
Q38834	852	Disease resistance RPP13-	no	no	0.916	0.724	0.263	4e-46
Q39214	926	Disease resistance protei	no	no	0.833	0.605	0.256	5e-41
P59584	910	Disease resistance protei	no	no	0.818	0.605	0.269	4e-35
P0C8S1	906	Probable disease resistan	no	no	0.812	0.603	0.263	3e-33

>sp|Q7XA40|RGA3_SOLBU Putative disease resistance protein RGA3 OS=Solanum bulbocastanum GN=RGA3 PE=2 SV=2

 Score =  333 bits (854), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 233/722 (32%), Positives = 364/722 (50%), Gaps = 119/722 (16%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A +  LL+ L        + ++ LV G + E  KL   F  IQAVL DA+++Q K +
Sbjct: 1   MAEAFLQVLLDNLTFF----IQGELGLVFGFEKEFKKLSSMFSMIQAVLEDAQEKQLKYK 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNT--ARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQ 118
            ++ WL +L   +Y + D+LD+  T  AR K  + G            + P    F +  
Sbjct: 57  AIKNWLQKLNVAAYEVDDILDDCKTEAARFKQAVLG-----------RYHPRTITFCYK- 104

Query: 119 TFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEK 178
                 +  ++K +  KLD IA+++  ++ +       + R Q+  ++   ++ GR++E+
Sbjct: 105 ------VGKRMKEMMEKLDAIAEERRNFHLDERIIERQAARRQTGFVLTEPKVYGREKEE 158

Query: 179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP 238
             +   L+   S     ++ ++ I+GMGG+GKTTLAQ  +ND  + E+F+ ++WVCVSD 
Sbjct: 159 DEIVKILINNVSYS--EEVPVLPILGMGGLGKTTLAQMVFNDQRITEHFNLKIWVCVSDD 216

Query: 239 FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHY 298
           FDE R+ KAI+E++EG      +L  L + ++  L GK++ L+LDD+W +D  KW+    
Sbjct: 217 FDEKRLIKAIVESIEGKSLGDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQEKWDNLRA 276

Query: 299 CLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW------------------- 339
            LK G  G+ IL+TTR E +  +M ++ +  +  LS+++CW                   
Sbjct: 277 VLKIGASGASILITTRLEKIGSIMGTLQLYQLSNLSQEDCWLLFKQRAFCHQTETSPKLM 336

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                    C G+PLAAKT+G LLRFKR   EWE + DSE+W L + E  +L  L LSY+
Sbjct: 337 EIGKEIVKKCGGVPLAAKTLGGLLRFKREESEWEHVRDSEIWNLPQDENSVLPALRLSYH 396

Query: 391 DLPPMIKRCFQYYE------------LIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
            LP  +++CF Y              LI LWMA  +++ +GN ELE +G E ++ L +RS
Sbjct: 397 HLPLDLRQCFAYCAVFPKDTKIEKEYLIALWMAHSFLLSKGNMELEDVGNEVWNELYLRS 456

Query: 439 FFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIA-----IEVDDDEEPLSLINTYQEK 493
           FFQE   + +      KMHD++HD A  +      +     I V DDE+ + ++  Y++ 
Sbjct: 457 FFQEI--EVKSGKTYFKMHDLIHDLATSMFSASASSRSIRQINVKDDEDMMFIVTNYKD- 513

Query: 494 LRHSMLVLGYE---ASFPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALR 549
               M+ +G+    +S+  S+FK   +LR L ++N            S F+QL       
Sbjct: 514 ----MMSIGFSEVVSSYSPSLFKRFVSLRVLNLSN------------SEFEQLP------ 551

Query: 550 IATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSL 609
                              +  L+HLRYL L G     LP+  C+L NLQ L++  C SL
Sbjct: 552 -----------------SSVGDLVHLRYLDLSGNKICSLPKRLCKLQNLQTLDLYNCQSL 594

Query: 610 KRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVV-RGGSKYGG-KACNL 667
             LP    KL +LR+L  D   L  +P  I  LT L+TL  FVV  R G + G  +  NL
Sbjct: 595 SCLPKQTSKLCSLRNLVLDHCPLTSMPPRIGLLTCLKTLGYFVVGERKGYQLGELRNLNL 654

Query: 668 EG 669
            G
Sbjct: 655 RG 656

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.
Solanum bulbocastanum (taxid: 147425)

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score =  328 bits (842), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 224/711 (31%), Positives = 350/711 (49%), Gaps = 111/711 (15%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A +  LL+ L S      + ++ L+ G  +E  +L   F  IQAVL DA+++Q   +
Sbjct: 1   MAEAFIQVLLDNLTSF----LKGELVLLFGFQDEFQRLSSMFSTIQAVLEDAQEKQLNNK 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
            +  WL +L   +Y + D+LDE+ T   +           Q +   + P    F      
Sbjct: 57  PLENWLQKLNAATYEVDDILDEYKTKATRFS---------QSEYGRYHPKVIPF------ 101

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            R  +  ++  +  KL  IA+++  ++ +       + R ++ S++   ++ GRD+EK  
Sbjct: 102 -RHKVGKRMDQVMKKLKAIAEERKNFHLHEKIVERQAVRRETGSVLTEPQVYGRDKEKDE 160

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +   L+   S+     + ++ I+GMGG+GKTTLAQ  +ND  V E+F  ++W+CVS+ FD
Sbjct: 161 IVKILINNVSDA--QHLSVLPILGMGGLGKTTLAQMVFNDQRVTEHFHSKIWICVSEDFD 218

Query: 241 ELRIAKAIIEALEGFVPTVGELN--SLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHY 298
           E R+ KAI+E++EG  P +GE++   L + ++  L GK++LL+LDD+W +D  KW     
Sbjct: 219 EKRLIKAIVESIEG-RPLLGEMDLAPLQKKLQELLNGKRYLLVLDDVWNEDQQKWANLRA 277

Query: 299 CLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW------------------- 339
            LK G  G+ +L TTR E V  +M ++    +  LS+++CW                   
Sbjct: 278 VLKVGASGASVLTTTRLEKVGSIMGTLQPYELSNLSQEDCWLLFMQRAFGHQEEINPNLV 337

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                      G+PLAAKT+G +L FKR    WE + DS +W L + E  +L  L LSY+
Sbjct: 338 AIGKEIVKKSGGVPLAAKTLGGILCFKREERAWEHVRDSPIWNLPQDESSILPALRLSYH 397

Query: 391 DLPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
            LP  +K+CF Y             +LI LWMA  +++ +GN ELE +G+E +  L +RS
Sbjct: 398 QLPLDLKQCFAYCAVFPKDAKMEKEKLISLWMAHGFLLSKGNMELEDVGDEVWKELYLRS 457

Query: 439 FFQEF-FKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHS 497
           FFQE   KD +      KMHD++HD A  L          +     +  IN +       
Sbjct: 458 FFQEIEVKDGKTYF---KMHDLIHDLATSL-------FSANTSSSNIREINKHSYT---H 504

Query: 498 MLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTW 557
           M+ +G+                        +V   + L  L ++   LR L +       
Sbjct: 505 MMSIGF-----------------------AEVVFFYTLPPL-EKFISLRVLNLGD----- 535

Query: 558 DVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIG 617
             ++ NK+   I  L+HLRYL L G G   LP+  C+L NLQ L+++ CT L  LP    
Sbjct: 536 --STFNKLPSSIGDLVHLRYLNLYGSGMRSLPKQLCKLQNLQTLDLQYCTKLCCLPKETS 593

Query: 618 KLVNLRHLTYDDS-CLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNL 667
           KL +LR+L  D S  L  +P  I  LT L+TL +FVV R      G+  NL
Sbjct: 594 KLGSLRNLLLDGSQSLTCMPPRIGSLTCLKTLGQFVVGRKKGYQLGELGNL 644

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA39|RGA4_SOLBU Putative disease resistance protein RGA4 OS=Solanum bulbocastanum GN=RGA4 PE=2 SV=1

 Score =  320 bits (821), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 222/712 (31%), Positives = 340/712 (47%), Gaps = 110/712 (15%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A +  LLE L S       +++ L+ G + E  KL   F  IQAVL DA+++Q K++
Sbjct: 1   MAEAFLQVLLENLTSF----IGDKLVLIFGFEKECEKLSSVFSTIQAVLQDAQEKQLKDK 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
            +  WL +L   +Y + D+L E     ++           Q ++  + P    F      
Sbjct: 57  AIENWLQKLNSAAYEVDDILGECKNEAIRFE---------QSRLGFYHPGIINF------ 101

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNF--NVIRSTENSERIQSTSLIDVSEIRGRDEEK 178
            R  I  ++K I  KLD I++++  ++F   +      +   ++  ++   ++ GRD+E+
Sbjct: 102 -RHKIGRRMKEIMEKLDAISEERRKFHFLEKITERQAAAATRETGFVLTEPKVYGRDKEE 160

Query: 179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP 238
             +   L+  ++  +  ++ +  I+GMGG+GKTTLAQ  +ND  V ++F+ ++WVCVSD 
Sbjct: 161 DEIVKILI--NNVNVAEELPVFPIIGMGGLGKTTLAQMIFNDERVTKHFNPKIWVCVSDD 218

Query: 239 FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHY 298
           FDE R+ K II  +E   P V +L S  + ++  L GK++LL+LDD+W DD  KW     
Sbjct: 219 FDEKRLIKTIIGNIERSSPHVEDLASFQKKLQELLNGKRYLLVLDDVWNDDLEKWAKLRA 278

Query: 299 CLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW------------------- 339
            L  G RG+ IL TTR E V  +M ++    +  LS  +                     
Sbjct: 279 VLTVGARGASILATTRLEKVGSIMGTLQPYHLSNLSPHDSLLLFMQRAFGQQKEANPNLV 338

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                    C G+PLAAKT+G LLRFKR   EWE + D+E+W L + E  +L  L LSY+
Sbjct: 339 AIGKEIVKKCGGVPLAAKTLGGLLRFKREESEWEHVRDNEIWSLPQDESSILPALRLSYH 398

Query: 391 DLPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
            LP  +++CF Y              LI LWMA  +++ +GN ELE +G E ++ L +RS
Sbjct: 399 HLPLDLRQCFAYCAVFPKDTKMIKENLITLWMAHGFLLSKGNLELEDVGNEVWNELYLRS 458

Query: 439 FFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSM 498
           FFQE    +       K+HD++HD A  L         + +       IN    K   S+
Sbjct: 459 FFQEIEAKSGNTYF--KIHDLIHDLATSLFSASASCGNIRE-------INVKDYKHTVSI 509

Query: 499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD 558
                 +S+  S+ K       F++  ++ +S + + Q                      
Sbjct: 510 GFAAVVSSYSPSLLKK------FVSLRVLNLSYSKLEQ---------------------- 541

Query: 559 VNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGK 618
                 +   I  L+HLRYL L       LPE  C+L NLQ L++  C SL  LP    K
Sbjct: 542 ------LPSSIGDLLHLRYLDLSCNNFRSLPERLCKLQNLQTLDVHNCYSLNCLPKQTSK 595

Query: 619 LVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGL 670
           L +LRHL  D   L   P  I  LT L+TL  F+V   GSK G +   L+ L
Sbjct: 596 LSSLRHLVVDGCPLTSTPPRIGLLTCLKTLGFFIV---GSKKGYQLGELKNL 644

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA42|RGA1_SOLBU Putative disease resistance protein RGA1 OS=Solanum bulbocastanum GN=RGA1 PE=2 SV=2

 Score =  314 bits (804), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 218/715 (30%), Positives = 345/715 (48%), Gaps = 114/715 (15%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A +  +L+ L S      + ++ L+ G  +E  +L   F  IQAVL DA+++Q  ++
Sbjct: 1   MAEAFIQVVLDNLTSF----LKGELVLLFGFQDEFQRLSSMFSTIQAVLEDAQEKQLNDK 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
            +  WL +L   +Y + D+LDE+ T   +           Q +   + P    F      
Sbjct: 57  PLENWLQKLNAATYEVDDILDEYKTKATRFL---------QSEYGRYHPKVIPF------ 101

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            R  +  ++  +  KL+ IA+++  ++         +   ++ S++   ++ GRD+EK  
Sbjct: 102 -RHKVGKRMDQVMKKLNAIAEERKKFHLQEKIIERQAATRETGSVLTEPQVYGRDKEKDE 160

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +   L+  +S+     + ++ I+GMGG+GKTTL+Q  +ND  V E F  ++W+C+SD F+
Sbjct: 161 IVKILINTASDA--QKLSVLPILGMGGLGKTTLSQMVFNDQRVTERFYPKIWICISDDFN 218

Query: 241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
           E R+ KAI+E++EG   +  +L  L + ++  L GK++ L+LDD+W +D  KW      L
Sbjct: 219 EKRLIKAIVESIEGKSLSDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQHKWANLRAVL 278

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW--------------------- 339
           K G  G+ +L TTR E V  +M ++    +  LS ++CW                     
Sbjct: 279 KVGASGAFVLTTTRLEKVGSIMGTLQPYELSNLSPEDCWFLFMQRAFGHQEEINPNLMAI 338

Query: 340 -------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDL 392
                  C G+PLAAKT+G +LRFKR   EWE + DS +W L + E  +L  L LSY+ L
Sbjct: 339 GKEIVKKCGGVPLAAKTLGGILRFKREEREWEHVRDSPIWNLPQDESSILPALRLSYHHL 398

Query: 393 PPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFF 440
           P  +++CF Y              LI  WMA  +++ +GN ELE +G E ++ L +RSFF
Sbjct: 399 PLDLRQCFVYCAVFPKDTKMAKENLIAFWMAHGFLLSKGNLELEDVGNEVWNELYLRSFF 458

Query: 441 QEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLV 500
           QE   + E      KMHD++HD A  L                    NT           
Sbjct: 459 QEI--EVESGKTYFKMHDLIHDLATSLFS-----------------ANT----------- 488

Query: 501 LGYEASFPISIFKAKNLRSLFIN--NTLIQVSLTHVLQSLFDQ-LKCLRALRIATLMNTW 557
                        + N+R +  N    ++ +    V+ S     L+   +LR+  L N+ 
Sbjct: 489 ------------SSSNIREINANYDGYMMSIGFAEVVSSYSPSLLQKFVSLRVLNLRNS- 535

Query: 558 DVNSTNKILKGIEKLIHLRYLRLVG-LGTEELPETCCELLNLQVLEIEQCTSLKRLPLGI 616
              + N++   I  L+HLRYL L G      LP+  C+L NLQ L++  C SL  LP   
Sbjct: 536 ---NLNQLPSSIGDLVHLRYLDLSGNFRIRNLPKRLCKLQNLQTLDLHYCDSLSCLPKQT 592

Query: 617 GKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVV-VRGGSKYGG-KACNLEG 669
            KL +LR+L  D   L   P  I  LT L++LS FV+  R G + G  K  NL G
Sbjct: 593 SKLGSLRNLLLDGCSLTSTPPRIGLLTCLKSLSCFVIGKRKGHQLGELKNLNLYG 647

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q9LRR4|R13L1_ARATH Putative disease resistance RPP13-like protein 1 OS=Arabidopsis thaliana GN=RPPL1 PE=3 SV=1

 Score =  299 bits (765), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 221/725 (30%), Positives = 353/725 (48%), Gaps = 97/725 (13%)

Query: 4   AIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVR 63
           A +  L + L+S   E  R   K     +N + +L    L I AVL+DAE++Q     V 
Sbjct: 11  AFLQALFQTLVS---EPFRSFFKRRELNENLLERLSTALLTITAVLIDAEEKQITNPVVE 67

Query: 64  LWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRR 123
            W+++L+DV Y+  D LD+  T  L+L I G ++    R     L      G        
Sbjct: 68  KWVNELRDVVYHAEDALDDIATEALRLNI-GAESSSSNR--LRQLRGRMSLGDFLDGNSE 124

Query: 124 DIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSSLKS 183
            +  +++ +  +L+ +A Q+++     + +    +R+ +TSL+D SE+ GRD++K  +  
Sbjct: 125 HLETRLEKVTIRLERLASQRNILGLKELTAMIPKQRLPTTSLVDESEVFGRDDDKDEIMR 184

Query: 184 KLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR 243
            L+ E+ ++  N I ++ IVG+GG+GKTTL+Q  YND  V  YF  ++W  VS+ FD  +
Sbjct: 185 FLIPENGKD--NGITVVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFK 242

Query: 244 IAKAIIEALEGFVPTVGELNSLLESIRASLVGK--KFLLILDDMWTDDYSKWEPFHYCLK 301
           I K + E++        +L+ L   ++  L G    FLL+LDD+W ++++ W+       
Sbjct: 243 ITKKVYESVTSRPCEFTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFI 302

Query: 302 NGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW---------------------- 339
           +  +GS+ILVTTR + VA +M ++HV +++ LS+ +CW                      
Sbjct: 303 HAAQGSQILVTTRSQRVASIMCAVHVHNLQPLSDGDCWSLFMKTVFGNQEPCLNREIGDL 362

Query: 340 -------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDL 392
                  C+GLPLA KT+G +LRF+    EWE +L S +W L   +  LL  L +SY  L
Sbjct: 363 AERIVHKCRGLPLAVKTLGGVLRFEGKVIEWERVLSSRIWDLPADKSNLLPVLRVSYYYL 422

Query: 393 PPMIKRCFQYY------------ELIKLWMAQDYI-MPEGNKELEIIGEEYFDYLAMRSF 439
           P  +KRCF Y             +++ LWMA+ ++     +K LE +G EYF  L  RS 
Sbjct: 423 PAHLKRCFAYCSIFPKGHAFEKDKVVLLWMAEGFLQQTRSSKNLEELGNEYFSELESRSL 482

Query: 440 FQEFFKDNEGVVVRCKMHDIVHDFAQFLTK------NECIAIEVDDDEEPLS-LINTYQE 492
            Q+          R  MHD +++ AQF +        +   ++V +    LS L + Y E
Sbjct: 483 LQK-------TKTRYIMHDFINELAQFASGEFSSKFEDGCKLQVSERTRYLSYLRDNYAE 535

Query: 493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQS-LFDQ------LKCL 545
            +        +EA           LR +    T + +SLT+  +S   DQ      L  L
Sbjct: 536 PME-------FEA-----------LREVKFLRTFLPLSLTNSSRSCCLDQMVSEKLLPTL 577

Query: 546 RALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQ 605
             LR+ +L +           K I    H R+L L     E+LP++ C + NLQ L +  
Sbjct: 578 TRLRVLSLSHYKIARLPPDFFKNIS---HARFLDLSRTELEKLPKSLCYMYNLQTLLLSY 634

Query: 606 CTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKAC 665
           C+SLK LP  I  L+NLR+L    + L  +P+   RL +L+TL+ F V    +  G +  
Sbjct: 635 CSSLKELPTDISNLINLRYLDLIGTKLRQMPRRFGRLKSLQTLTTFFV---SASDGSRIS 691

Query: 666 NLEGL 670
            L GL
Sbjct: 692 ELGGL 696

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LRR5|DRL21_ARATH Putative disease resistance protein At3g14460 OS=Arabidopsis thaliana GN=At3g14460 PE=3 SV=1

 Score =  264 bits (675), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 205/675 (30%), Positives = 321/675 (47%), Gaps = 90/675 (13%)

Query: 37  KLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVD 96
           +LK   +    VL DA+QR      V+ WL  +KD  +   D+LDE  T  L+ R+    
Sbjct: 38  RLKVALVTANPVLADADQRAEHVREVKHWLTGIKDAFFQAEDILDELQTEALRRRVVAE- 96

Query: 97  ALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAK--QKDMYNFNVIRST 154
                        A    G  Q       A++ K I  K++ + +  +  + +  VI   
Sbjct: 97  -------------AGGLGGLFQNLMAGREAIQ-KKIEPKMEKVVRLLEHHVKHIEVIGLK 142

Query: 155 ENSE------RIQSTSLID---VSEIRGRDEEKSSLKSKLLCESSEEI-INDIQIITIVG 204
           E SE      R  S S  D      + GR E+K +L + LL  S +EI I    +I++VG
Sbjct: 143 EYSETREPQWRQASRSRPDDLPQGRLVGRVEDKLALVNLLL--SDDEISIGKPAVISVVG 200

Query: 205 MGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNS 264
           M G+GKTTL +  +ND  V E+F+ +MW+     F+   + KA+++ +        +L S
Sbjct: 201 MPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDITSSAVNTEDLPS 260

Query: 265 LLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMES 324
           L   ++ +L GK+FLL+LDD W++  S+WE F     +   GSKI++TTR E V+ + ++
Sbjct: 261 LQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAEEGSKIVLTTRSEIVSTVAKA 320

Query: 325 IHVISIKELSEQECW------------------------------CKGLPLAAKTIGSLL 354
             +  +K ++ +ECW                              CKGLPLAA+ I S L
Sbjct: 321 EKIYQMKLMTNEECWELISRFAFGNISVGSINQELEGIGKRIAEQCKGLPLAARAIASHL 380

Query: 355 RFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYY----------- 403
           R K   ++W ++  +       +   +L  L LSY+ LPP +KRCF              
Sbjct: 381 RSKPNPDDWYAVSKN----FSSYTNSILPVLKLSYDSLPPQLKRCFALCSIFPKGHVFDR 436

Query: 404 -ELIKLWMAQDYI-MPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVH 461
            EL+ LWMA D +  P  ++ LE IG +Y   L  +SFFQ      +  +    MHD+++
Sbjct: 437 EELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQRL----DITMTSFVMHDLMN 492

Query: 462 DFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLF 521
           D A+ ++ + C  +E D+  E  S    +          + +      SI  A+ LR++ 
Sbjct: 493 DLAKAVSGDFCFRLEDDNIPEIPSTTRHFSFSRSQCDASVAFR-----SICGAEFLRTIL 547

Query: 522 INNTLIQVSLTHVLQSLFDQL-KCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRL 580
             N+   +    + + + + L   L  LRI +L + + + +  K LKG+ KL  LRYL L
Sbjct: 548 PFNSPTSLESLQLTEKVLNPLLNALSGLRILSLSH-YQITNLPKSLKGL-KL--LRYLDL 603

Query: 581 VGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQ 640
                +ELPE  C L NLQ L +  C  L  LP  I +L+NLR L    + L  +P GI+
Sbjct: 604 SSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDLVGTPLVEMPPGIK 663

Query: 641 RLTNLRTLSEFVVVR 655
           +L +L+ LS FV+ R
Sbjct: 664 KLRSLQKLSNFVIGR 678

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38834|R13L4_ARATH Disease resistance RPP13-like protein 4 OS=Arabidopsis thaliana GN=RPP13L4 PE=2 SV=2

 Score =  186 bits (473), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 188/714 (26%), Positives = 315/714 (44%), Gaps = 97/714 (13%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           MVDA+V+  LE+ ++I  E+ R     V     ++  L+     +Q+ L DAE+++   E
Sbjct: 1   MVDAVVTVFLEKTLNILEEKGRT----VSDYRKQLEDLQSELKYMQSFLKDAERQKRTNE 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
           T+R  +  L+++ Y   D+L +   A      +G D    QR   ++L           +
Sbjct: 57  TLRTLVADLRELVYEAEDILVDCQLA------DGDDG-NEQRSSNAWLSRLHPARVPLQY 109

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRST----ENSERIQSTSLIDVSEIRGRDE 176
           ++   + +++ IN ++  I  Q + Y F  I  +    +N     S+ + D +++ G + 
Sbjct: 110 KK---SKRLQEINERITKIKSQVEPY-FEFITPSNVGRDNGTDRWSSPVYDHTQVVGLEG 165

Query: 177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS 236
           +K  +K  L   +  +++    I+  VGMGG+GKTT+AQ  +ND ++   F++R+WV VS
Sbjct: 166 DKRKIKEWLFRSNDSQLL----IMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVS 221

Query: 237 DPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPF 296
             F E +I ++I+  L G      ++ +LL  I+  L+GK++L+++DD+W  + S W+  
Sbjct: 222 QTFTEEQIMRSILRNL-GDASVGDDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKI 280

Query: 297 HYCLKNGVRGSKILVTTRKETVARMMESIHVISIKE--LSEQECW--------------- 339
           +  L  G +G  ++VTTR E+VA+ +++    + +   LS    W               
Sbjct: 281 YQGLPRG-QGGSVIVTTRSESVAKRVQARDDKTHRPELLSPDNSWLLFCNVAFAANDGTC 339

Query: 340 ---------------CKGLPLAAKTIGSLLRFK-RTREEWESILD---SELWQLEEFEKG 380
                          CKGLPL  K +G LL  K     EW  I +    EL         
Sbjct: 340 ERPELEDVGKEIVTKCKGLPLTIKAVGGLLLCKDHVYHEWRRIAEHFQDELRGNTSETDN 399

Query: 381 LLAPLLLSYNDLPPMIKRC------------FQYYELIKLWMAQDYIMPEGNKELEIIGE 428
           +++ L LSY++LP  +K C                +L+  W+ + ++M    +     GE
Sbjct: 400 VMSSLQLSYDELPSHLKSCILTLSLYPEDCVIPKQQLVHGWIGEGFVMWRNGRSATESGE 459

Query: 429 EYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLIN 488
           + F  L  R   +   K   G ++ CK+HD+V D    + K +             S  N
Sbjct: 460 DCFSGLTNRCLIEVVDKTYSGTIITCKIHDMVRDLVIDIAKKD-------------SFSN 506

Query: 489 TYQEKLRHSMLVLGYEASFPISIFKAKN-LRSLFINNTLIQVS-LTHVLQSLFDQLKCLR 546
                 RH    LG   +F     K  + LR +       +V+ L   L   F   K LR
Sbjct: 507 PEGLNCRH----LGISGNFDEKQIKVNHKLRGVVSTTKTGEVNKLNSDLAKKFTDCKYLR 562

Query: 547 ALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTE-ELPETCCELLNLQVLEIEQ 605
            L I+   + +D    ++IL  I  L HL  L L       + P +  +L NLQ+L+   
Sbjct: 563 VLDISK--SIFDA-PLSEILDEIASLQHLACLSLSNTHPLIQFPRSMEDLHNLQILDASY 619

Query: 606 CTSLKRLPLGIGKLVNLRHLTYDD-SCLEFIPKGIQRLTNLRTLSEFVVVRGGS 658
           C +LK+L   I     L  L   +   LE  PKGI  L  L  L  F   R  +
Sbjct: 620 CQNLKQLQPCIVLFKKLLVLDMTNCGSLECFPKGIGSLVKLEVLLGFKPARSNN 673

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score =  169 bits (429), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 172/671 (25%), Positives = 296/671 (44%), Gaps = 110/671 (16%)

Query: 27  LVVGIDNEVAKLKHNFLAIQAVLVDAEQR------QFKEETVRLWLDQLKDVSYYMGDVL 80
           L+ G+  E+ K+K   L +++ L D  +           +  + ++   +D++Y + D+L
Sbjct: 23  LLSGVHGEIDKMKKELLIMKSFLEDTHKHGGNGSTTTTTQLFQTFVANTRDLAYQIEDIL 82

Query: 81  DEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQ-TFQRRDIAVKIKAINGKLDDI 139
           DE+        I G        + C+ +  A  F F +  + R  IA K+  +N  +  I
Sbjct: 83  DEFG-----YHIHGY-------RSCAKIWRA--FHFPRYMWARHSIAQKLGMVNVMIQSI 128

Query: 140 AK------QKDMYNFNVIRSTENSE-----RIQSTSLI-DVSEIRGRDEEKSSLKSKLLC 187
           +         + Y   ++   ++ +      I  +SL    + + G D  K  L  +LL 
Sbjct: 129 SDSMKRYYHSENYQAALLPPIDDGDAKWVNNISESSLFFSENSLVGIDAPKGKLIGRLLS 188

Query: 188 ESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA 247
              + I+     + +VGMGG GKTTL+   +    V  +F+   WV +S  +    + + 
Sbjct: 189 PEPQRIV-----VAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRT 243

Query: 248 IIEAL--EGFVPTVGELNS-----LLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
           +I+    E       EL S     L+E +   L  K+++++LDD+WT     W      L
Sbjct: 244 MIKEFYKEADTQIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTTGL--WREISIAL 301

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVIS--IKELSEQECW------------------- 339
            +G+ GS++++TTR   VA     I      I+ L E E W                   
Sbjct: 302 PDGIYGSRVMMTTRDMNVASFPYGIGSTKHEIELLKEDEAWVLFSNKAFPASLEQCRTQN 361

Query: 340 -----------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFE--KGLLAPLL 386
                      C+GLPLA  ++GS++  K+   EW+ +  +  W+L      K + + + 
Sbjct: 362 LEPIARKLVERCQGLPLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMF 421

Query: 387 LSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMPEGNKELEIIGEEYFDYL 434
           LS+NDLP  +KRCF Y              LI++WMAQ ++ P    + E + + Y + L
Sbjct: 422 LSFNDLPYPLKRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNEL 481

Query: 435 AMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKL 494
             R+  Q    +  G     KMHD++ + A  ++K E      +DD +      T  E  
Sbjct: 482 VYRNMLQVILWNPFGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAET-MENY 540

Query: 495 RHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLM 554
               L +  E + P SI +A NL SL     L+  S  H ++ L   L  LRAL +    
Sbjct: 541 GSRHLCIQKEMT-PDSI-RATNLHSL-----LVCSSAKHKME-LLPSLNLLRALDL---- 588

Query: 555 NTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL 614
              + +S +K+   +  + +L+YL L     +ELP+   +L+NL+ L  +  + ++ LPL
Sbjct: 589 ---EDSSISKLPDCLVTMFNLKYLNLSKTQVKELPKNFHKLVNLETLNTKH-SKIEELPL 644

Query: 615 GIGKLVNLRHL 625
           G+ KL  LR+L
Sbjct: 645 GMWKLKKLRYL 655

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|P59584|RP8HA_ARATH Disease resistance protein RPH8A OS=Arabidopsis thaliana GN=RPH8A PE=3 SV=1

 Score =  150 bits (378), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 178/661 (26%), Positives = 284/661 (42%), Gaps = 110/661 (16%)

Query: 1   MVDAIVSPLLEQLISI-SLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKE 59
           M +  VS  LE+L  + S E  R Q     GID ++  LK    ++Q++L DA+ ++   
Sbjct: 1   MAEGFVSFGLEKLWDLLSRESERLQ-----GIDEQLDGLKRQLRSLQSLLKDADAKKHGS 55

Query: 60  ETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQT 119
           + VR +L+ +KD+ +   D+++ +   +L+   +GV   V  R++  FL           
Sbjct: 56  DRVRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHV--RRLARFLT---------- 103

Query: 120 FQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGR--DEE 177
             R  +A  I+ I  ++ ++  +   +    I     S  +Q    +   EIR    D  
Sbjct: 104 -DRHKVASDIEGITKRISEVIGEMQSFGIQQIIDGGRSLSLQERQRVQ-REIRQTYPDSS 161

Query: 178 KSSLK------SKLLCESSEEIINDI-QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKR 230
           +S L       ++L+C   E   ND+ Q+++I GMGGIGKTTLA+  ++   V  +FD  
Sbjct: 162 ESDLVGVEQSVTELVCHLVE---NDVHQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGF 218

Query: 231 MWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLE-SIRASLV----GKKFLLILDDM 285
            WVCVS  F +  + + I++ L+   P  GE+  + E +I+  L       ++L++LDD+
Sbjct: 219 AWVCVSQQFTQKHVWQRILQELQ---PHDGEILQMDEYTIQGKLFQLLETGRYLVVLDDV 275

Query: 286 WTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMME-SIHVISIKELSEQECW----- 339
           W  +   W+          RG K+L+T+R E V    + +        L+ +E W     
Sbjct: 276 WKKE--DWDRIKAVFPRK-RGWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCER 332

Query: 340 ---------------------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELW 372
                                      C GLPLA K +G LL  K T  EW+ + D+   
Sbjct: 333 IVFPRRDETEVRLDEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGS 392

Query: 373 QL-------EEFEKGLLAPLLLSYNDLPPMIKRCF----QYYELIKLWMAQ--DYIMPEG 419
           Q+       +     +   L LSY DLP  +K CF     Y E  K++     +Y   EG
Sbjct: 393 QIVGGSCLDDNSLNSVYRILSLSYEDLPTHLKHCFLHLAHYPEDSKIYTQDLFNYWAAEG 452

Query: 420 ---NKELEIIGEEYFDYLAMRSFFQEFFKDN-----EGVVVRCKMHDIVHDFAQFLTKNE 471
                 ++  GE Y + L  R+       DN     E  +  C+MHD++ +      K E
Sbjct: 453 IYDGSTIQDSGEYYLEELVRRNL---VIADNRYLISEFKIKNCQMHDMMREVCLSKAKEE 509

Query: 472 CIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAK-NLRSLFINNTLIQVS 530
              +++  D    S IN  Q   R   L +    +F I   K    +RSL ++    +  
Sbjct: 510 NF-LQIIKDPTCTSTINA-QSPSRSRRLSIHSGKAFHILGHKRNAKVRSLIVSR--FEED 565

Query: 531 LTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE 590
                 S+F  L  LR L +     +W      K+   I  LIHLRYLRL G     LP 
Sbjct: 566 FWIRSASVFHNLTLLRVLDL-----SWVKFEGGKLPCSIGGLIHLRYLRLYGAVVSHLPS 620

Query: 591 T 591
           T
Sbjct: 621 T 621

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to RPP8, it does not specifically recognize the Emco5 avirulence protein from Hyaloperonospora parasitica.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8S1|RP8L2_ARATH Probable disease resistance RPP8-like protein 2 OS=Arabidopsis thaliana GN=RPP8L2 PE=1 SV=1

 Score =  144 bits (362), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 174/661 (26%), Positives = 280/661 (42%), Gaps = 114/661 (17%)

Query: 1   MVDAIVSPLLEQLISI-SLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKE 59
           M +A+VS  +E+L  + S E AR     + GID +V  LK     +Q++L DA+ ++ + 
Sbjct: 1   MAEAVVSFGVEKLWELLSRESAR-----LNGIDEQVDGLKRQLGRLQSLLKDADAKKNET 55

Query: 60  ETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQT 119
           E VR +L+ +KD+ Y   D+++ +    L+ + +G+   V  R +  FL           
Sbjct: 56  ERVRNFLEDVKDIVYDADDIIESFLLNELRGKEKGIKKQV--RTLACFL----------- 102

Query: 120 FQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVS-EIRGRDEEK 178
             RR  A  I+ I  ++ ++     M +  +    +   R  S SL +   EIR      
Sbjct: 103 VDRRKFASDIEGITKRISEVIV--GMQSLGIQHIADGGGR--SLSLQERQREIRQTFSRN 158

Query: 179 SSLKSKLLCESSEEII-----ND-IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMW 232
           S      L +S EE++     ND +Q++++ GMGGIGKTTLA+  ++   V  +FD   W
Sbjct: 159 SESDLVGLDQSVEELVDHLVENDSVQVVSVSGMGGIGKTTLARQVFHHDIVRRHFDGFSW 218

Query: 233 VCVSDPFDELRIAKAIIEALEGFVPTV---------GELNSLLESIRASLVGKKFLLILD 283
           VCVS  F    + + I++ L  +   +         GEL  LLES R       +LL+LD
Sbjct: 219 VCVSQQFTRKDVWQRILQDLRPYDEGIIQMDEYTLQGELFELLESGR-------YLLVLD 271

Query: 284 DMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMME-SIHVISIKELSEQECW--- 339
           D+W ++   W+       +  RG K+L+T+R E +    + +      + L+ ++ W   
Sbjct: 272 DVWKEE--DWDRIKAVFPHK-RGWKMLLTSRNEGLGLHADPTCFAFRPRILTPEQSWKLF 328

Query: 340 --------------------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQ 373
                                     C GLPLA K +G LL  K T  EW+ +  + +  
Sbjct: 329 ERIVSSRRDKTEFKVDEAMGKEMVTYCGGLPLAVKVLGGLLAKKHTVLEWKRVHSNIVTH 388

Query: 374 L-------EEFEKGLLAPLLLSYNDLPPMIKRCFQYYE------------LIKLWMAQDY 414
           +       ++    +   L LSY DLP  +K CF Y              L   W+A+  
Sbjct: 389 IVGKSGLSDDNSNSVYRVLSLSYEDLPMQLKHCFFYLAHFPEDYKIDVKILFNYWVAEGI 448

Query: 415 IMP-EGNKELEIIGEEYFDYLAMRSF--FQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNE 471
           I P      ++  GE Y + L  R+    +E +  +   +  C+MHD++ +      K E
Sbjct: 449 ITPFHDGSTIQDTGESYLEELVRRNMVVVEESYLTSR--IEYCQMHDMMREVCLSKAKEE 506

Query: 472 CIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFK-AKNLRSLFINNTLIQVS 530
                V       + IN  Q   R   LVL    +  +   K  K  RS+ I     +  
Sbjct: 507 NFIRVVKVPTTTSTTINA-QSPCRSRRLVLHSGNALHMLGHKDNKKARSVLIFGVEEKFW 565

Query: 531 LTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE 590
                Q       CL  LR+  L  ++      K+   I  LIHLR+L L   G   LP 
Sbjct: 566 KPRGFQ-------CLPLLRVLDL--SYVQFEGGKLPSSIGDLIHLRFLSLYEAGVSHLPS 616

Query: 591 T 591
           +
Sbjct: 617 S 617

Potential disease resistance protein.

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	673
224122712	945	cc-nbs-lrr resistance protein [Populus t	0.973	0.693	0.466	1e-173
224114824	941	cc-nbs-lrr resistance protein [Populus t	0.943	0.674	0.466	1e-166
224134406	987	cc-nbs-lrr resistance protein [Populus t	0.943	0.643	0.439	1e-160
359482790	923	PREDICTED: putative disease resistance p	0.965	0.704	0.437	1e-159
359482784	919	PREDICTED: putative disease resistance p	0.968	0.709	0.435	1e-157
359482792	922	PREDICTED: putative disease resistance p	0.961	0.701	0.428	1e-157
359482794	880	PREDICTED: putative disease resistance p	0.974	0.745	0.440	1e-157
359482800	1006	PREDICTED: putative disease resistance p	0.965	0.646	0.445	1e-155
224122696	906	cc-nbs-lrr resistance protein [Populus t	0.904	0.672	0.439	1e-155
147825450	927	hypothetical protein VITISV_000086 [Viti	0.971	0.705	0.438	1e-154

>gi|224122712|ref|XP_002318907.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859580|gb|EEE97127.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  614 bits (1584), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 336/721 (46%), Positives = 470/721 (65%), Gaps = 66/721 (9%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A++SP+LEQL +I  ++ +E++ LVVG+  +V KLK N L IQ+VL DA+++Q K++
Sbjct: 1   MAEALLSPILEQLTTIVAQQVQEEVNLVVGVKKQVDKLKSNLLDIQSVLEDADRKQVKDK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKV--CSFLPAASCFGFSQ 118
            VR W+D+LKD  Y M DVLDEW+TA L+ ++E  +     R+   CSFL  + CF F+Q
Sbjct: 61  AVRDWVDKLKDACYDMDDVLDEWSTAILRWKMEEAEENTHSRQKIRCSFL-GSPCFCFNQ 119

Query: 119 TFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEK 178
             +RRDIA+KIK ++ K+DDIAK++  Y F++ + T+  +R+ +TS +D S + GRD EK
Sbjct: 120 VVRRRDIALKIKEVSEKVDDIAKERAKYGFDLYKGTDELQRLTTTSFVDESSVIGRDGEK 179

Query: 179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP 238
            ++ SKLL ESS E   D+ +I++VG+GGIGKTTLAQ A+NDS+V  +F+K++WVCVS+P
Sbjct: 180 RNVVSKLLAESSHEA-RDVDVISLVGLGGIGKTTLAQLAFNDSEVTAHFEKKIWVCVSEP 238

Query: 239 FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHY 298
           FDE+RIAKAI+E LEG    + EL SLL+ +  S+ GK+ LL+LDD+WT+++ +WE    
Sbjct: 239 FDEIRIAKAILEQLEGRPTNLVELQSLLQGVSESITGKRLLLVLDDVWTENHGQWEQLKP 298

Query: 299 CLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW------------------- 339
            L    RGS+ILVTTRK+ VA MM + H I+I++LS++ C                    
Sbjct: 299 SLTGCARGSRILVTTRKDAVATMMGTDHRINIEKLSDEICRSIFNHVAFQERSEDERERL 358

Query: 340 ----------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKG-----LLAP 384
                     CKGLPLAAK +G L++ KRTREEWE +L SELW+L+E ++      +  P
Sbjct: 359 TDIGDKIANKCKGLPLAAKVLGGLMQSKRTREEWERVLSSELWRLDEVDRDQVESRIFIP 418

Query: 385 LLLSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMPEGNKELEIIGEEYFD 432
           LLLSY DLP +++RCF Y            YEL+K+WMAQ YI      ++E++GE YF 
Sbjct: 419 LLLSYYDLPSVVRRCFLYCAMFPKDYEMGKYELVKMWMAQGYIKETSGGDMELVGERYFH 478

Query: 433 YLAMRSFFQEFFKD-NEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQ 491
            LA RSFFQ+F  D  EG+  + KMHDIVHDFAQ++TKNEC+ ++V+      + + T  
Sbjct: 479 VLAARSFFQDFETDIFEGM--KFKMHDIVHDFAQYMTKNECLTVDVN--TLGGATVETSI 534

Query: 492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIA 551
           E++RH  +++  E SFP+SI KAK LRSL I+      SL   L  LF QL C+R+L ++
Sbjct: 535 ERVRHLSMMVSEETSFPVSIHKAKGLRSLLIDTR--DPSLGAALPDLFKQLTCIRSLNLS 592

Query: 552 TLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLK 610
                   +S  +I   + KLIHLR++ L   G  E LPET C+L NLQ L++  C SLK
Sbjct: 593 -------ASSIKEIPNEVGKLIHLRHVNLARCGELESLPETMCDLCNLQSLDVTWCRSLK 645

Query: 611 RLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGL 670
            LP  IGKL+ LRHL    S ++FIPKGI+R+T LRTL  F V  GG +   KA NL  L
Sbjct: 646 ELPNAIGKLIKLRHLRIYRSGVDFIPKGIERITCLRTLDVFKVC-GGGENESKAANLREL 704

Query: 671 R 671
           +
Sbjct: 705 K 705

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114824|ref|XP_002332291.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222832453|gb|EEE70930.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 326/699 (46%), Positives = 453/699 (64%), Gaps = 64/699 (9%)

Query: 22  REQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLD 81
           +E++ LV G+  +V KLK+N LAIQ+VL DA+++Q K++ +R W+D+LKDV Y M DVLD
Sbjct: 18  QEEVNLVGGVKKQVDKLKNNLLAIQSVLEDADRKQVKDKALRDWVDKLKDVCYDMDDVLD 77

Query: 82  EWNTARLKLRIEGVDALVPQRKV--CSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDI 139
           EW+TA L+ ++E  +   P RK   CSFL  +  F  +Q  QRRDIA+KIK +  K+DDI
Sbjct: 78  EWSTAILRWKMEEAEENTPSRKKIRCSFL-GSPFFCLNQVVQRRDIALKIKEVCEKVDDI 136

Query: 140 AKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQI 199
           AK++ MY F + R+T+  +RI STSL+D S + GRD+++ ++ SKLL ES +E   D+++
Sbjct: 137 AKERAMYGFELYRATDELQRITSTSLVDESSVIGRDDKREAVVSKLLGESIQEA-GDVEV 195

Query: 200 ITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTV 259
           I++VGMGGIGKTTLAQ A+ND +V  +F+K++WVCVSDPFDE+RI KAI+E LEG  P +
Sbjct: 196 ISLVGMGGIGKTTLAQLAFNDDEVTAHFEKKIWVCVSDPFDEVRIGKAILEQLEGRAPDL 255

Query: 260 GELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVA 319
            EL SLL+ +  S+ G++FLL+LDD+WT+++ +WE     L    RGS+ILVTTRK +VA
Sbjct: 256 VELQSLLQRVSESIKGERFLLVLDDVWTENHRQWEQLKPSLTGCARGSRILVTTRKHSVA 315

Query: 320 RMMESIHVISIKELSEQECW-----------------------------CKGLPLAAKTI 350
            MM + HVI++++LS++ C                              CKGLPLAAK +
Sbjct: 316 TMMGTGHVINLEKLSDEVCRSIFNHVAFQQRSKDERERLTDTGDKIANKCKGLPLAAKVL 375

Query: 351 GSLLRFKRTREEWESILDSELWQLEE-----FEKGLLAPLLLSYNDLPPMIKRCFQY--- 402
           G L++ KRTREEWE +  SELW L+E      E+G+  PLLLSY DLP M++RCF Y   
Sbjct: 376 GGLMQSKRTREEWERVFCSELWGLDEVDRDQVERGIFLPLLLSYYDLPSMVRRCFLYCAM 435

Query: 403 ---------YELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVR 453
                    YEL+K+W+AQ Y+      ++E +GE+YF  LA RSFFQ+ FK  +   VR
Sbjct: 436 FPKDYEMRKYELVKMWIAQGYLKETSGGDMEAVGEQYFQVLAARSFFQD-FKTYDREDVR 494

Query: 454 CKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFK 513
            KMHDIVHDFAQ++TKNEC+ ++V++  E  + + T  E++RH  ++L  E  FP+SI K
Sbjct: 495 FKMHDIVHDFAQYMTKNECLTVDVNNLRE--ATVETSIERVRHLSMMLSKETYFPVSIHK 552

Query: 514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLI 573
           AK LRSLFI+       L   L  +F QL C+R+L ++       ++   +I   + KLI
Sbjct: 553 AKGLRSLFIDAR--DPWLGAALPDVFKQLTCIRSLNLS-------MSLIKEIPNEVGKLI 603

Query: 574 HLRYLRLVG-LGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCL 632
           HLR+L L      E LPE  C+L  LQ L++  C SL  LP  IGKL+ LRHL    S +
Sbjct: 604 HLRHLNLADCYKLESLPEIMCDLCKLQSLDVTTCRSLWELPKAIGKLIKLRHLRICGSIV 663

Query: 633 EFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
            F+PKGI+R+T LRTL  F V  GG +   KA NL  L+
Sbjct: 664 AFMPKGIERITCLRTLDWFAVC-GGGEDESKAANLRELK 701

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134406|ref|XP_002321815.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222868811|gb|EEF05942.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  570 bits (1469), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 320/728 (43%), Positives = 451/728 (61%), Gaps = 93/728 (12%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA+VS +LEQ+I+I+  +   ++KLVVG++ E+  LK+NF AI+ VL DAE++Q K+ 
Sbjct: 1   MADALVSTILEQIITIARHQVEHEVKLVVGVEKEIQHLKNNFQAIRDVLEDAERKQLKDT 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIE--------------------------- 93
            V+ WL+ LKDVSY M DVLDEW+TA LK  +E                           
Sbjct: 61  AVKHWLNNLKDVSYDMDDVLDEWSTAVLKWEMEEAENALAPKSVVFSFLRSCCFCFRRAE 120

Query: 94  -GVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIR 152
              +AL P+  V SFL  + C  F +  +R DIA KI  +  KL+DIAK+K M+ F + +
Sbjct: 121 QAENALAPKSVVSSFL-CSFCCSFRRVARRHDIAHKIIEVGQKLEDIAKRKAMFGFELHK 179

Query: 153 STENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTT 212
           + E     Q+TS +DVS + GR++EK ++ SKLLC+SS+E    +Q+I+IVGMGG+GKTT
Sbjct: 180 AIEKEPDRQTTSFVDVSRVHGREDEKKNVISKLLCDSSQE-GRKVQVISIVGMGGLGKTT 238

Query: 213 LAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRAS 272
           LAQ AYN  ++  YF+KR+WVCVS PFDE  +AKAIIE L G  P + EL  L + I  S
Sbjct: 239 LAQLAYNADEIKTYFEKRIWVCVSHPFDENTVAKAIIEDLSGAAPNLVELEPLCKRISES 298

Query: 273 LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKE 332
           + GKKFLL+LDD+W D+  KWEP    LK G  GS+ILVTTRK+TVA+MMES + + + +
Sbjct: 299 IEGKKFLLVLDDVWEDNPRKWEPLKESLKCGAPGSRILVTTRKDTVAKMMESDYSLLLGK 358

Query: 333 LSEQECW-----------------------------CKGLPLAAKTIGSLLRFKRTREEW 363
           L+++ECW                             CKGLPLAAKT+G L++ K T E+W
Sbjct: 359 LTDEECWSVFSQVAFYGRSQDACEMFTEIGRQIVYRCKGLPLAAKTLGGLMQSKTTTEDW 418

Query: 364 ESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYY------------ELIKLWMA 411
           ++IL +ELW++EE EKG+  PLLLSY DLP  I+ CF Y             +LIK+WMA
Sbjct: 419 DNILSNELWEIEEVEKGIFPPLLLSYYDLPVAIRSCFTYCAMFPKDHVMERGKLIKMWMA 478

Query: 412 QDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNE 471
           Q Y+    +KE+E++G+ YF+ LA R+FFQ+F + +E   ++ KMHDIVHDFAQFL K+E
Sbjct: 479 QGYLKASPSKEMELVGKGYFEILATRAFFQDFQETDED-SIKFKMHDIVHDFAQFLMKDE 537

Query: 472 CIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFI---NNTLIQ 528
           C  +E D  +   +   ++ E+ RH+++ +   A FP SI+KA  LRSL I   N+T I 
Sbjct: 538 CFTVETDVLKRQKT--ESFYERARHAIMTVSNWARFPQSIYKAGKLRSLLIRSFNDTAIS 595

Query: 529 VSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN--KILKGIEKLIHLRYLRLVGLG-T 585
             L  +L+ L             T +  +D++++   +I   + KL+HLRYL        
Sbjct: 596 KPLLELLRKL-------------TYLRLFDLSASQIEEIPSDVGKLLHLRYLDFSYCKWL 642

Query: 586 EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNL 645
           +ELPET  +L NLQ L++  C +LK+LP  + KL+ LRHL    S + F+P+GI+ LT+L
Sbjct: 643 KELPETISDLYNLQSLDLTWCVALKKLPQKMRKLIRLRHLEIFGSGVAFLPRGIEELTSL 702

Query: 646 RTLSEFVV 653
           RTL+ F+V
Sbjct: 703 RTLTNFIV 710

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482790|ref|XP_002268671.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  568 bits (1463), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 314/718 (43%), Positives = 451/718 (62%), Gaps = 68/718 (9%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA+VS +LE+L S+  ++  EQ+ LV G+ +E+  LK    +++ VL DAE+RQ K++
Sbjct: 1   MADALVSIVLERLTSVVEQQIHEQVSLVQGVKSEIQSLKKTLRSVRDVLEDAERRQVKDK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
           +V+ WL+ LKD++Y M DVLDEW+ A L+ ++EGV+     +K  SF   + C  F Q  
Sbjct: 61  SVQGWLESLKDMAYEMEDVLDEWSIAILQFQMEGVENASTSKKKVSFCMPSPCICFKQVA 120

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            RRDIA+KIK I  +LDDI +++  +NF   RS E  +R+ +TS ID+SE+ GRD +K  
Sbjct: 121 SRRDIALKIKGIKQQLDDIERERIRFNFVSSRSEERPQRLITTSAIDISEVYGRDMDKKI 180

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +   LL +  +E  + + I++IVG GG+GKTTLAQ AY+ S+V  +FD+R+WVCVSDP+D
Sbjct: 181 ILDHLLGKMCQE-KSGLYIVSIVGTGGMGKTTLAQLAYSHSEVKVHFDERIWVCVSDPYD 239

Query: 241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
            +R+ +AI+EAL+     + +L ++ + I+  + G+KFLL+LDD+WT+D   WE     L
Sbjct: 240 PIRVCRAIVEALQKKPCHLHDLEAVQQEIQTCIAGQKFLLVLDDVWTEDNQLWEQLKNTL 299

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVISIKELS--------------EQECW------- 339
             G  GS+IL TTRKE+V +MM + +   + ELS              E+  W       
Sbjct: 300 HCGAAGSRILATTRKESVVKMMRATYKHPLGELSSEQSRALFHQIAFYERSTWEKEEELK 359

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                    CKGLPLA KT+G+LLR K + EEW+++L+SE+WQL+EFE+ +   LLLSY 
Sbjct: 360 EIGEKIADKCKGLPLAIKTLGNLLRIKNSEEEWKNVLNSEVWQLDEFERDISPALLLSYY 419

Query: 391 DLPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
           DLPP I+RCF +             ELIKLWMAQ Y+  +G+KE+E++G  YF+YLA RS
Sbjct: 420 DLPPAIQRCFSFCAVFPKDSVIERDELIKLWMAQSYLKSDGSKEMEMVGRTYFEYLAARS 479

Query: 439 FFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSM 498
           FFQ+F KD++G ++ CKMHDIVHDFAQFLT NEC  +EVD+ ++    ++ + +K+RH+ 
Sbjct: 480 FFQDFEKDDDGNIIHCKMHDIVHDFAQFLTLNECFIVEVDNQKK--GSMDLFFQKIRHAT 537

Query: 499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD 558
           LV+        S    KNL +L           + VL++L   L CLRAL         D
Sbjct: 538 LVVRESTPNFASTCNMKNLHTLLAKRAFD----SRVLEAL-GHLTCLRAL---------D 583

Query: 559 VNSTN---KILKGIEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPL 614
           + S     ++ K + KLIHLRYL L    +  ELPET C+L NLQ L I+ C+ L++LP 
Sbjct: 584 LRSNQLIEELPKEVGKLIHLRYLNLSYCDSLRELPETICDLYNLQTLNIQACSRLQKLPQ 643

Query: 615 GIGKLVNLRHL-TYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
            +GKL+NLRHL  YD   L+ +PKGI RL++L+TL  F+V    S +G   C +E LR
Sbjct: 644 AMGKLINLRHLENYDADDLQGLPKGIGRLSSLQTLDVFIV----SSHGNDECQIEDLR 697

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482784|ref|XP_002269044.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 311/714 (43%), Positives = 454/714 (63%), Gaps = 62/714 (8%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA++S +LE+L S+  ++ R+++ LV+G++ E+  L     +++ VL DAE+RQ KE+
Sbjct: 1   MADALLSIVLERLASVVEQQIRDELTLVLGVEAEIQSLTDTLRSVRDVLEDAERRQVKEK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVD-ALVPQRKVCSFLPAASCFGFSQT 119
           +V+ WL++LKD++Y M DV+DEW+TA L+L+I+G + A + ++KV S +P+  CF   Q 
Sbjct: 61  SVQGWLERLKDMAYQMDDVVDEWSTAILQLQIKGAESASMSKKKVSSCIPSP-CFCLKQV 119

Query: 120 FQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKS 179
             RRDIA+KIK I  +LD IA Q+  +NF +   +E  +R  +TS +D+ E+ GRD +K+
Sbjct: 120 ASRRDIALKIKGIKQQLDVIASQRSQFNF-ISSLSEEPQRFITTSQLDIPEVYGRDMDKN 178

Query: 180 SLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF 239
           ++   LL E+ +E  +   II+IVG GG+GKTTLAQ AYN  +V  +FD+R+WVCVSDPF
Sbjct: 179 TILGHLLGETCQETESGPHIISIVGTGGMGKTTLAQLAYNHPEVKAHFDERIWVCVSDPF 238

Query: 240 DELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYC 299
           D +RI + I+E L+   P +  L +L + I+  + GKKFLL+LDD+WT+++  WE  +  
Sbjct: 239 DPIRIFREIVEILQRESPNLHSLEALQQKIQTCIAGKKFLLVLDDVWTENHQLWEQLNST 298

Query: 300 LKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW-------------------- 339
           L  G  GS+ILVTTRKE+V  MM + ++ S+ +LSE +                      
Sbjct: 299 LSCGGVGSRILVTTRKESVVEMMRTTYMHSLGKLSEDKSRALFYQIAFYGKNREKMEDFQ 358

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                    CKGLPLA KT+G+L+R K  REEWE++L SE+W+L+ F + +   LLLSY 
Sbjct: 359 EIGEKIADKCKGLPLAIKTLGNLMRSKHNREEWENVLCSEVWKLDVFGRDISPALLLSYY 418

Query: 391 DLPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
           DLPP IKRCF +             ELIKLWMAQ Y+  +G+KE+E++G EYF+YLA RS
Sbjct: 419 DLPPTIKRCFSFCAVFPKDSVIERDELIKLWMAQSYLKSDGSKEMEMVGREYFEYLAARS 478

Query: 439 FFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSM 498
           FFQ+F KD +  ++RCKMHDIVHDFAQFLT+NEC  +EVD+ ++    ++ + +K+ H+ 
Sbjct: 479 FFQDFEKDGDDDIIRCKMHDIVHDFAQFLTQNECFVVEVDNQKK--GSMDLFFQKICHAT 536

Query: 499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD 558
           LV+        S    KNL +L   +       + VL++L   L CLRAL +     +W+
Sbjct: 537 LVVQESTLNFASTCNMKNLHTLLAKSAFD----SRVLEAL-GHLTCLRALDL-----SWN 586

Query: 559 VNSTNKILKGIEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIG 617
                ++ K + KLIHLRYL L    +  ELPET C+L NLQ L I+ C SL++LP  +G
Sbjct: 587 -QLIEELPKEVGKLIHLRYLDLSRCQSLRELPETICDLYNLQTLNIQYCISLQKLPQAMG 645

Query: 618 KLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
           KL+NLRHL      L+ +PKGI RL++L+TL  F+V    S +G   C +  LR
Sbjct: 646 KLINLRHLENYTRSLKGLPKGIGRLSSLQTLDVFIV----SSHGNDECQIGDLR 695

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482792|ref|XP_002268589.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/718 (42%), Positives = 457/718 (63%), Gaps = 71/718 (9%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA++S +LE+L S+  ++ R+++ LV+G++ E+  L     +++ VL DAE+RQ KE+
Sbjct: 1   MADALLSIVLERLASVVEQQIRDELTLVLGVEAEIQSLTDTLRSVRDVLEDAERRQVKEK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVD-ALVPQRKVCSFLPAASCFGFSQT 119
            V+ WL++LKD++Y M DV+DEW+TA L+L+I+G + A + ++KV S +P+  CF   Q 
Sbjct: 61  AVQGWLERLKDMAYQMDDVVDEWSTAILQLQIKGAESASMSKKKVSSCIPSP-CFCLKQV 119

Query: 120 FQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKS 179
             RRDIA+K+K+I  +LD IA Q+  +NF +   +E  +R  +TS +D+ E+ GRD +K+
Sbjct: 120 ASRRDIALKVKSIKQQLDVIASQRSQFNF-ISSLSEEPQRFITTSQLDIPEVYGRDMDKN 178

Query: 180 SLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF 239
           ++   LL E+ +E  +   II+IVG GG+GKTTLAQ AYN  +V  +FD+R+WVCVSDPF
Sbjct: 179 TILGHLLGETCQETKSGPYIISIVGTGGMGKTTLAQLAYNHPEVKAHFDERIWVCVSDPF 238

Query: 240 DELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYC 299
           D +RI + I+E L+G  P +  L +L + I+  + GKKFL++LDD+WT+++  W      
Sbjct: 239 DPIRIFREIVEILQGESPNLHSLEALQQKIQTYIAGKKFLIVLDDVWTENHQLWGQLKST 298

Query: 300 LKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW-------------------- 339
           L  G  GS+IL TTRKE+V +M+ + +  S++ELS ++                      
Sbjct: 299 LNCGGVGSRILATTRKESVVKMVGTTYTHSLEELSREQARALFHQIAFFEKSREKVEELN 358

Query: 340 ---------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
                    CKGLPLA KT+G+L+R K  REEWE++L SE+W L+EFE+ +   LLLSY+
Sbjct: 359 EIGENIADKCKGLPLAIKTLGNLMRSKHNREEWENVLCSEVWHLDEFERDISPALLLSYH 418

Query: 391 DLPPMIKRCFQY------------YELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRS 438
           DLPP I+RCF +             ELIKLWMAQ Y+  +G KE+E++G  YF+YLA RS
Sbjct: 419 DLPPAIQRCFSFCAVFPKDSVIVRAELIKLWMAQSYLKSDGCKEMEMVGRTYFEYLAARS 478

Query: 439 FFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSM 498
           FFQ+F KD++G ++RCKMHDIVHDFAQFLT+NEC  +EVD+ ++    ++ + +K+RH+ 
Sbjct: 479 FFQDFEKDDDGNIIRCKMHDIVHDFAQFLTQNECFIVEVDNQKK--GSMDLFFQKIRHAT 536

Query: 499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD 558
           LV+        S    KNL +L           + VL++L + L CLRAL +        
Sbjct: 537 LVVRESTPNFASTCNMKNLHTLLAKKAFD----SRVLEALGN-LTCLRALDL-------- 583

Query: 559 VNSTNKIL----KGIEKLIHLRYLRL-VGLGTEELPETCCELLNLQVLEIEQCTSLKRLP 613
             S N+++    K + KLIHLRYL L +     ELPET C+L NLQ L I+ C  +++LP
Sbjct: 584 --SRNRLIEELPKEVGKLIHLRYLNLSLCYSLRELPETICDLYNLQTLNIQGCI-IRKLP 640

Query: 614 LGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
             +GKL+NLRHL   ++ L+ +PKGI RL++L+TL  F+V    S +G   C +  LR
Sbjct: 641 QAMGKLINLRHLENYNTRLKGLPKGIGRLSSLQTLDVFIV----SSHGNDECQIGDLR 694

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482794|ref|XP_002268547.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  560 bits (1443), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 307/697 (44%), Positives = 444/697 (63%), Gaps = 41/697 (5%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA++S +L +L S+  ++ R+++ LV+G++ E+  L     +++ VL DAE+RQ KE+
Sbjct: 1   MADALLSIVLTRLASVVGQQIRDELTLVLGVEAEIQSLTDTLRSVRDVLEDAERRQVKEK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
           +V+ WL++LKD++Y M DV+DEW+TA L+L+I+G ++    +KV S +P+  CF   Q  
Sbjct: 61  SVQGWLERLKDMAYQMDDVVDEWSTAILQLQIKGAESASMSKKVSSCIPSP-CFCLKQVA 119

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            RRDIA+K+K+I  +LD IA Q+  +NF +   +E  +R  +TS +D+ E+ GRD +K++
Sbjct: 120 SRRDIALKVKSIKQQLDVIASQRSQFNF-ISSLSEEPQRFITTSQLDIPEVYGRDMDKNT 178

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +   LL E+ +E  +   II+IVG GG+GKTTLAQ AYN  +V  +FD+R+WVCVSDPFD
Sbjct: 179 ILGHLLGETCQETKSGPYIISIVGTGGMGKTTLAQLAYNHPEVKAHFDERIWVCVSDPFD 238

Query: 241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
            +RI + I+E L+G  P +  L +L + I+  + GKKFL++LDD+WT+++  W      L
Sbjct: 239 PIRIFREIVEILQGESPNLHSLEALQQKIQTCIAGKKFLIVLDDVWTENHQLWGQLKSTL 298

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVISIKELSEQEC------------WCKGLPLAAK 348
             G  GS+IL TT++ +  +     H I+  E S ++              CKGLPLA K
Sbjct: 299 NCGGVGSRILATTQELSQEQARALFHQIAFFEKSREKVEELKEIGEKIADKCKGLPLAIK 358

Query: 349 TIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYY----- 403
           T+G+L+R K  +EEWE++L+SE+WQL+EFE+ +   LLLSY DLPP IKRCF +      
Sbjct: 359 TLGNLMRLKNNKEEWENVLNSEVWQLDEFERDICPALLLSYYDLPPAIKRCFSFCAVFPK 418

Query: 404 -------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKM 456
                  ELI+LWMAQ+Y+  + +KE+E++G EYF+YLA RSFFQ+F KD +  ++RCKM
Sbjct: 419 DSVIKIDELIRLWMAQNYLNSDASKEMEMVGREYFEYLAARSFFQDFEKDGDDDIIRCKM 478

Query: 457 HDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKN 516
           HDIVHDFAQFLTKNEC  + V++ EE      T  +K+RH+ L+        +S +K KN
Sbjct: 479 HDIVHDFAQFLTKNECFIMNVENAEE--GRTKTSFQKIRHATLIGQQRYPNFVSTYKMKN 536

Query: 517 LRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLR 576
           L +L +  T    S    L +LF  L CLRAL +A   N   +    ++ K + KLIHL+
Sbjct: 537 LHTLLLKFTFSSTS-DEALPNLFQHLTCLRALNLAR--NPLIM----ELPKAVGKLIHLK 589

Query: 577 YLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSC-LEF 634
           YL L       ELPET C+L NLQ L I +C SL  LP  +GKL+NLRHL    +  L+ 
Sbjct: 590 YLSLSDCHKLRELPETICDLYNLQTLNISRCFSLVELPQAMGKLINLRHLQNCGALDLKG 649

Query: 635 IPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
           +PKGI RL +L+TL EFVV    S  G   C +  LR
Sbjct: 650 LPKGIARLNSLQTLEEFVV----SSDGDAECKIGDLR 682

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482800|ref|XP_003632842.1| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 319/716 (44%), Positives = 438/716 (61%), Gaps = 66/716 (9%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA+VS +LE+L S+      +Q+ LVVG+ +EV  L     +I+AVL DAE+RQF EE
Sbjct: 1   MADALVSIVLERLASV----LEQQVTLVVGVGSEVDNLNSTLQSIRAVLADAEKRQFSEE 56

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
            V++WL++LKD+SY M DV+D WNTA LKL+I   +  +P+ K+ S LP+  C  F Q  
Sbjct: 57  LVKVWLERLKDISYQMDDVVDGWNTALLKLQIGAENPCIPKLKISSCLPSP-CVCFKQVL 115

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            R DI +KIK I  +LD IA +++ +NF    + +   R  ++S+IDVS+  GRD +   
Sbjct: 116 LRCDIGIKIKDIRKQLDAIANERNQFNFVSSSTIQQPHRRMTSSVIDVSQFCGRDADMDV 175

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +  KLL  SS+E  + + II+IVGMGGIGKTTLAQ AYND  V  YF +RMWVCVSDPFD
Sbjct: 176 IIDKLLGGSSQES-SSLYIISIVGMGGIGKTTLAQLAYNDDRVKAYFHERMWVCVSDPFD 234

Query: 241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
            + I++AI+EAL+       EL ++ + I   +  KKFLL+LDD+WT++Y  WE     L
Sbjct: 235 PVTISRAILEALQKESCDFHELENVEQKICTLIADKKFLLVLDDVWTENYELWEKVESSL 294

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW--------------------- 339
           K G  GS+ILVTTRK+ V+ MM + +   ++ELSE +CW                     
Sbjct: 295 KGGAPGSRILVTTRKDDVSTMMGTTYKHPLRELSEGQCWSLFSNIAFCGRSREKVEELEN 354

Query: 340 --------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYND 391
                   C+GLPLAAK +GSL+R K  +E WESIL++E+WQL+  EK L  PLLLSY D
Sbjct: 355 IGRKIADKCRGLPLAAKVLGSLMRLKDNKENWESILNNEIWQLDVIEKHLSTPLLLSYYD 414

Query: 392 LPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSF 439
           L P +KRCF Y              LIKLWMA  Y+   G+ E+E  G +YF+ L  RS 
Sbjct: 415 LSPAVKRCFSYCAVFPKDQIISKDRLIKLWMANSYLNSRGSIEMEKTGGDYFEDLVSRSL 474

Query: 440 FQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSML 499
           FQ+F +DNE  ++ CKMHDIVHD AQ LTKNEC  +E DD++E + + +++Q K RH+ L
Sbjct: 475 FQDFRRDNEDNIISCKMHDIVHDLAQSLTKNECFILEFDDEKE-VRMASSFQ-KARHATL 532

Query: 500 VLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDV 559
           ++   A FP +I   K L +LF+   +   +      +LF  L CLRAL         D+
Sbjct: 533 IITPWAGFPSTIHNLKYLHTLFVGRVVNLNTTAQPPPNLFKHLVCLRAL---------DL 583

Query: 560 NSTNKIL---KGIEKLIHLRYLRLV-GLGTEELPETCCELLNLQVLEIEQCTSLKRLPLG 615
           +    I+   + + KL+HLR+L L   L   ELPET C+L NLQ L +     L +LP G
Sbjct: 584 SGHRLIVELPRNLGKLMHLRFLNLSNNLMRGELPETICDLYNLQTLILSDL--LIKLPQG 641

Query: 616 IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
           + KL+NLRHL ++ S +  +PKGI RLT+LRTL+EF ++  G    G+  NL  LR
Sbjct: 642 MRKLINLRHLEWEGSRVLMLPKGIGRLTSLRTLTEFRII--GVCKIGELKNLNSLR 695

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122696|ref|XP_002318903.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859576|gb|EEE97123.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  554 bits (1427), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 315/716 (43%), Positives = 438/716 (61%), Gaps = 107/716 (14%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M +A++SP+LEQL +I  ++ +E++ LVVG+  +  KLK N L IQ+VL DA+++Q K++
Sbjct: 1   MAEALLSPILEQLTTIVAQQVQEEVNLVVGVKKQCDKLKSNLLDIQSVLEDADRKQVKDK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKV--CSFLPAASCFGFSQ 118
            VR WLD+LKD  Y M DVLDEW+TA L+ ++E  +     R+   CSFL  + CF F+Q
Sbjct: 61  AVRDWLDKLKDACYDMDDVLDEWSTAILRWKMEEAEENTRSRQKMRCSFL-RSPCFCFNQ 119

Query: 119 TFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEK 178
             +RRDIA+KIK +  K+DDIAK++  Y F+  R+T+  +R+ STS +D           
Sbjct: 120 VVRRRDIALKIKEVCEKVDDIAKERAKYGFDPYRATDELQRLTSTSFVD----------- 168

Query: 179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP 238
                    ESSE    D+ +I++VG+GG+GKTTLAQ A+ND++V  +F+K++WVCVS+P
Sbjct: 169 ---------ESSE--ARDVDVISLVGLGGMGKTTLAQLAFNDAEVTAHFEKKIWVCVSEP 217

Query: 239 FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHY 298
           FDE+RIAKAIIE LEG    + EL SLL+ +  S+ GK+FLL+LDD+WT+++ +WEP   
Sbjct: 218 FDEVRIAKAIIEQLEGSPTNLVELQSLLQRVSESIKGKRFLLVLDDVWTENHGQWEPLKL 277

Query: 299 CLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW------------------- 339
            LK G  GS+ILVTTRK +VA MM + H+I+++ LS++ C                    
Sbjct: 278 SLKGGAPGSRILVTTRKHSVATMMGTDHMINLERLSDEVCRSIFNHVAFHKRSKDECERL 337

Query: 340 ----------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSY 389
                     CKGLPLAAK                         LE  E+G+  PLLLSY
Sbjct: 338 TEISDKIANKCKGLPLAAK-------------------------LEHVERGIFPPLLLSY 372

Query: 390 NDLPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMR 437
            DLP +++RCF Y             EL+K+WMAQ Y+      ++E++GE+YF  LA R
Sbjct: 373 YDLPSVVRRCFLYCAMFPKDYEMVKDELVKMWMAQGYLKETSGGDMELVGEQYFQVLAAR 432

Query: 438 SFFQEFFKD-NEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRH 496
           SFFQ+F  D +EG+    KMHDIVHDFAQ++TKNEC+ ++V+      + + T  E++RH
Sbjct: 433 SFFQDFETDEDEGMTF--KMHDIVHDFAQYMTKNECLTVDVNTLGG--ATVETSIERVRH 488

Query: 497 SMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNT 556
             ++L  E SFP+SI KAK LRSL I+      SL   L  LF QL C+R+L ++     
Sbjct: 489 LSMMLPNETSFPVSIHKAKGLRSLLIDTR--DPSLGAALPDLFKQLTCIRSLNLSR---- 542

Query: 557 WDVNSTNKILKGIEKLIHLRYLRLV-GLGTEELPETCCELLNLQVLEIEQCTSLKRLPLG 615
              +   +I   + KLIHLR+L L   +  E LPET C+L NLQ L++  C SLK LP  
Sbjct: 543 ---SQIKEIPNEVGKLIHLRHLNLAWCVELESLPETICDLCNLQSLDVTWCRSLKELPKA 599

Query: 616 IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
           IGKL+ LRHL  D S + FIPKGI+R+T LRTL +F V  GG +   KA NL  L+
Sbjct: 600 IGKLIKLRHLWIDSSGVAFIPKGIERITCLRTLDKFTVC-GGGENESKAANLRELK 654

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147825450|emb|CAN71072.1| hypothetical protein VITISV_000086 [Vitis vinifera]

 Score =  550 bits (1417), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 315/718 (43%), Positives = 447/718 (62%), Gaps = 64/718 (8%)

Query: 1   MVDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
           M DA+VS +LE+L S++ ++  EQ+ LV+G+D+E+  LK    +++ VL DAE+RQ KE+
Sbjct: 1   MADALVSIVLERLKSVAEQQIHEQVSLVLGVDSEIESLKSTLRSVRNVLEDAERRQVKEK 60

Query: 61  TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
           +V+ WL+ LKD++Y M DVLDEW+   L  ++EGV+     +K  SF   + C  F Q  
Sbjct: 61  SVQDWLESLKDMAYQMEDVLDEWSIPILPFQMEGVENASTSKKKVSFCMPSPCICFKQVA 120

Query: 121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDEEKSS 180
            RRDIA+KIK I  KLDDI ++K+ +NF   RS E S+ I +TS ID+SE+ GRD +K  
Sbjct: 121 SRRDIALKIKGIKKKLDDIEREKNRFNFVSSRSEERSQPITATSAIDISEVYGRDMDKEI 180

Query: 181 LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD 240
           +   LL +  +E  + + I++IVG GG+GKTTLAQ AY+ S+V  +FD+R+WVCVSDPFD
Sbjct: 181 ILDHLLGKKCQE-KSGLYIVSIVGTGGMGKTTLAQLAYSHSEVEFHFDERIWVCVSDPFD 239

Query: 241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCL 300
             R+ +AI+EALE     + +L +L + I+  + GKKFLL+LDD+WT+++  WE     L
Sbjct: 240 PSRVCRAIVEALEKESCNLHDLEALQQKIQTCIGGKKFLLVLDDVWTENHQLWEQLKSIL 299

Query: 301 KNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW--------------------- 339
             G  GS+ILVTTR E V  MM + ++ S+ +LSE +                       
Sbjct: 300 SCGAVGSRILVTTRNENVVEMMRTTYMHSLGKLSEDKSRELFYQIAFSGKNREKMEDLKE 359

Query: 340 --------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYND 391
                   CKGLPLA KT+G+L+R K  REEWE++L SE+W+L+ F   +   LLLSY+D
Sbjct: 360 IGEKIADKCKGLPLAIKTLGNLMRSKHNREEWENVLCSEVWKLDVFGIYISPALLLSYHD 419

Query: 392 LPPMIKRCFQYY------------ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSF 439
           LPP I+RCF +             ELIKLWMAQ Y+  + +KE+E++G  YF+YLA RSF
Sbjct: 420 LPPEIQRCFSFCAVFPKDSVIWSDELIKLWMAQSYLNSDRSKEMEMVGRTYFEYLAARSF 479

Query: 440 FQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSML 499
           FQ+F KD++G ++ CKMHDIVHDFAQFLT+NEC  +EVD+ ++    ++ + +K+RH+ L
Sbjct: 480 FQDFEKDDDGNIICCKMHDIVHDFAQFLTQNECFIVEVDNQKK--GSMDLFFQKIRHATL 537

Query: 500 VLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDV 559
           V+        S    KNL +L          +   L +L   L CLRAL +         
Sbjct: 538 VVRESTPNFASTCNMKNLHTLLAKEEFBISXVLEALXNLLRHLTCLRALDL--------- 588

Query: 560 NSTNKIL----KGIEKLIHLRYLRL-VGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL 614
            S N+++    K + KLIHLRYL L +     ELPET C+L NLQ L IE C+SL++LP 
Sbjct: 589 -SRNRLIEELPKEVGKLIHLRYLNLSLCYRLRELPETICDLYNLQTLNIEGCSSLQKLPQ 647

Query: 615 GIGKLVNLRHL-TYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLR 671
            +GKL+NLRHL   +   L+ +PKGI RL++L+TL  F+V    S +G   C +  LR
Sbjct: 648 AMGKLINLRHLENCNTGSLKGLPKGIGRLSSLQTLDVFIV----SSHGNDECQIGDLR 701

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	673
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.450	0.287	0.303	9.6e-65
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.451	0.213	0.320	1.1e-54
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.453	0.169	0.288	1.9e-37
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.450	0.355	0.256	1.1e-36
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.332	0.241	0.296	1.2e-33
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.199	0.158	0.340	4.1e-29
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.416	0.308	0.245	2.9e-26
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.414	0.307	0.260	3.5e-26
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.447	0.334	0.25	1.6e-25
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.196	0.145	0.309	1.5e-24

TAIR|locus:2091672 AT3G14470 [Arabidopsis thaliana (taxid:3702)]

 Score = 409 (149.0 bits), Expect = 9.6e-65, Sum P(2) = 9.6e-65
 Identities = 94/310 (30%), Positives = 160/310 (51%)

Query:    32 DNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLR 91
             +N + +L    L I AVL+DAE++Q     V  W+++L+DV Y+  D LD+  T  L+L 
Sbjct:    36 ENLLERLSTALLTITAVLIDAEEKQITNPVVEKWVNELRDVVYHAEDALDDIATEALRLN 95

Query:    92 IEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVI 151
             I G ++    R     L      G         +  +++ +  +L+ +A Q+++     +
Sbjct:    96 I-GAESSSSNR--LRQLRGRMSLGDFLDGNSEHLETRLEKVTIRLERLASQRNILGLKEL 152

Query:   152 RSTENSERIQSTSLIDVSEIRGRDXXXXXXXXXXXXXXXXXXXXXXXXXXXVGMGGIGKT 211
              +    +R+ +TSL+D SE+ GRD                           VG+GG+GKT
Sbjct:   153 TAMIPKQRLPTTSLVDESEVFGRDDDKDEIMRFLIPENGKDNGITVVAI--VGIGGVGKT 210

Query:   212 TLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA 271
             TL+Q  YND  V  YF  ++W  VS+ FD  +I K + E++        +L+ L   ++ 
Sbjct:   211 TLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPCEFTDLDVLQVKLKE 270

Query:   272 SLVGK--KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVIS 329
              L G    FLL+LDD+W ++++ W+       +  +GS+ILVTTR + VA +M ++HV +
Sbjct:   271 RLTGTGLPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQRVASIMCAVHVHN 330

Query:   330 IKELSEQECW 339
             ++ LS+ +CW
Sbjct:   331 LQPLSDGDCW 340

GO:0005576 "extracellular region" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:2091662 AT3G14460 [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 1.1e-54, Sum P(3) = 1.1e-54
 Identities = 109/340 (32%), Positives = 163/340 (47%)

Query:   331 KELSEQECWCKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYN 390
             K ++EQ   CKGLPLAA+ I S LR K   ++W ++  +       +   +L  L LSY+
Sbjct:   360 KRIAEQ---CKGLPLAARAIASHLRSKPNPDDWYAVSKN----FSSYTNSILPVLKLSYD 412

Query:   391 DLPPMIKRCFQYY------------ELIKLWMAQDYI-MPEGNKELEIIGEEYFDYLAMR 437
              LPP +KRCF               EL+ LWMA D +  P  ++ LE IG +Y   L  +
Sbjct:   413 SLPPQLKRCFALCSIFPKGHVFDREELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQ 472

Query:   438 SFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHS 497
             SFFQ      +  +    MHD+++D A+ ++ + C  +E  DD  P     T       S
Sbjct:   473 SFFQRL----DITMTSFVMHDLMNDLAKAVSGDFCFRLE--DDNIPEIPSTTRHFSFSRS 526

Query:   498 MLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQL-KCLRALRIATLMN 555
                   +AS    SI  A+ LR++   N+   +    + + + + L   L  LRI +L +
Sbjct:   527 QC----DASVAFRSICGAEFLRTILPFNSPTSLESLQLTEKVLNPLLNALSGLRILSLSH 582

Query:   556 TWDVNSTNKILKGIEKLIHLRYLRLVGXXXXXXXXXXXXXXNLQVLEIEQCTSLKRLPLG 615
              + + +  K LKG+ KL  LRYL L                NLQ L +  C  L  LP  
Sbjct:   583 -YQITNLPKSLKGL-KL--LRYLDLSSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKS 638

Query:   616 IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVR 655
             I +L+NLR L    + L  +P GI++L +L+ LS FV+ R
Sbjct:   639 IAELINLRLLDLVGTPLVEMPPGIKKLRSLQKLSNFVIGR 678

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|O48647 O48647 "XA1" [Oryza sativa (taxid:4530)]

 Score = 278 (102.9 bits), Expect = 1.9e-37, Sum P(3) = 1.9e-37
 Identities = 96/333 (28%), Positives = 157/333 (47%)

Query:   341 KGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCF 400
             KG PLAAKT+GSLL    T + W+SI+ SE W+  +   G++  L LSY+ L   +++C 
Sbjct:   502 KGNPLAAKTVGSLLGTNLTIDHWDSIIKSEEWKSLQQAYGIMQALKLSYDHLSNPLQQCV 561

Query:   401 QY-------Y-----ELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNE 448
              Y       Y     +LI++W+AQ ++  E +++LE  G +Y   L    F Q+  +   
Sbjct:   562 SYCSLFPKGYSFSKAQLIQIWIAQGFV-EESSEKLEQKGWKYLAELVNSGFLQQV-ESTR 619

Query:   449 GVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEE--P----LSLINTYQEKLRHSMLVLG 502
                    MHD++HD AQ +++ E   I+  +  E  P    LS++ T     +     + 
Sbjct:   620 FSSEYFVMHDLMHDLAQKVSQTEYATIDGSECTELAPSIRHLSIV-TDSAYRKEKYRNIS 678

Query:   503 YEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNST 562
                 F   + K K+ RS   +  LI    +H  +   D  K  + LR+  +  T+    +
Sbjct:   679 RNEVFEKRLMKVKS-RSKLRSLVLIGQYDSHFFKYFKDAFKEAQHLRLLQITATYA--DS 735

Query:   563 NKILKGIEKLIHLRYLRLVGXXXXXXX-XXXXXXXNLQVLEIEQCTSLKRLPLGIGKLVN 621
             +  L  +    HLRYL++V                +LQVL+I     + R+   I  L++
Sbjct:   736 DSFLSSLVNSTHLRYLKIVTEESGRTLPRSLRKYYHLQVLDIGYRFGIPRISNDINNLLS 795

Query:   622 LRHLT-YDDSCLEFIPKGIQRLTNLRTLSEFVV 653
             LRHL  YD+ C       I ++T+L+ L  F+V
Sbjct:   796 LRHLVAYDEVCSSIA--NIGKMTSLQELGNFIV 826

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.1e-36, Sum P(2) = 1.1e-36
 Identities = 84/328 (25%), Positives = 158/328 (48%)

Query:     1 MVDAIVSPXXXXXXXXXXXXAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEE 60
             MVDA+V+               E+ + V     ++  L+     +Q+ L DAE+++   E
Sbjct:     1 MVDAVVT----VFLEKTLNILEEKGRTVSDYRKQLEDLQSELKYMQSFLKDAERQKRTNE 56

Query:    61 TVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTF 120
             T+R  +  L+++ Y   D+L +   A      +G D    QR   ++L           +
Sbjct:    57 TLRTLVADLRELVYEAEDILVDCQLA------DGDDGN-EQRSSNAWLSRLHPARVPLQY 109

Query:   121 QRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRST----ENSERIQSTSLIDVSEIRGRDX 176
             ++   + +++ IN ++  I  Q + Y F  I  +    +N     S+ + D +++ G + 
Sbjct:   110 KK---SKRLQEINERITKIKSQVEPY-FEFITPSNVGRDNGTDRWSSPVYDHTQVVGLEG 165

Query:   177 XXXXXXXXXXXXXXXXXXXXXXXXXXVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS 236
                                       VGMGG+GKTT+AQ  +ND ++   F++R+WV VS
Sbjct:   166 DKRKIKEWLFRSNDSQLLIMAF----VGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVS 221

Query:   237 DPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPF 296
               F E +I ++I+  L G      ++ +LL  I+  L+GK++L+++DD+W  + S W+  
Sbjct:   222 QTFTEEQIMRSILRNL-GDASVGDDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKI 280

Query:   297 HYCLKNGVRGSKILVTTRKETVARMMES 324
             +  L  G +G  ++VTTR E+VA+ +++
Sbjct:   281 YQGLPRG-QGGSVIVTTRSESVAKRVQA 307

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 225 (84.3 bits), Expect = 1.2e-33, Sum P(4) = 1.2e-33
 Identities = 76/256 (29%), Positives = 125/256 (48%)

Query:   340 CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEE-FEKGLLAPLL-LSYNDLPPMIK 397
             C+GLPLA  ++GS++  K+   EW+ +  +  W+L    E  ++  ++ LS+NDLP  +K
Sbjct:   373 CQGLPLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYPLK 432

Query:   398 RCFQY-------YE-----LIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFK 445
             RCF Y       Y      LI++WMAQ ++ P    + E + + Y + L  R+  Q    
Sbjct:   433 RCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNELVYRNMLQVILW 492

Query:   446 DNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEK-LRHSMLVLGYE 504
             +  G     KMHD++ + A  ++K E      +DD +      T +    RH  L +  E
Sbjct:   493 NPFGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRH--LCIQKE 550

Query:   505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK 564
              + P SI +A NL SL     L+  S  H ++ L   L  LRAL +       + +S +K
Sbjct:   551 MT-PDSI-RATNLHSL-----LVCSSAKHKME-LLPSLNLLRALDL-------EDSSISK 595

Query:   565 ILKGIEKLIHLRYLRL 580
             +   +  + +L+YL L
Sbjct:   596 LPDCLVTMFNLKYLNL 611

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009626 "plant-type hypersensitive response" evidence=IDA

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 4.1e-29, Sum P(3) = 4.1e-29
 Identities = 49/144 (34%), Positives = 77/144 (53%)

Query:   204 GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE----LRIAKA--IIEALEGFVP 257
             GMGG+GKT LA+  YN  DV   FD R W  VS  +      +RI ++  I+ A E    
Sbjct:   192 GMGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIRSLGIVSAEEMEKI 251

Query:   258 TVGELNSLLESIRASLV-GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE 316
              + E +  LE     L+ GK +++++DD+W  D   WE     L    RGSK+++TTR  
Sbjct:   252 KMFEEDEELEVYLYGLLEGKNYMVVVDDVWDPD--AWESLKRALPCDHRGSKVIITTRIR 309

Query:   317 TVARMME-SIHVISIKELSEQECW 339
              +A  +E +++   ++ L+ +E W
Sbjct:   310 AIAEGVEGTVYAHKLRFLTFEESW 333

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 209 (78.6 bits), Expect = 2.9e-26, Sum P(2) = 2.9e-26
 Identities = 75/306 (24%), Positives = 137/306 (44%)

Query:    21 AREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVL 80
             +RE  +L  GID ++  LK    ++Q++L DA+ ++   + VR +L+ +KD+ +   D++
Sbjct:    18 SRESERLQ-GIDGQLDGLKRQLRSLQSLLKDADAKKHGSDRVRNFLEDVKDLVFDAEDII 76

Query:    81 DEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIA 140
             + +   +L  + +GV   V  R++  FL             R  +A  I+ I  ++ ++ 
Sbjct:    77 ESYVLNKLSGKGKGVKKHV--RRLACFLT-----------DRHKVASDIEGITKRISEVI 123

Query:   141 KQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGR--DXXXXXXXXXXXXXXXXXXXXXXX 198
              +   +    I     S  +Q    +   EIR    D                       
Sbjct:   124 GEMQSFGIQQIIDGGRSLSLQERQRVQ-REIRQTYPDSSESDLVGVEQSVKELVGHLVEN 182

Query:   199 XXXXV----GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG 254
                 V    GMGGIGKTTLA+  ++   V  +FD   WVCVS  F +  + + I++ L+ 
Sbjct:   183 DVHQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELQP 242

Query:   255 FVPTVGELN--SLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVT 312
                 + +++  +L   +   L   ++L++LDD+W  +   W+          RG K+L+T
Sbjct:   243 HDGDILQMDEYALQRKLFQLLEAGRYLVVLDDVWKKE--DWDVIKAVFPRK-RGWKMLLT 299

Query:   313 TRKETV 318
             +R E V
Sbjct:   300 SRNEGV 305

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0051707 "response to other organism" evidence=IMP

TAIR|locus:2152536 AT5G48620 [Arabidopsis thaliana (taxid:3702)]

 Score = 211 (79.3 bits), Expect = 3.5e-26, Sum P(3) = 3.5e-26
 Identities = 80/307 (26%), Positives = 135/307 (43%)

Query:    21 AREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVL 80
             +RE  +L  GID ++  LK    ++Q++L DA+ ++   + VR +L+ +KD+ +   D++
Sbjct:    18 SRESERLQ-GIDEQLDGLKRQLRSLQSLLKDADAKKHGSDRVRNFLEDVKDLVFDAEDII 76

Query:    81 DEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIA 140
             + +     KLR EG       R++  FL             R  +A  I+ I  ++ D+ 
Sbjct:    77 ESY--VLNKLRGEGKGVKKHVRRLARFLT-----------DRHKVASDIEGITKRISDVI 123

Query:   141 KQKDMYNFNVIRSTENSERIQSTSLIDVSEIRGR--DXXXXXXXXXXXXXXXXXXXXXXX 198
              +   +    I     S  +Q    +   EIR    D                       
Sbjct:   124 GEMQSFGIQQIIDGVRSLSLQERQRVQ-REIRQTYPDSSESDLVGVEQSVEELVGHLVEN 182

Query:   199 XXXXV----GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALE- 253
                 V    GMGGIGKTTLA+  ++   V  +FD   WVCVS  F    + + I++ L+ 
Sbjct:   183 DIYQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRILQELQP 242

Query:   254 --GFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILV 311
               G +  + E ++L   +   L   ++LL+LDD+W  +   W+          RG K+L+
Sbjct:   243 HDGNILQMDE-SALQPKLFQLLETGRYLLVLDDVWKKE--DWDRIKAVFPRK-RGWKMLL 298

Query:   312 TTRKETV 318
             T+R E V
Sbjct:   299 TSRNEGV 305

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 1.6e-25, Sum P(3) = 1.6e-25
 Identities = 81/324 (25%), Positives = 143/324 (44%)

Query:    22 REQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLD 81
             RE  +L  GID +V  LK     +Q++L DA+ ++   + VR +L+ +KD+ +   D+++
Sbjct:    19 RESERLN-GIDEQVDGLKRQLRGLQSLLKDADAKKHGSDRVRNFLEDVKDLVFDAEDIIE 77

Query:    82 EWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAK 141
              +     KLR EG       R++  FL                I  +I  + G++  +  
Sbjct:    78 SY--VLNKLRGEGKGVKNHVRRLACFLTDRH----KVASDIEGITKRISKVIGEMQSLGI 131

Query:   142 QKDMYNFNVIRSTENSERIQSTSLIDVSEIRGRDXXXXXXXXXXXXXXXXXXXXXXXXXX 201
             Q+ + +     S ++ +R    +  + SE    D                          
Sbjct:   132 QQQIIDGGRSLSLQDIQREIRQTFPNSSE---SDLVGVEQSVEELVGPMVEIDNIQVVSI 188

Query:   202 XVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGE 261
               GMGGIGKTTLA+  ++   V  +FD   WVCVS  F +  + + I++ L    P  GE
Sbjct:   189 S-GMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELR---PHDGE 244

Query:   262 LNSLLE-SIRASLVGK----KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE 316
             +  + E +I+  L       ++L++LDD+W ++   W+          RG K+L+T+R E
Sbjct:   245 ILQMDEYTIQGKLFQLLETGRYLVVLDDVWKEE--DWDRIKEVFPRK-RGWKMLLTSRNE 301

Query:   317 TVARMMESIHV-ISIKELSEQECW 339
              V    +   +    + L+ +E W
Sbjct:   302 GVGLHADPTCLSFRARILNPKESW 325

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 1.5e-24, Sum P(4) = 1.5e-24
 Identities = 44/142 (30%), Positives = 71/142 (50%)

Query:   204 GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELN 263
             GMGG+GKTTLA+  +N  DV   FD+  WVCVS  F    + + I++ L         L 
Sbjct:   190 GMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSREKKDEILQ 249

Query:   264 ----SLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVA 319
                  L + +   L   K L++ DD+W D+   W+          +G K+L+T++ E+VA
Sbjct:   250 MEEAELHDKLFQLLETSKSLIVFDDIWKDE--DWDLIKPIFPPN-KGWKVLLTSQNESVA 306

Query:   320 RMMESIHVISIKE--LSEQECW 339
              +   I  ++ K   L+ ++ W
Sbjct:   307 -VRGDIKYLNFKPECLAIEDSW 327

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_XII001317 cc-nbs-lrr resistance protein (945 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	673
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	8e-52
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.004

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score =  180 bits (459), Expect = 8e-52
 Identities = 100/290 (34%), Positives = 148/290 (51%), Gaps = 52/290 (17%)

Query: 174 RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV 233
           R++   +L  KLL  S       + ++ IVGMGG+GKTTLA+  YND  V  +FD   WV
Sbjct: 1   REDMIEALIEKLLEMSDN-----LGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWV 55

Query: 234 CVSDPFDELRIAKAIIEALEGFVPTVGELN--SLLESIRASLVGKKFLLILDDMWTDDYS 291
            VS  + E R+ K I++ L        E N   L   I+ +L+ K+FLL+LDD+W  + +
Sbjct: 56  VVSKTYTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVW--EKN 113

Query: 292 KWEPFHYCLKNGVRGSKILVTTRKETVA-RMMESIHVISIKELSEQECW----------- 339
            W+       +G  GS+++VTTR E+VA RM  +     ++ L  +E W           
Sbjct: 114 DWDKIGVPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKE 173

Query: 340 -----------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFE--KG 380
                            CKGLPLA K +G LL FK T +EWE +L+    +L   +    
Sbjct: 174 LPPCPELEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNE 233

Query: 381 LLAPLLLSYNDLPPMIKRCFQYY------------ELIKLWMAQDYIMPE 418
           +L+ L LSY++LP  +KRCF Y             +LIKLW+A+ +++P 
Sbjct: 234 VLSILSLSYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIAEGFVIPS 283

Length = 285

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 25/134 (18%), Positives = 44/134 (32%), Gaps = 21/134 (15%)

Query: 173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLA----QFAYNDSDVFEYFD 228
           GR+EE   L   L              + + G  G GKT+L     +     +   +  +
Sbjct: 4   GREEELERLLDAL----RRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAE 59

Query: 229 KRMWVCVSDPF------------DELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK 276
           +      S                EL + +  + A  G     G  + +    R     +
Sbjct: 60  RNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARAR 119

Query: 277 KFLLILDDM-WTDD 289
             +L+LDD+ W D+
Sbjct: 120 PLVLVLDDLQWADE 133

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	673
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.4
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.31
PRK04841	903	transcriptional regulator MalT; Provisional	99.18
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.1
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.09
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.08
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.03
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.03
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.9
KOG0472	565	consensus Leucine-rich repeat protein [Function un	98.88
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.87
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.83
PF05729	166	NACHT: NACHT domain	98.83
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.76
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.76
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.73
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.69
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.63
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.59
PTZ00202	550	tuzin; Provisional	98.53
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.53
PF13173	128	AAA_14: AAA domain	98.53
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.53
cd01128	249	rho_factor Transcription termination factor rho is	98.52
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.52
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.51
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.47
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.43
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.42
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.41
PRK09376	416	rho transcription termination factor Rho; Provisio	98.4
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.4
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.39
PRK06893	229	DNA replication initiation factor; Validated	98.36
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.36
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.32
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.31
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.29
PRK13342	413	recombination factor protein RarA; Reviewed	98.27
PLN03150	623	hypothetical protein; Provisional	98.25
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.24
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.23
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.22
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.22
TIGR00767	415	rho transcription termination factor Rho. Members	98.2
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.2
KOG2028	554	consensus ATPase related to the helicase subunit o	98.18
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.17
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.17
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.15
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.12
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.12
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.09
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.09
PRK12402	337	replication factor C small subunit 2; Reviewed	98.06
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.06
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.03
PRK13341	725	recombination factor protein RarA/unknown domain f	98.03
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	98.01
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.01
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.01
PLN03150	623	hypothetical protein; Provisional	97.98
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.98
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	97.93
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.93
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.91
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.91
PLN03025	319	replication factor C subunit; Provisional	97.9
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.89
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.88
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.87
PRK08727	233	hypothetical protein; Validated	97.81
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.81
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.8
COG3899	849	Predicted ATPase [General function prediction only	97.79
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.78
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.77
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.76
KOG4237	498	consensus Extracellular matrix protein slit, conta	97.75
PHA02544	316	44 clamp loader, small subunit; Provisional	97.73
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.71
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.71
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.7
PRK04195	482	replication factor C large subunit; Provisional	97.7
PRK09087	226	hypothetical protein; Validated	97.7
PRK08116	268	hypothetical protein; Validated	97.7
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.69
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.69
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.68
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.68
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.67
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.67
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.66
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.65
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.64
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.63
PRK08084	235	DNA replication initiation factor; Provisional	97.61
PF00004	132	AAA: ATPase family associated with various cellula	97.61
smart00382	148	AAA ATPases associated with a variety of cellular	97.61
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.6
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.6
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.58
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.57
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.56
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.55
PRK15386	426	type III secretion protein GogB; Provisional	97.55
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.51
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.51
PRK08118	167	topology modulation protein; Reviewed	97.49
COG3903	414	Predicted ATPase [General function prediction only	97.48
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.47
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.46
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.46
PRK05642	234	DNA replication initiation factor; Validated	97.44
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.43
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.42
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.41
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.41
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.41
PRK10536	262	hypothetical protein; Provisional	97.41
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.39
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.38
PRK15386	426	type III secretion protein GogB; Provisional	97.36
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.35
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.35
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.35
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.34
PRK12422	445	chromosomal replication initiation protein; Provis	97.32
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.31
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.31
PRK08181	269	transposase; Validated	97.26
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.23
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.22
CHL00181	287	cbbX CbbX; Provisional	97.2
PRK09183	259	transposase/IS protein; Provisional	97.19
PRK07952	244	DNA replication protein DnaC; Validated	97.18
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.18
PRK07261	171	topology modulation protein; Provisional	97.18
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.17
PRK12377	248	putative replication protein; Provisional	97.17
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.17
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.16
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.16
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.16
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.16
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.15
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.14
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.13
KOG4237	498	consensus Extracellular matrix protein slit, conta	97.12
PRK06921	266	hypothetical protein; Provisional	97.09
PRK06620	214	hypothetical protein; Validated	97.09
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.07
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.06
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.05
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.05
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.04
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.04
PRK06526	254	transposase; Provisional	97.02
CHL00095	821	clpC Clp protease ATP binding subunit	97.01
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.99
PF14516	331	AAA_35: AAA-like domain	96.98
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.97
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.96
PRK10865	857	protein disaggregation chaperone; Provisional	96.95
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	96.95
PRK08939	306	primosomal protein DnaI; Reviewed	96.94
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.94
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.94
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.93
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.9
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	96.9
PRK12608	380	transcription termination factor Rho; Provisional	96.88
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.87
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.87
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.87
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.87
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.86
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.85
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.84
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.84
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.84
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.83
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.8
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.8
PRK05541	176	adenylylsulfate kinase; Provisional	96.79
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.79
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	96.79
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.78
PRK06835	329	DNA replication protein DnaC; Validated	96.77
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.75
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.73
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.72
PRK04296	190	thymidine kinase; Provisional	96.72
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.71
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.71
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.7
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.7
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.7
PRK10865	857	protein disaggregation chaperone; Provisional	96.69
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.67
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.67
PRK06696	223	uridine kinase; Validated	96.65
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.62
PRK13695	174	putative NTPase; Provisional	96.62
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.6
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.59
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.58
CHL00095	821	clpC Clp protease ATP binding subunit	96.57
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.54
PHA00729	226	NTP-binding motif containing protein	96.52
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.52
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.51
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.5
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.5
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.48
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.46
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.45
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.45
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.45
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.44
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.43
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.41
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.38
PRK06067	234	flagellar accessory protein FlaH; Validated	96.35
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.34
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.34
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.33
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.31
cd03246	173	ABCC_Protease_Secretion This family represents the	96.31
PRK09354	349	recA recombinase A; Provisional	96.29
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.29
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.26
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.25
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.24
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.23
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.22
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.21
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.21
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.21
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.2
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.2
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.17
PHA02244	383	ATPase-like protein	96.17
CHL00176	638	ftsH cell division protein; Validated	96.16
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.15
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.13
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.12
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.12
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.12
PRK15455	644	PrkA family serine protein kinase; Provisional	96.11
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.09
PRK07667	193	uridine kinase; Provisional	96.09
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.08
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.08
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	96.08
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.07
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.06
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.05
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.05
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	96.04
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.04
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.03
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.01
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.01
PRK14974	336	cell division protein FtsY; Provisional	95.98
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.97
PTZ00035	337	Rad51 protein; Provisional	95.94
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.94
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.92
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.91
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	95.89
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	95.89
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.88
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.87
PRK05480	209	uridine/cytidine kinase; Provisional	95.86
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.85
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.84
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.76
PRK08233	182	hypothetical protein; Provisional	95.75
cd03215	182	ABC_Carb_Monos_II This family represents domain II	95.72
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.72
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	95.7
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	95.7
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.7
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	95.69
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.69
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.69
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.67
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.66
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.65
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.64
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.64
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	95.63
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	95.62
PTZ00301	210	uridine kinase; Provisional	95.62
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.61
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	95.61
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.6
TIGR00959	428	ffh signal recognition particle protein. This mode	95.59
PRK05439	311	pantothenate kinase; Provisional	95.59
PRK10867	433	signal recognition particle protein; Provisional	95.58
PRK11608	326	pspF phage shock protein operon transcriptional ac	95.57
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	95.57
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.57
PRK06547	172	hypothetical protein; Provisional	95.56
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.56
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.56
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.54
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.53
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	95.53
PRK13531	498	regulatory ATPase RavA; Provisional	95.51
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.49
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.48
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	95.44
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	95.43
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	95.42
PRK06762	166	hypothetical protein; Provisional	95.42
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.41
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	95.4
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	95.4
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	95.37
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.36
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.36
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.33
PRK00889	175	adenylylsulfate kinase; Provisional	95.31
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.29
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.29
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.25
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.25
PRK09580	248	sufC cysteine desulfurase ATPase component; Review	95.2
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.19
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.18
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.16
PRK03839	180	putative kinase; Provisional	95.16
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.16
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.14
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.13
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.11
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.1
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.1
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	95.07
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	95.06
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.03
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.03
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.02
PRK03846	198	adenylylsulfate kinase; Provisional	95.02
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.02
PTZ00088	229	adenylate kinase 1; Provisional	95.0
PRK07594	433	type III secretion system ATPase SsaN; Validated	94.98
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	94.94
PRK04040	188	adenylate kinase; Provisional	94.94
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.94
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.91
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	94.91
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.89
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	94.89
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	94.86
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	94.86
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	94.86
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.84
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.84
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.83
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	94.83
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	94.81
PRK15064	530	ABC transporter ATP-binding protein; Provisional	94.8
PRK00625	173	shikimate kinase; Provisional	94.8
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.79
PTZ00185	574	ATPase alpha subunit; Provisional	94.78
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	94.77
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	94.76
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.75
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	94.74
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	94.74
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	94.72
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.72
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.71
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	94.71
PRK07993	334	DNA polymerase III subunit delta'; Validated	94.7
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	94.7
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	94.69
PRK00131	175	aroK shikimate kinase; Reviewed	94.69
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.67
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	94.66
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	94.65
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	94.65
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	94.64
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	94.64
PRK04328	249	hypothetical protein; Provisional	94.63
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.62
PRK05022	509	anaerobic nitric oxide reductase transcription reg	94.61
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.61
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.6
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	94.6
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	94.58
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.53
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	94.53
PRK05922	434	type III secretion system ATPase; Validated	94.53
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.53
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	94.52
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	94.51
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.49
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	94.49
PRK08149	428	ATP synthase SpaL; Validated	94.47
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	94.47
PRK06217	183	hypothetical protein; Validated	94.47
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	94.42
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.39
PRK14738	206	gmk guanylate kinase; Provisional	94.37
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	94.37
PRK12678	672	transcription termination factor Rho; Provisional	94.33
KOG2123	388	consensus Uncharacterized conserved protein [Funct	94.32
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.32
PRK00300	205	gmk guanylate kinase; Provisional	94.31
PRK06936	439	type III secretion system ATPase; Provisional	94.31
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	94.3
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.29
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	94.29
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	94.28
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	94.27
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.26
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.26
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	94.26
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	94.25
PF07726	131	AAA_3: ATPase family associated with various cellu	94.23
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	94.2
PRK04132	846	replication factor C small subunit; Provisional	94.19
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.17
PRK13409	590	putative ATPase RIL; Provisional	94.17
COG0488	530	Uup ATPase components of ABC transporters with dup	94.17
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.17
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.16
PRK13949	169	shikimate kinase; Provisional	94.14
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	94.14
PLN02318	656	phosphoribulokinase/uridine kinase	94.13
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.12
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.11
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	94.1
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	94.1
COG0488	530	Uup ATPase components of ABC transporters with dup	94.09
PTZ00494	664	tuzin-like protein; Provisional	94.09
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	94.07
PRK11823	446	DNA repair protein RadA; Provisional	94.05
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	94.04
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	94.04
PRK09099	441	type III secretion system ATPase; Provisional	94.03
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	94.02
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.02
PRK13947	171	shikimate kinase; Provisional	94.01
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	93.99
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	93.98
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.98
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	93.96
PRK05973	237	replicative DNA helicase; Provisional	93.94
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	93.92
COG4181	228	Predicted ABC-type transport system involved in ly	93.92
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	93.9
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	93.9
PRK14737	186	gmk guanylate kinase; Provisional	93.88
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.88
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	93.88
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	93.88
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	93.87
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	93.87
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	93.86
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	93.86
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	93.86
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	93.86
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	93.84
COG4240	300	Predicted kinase [General function prediction only	93.82
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	93.82
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	93.8
cd03269	210	ABC_putative_ATPase This subfamily is involved in	93.8
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	93.77
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	93.75
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	93.74
PRK14530	215	adenylate kinase; Provisional	93.74
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.73
PRK13409	590	putative ATPase RIL; Provisional	93.73
PRK13975	196	thymidylate kinase; Provisional	93.72
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	93.7
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.69
PRK05057	172	aroK shikimate kinase I; Reviewed	93.68
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.67
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	93.66
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	93.66
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	93.66
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	93.66
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	93.66
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	93.66
PRK10416	318	signal recognition particle-docking protein FtsY;	93.65
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.64
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	93.64
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	93.64
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	93.63
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.62
PRK13765	637	ATP-dependent protease Lon; Provisional	93.59
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	93.58

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=2.4e-77  Score=675.49  Aligned_cols=618  Identities=27%  Similarity=0.400  Sum_probs=488.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHhhhhhhhhHHH
Q 005860            3 DAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDE   82 (673)
Q Consensus         3 ~a~v~~~~~~l~~~l~~~~~~e~~~~~~~~~~i~~L~~~L~~i~~~l~~a~~~~~~~~~~~~wl~~lr~~ay~~ed~lD~   82 (673)
                      ++.++..++++.+.    +.++...+.+.++.+..|++.|..+++++++|+.++.....+..|...+++++|++||+++.
T Consensus         2 ~~~~s~~~~~~~~~----l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~   77 (889)
T KOG4658|consen    2 GACVSFGVEKLDQL----LNRESECLDGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWL   77 (889)
T ss_pred             CeEEEEehhhHHHH----HHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566666777665    56677888999999999999999999999999999988889999999999999999999999


Q ss_pred             HHHHHHHHHHhccCCCCcccccccccCCccccCccchhhhHHHHHHHHHHHHHHHHHHhhcccCCccc----ccC-CCCc
Q 005860           83 WNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNV----IRS-TENS  157 (673)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~l~~i~~~~~~~~~~~----~~~-~~~~  157 (673)
                      |.......+..+.-...  ....+.+      |..  ..++..+..+..+.+++.++.+....+....    ... ..+.
T Consensus        78 ~~v~~~~~~~~~~l~~~--~~~~~~~------c~~--~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~  147 (889)
T KOG4658|consen   78 FLVEEIERKANDLLSTR--SVERQRL------CLC--GFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPR  147 (889)
T ss_pred             HHHHHHHHHHhHHhhhh--HHHHHHH------hhh--hhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccch
Confidence            98776554322211000  0000101      000  2334455555555555555555444443222    111 1111


Q ss_pred             ccccccccccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc-ccccCCeEEEEEcC
Q 005860          158 ERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD-VFEYFDKRMWVCVS  236 (673)
Q Consensus       158 ~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~vs  236 (673)
                      ....+.+.....+ ||.+..++++.+.|.+++       ..+++|+||||+||||||+.++|+.. ++.+||.++||+||
T Consensus       148 ~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~-------~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VS  219 (889)
T KOG4658|consen  148 EKVETRPIQSESD-VGLETMLEKLWNRLMEDD-------VGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVS  219 (889)
T ss_pred             hhcccCCCCcccc-ccHHHHHHHHHHHhccCC-------CCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEc
Confidence            1223333333334 999999999999998776       38999999999999999999999987 99999999999999


Q ss_pred             CcccHHHHHHHHHHHhhCCCCCcC--cHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC
Q 005860          237 DPFDELRIAKAIIEALEGFVPTVG--ELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       237 ~~~~~~~~~~~i~~~l~~~~~~~~--~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                      +.++...++.+|+..++..+....  +.++++..+.+.|++|||+|||||||+.  .+|+.+..++|...+||||++|||
T Consensus       220 k~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~--~dw~~I~~~~p~~~~g~KvvlTTR  297 (889)
T KOG4658|consen  220 KEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEE--VDWDKIGVPFPSRENGSKVVLTTR  297 (889)
T ss_pred             ccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEEEeccccc--ccHHhcCCCCCCccCCeEEEEEec
Confidence            999999999999999988544322  2478899999999999999999999986  469999999999999999999999


Q ss_pred             ChhHHHh-ccccceeecCCCCccccc----------------------------cCCchhhHHHHhhhhccCCCHHHHHH
Q 005860          315 KETVARM-MESIHVISIKELSEQECW----------------------------CKGLPLAAKTIGSLLRFKRTREEWES  365 (673)
Q Consensus       315 ~~~v~~~-~~~~~~~~l~~L~~~~~~----------------------------c~GlPLai~~~~~~L~~~~~~~~w~~  365 (673)
                      ++.|+.. |++...+++++|+.+|||                            |+|+|||++++|+.|+.|++.++|++
T Consensus       298 s~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~  377 (889)
T KOG4658|consen  298 SEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRR  377 (889)
T ss_pred             cHhhhhccccCCccccccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHH
Confidence            9999999 888999999999999999                            99999999999999999999999999


Q ss_pred             HHhhhccc----chhhhhccchhhhhcccCCChhhhhhhch------------HHHHHHHHHcCCCCC-CCCCcHHHHHH
Q 005860          366 ILDSELWQ----LEEFEKGLLAPLLLSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMP-EGNKELEIIGE  428 (673)
Q Consensus       366 ~l~~~~~~----~~~~~~~i~~~l~~sy~~L~~~~k~cfl~------------~~l~~~w~a~g~i~~-~~~~~~e~~~~  428 (673)
                      +.+...+.    ..+..+.++++|++||+.||+++|.||+|            ..|+.+|+||||+.+ ..+.+++++|+
T Consensus       378 ~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~  457 (889)
T KOG4658|consen  378 ALNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGY  457 (889)
T ss_pred             HHccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchH
Confidence            99876554    23346789999999999999999999999            799999999999988 45788999999


Q ss_pred             HHHHHHHhcccccccccCCCCcEeEEEeChHHHHHHHHhcc-----cceEEEEecCCCCcccccccccCceEEEEEEcCC
Q 005860          429 EYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTK-----NECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGY  503 (673)
Q Consensus       429 ~~~~~L~~~sli~~~~~~~~~~~~~~~mHdlv~~~a~~i~~-----~e~~~~~~~~~~~~~~~~~~~~~~~r~l~l~~~~  503 (673)
                      .|+.+|++++|++.....  ++..+|+|||+|||+|.++++     .++.++..+.... .......+..+|++++..+.
T Consensus       458 ~~i~~LV~~~Ll~~~~~~--~~~~~~kmHDvvRe~al~ias~~~~~~e~~iv~~~~~~~-~~~~~~~~~~~rr~s~~~~~  534 (889)
T KOG4658|consen  458 DYIEELVRASLLIEERDE--GRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLS-EIPQVKSWNSVRRMSLMNNK  534 (889)
T ss_pred             HHHHHHHHHHHHhhcccc--cceeEEEeeHHHHHHHHHHhccccccccceEEECCcCcc-ccccccchhheeEEEEeccc
Confidence            999999999999876543  566799999999999999999     6664444331111 01222345678999998887


Q ss_pred             CCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhccccccccccccceecC
Q 005860          504 EASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILKGIEKLIHLRYLRLVG  582 (673)
Q Consensus       504 ~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~~i~~L~~Lr~L~L~~  582 (673)
                      ....+... .+++|+||.+.++..  .+......+|..++.|+||||++       |. +.++|++|+.|.|||||+|++
T Consensus       535 ~~~~~~~~-~~~~L~tLll~~n~~--~l~~is~~ff~~m~~LrVLDLs~-------~~~l~~LP~~I~~Li~LryL~L~~  604 (889)
T KOG4658|consen  535 IEHIAGSS-ENPKLRTLLLQRNSD--WLLEISGEFFRSLPLLRVLDLSG-------NSSLSKLPSSIGELVHLRYLDLSD  604 (889)
T ss_pred             hhhccCCC-CCCccceEEEeecch--hhhhcCHHHHhhCcceEEEECCC-------CCccCcCChHHhhhhhhhcccccC
Confidence            65544433 456899999988752  34566677899999999999998       55 789999999999999999999


Q ss_pred             CCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCeeEEccCC
Q 005860          583 LGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRGG  657 (673)
Q Consensus       583 ~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~~~~~~~  657 (673)
                      |.+..||.++++|+.|.+||+..+..+..+|..+..|.+||+|.+.......--..++.+.+|++|..+.+...+
T Consensus       605 t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s  679 (889)
T KOG4658|consen  605 TGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISS  679 (889)
T ss_pred             CCccccchHHHHHHhhheeccccccccccccchhhhcccccEEEeeccccccchhhHHhhhcccchhhheeecch
Confidence            999999999999999999999998878888877777999999997665432222335566666666666665444

>PLN03210 Resistant to P

Probab=100.00  E-value=1.2e-48  Score=466.13  Aligned_cols=481  Identities=21%  Similarity=0.275  Sum_probs=341.1

Q ss_pred             HHHHHHHHHHHHHHHhhcccCCccccc---------CCCCcccccccccccCCcceechhhHHHHHHHhccCCcccccCC
Q 005860          126 AVKIKAINGKLDDIAKQKDMYNFNVIR---------STENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIIND  196 (673)
Q Consensus       126 ~~~i~~~~~~l~~i~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~  196 (673)
                      ..+++++++.|.+++.... +.+....         ..........++..+.+++|||+++++++..+|..+.     ++
T Consensus       133 ~~~~~~w~~al~~~~~~~g-~~~~~~~~E~~~i~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~-----~~  206 (1153)
T PLN03210        133 EDEKIQWKQALTDVANILG-YHSQNWPNEAKMIEEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLES-----EE  206 (1153)
T ss_pred             hhHHHHHHHHHHHHhCcCc-eecCCCCCHHHHHHHHHHHHHHhhccccCcccccccchHHHHHHHHHHHcccc-----Cc
Confidence            3578888888888875332 2221100         0011112223334456789999999999999886543     56


Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc---CCc-----------cc-HHHHHHHHHHHhhCCCC-CcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV---SDP-----------FD-ELRIAKAIIEALEGFVP-TVG  260 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~-----------~~-~~~~~~~i~~~l~~~~~-~~~  260 (673)
                      +++|+||||||+||||||+++|+.  +..+|++.+|+..   +..           ++ ...++.+++.++..... ...
T Consensus       207 ~~vvgI~G~gGiGKTTLA~~l~~~--l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~  284 (1153)
T PLN03210        207 VRMVGIWGSSGIGKTTIARALFSR--LSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIY  284 (1153)
T ss_pred             eEEEEEEcCCCCchHHHHHHHHHH--HhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccC
Confidence            899999999999999999999995  7789999888742   111           01 12344555555433221 111


Q ss_pred             cHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeecCCCCccccc-
Q 005860          261 ELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW-  339 (673)
Q Consensus       261 ~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l~~L~~~~~~-  339 (673)
                      .    ...+++.+++||+||||||||+  ..+|+.+.....+.++||+||||||++.++..++..++|+++.|++++|| 
T Consensus       285 ~----~~~~~~~L~~krvLLVLDdv~~--~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~  358 (1153)
T PLN03210        285 H----LGAMEERLKHRKVLIFIDDLDD--QDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALE  358 (1153)
T ss_pred             C----HHHHHHHHhCCeEEEEEeCCCC--HHHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHH
Confidence            1    2457788999999999999975  46899988877788899999999999999988888899999999999998 


Q ss_pred             --------------------------cCCchhhHHHHhhhhccCCCHHHHHHHHhhhcccchhhhhccchhhhhcccCCC
Q 005860          340 --------------------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLP  393 (673)
Q Consensus       340 --------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~  393 (673)
                                                |+|+|||++++|+.|+.+ +..+|+.++++..+.   .+.++.++|++||++|+
T Consensus       359 LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k-~~~~W~~~l~~L~~~---~~~~I~~~L~~SYd~L~  434 (1153)
T PLN03210        359 MFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGR-DKEDWMDMLPRLRNG---LDGKIEKTLRVSYDGLN  434 (1153)
T ss_pred             HHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCC-CHHHHHHHHHHHHhC---ccHHHHHHHHHhhhccC
Confidence                                      999999999999999876 689999999876543   34578999999999998


Q ss_pred             h-hhhhhhch---------HHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHhcccccccccCCCCcEeEEEeChHHHHH
Q 005860          394 P-MIKRCFQY---------YELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDF  463 (673)
Q Consensus       394 ~-~~k~cfl~---------~~l~~~w~a~g~i~~~~~~~~e~~~~~~~~~L~~~sli~~~~~~~~~~~~~~~mHdlv~~~  463 (673)
                      + ..|.||++         .+.+..|.+.+....          +..++.|+++||++...    +   ++.|||++|++
T Consensus       435 ~~~~k~~Fl~ia~ff~~~~~~~v~~~l~~~~~~~----------~~~l~~L~~ksLi~~~~----~---~~~MHdLl~~~  497 (1153)
T PLN03210        435 NKKDKAIFRHIACLFNGEKVNDIKLLLANSDLDV----------NIGLKNLVDKSLIHVRE----D---IVEMHSLLQEM  497 (1153)
T ss_pred             ccchhhhhheehhhcCCCCHHHHHHHHHhcCCCc----------hhChHHHHhcCCEEEcC----C---eEEhhhHHHHH
Confidence            7 59999998         345667777665432          22388999999997632    1   68999999999


Q ss_pred             HHHhcccceE------EEEecCCCCcccccccccCceEEEEEEcCCCCcc---ccccccccccchhhhccchhhh-----
Q 005860          464 AQFLTKNECI------AIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASF---PISIFKAKNLRSLFINNTLIQV-----  529 (673)
Q Consensus       464 a~~i~~~e~~------~~~~~~~~~~~~~~~~~~~~~r~l~l~~~~~~~~---~~~~~~~~~Lr~L~l~~~~~~~-----  529 (673)
                      |+.+++.+..      +..................+++.+++........   ...+..|++|+.|.+..+....     
T Consensus       498 ~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~~L~~L~~~~~~~~~~~~~~  577 (1153)
T PLN03210        498 GKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFLKFYTKKWDQKKEVR  577 (1153)
T ss_pred             HHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCccccEEEEecccccccccce
Confidence            9999876531      1111000000011122334566666654433211   2234456666666554321000     


Q ss_pred             -h--------------------hhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCC-Ccc
Q 005860          530 -S--------------------LTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG-TEE  587 (673)
Q Consensus       530 -~--------------------~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~-i~~  587 (673)
                       .                    ....+|..| .+.+|+.|++.+       +.+..+|..+..+++|++|+|+++. ++.
T Consensus       578 ~~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f-~~~~L~~L~L~~-------s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~  649 (1153)
T PLN03210        578 WHLPEGFDYLPPKLRLLRWDKYPLRCMPSNF-RPENLVKLQMQG-------SKLEKLWDGVHSLTGLRNIDLRGSKNLKE  649 (1153)
T ss_pred             eecCcchhhcCcccEEEEecCCCCCCCCCcC-CccCCcEEECcC-------ccccccccccccCCCCCEEECCCCCCcCc
Confidence             0                    001122222 356777888877       7888888889999999999999887 888


Q ss_pred             cchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccc-cccccccccCCCCCCCCcCCee
Q 005860          588 LPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDD-SCLEFIPKGIQRLTNLRTLSEF  651 (673)
Q Consensus       588 LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~-~~l~~lP~~i~~L~~L~~L~~~  651 (673)
                      +|. ++.+++|++|+|++|..+..+|..+++|++|++|++++ +.+..+|.++ ++++|+.|...
T Consensus       650 ip~-ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~L~Ls  712 (1153)
T PLN03210        650 IPD-LSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI-NLKSLYRLNLS  712 (1153)
T ss_pred             CCc-cccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcC-CCCCCCEEeCC
Confidence            885 88899999999999998999999999999999999764 5688888776 67777776543

syringae 6; Provisional

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=100.00  E-value=3.6e-38  Score=323.15  Aligned_cols=238  Identities=39%  Similarity=0.634  Sum_probs=195.3

Q ss_pred             chhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          174 RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       174 r~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ||.++++|.+.|....     ++.++|+|+||||+||||||++++++..++.+|+.++|+.++...+...++..|+.+++
T Consensus         1 re~~~~~l~~~L~~~~-----~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~   75 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNS-----NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLG   75 (287)
T ss_dssp             -HHHHHHHHHHHHTTT-----TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHhhCCC-----CCeEEEEEEcCCcCCcceeeeeccccccccccccccccccccccccccccccccccccc
Confidence            7899999999998754     45899999999999999999999998778899999999999999999999999999998


Q ss_pred             CCCC---CcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhccc-cceee
Q 005860          254 GFVP---TVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMES-IHVIS  329 (673)
Q Consensus       254 ~~~~---~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~-~~~~~  329 (673)
                      ....   ...+.++....+.+.|+++++||||||||+.  ..|+.+...++.+..||+||||||+..++..++. ...++
T Consensus        76 ~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~  153 (287)
T PF00931_consen   76 EPDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDE--EDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIE  153 (287)
T ss_dssp             CC-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SH--HHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEE
T ss_pred             ccccccccccccccccccchhhhccccceeeeeeeccc--cccccccccccccccccccccccccccccccccccccccc
Confidence            8743   4467788999999999999999999999764  5888888888887889999999999999887665 78999


Q ss_pred             cCCCCccccc----------------------------cCCchhhHHHHhhhhccCCCHHHHHHHHhhhcccch---hhh
Q 005860          330 IKELSEQECW----------------------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLE---EFE  378 (673)
Q Consensus       330 l~~L~~~~~~----------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l~~~~~~~~---~~~  378 (673)
                      +++|+.+|++                            |+|+|||++++|++|+.+.+..+|+.+++...+...   +..
T Consensus       154 l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~  233 (287)
T PF00931_consen  154 LEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYD  233 (287)
T ss_dssp             CSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSC
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            9999999998                            999999999999999766678899998876554432   235


Q ss_pred             hccchhhhhcccCCChhhhhhhch------------HHHHHHHHHcCCCCCC
Q 005860          379 KGLLAPLLLSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMPE  418 (673)
Q Consensus       379 ~~i~~~l~~sy~~L~~~~k~cfl~------------~~l~~~w~a~g~i~~~  418 (673)
                      ..+..++.+||+.||++.|.||+|            ..++.+|+++|||...
T Consensus       234 ~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~~  285 (287)
T PF00931_consen  234 RSVFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISSK  285 (287)
T ss_dssp             HHHHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC--
T ss_pred             ccccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCccc
Confidence            678999999999999999999999            7999999999999764

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.40  E-value=1.1e-14  Score=128.00  Aligned_cols=139  Identities=27%  Similarity=0.338  Sum_probs=117.2

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh--hhcccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN--KILKGI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~--~lp~~i  569 (673)
                      .++..+.+..+....+|.++.++++||.|.+.-+..     ..+|.-|+.++-|.+|||.+       +.+.  .+|..+
T Consensus        56 ~nlevln~~nnqie~lp~~issl~klr~lnvgmnrl-----~~lprgfgs~p~levldlty-------nnl~e~~lpgnf  123 (264)
T KOG0617|consen   56 KNLEVLNLSNNQIEELPTSISSLPKLRILNVGMNRL-----NILPRGFGSFPALEVLDLTY-------NNLNENSLPGNF  123 (264)
T ss_pred             hhhhhhhcccchhhhcChhhhhchhhhheecchhhh-----hcCccccCCCchhhhhhccc-------cccccccCCcch
Confidence            445556666666677788888888888887765432     45677788999999999998       7754  489999


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLT  643 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~  643 (673)
                      ..|..||.|.|+.|.++-+|+.+++|++||.|.++.+. +-++|.+++.|+.||.|++.+|.+..+|++++++.
T Consensus       124 f~m~tlralyl~dndfe~lp~dvg~lt~lqil~lrdnd-ll~lpkeig~lt~lrelhiqgnrl~vlppel~~l~  196 (264)
T KOG0617|consen  124 FYMTTLRALYLGDNDFEILPPDVGKLTNLQILSLRDND-LLSLPKEIGDLTRLRELHIQGNRLTVLPPELANLD  196 (264)
T ss_pred             hHHHHHHHHHhcCCCcccCChhhhhhcceeEEeeccCc-hhhCcHHHHHHHHHHHHhcccceeeecChhhhhhh
Confidence            99999999999999999999999999999999999965 88999999999999999999999999999888764

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.31  E-value=4.9e-14  Score=123.90  Aligned_cols=145  Identities=29%  Similarity=0.351  Sum_probs=95.8

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      .+.++.++.+.....|+.+..+.+|.+|.++++..     ..+|..++.++.|+.|++.-       +.+..+|..+|.+
T Consensus        34 ~ITrLtLSHNKl~~vppnia~l~nlevln~~nnqi-----e~lp~~issl~klr~lnvgm-------nrl~~lprgfgs~  101 (264)
T KOG0617|consen   34 NITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQI-----EELPTSISSLPKLRILNVGM-------NRLNILPRGFGSF  101 (264)
T ss_pred             hhhhhhcccCceeecCCcHHHhhhhhhhhcccchh-----hhcChhhhhchhhhheecch-------hhhhcCccccCCC
Confidence            44555566565566666666677777777766653     34555566667777777666       6666667777777


Q ss_pred             cccccceecCCCC--cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCe
Q 005860          573 IHLRYLRLVGLGT--EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       573 ~~Lr~L~L~~~~i--~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~  650 (673)
                      +.|..|||..|++  ..||..+..++-|+.|+|+++. ++.+|.++++|++|+.|.++.|.+-.+|.++|.|+.|+.|..
T Consensus       102 p~levldltynnl~e~~lpgnff~m~tlralyl~dnd-fe~lp~dvg~lt~lqil~lrdndll~lpkeig~lt~lrelhi  180 (264)
T KOG0617|consen  102 PALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDND-FEILPPDVGKLTNLQILSLRDNDLLSLPKEIGDLTRLRELHI  180 (264)
T ss_pred             chhhhhhccccccccccCCcchhHHHHHHHHHhcCCC-cccCChhhhhhcceeEEeeccCchhhCcHHHHHHHHHHHHhc
Confidence            7777777766663  3466666666666777776643 667777777777777777777777777777777776666643

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.18  E-value=6.2e-10  Score=132.83  Aligned_cols=268  Identities=16%  Similarity=0.191  Sum_probs=155.6

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcC-CcccHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS-DPFDELRIAK  246 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~~~~  246 (673)
                      ++.++-|+.-.+.+    ...      ...+++.|+|++|.||||++......      ++.++|+++. .+.++..+..
T Consensus        13 ~~~~~~R~rl~~~l----~~~------~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~   76 (903)
T PRK04841         13 LHNTVVRERLLAKL----SGA------NNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFAS   76 (903)
T ss_pred             ccccCcchHHHHHH----hcc------cCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHH
Confidence            34567776555444    222      34789999999999999999888753      2368999985 4456677778


Q ss_pred             HHHHHhhCCCCC-------------cCcHHHHHHHHHHHhC--CCeEEEEEcCCCCCCccchh-hhhhhccCCCCCeEEE
Q 005860          247 AIIEALEGFVPT-------------VGELNSLLESIRASLV--GKKFLLILDDMWTDDYSKWE-PFHYCLKNGVRGSKIL  310 (673)
Q Consensus       247 ~i~~~l~~~~~~-------------~~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~~~~~~-~l~~~l~~~~~gs~ii  310 (673)
                      .++..+......             ..+.......+...+.  +.+++|||||+..-+..... .+...+.....+.++|
T Consensus        77 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv  156 (903)
T PRK04841         77 YLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLV  156 (903)
T ss_pred             HHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEE
Confidence            888877532111             0122233333333332  68999999999554333333 3433344445667888


Q ss_pred             EEcCChhH---HHhccccceeecC----CCCccccc----------------------cCCchhhHHHHhhhhccCCC-H
Q 005860          311 VTTRKETV---ARMMESIHVISIK----ELSEQECW----------------------CKGLPLAAKTIGSLLRFKRT-R  360 (673)
Q Consensus       311 vTtr~~~v---~~~~~~~~~~~l~----~L~~~~~~----------------------c~GlPLai~~~~~~L~~~~~-~  360 (673)
                      ||||...-   ...........+.    +|+.+|+.                      |+|.|+++..++..++.... .
T Consensus       157 ~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~  236 (903)
T PRK04841        157 VLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIEAAESSRLCDDVEGWATALQLIALSARQNNSSL  236 (903)
T ss_pred             EEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCCHHHHHHHHHHhCChHHHHHHHHHHHhhCCCch
Confidence            99997421   1111112233444    67777764                      99999999998877754321 1


Q ss_pred             HHHHHHHhhhcccchh-hhhccchhhh-hcccCCChhhhhhhchHHHHH---HHHHcCCCCCCCCCcHHHHHHHHHHHHH
Q 005860          361 EEWESILDSELWQLEE-FEKGLLAPLL-LSYNDLPPMIKRCFQYYELIK---LWMAQDYIMPEGNKELEIIGEEYFDYLA  435 (673)
Q Consensus       361 ~~w~~~l~~~~~~~~~-~~~~i~~~l~-~sy~~L~~~~k~cfl~~~l~~---~w~a~g~i~~~~~~~~e~~~~~~~~~L~  435 (673)
                      ...   ..    .+.. ....+...+. -.++.||++.+..++...+..   ...+..+..       .+.+...+++|.
T Consensus       237 ~~~---~~----~~~~~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~~~~~~l~~~l~~-------~~~~~~~L~~l~  302 (903)
T PRK04841        237 HDS---AR----RLAGINASHLSDYLVEEVLDNVDLETRHFLLRCSVLRSMNDALIVRVTG-------EENGQMRLEELE  302 (903)
T ss_pred             hhh---hH----hhcCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccccCCHHHHHHHcC-------CCcHHHHHHHHH
Confidence            111   11    1100 0112333332 347799999988876633321   111211111       112356789999


Q ss_pred             hcccccccccCCCCcEeEEEeChHHHHHHHHhc
Q 005860          436 MRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLT  468 (673)
Q Consensus       436 ~~sli~~~~~~~~~~~~~~~mHdlv~~~a~~i~  468 (673)
                      ..+++..... ..+  ..|++|++++++.+...
T Consensus       303 ~~~l~~~~~~-~~~--~~yr~H~L~r~~l~~~l  332 (903)
T PRK04841        303 RQGLFIQRMD-DSG--EWFRYHPLFASFLRHRC  332 (903)
T ss_pred             HCCCeeEeec-CCC--CEEehhHHHHHHHHHHH
Confidence            9998743211 112  25778999999987654

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.10  E-value=6.3e-11  Score=142.21  Aligned_cols=149  Identities=21%  Similarity=0.241  Sum_probs=99.2

Q ss_pred             cCceEEEEEEcCCCC-ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhccc
Q 005860          491 QEKLRHSMLVLGYEA-SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKG  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~-~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~  568 (673)
                      ..+++.+.+..+... ..|..+..+++|++|++.++..    ...+|..+.++++|++|++++       |.+. .+|..
T Consensus       139 l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~l----~~~~p~~~~~l~~L~~L~L~~-------n~l~~~~p~~  207 (968)
T PLN00113        139 IPNLETLDLSNNMLSGEIPNDIGSFSSLKVLDLGGNVL----VGKIPNSLTNLTSLEFLTLAS-------NQLVGQIPRE  207 (968)
T ss_pred             cCCCCEEECcCCcccccCChHHhcCCCCCEEECccCcc----cccCChhhhhCcCCCeeeccC-------CCCcCcCChH
Confidence            345666666665543 3455566677777777776652    234455666777777777777       6643 46777


Q ss_pred             cccccccccceecCCCC-cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc-cccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE-FIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i-~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~-~lP~~i~~L~~L~  646 (673)
                      ++++.+|++|+|++|.+ ..+|..++++++|++|++++|.....+|..++++++|++|+++.|.+. .+|..++++++|+
T Consensus       208 l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~  287 (968)
T PLN00113        208 LGQMKSLKWIYLGYNNLSGEIPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLI  287 (968)
T ss_pred             HcCcCCccEEECcCCccCCcCChhHhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcC
Confidence            77777777777777774 367777777777777777776644467777777777777777777664 4666677777666


Q ss_pred             cCCe
Q 005860          647 TLSE  650 (673)
Q Consensus       647 ~L~~  650 (673)
                      .|..
T Consensus       288 ~L~L  291 (968)
T PLN00113        288 SLDL  291 (968)
T ss_pred             EEEC
Confidence            6543

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.09  E-value=7.1e-12  Score=130.69  Aligned_cols=132  Identities=21%  Similarity=0.251  Sum_probs=96.3

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..++.|+++..+........+..++.||++++..|...   ...+|.-+-.++.|.+|||+.       +++.+.|..+.
T Consensus        54 lqkLEHLs~~HN~L~~vhGELs~Lp~LRsv~~R~N~LK---nsGiP~diF~l~dLt~lDLSh-------NqL~EvP~~LE  123 (1255)
T KOG0444|consen   54 LQKLEHLSMAHNQLISVHGELSDLPRLRSVIVRDNNLK---NSGIPTDIFRLKDLTILDLSH-------NQLREVPTNLE  123 (1255)
T ss_pred             HhhhhhhhhhhhhhHhhhhhhccchhhHHHhhhccccc---cCCCCchhcccccceeeecch-------hhhhhcchhhh
Confidence            45677888877777666667777888888888776631   122333344778888888888       88888888887


Q ss_pred             cccccccceecCCCCcccchhhh-cCCCccEEEeccCCCCccccccccccccCCeeeccccccc
Q 005860          571 KLIHLRYLRLVGLGTEELPETCC-ELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~-~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      .-+++-.|+|+.|+|..+|.+++ +|+-|-+||||++. ++.+|..+.+|.+|+.|.+++|.+.
T Consensus       124 ~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS~Nr-Le~LPPQ~RRL~~LqtL~Ls~NPL~  186 (1255)
T KOG0444|consen  124 YAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLSNNR-LEMLPPQIRRLSMLQTLKLSNNPLN  186 (1255)
T ss_pred             hhcCcEEEEcccCccccCCchHHHhhHhHhhhccccch-hhhcCHHHHHHhhhhhhhcCCChhh
Confidence            77778888888888888885543 67777788888754 7888888888888888887777643

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.08  E-value=8.4e-11  Score=141.13  Aligned_cols=171  Identities=23%  Similarity=0.168  Sum_probs=135.8

Q ss_pred             cCceEEEEEEcCCC-CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhccc
Q 005860          491 QEKLRHSMLVLGYE-ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKG  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~-~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~  568 (673)
                      ..+++.+.+..+.. ...|..+.++++|++|.+.++..    ...+|..+.++++|+.|++++       +.+. .+|..
T Consensus       163 l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l----~~~~p~~l~~l~~L~~L~L~~-------n~l~~~~p~~  231 (968)
T PLN00113        163 FSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQL----VGQIPRELGQMKSLKWIYLGY-------NNLSGEIPYE  231 (968)
T ss_pred             CCCCCEEECccCcccccCChhhhhCcCCCeeeccCCCC----cCcCChHHcCcCCccEEECcC-------CccCCcCChh
Confidence            46789999988765 35677788999999999998863    344677788999999999999       8755 68889


Q ss_pred             cccccccccceecCCCC-cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc-cccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE-FIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i-~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~-~lP~~i~~L~~L~  646 (673)
                      ++.+++|++|+|++|.+ ..+|.+++++++|++|++++|.....+|..++++++|++|+++.|.+. .+|..++++++|+
T Consensus       232 l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~  311 (968)
T PLN00113        232 IGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNSLSGEIPELVIQLQNLE  311 (968)
T ss_pred             HhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECcCCeeccCCChhHcCCCCCc
Confidence            99999999999999995 578999999999999999998745678999999999999999988876 5777788888888


Q ss_pred             cCCeeEEcc--CCccCCCccccCCCCCC
Q 005860          647 TLSEFVVVR--GGSKYGGKACNLEGLRY  672 (673)
Q Consensus       647 ~L~~~~~~~--~~~~~~~~~~~l~~L~~  672 (673)
                      .|......-  ..+..+..+.+|+.|.+
T Consensus       312 ~L~l~~n~~~~~~~~~~~~l~~L~~L~L  339 (968)
T PLN00113        312 ILHLFSNNFTGKIPVALTSLPRLQVLQL  339 (968)
T ss_pred             EEECCCCccCCcCChhHhcCCCCCEEEC
Confidence            876543221  11122344556665544

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=99.03  E-value=2.9e-11  Score=120.23  Aligned_cols=146  Identities=21%  Similarity=0.228  Sum_probs=123.5

Q ss_pred             eEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccccc
Q 005860          494 LRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLI  573 (673)
Q Consensus       494 ~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~  573 (673)
                      +..+.+..+.....|..+..++.+.|..+..+.    ...++|..++.+++|..|+|++       +.+..+|..++.+.
T Consensus       390 Vt~VnfskNqL~elPk~L~~lkelvT~l~lsnn----~isfv~~~l~~l~kLt~L~L~N-------N~Ln~LP~e~~~lv  458 (565)
T KOG0472|consen  390 VTSVNFSKNQLCELPKRLVELKELVTDLVLSNN----KISFVPLELSQLQKLTFLDLSN-------NLLNDLPEEMGSLV  458 (565)
T ss_pred             eEEEecccchHhhhhhhhHHHHHHHHHHHhhcC----ccccchHHHHhhhcceeeeccc-------chhhhcchhhhhhh
Confidence            556667777777788877777777776655443    2356778889999999999999       99999999999999


Q ss_pred             ccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeeccccccccccccCCCCCCCCcCCee
Q 005860          574 HLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEF  651 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~  651 (673)
                      .||.|+++.|.+..+|..+..++-|+++-.+++. +.++|.+ +.+|.+|..||+..|.+..+|+++|++++|++|...
T Consensus       459 ~Lq~LnlS~NrFr~lP~~~y~lq~lEtllas~nq-i~~vd~~~l~nm~nL~tLDL~nNdlq~IPp~LgnmtnL~hLeL~  536 (565)
T KOG0472|consen  459 RLQTLNLSFNRFRMLPECLYELQTLETLLASNNQ-IGSVDPSGLKNMRNLTTLDLQNNDLQQIPPILGNMTNLRHLELD  536 (565)
T ss_pred             hhheecccccccccchHHHhhHHHHHHHHhcccc-ccccChHHhhhhhhcceeccCCCchhhCChhhccccceeEEEec
Confidence            9999999999999999988888889998888755 8888765 999999999999999999999999999999988543

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.03  E-value=2.2e-11  Score=127.06  Aligned_cols=146  Identities=27%  Similarity=0.308  Sum_probs=111.3

Q ss_pred             EEEEcCCCCccccccccccccchhhhccchhhh---------------------hhhhhHHHHhhhCCccceeeeccccc
Q 005860          497 SMLVLGYEASFPISIFKAKNLRSLFINNTLIQV---------------------SLTHVLQSLFDQLKCLRALRIATLMN  555 (673)
Q Consensus       497 l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~---------------------~~~~~~~~~~~~l~~L~~L~L~~~~~  555 (673)
                      +.++.+....+|+.+..+.+|++|.+++|....                     .....+|..+..+.+|+-+|++.   
T Consensus       155 LDLS~NrLe~LPPQ~RRL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~---  231 (1255)
T KOG0444|consen  155 LDLSNNRLEMLPPQIRRLSMLQTLKLSNNPLNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSE---  231 (1255)
T ss_pred             hccccchhhhcCHHHHHHhhhhhhhcCCChhhHHHHhcCccchhhhhhhcccccchhhcCCCchhhhhhhhhccccc---
Confidence            344444445566666666666666666654210                     01123455567777788888888   


Q ss_pred             cccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc--
Q 005860          556 TWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE--  633 (673)
Q Consensus       556 ~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~--  633 (673)
                          +.+..+|+.+-++.+|+-|+|++|.|++|--.++...+|++|++|.+. +..+|+.+.+|++|+.|.+..|.+.  
T Consensus       232 ----N~Lp~vPecly~l~~LrrLNLS~N~iteL~~~~~~W~~lEtLNlSrNQ-Lt~LP~avcKL~kL~kLy~n~NkL~Fe  306 (1255)
T KOG0444|consen  232 ----NNLPIVPECLYKLRNLRRLNLSGNKITELNMTEGEWENLETLNLSRNQ-LTVLPDAVCKLTKLTKLYANNNKLTFE  306 (1255)
T ss_pred             ----cCCCcchHHHhhhhhhheeccCcCceeeeeccHHHHhhhhhhccccch-hccchHHHhhhHHHHHHHhccCccccc
Confidence                888888888888999999999999999998888888999999999865 9999999999999999998888754  


Q ss_pred             cccccCCCCCCCCcCCe
Q 005860          634 FIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       634 ~lP~~i~~L~~L~~L~~  650 (673)
                      .+|++||+|..|..+..
T Consensus       307 GiPSGIGKL~~Levf~a  323 (1255)
T KOG0444|consen  307 GIPSGIGKLIQLEVFHA  323 (1255)
T ss_pred             CCccchhhhhhhHHHHh
Confidence            79999999998887743

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.90  E-value=3.7e-08  Score=99.82  Aligned_cols=137  Identities=18%  Similarity=0.167  Sum_probs=82.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHH----HH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIR----AS  272 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~----~~  272 (673)
                      ..++.|+|++|+|||||++.+++..... .+ ..+|+ +....+..+++..|...++..... .+.......+.    ..
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~-~~~~~~~~~l~~~l~~~  118 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETEG-RDKAALLRELEDFLIEQ  118 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCCC-CCHHHHHHHHHHHHHHH
Confidence            4589999999999999999999863321 11 22333 333457778999999888765432 22222233333    32


Q ss_pred             -hCCCeEEEEEcCCCCCCccchhhhhhhccC---CCCCeEEEEEcCChhHHHhcc----------ccceeecCCCCcccc
Q 005860          273 -LVGKKFLLILDDMWTDDYSKWEPFHYCLKN---GVRGSKILVTTRKETVARMME----------SIHVISIKELSEQEC  338 (673)
Q Consensus       273 -l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~---~~~gs~iivTtr~~~v~~~~~----------~~~~~~l~~L~~~~~  338 (673)
                       ..+++++||+||+|.-+...++.+......   ......|++|... .....+.          ....+++++++.+|.
T Consensus       119 ~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~-~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~  197 (269)
T TIGR03015       119 FAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQP-EFRETLQSPQLQQLRQRIIASCHLGPLDREET  197 (269)
T ss_pred             HhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCH-HHHHHHcCchhHHHHhheeeeeeCCCCCHHHH
Confidence             367889999999987665566665533221   1222344555543 2222211          134567888887775

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=98.88  E-value=1.7e-10  Score=114.96  Aligned_cols=134  Identities=22%  Similarity=0.342  Sum_probs=99.1

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      .+.+.|+....+....+|+.+..+..|.-|++..+..     .++| .|.++..|..|++..       ++++.+|..++
T Consensus       182 m~~L~~ld~~~N~L~tlP~~lg~l~~L~~LyL~~Nki-----~~lP-ef~gcs~L~Elh~g~-------N~i~~lpae~~  248 (565)
T KOG0472|consen  182 MKRLKHLDCNSNLLETLPPELGGLESLELLYLRRNKI-----RFLP-EFPGCSLLKELHVGE-------NQIEMLPAEHL  248 (565)
T ss_pred             HHHHHhcccchhhhhcCChhhcchhhhHHHHhhhccc-----ccCC-CCCccHHHHHHHhcc-------cHHHhhHHHHh
Confidence            3455666666666677777777777777777777653     3344 466777777777777       77888887776


Q ss_pred             -cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccC
Q 005860          571 -KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       571 -~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i  639 (673)
                       +|.+|..|||+.|.++++|..+|.|.+|++||+|++. +..+|-++|+| .|+.|-+.+|.++.+-.+|
T Consensus       249 ~~L~~l~vLDLRdNklke~Pde~clLrsL~rLDlSNN~-is~Lp~sLgnl-hL~~L~leGNPlrTiRr~i  316 (565)
T KOG0472|consen  249 KHLNSLLVLDLRDNKLKEVPDEICLLRSLERLDLSNND-ISSLPYSLGNL-HLKFLALEGNPLRTIRREI  316 (565)
T ss_pred             cccccceeeeccccccccCchHHHHhhhhhhhcccCCc-cccCCcccccc-eeeehhhcCCchHHHHHHH
Confidence             7788888888888888888888888888888888754 88888888888 7888888888777665443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.87  E-value=2.1e-08  Score=107.66  Aligned_cols=169  Identities=15%  Similarity=0.139  Sum_probs=106.2

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      .|+.++||++++++|...|...-.   ......+.|+|++|+|||++++.++++.......-..+++.+....+...++.
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~---~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~  104 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALR---GSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFS  104 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhC---CCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHH
Confidence            456899999999999998844321   12234578999999999999999998632222123466777776677888999


Q ss_pred             HHHHHhhCCC-C-CcCcHHHHHHHHHHHhC--CCeEEEEEcCCCCCC----ccchhhhhhhccCCCCCeE--EEEEcCCh
Q 005860          247 AIIEALEGFV-P-TVGELNSLLESIRASLV--GKKFLLILDDMWTDD----YSKWEPFHYCLKNGVRGSK--ILVTTRKE  316 (673)
Q Consensus       247 ~i~~~l~~~~-~-~~~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~----~~~~~~l~~~l~~~~~gs~--iivTtr~~  316 (673)
                      .|++++.... + ...+.++....+.+.+.  +++.+||||+++.-.    ...+..+...+.. ..+++  +|.++...
T Consensus       105 ~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~-~~~~~v~vI~i~~~~  183 (394)
T PRK00411        105 EIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEE-YPGARIGVIGISSDL  183 (394)
T ss_pred             HHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhc-cCCCeEEEEEEECCc
Confidence            9999997632 2 22345666777777765  467899999995421    1122222222211 23333  56666654


Q ss_pred             hHHHhccc-------cceeecCCCCccccc
Q 005860          317 TVARMMES-------IHVISIKELSEQECW  339 (673)
Q Consensus       317 ~v~~~~~~-------~~~~~l~~L~~~~~~  339 (673)
                      .+......       ...+.+++++.++..
T Consensus       184 ~~~~~l~~~~~s~~~~~~i~f~py~~~e~~  213 (394)
T PRK00411        184 TFLYILDPRVKSVFRPEEIYFPPYTADEIF  213 (394)
T ss_pred             chhhhcCHHHHhcCCcceeecCCCCHHHHH
Confidence            43332211       235677777776643

>PLN03210 Resistant to P

Probab=98.83  E-value=3.3e-09  Score=128.17  Aligned_cols=122  Identities=25%  Similarity=0.310  Sum_probs=69.5

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~~i  569 (673)
                      +.++|.+.+..+....+|..+ .+.+|+.|.+.++..     ..++..+..+++|+.|+|++       +. +..+| .+
T Consensus       588 p~~Lr~L~~~~~~l~~lP~~f-~~~~L~~L~L~~s~l-----~~L~~~~~~l~~Lk~L~Ls~-------~~~l~~ip-~l  653 (1153)
T PLN03210        588 PPKLRLLRWDKYPLRCMPSNF-RPENLVKLQMQGSKL-----EKLWDGVHSLTGLRNIDLRG-------SKNLKEIP-DL  653 (1153)
T ss_pred             CcccEEEEecCCCCCCCCCcC-CccCCcEEECcCccc-----cccccccccCCCCCEEECCC-------CCCcCcCC-cc
Confidence            456777777766666666554 456777777766542     12233345566666666665       33 33343 35


Q ss_pred             ccccccccceecCCC-CcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeec
Q 005860          570 EKLIHLRYLRLVGLG-TEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTY  627 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~-i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l  627 (673)
                      +.+++|++|+|++|. +..+|.++++|++|+.|++++|+++..+|..+ ++++|++|++
T Consensus       654 s~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~L~L  711 (1153)
T PLN03210        654 SMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI-NLKSLYRLNL  711 (1153)
T ss_pred             ccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcC-CCCCCCEEeC
Confidence            555666666666655 55566666666666666666665566665544 4444444443

syringae 6; Provisional

>PF05729 NACHT: NACHT domain

Probab=98.83  E-value=1.1e-08  Score=95.31  Aligned_cols=134  Identities=20%  Similarity=0.283  Sum_probs=78.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcccccc----CCeEEEEEcCCcccHH---HHHHHHHHHhhCCCCCcCcHHHHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEY----FDKRMWVCVSDPFDEL---RIAKAIIEALEGFVPTVGELNSLLESIR  270 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~~l~  270 (673)
                      +++.|+|.+|+||||+++.++........    +...+|+.........   .+...|.........   ....   .+.
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~---~~~~---~~~   74 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIA---PIEE---LLQ   74 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchh---hhHH---HHH
Confidence            57899999999999999998876332222    4456677665543332   333333333322211   1111   122


Q ss_pred             H-HhCCCeEEEEEcCCCCCCc--c-----chhhhh-hhccC-CCCCeEEEEEcCChhH---HHhccccceeecCCCCccc
Q 005860          271 A-SLVGKKFLLILDDMWTDDY--S-----KWEPFH-YCLKN-GVRGSKILVTTRKETV---ARMMESIHVISIKELSEQE  337 (673)
Q Consensus       271 ~-~l~~kr~LlVLDdvw~~~~--~-----~~~~l~-~~l~~-~~~gs~iivTtr~~~v---~~~~~~~~~~~l~~L~~~~  337 (673)
                      . .-+.++++||||++.+-..  .     .+..+. ..+.. ..++.++|||||....   .........+++.+|++++
T Consensus        75 ~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~  154 (166)
T PF05729_consen   75 ELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEED  154 (166)
T ss_pred             HHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHH
Confidence            2 2257899999999832111  0     122222 22222 3568999999998765   3334445678999998765

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=98.76  E-value=6.5e-10  Score=115.55  Aligned_cols=130  Identities=21%  Similarity=0.306  Sum_probs=84.1

Q ss_pred             CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCC
Q 005860          505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG  584 (673)
Q Consensus       505 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~  584 (673)
                      ..+|..+.++..|..|+++.+..     ..+|..+..++ |++|-+++       +.+..+|+.|+.+.+|..|+.+.|.
T Consensus       111 r~ip~~i~~L~~lt~l~ls~Nql-----S~lp~~lC~lp-Lkvli~sN-------Nkl~~lp~~ig~~~tl~~ld~s~ne  177 (722)
T KOG0532|consen  111 RTIPEAICNLEALTFLDLSSNQL-----SHLPDGLCDLP-LKVLIVSN-------NKLTSLPEEIGLLPTLAHLDVSKNE  177 (722)
T ss_pred             eecchhhhhhhHHHHhhhccchh-----hcCChhhhcCc-ceeEEEec-------CccccCCcccccchhHHHhhhhhhh
Confidence            34455566666666666666543     22333333333 67777777       6677777777766777777777777


Q ss_pred             CcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          585 TEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       585 i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      +..+|+.+++|..|+.|+++.++ +..+|.+++.|+ |..||++||++..+|-.|.+|+.||+|.
T Consensus       178 i~slpsql~~l~slr~l~vrRn~-l~~lp~El~~Lp-Li~lDfScNkis~iPv~fr~m~~Lq~l~  240 (722)
T KOG0532|consen  178 IQSLPSQLGYLTSLRDLNVRRNH-LEDLPEELCSLP-LIRLDFSCNKISYLPVDFRKMRHLQVLQ  240 (722)
T ss_pred             hhhchHHhhhHHHHHHHHHhhhh-hhhCCHHHhCCc-eeeeecccCceeecchhhhhhhhheeee
Confidence            77777777777777777777644 667776666543 6667777777777776677777776653

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.76  E-value=9e-08  Score=101.59  Aligned_cols=118  Identities=19%  Similarity=0.176  Sum_probs=81.1

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc-ccC---CeEEEEEcCCcccHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF-EYF---DKRMWVCVSDPFDEL  242 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F---~~~~wv~vs~~~~~~  242 (673)
                      .|+.++||++++++|...|...-.   ......+.|+|++|+|||++++.+++...-. ...   -..+|+.+....+..
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~---~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~   89 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILR---GSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLY   89 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHc---CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHH
Confidence            345899999999999999864211   1224568999999999999999999852110 111   135677777766788


Q ss_pred             HHHHHHHHHhh---CCCC-CcCcHHHHHHHHHHHh--CCCeEEEEEcCCCC
Q 005860          243 RIAKAIIEALE---GFVP-TVGELNSLLESIRASL--VGKKFLLILDDMWT  287 (673)
Q Consensus       243 ~~~~~i~~~l~---~~~~-~~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~  287 (673)
                      .++..|++++.   ...+ ...+.++....+.+.+  .+++++||||++..
T Consensus        90 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~  140 (365)
T TIGR02928        90 QVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDY  140 (365)
T ss_pred             HHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhh
Confidence            89999999994   2211 1223445555566655  35689999999944

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.73  E-value=1e-08  Score=101.33  Aligned_cols=43  Identities=35%  Similarity=0.387  Sum_probs=35.3

Q ss_pred             ceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          171 IRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       171 ~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+||+.++++|.+++..+.       .+.+.|+|+.|+|||+|++.+.+.
T Consensus         1 F~gR~~el~~l~~~l~~~~-------~~~~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP-------SQHILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH---------SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhc-------CcEEEEEcCCcCCHHHHHHHHHHH
Confidence            7899999999999886543       467899999999999999999985

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.69  E-value=1e-06  Score=96.98  Aligned_cols=279  Identities=21%  Similarity=0.250  Sum_probs=156.8

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAK  246 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~  246 (673)
                      +...|-|..-.+.    |...      .+.+.+.|..++|.|||||+-.....   ...=..+.|.+..+ +.++..+..
T Consensus        18 ~~~~v~R~rL~~~----L~~~------~~~RL~li~APAGfGKttl~aq~~~~---~~~~~~v~Wlslde~dndp~rF~~   84 (894)
T COG2909          18 PDNYVVRPRLLDR----LRRA------NDYRLILISAPAGFGKTTLLAQWREL---AADGAAVAWLSLDESDNDPARFLS   84 (894)
T ss_pred             cccccccHHHHHH----HhcC------CCceEEEEeCCCCCcHHHHHHHHHHh---cCcccceeEeecCCccCCHHHHHH
Confidence            4456666654444    4333      35899999999999999999888651   12234689998765 457888999


Q ss_pred             HHHHHhhCCCCCc-------------CcHHHHHHHHHHHhC--CCeEEEEEcCCCCCCccchh-hhhhhccCCCCCeEEE
Q 005860          247 AIIEALEGFVPTV-------------GELNSLLESIRASLV--GKKFLLILDDMWTDDYSKWE-PFHYCLKNGVRGSKIL  310 (673)
Q Consensus       247 ~i~~~l~~~~~~~-------------~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~~~~~~-~l~~~l~~~~~gs~ii  310 (673)
                      .++..++.-.++.             .+...+...+...+.  .++..+||||-.-......+ .+...+.....+-..|
T Consensus        85 yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lv  164 (894)
T COG2909          85 YLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLV  164 (894)
T ss_pred             HHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEE
Confidence            9999987543322             223334444554443  46899999997543333343 3555556677788999


Q ss_pred             EEcCChhHHHh---ccccceeecC----CCCccccc----cC-CchhhHHHHhhhhccCCCHHHHHHHHhhhcc--c---
Q 005860          311 VTTRKETVARM---MESIHVISIK----ELSEQECW----CK-GLPLAAKTIGSLLRFKRTREEWESILDSELW--Q---  373 (673)
Q Consensus       311 vTtr~~~v~~~---~~~~~~~~l~----~L~~~~~~----c~-GlPLai~~~~~~L~~~~~~~~w~~~l~~~~~--~---  373 (673)
                      ||||+.--...   --....++++    .++.+|+-    |. |+|+--..+..+..   ..+-|-..+.-..-  .   
T Consensus       165 v~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld~~~~~~L~~---~teGW~~al~L~aLa~~~~~  241 (894)
T COG2909         165 VTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLDAADLKALYD---RTEGWAAALQLIALALRNNT  241 (894)
T ss_pred             EEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCChHHHHHHHh---hcccHHHHHHHHHHHccCCC
Confidence            99998632211   0011122222    24445543    33 36665555544442   23445444321100  0   


Q ss_pred             --------chhhhhccchh-hhhcccCCChhhhhhhchHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHhcccccccc
Q 005860          374 --------LEEFEKGLLAP-LLLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFF  444 (673)
Q Consensus       374 --------~~~~~~~i~~~-l~~sy~~L~~~~k~cfl~~~l~~~w~a~g~i~~~~~~~~e~~~~~~~~~L~~~sli~~~~  444 (673)
                              +....+.+..- ..--++.||+++|..++-.......-++ ++..-   +-++-+...+++|.+++||-..-
T Consensus       242 ~~~q~~~~LsG~~~~l~dYL~eeVld~Lp~~l~~FLl~~svl~~f~~e-L~~~L---tg~~ng~amLe~L~~~gLFl~~L  317 (894)
T COG2909         242 SAEQSLRGLSGAASHLSDYLVEEVLDRLPPELRDFLLQTSVLSRFNDE-LCNAL---TGEENGQAMLEELERRGLFLQRL  317 (894)
T ss_pred             cHHHHhhhccchHHHHHHHHHHHHHhcCCHHHHHHHHHHHhHHHhhHH-HHHHH---hcCCcHHHHHHHHHhCCCceeee
Confidence                    00001111111 2235678899988866653333332221 11110   11223456789999999875432


Q ss_pred             cCCCCcEeEEEeChHHHHHHHHhcc
Q 005860          445 KDNEGVVVRCKMHDIVHDFAQFLTK  469 (673)
Q Consensus       445 ~~~~~~~~~~~mHdlv~~~a~~i~~  469 (673)
                      .+.   ..-|+.|.++.||.+.-..
T Consensus       318 dd~---~~WfryH~LFaeFL~~r~~  339 (894)
T COG2909         318 DDE---GQWFRYHHLFAEFLRQRLQ  339 (894)
T ss_pred             cCC---CceeehhHHHHHHHHhhhc
Confidence            222   2268999999999876544

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.63  E-value=5.8e-08  Score=86.56  Aligned_cols=117  Identities=20%  Similarity=0.162  Sum_probs=80.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccc---ccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVF---EYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      -+++.|+|.+|+|||++++.+.++....   ..-..++|+.++...+...+...|+++++.......+.+++...+.+.+
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            4789999999999999999999852110   0034567999988889999999999999988666566677778888877


Q ss_pred             CCC-eEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCC
Q 005860          274 VGK-KFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       274 ~~k-r~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~  315 (673)
                      ... ..+||+|++..- +...++.+.....  ..+.+||++.+.
T Consensus        84 ~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            654 459999999443 3333444433322  567777777654

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.59  E-value=2.3e-08  Score=92.35  Aligned_cols=131  Identities=24%  Similarity=0.260  Sum_probs=58.9

Q ss_pred             cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhh
Q 005860          513 KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETC  592 (673)
Q Consensus       513 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i  592 (673)
                      +..+++.|.+.++.+     ..+...-..+..|++|++++       |.+..+. .+..|++|+.|++++|.|+.+++.+
T Consensus        17 n~~~~~~L~L~~n~I-----~~Ie~L~~~l~~L~~L~Ls~-------N~I~~l~-~l~~L~~L~~L~L~~N~I~~i~~~l   83 (175)
T PF14580_consen   17 NPVKLRELNLRGNQI-----STIENLGATLDKLEVLDLSN-------NQITKLE-GLPGLPRLKTLDLSNNRISSISEGL   83 (175)
T ss_dssp             ------------------------S--TT-TT--EEE-TT-------S--S--T-T----TT--EEE--SS---S-CHHH
T ss_pred             ccccccccccccccc-----ccccchhhhhcCCCEEECCC-------CCCcccc-CccChhhhhhcccCCCCCCccccch
Confidence            455788999988874     11222212567899999999       9988875 5888999999999999999998766


Q ss_pred             h-cCCCccEEEeccCCCCccccc--cccccccCCeeeccccccccccc----cCCCCCCCCcCCeeEEccCC
Q 005860          593 C-ELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIPK----GIQRLTNLRTLSEFVVVRGG  657 (673)
Q Consensus       593 ~-~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP~----~i~~L~~L~~L~~~~~~~~~  657 (673)
                      . .+++|+.|+++++. +..+-+  .+..+++|++|++.+|++...+.    -|..+++|+.|++-.|....
T Consensus        84 ~~~lp~L~~L~L~~N~-I~~l~~l~~L~~l~~L~~L~L~~NPv~~~~~YR~~vi~~lP~Lk~LD~~~V~~~E  154 (175)
T PF14580_consen   84 DKNLPNLQELYLSNNK-ISDLNELEPLSSLPKLRVLSLEGNPVCEKKNYRLFVIYKLPSLKVLDGQDVTEEE  154 (175)
T ss_dssp             HHH-TT--EEE-TTS----SCCCCGGGGG-TT--EEE-TT-GGGGSTTHHHHHHHH-TT-SEETTEETTS-B
T ss_pred             HHhCCcCCEEECcCCc-CCChHHhHHHHcCCCcceeeccCCcccchhhHHHHHHHHcChhheeCCEEccHHH
Confidence            4 69999999999865 666542  46788999999999998876542    35779999999999987654

>PTZ00202 tuzin; Provisional

Probab=98.53  E-value=1.2e-06  Score=90.12  Aligned_cols=110  Identities=19%  Similarity=0.251  Sum_probs=73.9

Q ss_pred             ccccccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH
Q 005860          162 STSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE  241 (673)
Q Consensus       162 ~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  241 (673)
                      ...+.+.+.|+||+.+..++...|...+.    ...+++.|+|++|+|||||++.+.....    + . .++.-+.  +.
T Consensus       255 ~~lPa~~~~FVGReaEla~Lr~VL~~~d~----~~privvLtG~~G~GKTTLlR~~~~~l~----~-~-qL~vNpr--g~  322 (550)
T PTZ00202        255 QSAPAVIRQFVSREAEESWVRQVLRRLDT----AHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-P-AVFVDVR--GT  322 (550)
T ss_pred             cCCCCCccCCCCcHHHHHHHHHHHhccCC----CCceEEEEECCCCCCHHHHHHHHHhcCC----c-e-EEEECCC--CH
Confidence            34556678999999999999999865442    2356999999999999999999987532    1 2 3332233  67


Q ss_pred             HHHHHHHHHHhhCCCCCc-C-cHHHHHHHHHHHh-C-CCeEEEEEc
Q 005860          242 LRIAKAIIEALEGFVPTV-G-ELNSLLESIRASL-V-GKKFLLILD  283 (673)
Q Consensus       242 ~~~~~~i~~~l~~~~~~~-~-~~~~~~~~l~~~l-~-~kr~LlVLD  283 (673)
                      .++++.|+.+|+.+.... . -.+.+.+.+.+.- . +++.+||+-
T Consensus       323 eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~  368 (550)
T PTZ00202        323 EDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLLVLK  368 (550)
T ss_pred             HHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            999999999999742211 1 1233333333322 3 677777765

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.53  E-value=2.6e-08  Score=114.71  Aligned_cols=103  Identities=29%  Similarity=0.329  Sum_probs=84.7

Q ss_pred             ccceeeeccccccccccc--hhhhcc-ccccccccccceecCCC-CcccchhhhcCCCccEEEeccCCCCcccccccccc
Q 005860          544 CLRALRIATLMNTWDVNS--TNKILK-GIEKLIHLRYLRLVGLG-TEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKL  619 (673)
Q Consensus       544 ~L~~L~L~~~~~~~~~~~--~~~lp~-~i~~L~~Lr~L~L~~~~-i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  619 (673)
                      .|+.|-+.+       +.  +..++. .+..|++|++|||++|. +.+||++|++|.+|++|+++++. +..+|.++++|
T Consensus       546 ~L~tLll~~-------n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~-I~~LP~~l~~L  617 (889)
T KOG4658|consen  546 KLRTLLLQR-------NSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTG-ISHLPSGLGNL  617 (889)
T ss_pred             ccceEEEee-------cchhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCC-ccccchHHHHH
Confidence            577777777       54  444444 37779999999999988 99999999999999999999977 99999999999


Q ss_pred             ccCCeeecccccccccccc-CCCCCCCCcCCeeEEc
Q 005860          620 VNLRHLTYDDSCLEFIPKG-IQRLTNLRTLSEFVVV  654 (673)
Q Consensus       620 ~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~~~~~~  654 (673)
                      ++|.||++..+.-...+++ +..|++|++|..+...
T Consensus       618 k~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~  653 (889)
T KOG4658|consen  618 KKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSA  653 (889)
T ss_pred             HhhheeccccccccccccchhhhcccccEEEeeccc
Confidence            9999999876654333344 4559999999888776

>PF13173 AAA_14: AAA domain

Probab=98.53  E-value=3.3e-07  Score=81.24  Aligned_cols=119  Identities=24%  Similarity=0.271  Sum_probs=78.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      +++.|.|+.|+|||||+++++++..   ....++|++..+.........                + ....+.+....++
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~----------------~-~~~~~~~~~~~~~   62 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADP----------------D-LLEYFLELIKPGK   62 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhh----------------h-hHHHHHHhhccCC
Confidence            6899999999999999999887522   335677887665433211000                0 2333444444478


Q ss_pred             EEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhc------cccceeecCCCCcccc
Q 005860          278 FLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMM------ESIHVISIKELSEQEC  338 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~------~~~~~~~l~~L~~~~~  338 (673)
                      .+|+||++.  ....|......+.+..+..+|++|+.+......-      +-...++|.||+-.|.
T Consensus        63 ~~i~iDEiq--~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   63 KYIFIDEIQ--YLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             cEEEEehhh--hhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            899999994  3456777666666655667999999877665331      2245678888886653

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=98.53  E-value=6e-07  Score=81.42  Aligned_cols=125  Identities=18%  Similarity=0.140  Sum_probs=72.8

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHH
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEA  251 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  251 (673)
                      .|++..++.+...+....       .+.+.|+|.+|+||||+|+.+++...  ..-..++++..++..........+...
T Consensus         1 ~~~~~~~~~i~~~~~~~~-------~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~~~~~~~~~~~~~~   71 (151)
T cd00009           1 VGQEEAIEALREALELPP-------PKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGHF   71 (151)
T ss_pred             CchHHHHHHHHHHHhCCC-------CCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhhhhhhHHHHHhhhh
Confidence            478888888888875432       46788999999999999999999632  222346666655433322211111000


Q ss_pred             hhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCC------CCCeEEEEEcCChh
Q 005860          252 LEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNG------VRGSKILVTTRKET  317 (673)
Q Consensus       252 l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~------~~gs~iivTtr~~~  317 (673)
                                  ............++.+||+||++.-.......+...+...      ..+..||+||....
T Consensus        72 ------------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 ------------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ------------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                        0011122233456789999999643122222333333322      36778888888643

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.52  E-value=1.5e-07  Score=92.67  Aligned_cols=88  Identities=20%  Similarity=0.112  Sum_probs=62.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc--ccHHHHHHHHHHHhhCCCCCcCc---H---HHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP--FDELRIAKAIIEALEGFVPTVGE---L---NSLLES  268 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~l~~~~~~~~~---~---~~~~~~  268 (673)
                      -..++|+|++|+|||||++.++++.... +|+.++|+.+++.  .++.++++.+...+-....+...   .   ......
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~   94 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEK   94 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHH
Confidence            4579999999999999999999985544 8999999997776  78999999984333222111111   1   122222


Q ss_pred             HHHH-hCCCeEEEEEcCC
Q 005860          269 IRAS-LVGKKFLLILDDM  285 (673)
Q Consensus       269 l~~~-l~~kr~LlVLDdv  285 (673)
                      .... -.++++++++|++
T Consensus        95 a~~~~~~G~~vll~iDei  112 (249)
T cd01128          95 AKRLVEHGKDVVILLDSI  112 (249)
T ss_pred             HHHHHHCCCCEEEEEECH
Confidence            2222 3589999999999

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.52  E-value=1.8e-08  Score=105.17  Aligned_cols=147  Identities=21%  Similarity=0.268  Sum_probs=87.2

Q ss_pred             CceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-cc
Q 005860          492 EKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i  569 (673)
                      +++.++.+..+..... ..+++.+..|+.|++++|.+    ..+-.+.++..+.|..|+|+.       +.++.+++ ++
T Consensus       269 ~kme~l~L~~N~l~~vn~g~lfgLt~L~~L~lS~NaI----~rih~d~WsftqkL~~LdLs~-------N~i~~l~~~sf  337 (873)
T KOG4194|consen  269 EKMEHLNLETNRLQAVNEGWLFGLTSLEQLDLSYNAI----QRIHIDSWSFTQKLKELDLSS-------NRITRLDEGSF  337 (873)
T ss_pred             cccceeecccchhhhhhcccccccchhhhhccchhhh----heeecchhhhcccceeEeccc-------cccccCChhHH
Confidence            4555666655544332 23456677777777777652    233344556666777777777       77666644 56


Q ss_pred             ccccccccceecCCCCcccch-hhhcCCCccEEEeccCCC---CccccccccccccCCeeecccccccccccc-CCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTS---LKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTN  644 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~---l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~  644 (673)
                      ..|..|..|+|+.|.+..+-+ .+..+.+|++|||+.+.-   ++.--..+..|++|+.|.+.+|.++.+|.. +..|.+
T Consensus       338 ~~L~~Le~LnLs~Nsi~~l~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~gNqlk~I~krAfsgl~~  417 (873)
T KOG4194|consen  338 RVLSQLEELNLSHNSIDHLAEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTGNQLKSIPKRAFSGLEA  417 (873)
T ss_pred             HHHHHhhhhcccccchHHHHhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecCceeeecchhhhccCcc
Confidence            666677777777777666643 455566777777765431   122222345566677777777777666643 555666


Q ss_pred             CCcCC
Q 005860          645 LRTLS  649 (673)
Q Consensus       645 L~~L~  649 (673)
                      |+.|+
T Consensus       418 LE~Ld  422 (873)
T KOG4194|consen  418 LEHLD  422 (873)
T ss_pred             cceec
Confidence            66554

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=98.51  E-value=1.3e-08  Score=111.79  Aligned_cols=149  Identities=21%  Similarity=0.267  Sum_probs=94.7

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhh------------------hhhhHHHHhhhCCccceeeecc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVS------------------LTHVLQSLFDQLKCLRALRIAT  552 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~------------------~~~~~~~~~~~l~~L~~L~L~~  552 (673)
                      +.++..+.+..+....+|.++..+.+|..+....+.+..-                  -...+|.+..++++|++|+|..
T Consensus       240 p~nl~~~dis~n~l~~lp~wi~~~~nle~l~~n~N~l~~lp~ri~~~~~L~~l~~~~nel~yip~~le~~~sL~tLdL~~  319 (1081)
T KOG0618|consen  240 PLNLQYLDISHNNLSNLPEWIGACANLEALNANHNRLVALPLRISRITSLVSLSAAYNELEYIPPFLEGLKSLRTLDLQS  319 (1081)
T ss_pred             cccceeeecchhhhhcchHHHHhcccceEecccchhHHhhHHHHhhhhhHHHHHhhhhhhhhCCCcccccceeeeeeehh
Confidence            4567777777777667777777777777777666543100                  0123445566788888888877


Q ss_pred             ccccccccchhhhccc--------------------------------------------------cccccccccceecC
Q 005860          553 LMNTWDVNSTNKILKG--------------------------------------------------IEKLIHLRYLRLVG  582 (673)
Q Consensus       553 ~~~~~~~~~~~~lp~~--------------------------------------------------i~~L~~Lr~L~L~~  582 (673)
                             +.+..+|+.                                                  +...+||+.|+|+.
T Consensus       320 -------N~L~~lp~~~l~v~~~~l~~ln~s~n~l~~lp~~~e~~~~~Lq~LylanN~Ltd~c~p~l~~~~hLKVLhLsy  392 (1081)
T KOG0618|consen  320 -------NNLPSLPDNFLAVLNASLNTLNVSSNKLSTLPSYEENNHAALQELYLANNHLTDSCFPVLVNFKHLKVLHLSY  392 (1081)
T ss_pred             -------ccccccchHHHhhhhHHHHHHhhhhccccccccccchhhHHHHHHHHhcCcccccchhhhccccceeeeeecc
Confidence                   333333321                                                  23456777777777


Q ss_pred             CCCcccc-hhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          583 LGTEELP-ETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       583 ~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      |.+..+| ..+.+|..|+.|+|||+. +..+|..+.++..|++|...+|.+..+| .+..++.|+++
T Consensus       393 NrL~~fpas~~~kle~LeeL~LSGNk-L~~Lp~tva~~~~L~tL~ahsN~l~~fP-e~~~l~qL~~l  457 (1081)
T KOG0618|consen  393 NRLNSFPASKLRKLEELEELNLSGNK-LTTLPDTVANLGRLHTLRAHSNQLLSFP-ELAQLPQLKVL  457 (1081)
T ss_pred             cccccCCHHHHhchHHhHHHhcccch-hhhhhHHHHhhhhhHHHhhcCCceeech-hhhhcCcceEE
Confidence            7777777 345667777777777754 7777777777777777777777777776 45555544443

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.47  E-value=7.6e-08  Score=100.66  Aligned_cols=145  Identities=21%  Similarity=0.273  Sum_probs=99.6

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-ccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIE  570 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~  570 (673)
                      .++..+++..+....+|.......+|..|++.+|.+    .......+.-++.||+|||+.       +.+.++|. ++.
T Consensus       102 ~nLq~v~l~~N~Lt~IP~f~~~sghl~~L~L~~N~I----~sv~se~L~~l~alrslDLSr-------N~is~i~~~sfp  170 (873)
T KOG4194|consen  102 PNLQEVNLNKNELTRIPRFGHESGHLEKLDLRHNLI----SSVTSEELSALPALRSLDLSR-------NLISEIPKPSFP  170 (873)
T ss_pred             CcceeeeeccchhhhcccccccccceeEEeeecccc----ccccHHHHHhHhhhhhhhhhh-------chhhcccCCCCC
Confidence            456666666666666665444556677777777653    233344566677888888888       77777764 455


Q ss_pred             cccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccccc-ccCCCCCCCCc
Q 005860          571 KLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIP-KGIQRLTNLRT  647 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP-~~i~~L~~L~~  647 (673)
                      .=.++++|+|++|.|+.+- ..+..|.+|-+|.|+.+. +..+|. .|.+|++|+.|++..|.++.+- ..|..|.+||.
T Consensus       171 ~~~ni~~L~La~N~It~l~~~~F~~lnsL~tlkLsrNr-ittLp~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~n  249 (873)
T KOG4194|consen  171 AKVNIKKLNLASNRITTLETGHFDSLNSLLTLKLSRNR-ITTLPQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQN  249 (873)
T ss_pred             CCCCceEEeeccccccccccccccccchheeeecccCc-ccccCHHHhhhcchhhhhhccccceeeehhhhhcCchhhhh
Confidence            5567888888888887775 567778888888888765 888885 4566888888888877766541 22455666665


Q ss_pred             C
Q 005860          648 L  648 (673)
Q Consensus       648 L  648 (673)
                      |
T Consensus       250 l  250 (873)
T KOG4194|consen  250 L  250 (873)
T ss_pred             h
Confidence            5

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.43  E-value=3.3e-07  Score=87.02  Aligned_cols=48  Identities=25%  Similarity=0.344  Sum_probs=32.7

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      .|+||+++++++...|....    ....+.+.|+|.+|+|||+|++.++...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~----~~~~~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQ----SGSPRNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTS----S-----EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHH----cCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999995222    2456899999999999999999988863

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.42  E-value=1.8e-06  Score=89.93  Aligned_cols=156  Identities=17%  Similarity=0.124  Sum_probs=80.6

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      -.+|+|++..++.+..++......  ......+.|+|++|+||||||+.+.+...  ..+   .++..+ .......+..
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~~--~~~~~~~ll~GppG~GKT~la~~ia~~l~--~~~---~~~~~~-~~~~~~~l~~   95 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKKR--GEALDHVLLYGPPGLGKTTLANIIANEMG--VNI---RITSGP-ALEKPGDLAA   95 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHhc--CCCCCcEEEECCCCccHHHHHHHHHHHhC--CCe---EEEecc-cccChHHHHH
Confidence            357999999999998877532110  12356788999999999999999999632  221   122211 1111222333


Q ss_pred             HHHHhhCCC----CCcCcH-HHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhc
Q 005860          248 IIEALEGFV----PTVGEL-NSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMM  322 (673)
Q Consensus       248 i~~~l~~~~----~~~~~~-~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~  322 (673)
                      ++..+....    ++.+.+ ....+.+...+.+.+..+|+|+..+.  ..+.   ..+   .+.+-|..||+...+....
T Consensus        96 ~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~--~~~~---~~l---~~~~li~at~~~~~l~~~L  167 (328)
T PRK00080         96 ILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAA--RSIR---LDL---PPFTLIGATTRAGLLTSPL  167 (328)
T ss_pred             HHHhcccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccc--ccee---ecC---CCceEEeecCCcccCCHHH
Confidence            333332211    000100 11223344455555666666655221  1111   011   1245566677754333221


Q ss_pred             cc--cceeecCCCCccccc
Q 005860          323 ES--IHVISIKELSEQECW  339 (673)
Q Consensus       323 ~~--~~~~~l~~L~~~~~~  339 (673)
                      ..  ...+++++++.++..
T Consensus       168 ~sRf~~~~~l~~~~~~e~~  186 (328)
T PRK00080        168 RDRFGIVQRLEFYTVEELE  186 (328)
T ss_pred             HHhcCeeeecCCCCHHHHH
Confidence            11  346788888888764

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=98.41  E-value=2.3e-08  Score=104.28  Aligned_cols=141  Identities=22%  Similarity=0.326  Sum_probs=103.9

Q ss_pred             EEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccc
Q 005860          499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYL  578 (673)
Q Consensus       499 l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L  578 (673)
                      +..+....+|..++.+ -|+.|++.++..     ..+|.-+..+..|..||.+.       |.+..+|+.++.|..|+-|
T Consensus       128 ls~NqlS~lp~~lC~l-pLkvli~sNNkl-----~~lp~~ig~~~tl~~ld~s~-------nei~slpsql~~l~slr~l  194 (722)
T KOG0532|consen  128 LSSNQLSHLPDGLCDL-PLKVLIVSNNKL-----TSLPEEIGLLPTLAHLDVSK-------NEIQSLPSQLGYLTSLRDL  194 (722)
T ss_pred             hccchhhcCChhhhcC-cceeEEEecCcc-----ccCCcccccchhHHHhhhhh-------hhhhhchHHhhhHHHHHHH
Confidence            3333334445555443 377787777753     33444455777888888888       8888899999999999999


Q ss_pred             eecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCeeEEc
Q 005860          579 RLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVV  654 (673)
Q Consensus       579 ~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~~~~  654 (673)
                      +++.|.+..+|+.++.|+ |..||++ |+++..+|-.|.+|+.|++|.+.+|.+..-|..|.....+..+.+....
T Consensus       195 ~vrRn~l~~lp~El~~Lp-Li~lDfS-cNkis~iPv~fr~m~~Lq~l~LenNPLqSPPAqIC~kGkVHIFKyL~~q  268 (722)
T KOG0532|consen  195 NVRRNHLEDLPEELCSLP-LIRLDFS-CNKISYLPVDFRKMRHLQVLQLENNPLQSPPAQICEKGKVHIFKYLSTQ  268 (722)
T ss_pred             HHhhhhhhhCCHHHhCCc-eeeeecc-cCceeecchhhhhhhhheeeeeccCCCCCChHHHHhccceeeeeeecch
Confidence            999988889998888665 8889998 4568999999999999999999998888877666555555555554443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.40  E-value=4.7e-07  Score=92.77  Aligned_cols=88  Identities=18%  Similarity=0.106  Sum_probs=60.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc--cHHHHHHHHHHHhhCCCCCcCcH------HHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF--DELRIAKAIIEALEGFVPTVGEL------NSLLES  268 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~l~~~~~~~~~~------~~~~~~  268 (673)
                      -...+|+|++|+||||||+.||++.... +|+.++||.+++..  ++.++++.|...+-....+....      ......
T Consensus       169 GQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~  247 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEK  247 (416)
T ss_pred             CceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHH
Confidence            4568999999999999999999975443 89999999999887  77778877763322222111111      111111


Q ss_pred             HHHH-hCCCeEEEEEcCC
Q 005860          269 IRAS-LVGKKFLLILDDM  285 (673)
Q Consensus       269 l~~~-l~~kr~LlVLDdv  285 (673)
                      .+.. -.+++++|++|++
T Consensus       248 Ae~~~e~G~dVlL~iDsI  265 (416)
T PRK09376        248 AKRLVEHGKDVVILLDSI  265 (416)
T ss_pred             HHHHHHcCCCEEEEEECh
Confidence            2221 3689999999999

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.40  E-value=8.1e-07  Score=89.83  Aligned_cols=133  Identities=21%  Similarity=0.340  Sum_probs=81.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|-+..+.++++   .       ..+.-.-.||++|+||||||+.+...  ....|     ..+|-..+-.+-++++
T Consensus        30 ~HLlg~~~~lrr~v~---~-------~~l~SmIl~GPPG~GKTTlA~liA~~--~~~~f-----~~~sAv~~gvkdlr~i   92 (436)
T COG2256          30 EHLLGEGKPLRRAVE---A-------GHLHSMILWGPPGTGKTTLARLIAGT--TNAAF-----EALSAVTSGVKDLREI   92 (436)
T ss_pred             HhhhCCCchHHHHHh---c-------CCCceeEEECCCCCCHHHHHHHHHHh--hCCce-----EEeccccccHHHHHHH
Confidence            344555555555443   2       34666789999999999999999985  33444     3333322222222222


Q ss_pred             HHHhhCCCCCcCcHHHHHHHH-HHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEE--EcCChhH---HHhc
Q 005860          249 IEALEGFVPTVGELNSLLESI-RASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILV--TTRKETV---ARMM  322 (673)
Q Consensus       249 ~~~l~~~~~~~~~~~~~~~~l-~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iiv--Ttr~~~v---~~~~  322 (673)
                      +                 +.- +....+++.+|++|.|..-+..+-+.+.   +.-.+|.-|+|  ||-+...   ....
T Consensus        93 ~-----------------e~a~~~~~~gr~tiLflDEIHRfnK~QQD~lL---p~vE~G~iilIGATTENPsF~ln~ALl  152 (436)
T COG2256          93 I-----------------EEARKNRLLGRRTILFLDEIHRFNKAQQDALL---PHVENGTIILIGATTENPSFELNPALL  152 (436)
T ss_pred             H-----------------HHHHHHHhcCCceEEEEehhhhcChhhhhhhh---hhhcCCeEEEEeccCCCCCeeecHHHh
Confidence            2                 222 2334589999999999776666666553   44456777776  5555431   1222


Q ss_pred             cccceeecCCCCcccc
Q 005860          323 ESIHVISIKELSEQEC  338 (673)
Q Consensus       323 ~~~~~~~l~~L~~~~~  338 (673)
                      .-..+|.+++|+.++-
T Consensus       153 SR~~vf~lk~L~~~di  168 (436)
T COG2256         153 SRARVFELKPLSSEDI  168 (436)
T ss_pred             hhhheeeeecCCHHHH
Confidence            3468899999998873

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.39  E-value=2.2e-07  Score=105.50  Aligned_cols=122  Identities=19%  Similarity=0.324  Sum_probs=66.4

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK  571 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~  571 (673)
                      +.++.+.+..+....+|..+.  ++|++|.+.+|.+    .. +|..+  ...|+.|+|++       |.+..+|..+. 
T Consensus       199 ~~L~~L~Ls~N~LtsLP~~l~--~nL~~L~Ls~N~L----ts-LP~~l--~~~L~~L~Ls~-------N~L~~LP~~l~-  261 (754)
T PRK15370        199 EQITTLILDNNELKSLPENLQ--GNIKTLYANSNQL----TS-IPATL--PDTIQEMELSI-------NRITELPERLP-  261 (754)
T ss_pred             cCCcEEEecCCCCCcCChhhc--cCCCEEECCCCcc----cc-CChhh--hccccEEECcC-------CccCcCChhHh-
Confidence            456666666666655555433  4677777766653    11 22211  13566666666       66666665553 


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccc
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                       .+|++|+|++|.+..+|..+.  .+|++|++++|+ +..+|..+.  .+|++|++++|.+..+|
T Consensus       262 -s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~-Lt~LP~~lp--~sL~~L~Ls~N~Lt~LP  320 (754)
T PRK15370        262 -SALQSLDLFHNKISCLPENLP--EELRYLSVYDNS-IRTLPAHLP--SGITHLNVQSNSLTALP  320 (754)
T ss_pred             -CCCCEEECcCCccCccccccC--CCCcEEECCCCc-cccCcccch--hhHHHHHhcCCccccCC
Confidence             356666666666666665543  366666666654 555554332  23444444444444444

>PRK06893 DNA replication initiation factor; Validated

Probab=98.36  E-value=1.4e-06  Score=85.62  Aligned_cols=116  Identities=16%  Similarity=0.202  Sum_probs=70.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      .+.+.|+|++|+|||+||+++++.  .......+.|++++..   .....                     .+.+.+. +
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~~~---~~~~~---------------------~~~~~~~-~   91 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLSKS---QYFSP---------------------AVLENLE-Q   91 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHHHh---hhhhH---------------------HHHhhcc-c
Confidence            357899999999999999999986  3333445677766421   00000                     1111222 2


Q ss_pred             eEEEEEcCCCCCC-ccchhh-hhhhccCC-CCCeEEEEE-cCC---------hhHHHhccccceeecCCCCccccc
Q 005860          277 KFLLILDDMWTDD-YSKWEP-FHYCLKNG-VRGSKILVT-TRK---------ETVARMMESIHVISIKELSEQECW  339 (673)
Q Consensus       277 r~LlVLDdvw~~~-~~~~~~-l~~~l~~~-~~gs~iivT-tr~---------~~v~~~~~~~~~~~l~~L~~~~~~  339 (673)
                      .-+|||||+|... ...|+. +...+... ..|+.+||+ +..         ..+...+.....++++++++++.+
T Consensus        92 ~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~  167 (229)
T PRK06893         92 QDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKI  167 (229)
T ss_pred             CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHH
Confidence            3489999998642 234553 33333322 345566554 443         355666666778899999988866

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.36  E-value=6.8e-06  Score=84.85  Aligned_cols=155  Identities=15%  Similarity=0.097  Sum_probs=82.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+|+|+++.++.|..++......  ......+.++|++|+|||+||+.+.+...  ..|   ..+..+...... .+...
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~--~~~~~~~ll~Gp~G~GKT~la~~ia~~~~--~~~---~~~~~~~~~~~~-~l~~~   75 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMR--QEALDHLLLYGPPGLGKTTLAHIIANEMG--VNL---KITSGPALEKPG-DLAAI   75 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhc--CCCCCeEEEECCCCCCHHHHHHHHHHHhC--CCE---EEeccchhcCch-hHHHH
Confidence            47999999999999888532210  12345678999999999999999998532  222   122211111111 22223


Q ss_pred             HHHhhCCC----CCcCcH-HHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhcc
Q 005860          249 IEALEGFV----PTVGEL-NSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMME  323 (673)
Q Consensus       249 ~~~l~~~~----~~~~~~-~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~  323 (673)
                      +..+....    ++.+.+ ......+...+.+.+..+|+++.++.  ..+..   .+   .+.+-|..||+...+....-
T Consensus        76 l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~--~~~~~---~~---~~~~li~~t~~~~~l~~~l~  147 (305)
T TIGR00635        76 LTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSA--RSVRL---DL---PPFTLVGATTRAGMLTSPLR  147 (305)
T ss_pred             HHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccc--cceee---cC---CCeEEEEecCCccccCHHHH
Confidence            33332211    000100 12234455566666677777766332  22221   11   12455666777644333211


Q ss_pred             --ccceeecCCCCccccc
Q 005860          324 --SIHVISIKELSEQECW  339 (673)
Q Consensus       324 --~~~~~~l~~L~~~~~~  339 (673)
                        ....+++++++.++..
T Consensus       148 sR~~~~~~l~~l~~~e~~  165 (305)
T TIGR00635       148 DRFGIILRLEFYTVEELA  165 (305)
T ss_pred             hhcceEEEeCCCCHHHHH
Confidence              1345788888887764

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.32  E-value=4.6e-07  Score=83.84  Aligned_cols=106  Identities=20%  Similarity=0.274  Sum_probs=40.9

Q ss_pred             hhCCccceeeeccccccccccchhhhccccc-cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccc-c
Q 005860          540 DQLKCLRALRIATLMNTWDVNSTNKILKGIE-KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGI-G  617 (673)
Q Consensus       540 ~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~-~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i-~  617 (673)
                      .+...++.|+|.+       +.+..+ +.++ .+.+|+.|+|++|.|+.++ .+..|++|++|+++++. +..++..+ .
T Consensus        16 ~n~~~~~~L~L~~-------n~I~~I-e~L~~~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~N~-I~~i~~~l~~   85 (175)
T PF14580_consen   16 NNPVKLRELNLRG-------NQISTI-ENLGATLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSNNR-ISSISEGLDK   85 (175)
T ss_dssp             ----------------------------S--TT-TT--EEE-TTS--S--T-T----TT--EEE--SS----S-CHHHHH
T ss_pred             ccccccccccccc-------cccccc-cchhhhhcCCCEEECCCCCCcccc-CccChhhhhhcccCCCC-CCccccchHH
Confidence            3445789999999       888776 4566 6889999999999999997 48889999999999866 99997666 4


Q ss_pred             ccccCCeeeccccccccccccCCCCCCCCcCCeeEEccC
Q 005860          618 KLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRG  656 (673)
Q Consensus       618 ~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~~~~~~  656 (673)
                      .+++|++|++++|.+..+ ..+..|..+..|.......+
T Consensus        86 ~lp~L~~L~L~~N~I~~l-~~l~~L~~l~~L~~L~L~~N  123 (175)
T PF14580_consen   86 NLPNLQELYLSNNKISDL-NELEPLSSLPKLRVLSLEGN  123 (175)
T ss_dssp             H-TT--EEE-TTS---SC-CCCGGGGG-TT--EEE-TT-
T ss_pred             hCCcCCEEECcCCcCCCh-HHhHHHHcCCCcceeeccCC
Confidence            689999999999999877 45666666666666666544

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=98.31  E-value=4.6e-07  Score=97.32  Aligned_cols=143  Identities=28%  Similarity=0.319  Sum_probs=66.8

Q ss_pred             eEEEEEEcCCCCcccccccccc-ccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          494 LRHSMLVLGYEASFPISIFKAK-NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       494 ~r~l~l~~~~~~~~~~~~~~~~-~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      +..+.+..+....+++....++ +|+.|.+.++..     ..++..+..++.|+.|+++.       +.+..+|...+.+
T Consensus       118 l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i-----~~l~~~~~~l~~L~~L~l~~-------N~l~~l~~~~~~~  185 (394)
T COG4886         118 LTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKI-----ESLPSPLRNLPNLKNLDLSF-------NDLSDLPKLLSNL  185 (394)
T ss_pred             eeEEecCCcccccCccccccchhhcccccccccch-----hhhhhhhhccccccccccCC-------chhhhhhhhhhhh
Confidence            4444444444444444443342 555555555442     11212334555555555555       5555555555455


Q ss_pred             cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          573 IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..|+.|+++++.+..+|..+..+.+|++|.++++. +...|..+.++.+|..|.+.++.+..+|..++.+++|++|.
T Consensus       186 ~~L~~L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~-~~~~~~~~~~~~~l~~l~l~~n~~~~~~~~~~~l~~l~~L~  261 (394)
T COG4886         186 SNLNNLDLSGNKISDLPPEIELLSALEELDLSNNS-IIELLSSLSNLKNLSGLELSNNKLEDLPESIGNLSNLETLD  261 (394)
T ss_pred             hhhhheeccCCccccCchhhhhhhhhhhhhhcCCc-ceecchhhhhcccccccccCCceeeeccchhccccccceec
Confidence            55555555555555555544444445555555432 33344444444444444444444444344444444444443

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.29  E-value=5.9e-08  Score=93.47  Aligned_cols=131  Identities=22%  Similarity=0.195  Sum_probs=88.3

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      |..+..+.++.+.+..+..+..-.+++|.|+++.|..     ....+ +..+.+|..|||++       +.+.++-..-.
T Consensus       283 Wq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i-----~~v~n-La~L~~L~~LDLS~-------N~Ls~~~Gwh~  349 (490)
T KOG1259|consen  283 WQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRI-----RTVQN-LAELPQLQLLDLSG-------NLLAECVGWHL  349 (490)
T ss_pred             HhhhhhccccccchhhhhhhhhhccceeEEeccccce-----eeehh-hhhcccceEeeccc-------chhHhhhhhHh
Confidence            3445556666666666655665667777777777653     11111 45667777788877       76666655555


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccc--cccccccCCeeecccccccccc
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +|-+.+.|.|.+|.++.| +.+++|++|..||+++++ ++.+..  +||+|+.|++|.+.+|.+..+|
T Consensus       350 KLGNIKtL~La~N~iE~L-SGL~KLYSLvnLDl~~N~-Ie~ldeV~~IG~LPCLE~l~L~~NPl~~~v  415 (490)
T KOG1259|consen  350 KLGNIKTLKLAQNKIETL-SGLRKLYSLVNLDLSSNQ-IEELDEVNHIGNLPCLETLRLTGNPLAGSV  415 (490)
T ss_pred             hhcCEeeeehhhhhHhhh-hhhHhhhhheeccccccc-hhhHHHhcccccccHHHHHhhcCCCccccc
Confidence            666677777877777666 457788888888888755 766653  6788888888888777777665

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.27  E-value=1.9e-06  Score=92.53  Aligned_cols=137  Identities=21%  Similarity=0.339  Sum_probs=79.1

Q ss_pred             CcceechhhHHH---HHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          169 SEIRGRDEEKSS---LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       169 ~~~vGr~~~~~~---l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      ++++|.+..+..   +..++....       ...+.|+|++|+||||||+.+.+..  ...|     +.++......+-.
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~~-------~~~ilL~GppGtGKTtLA~~ia~~~--~~~~-----~~l~a~~~~~~~i   77 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAGR-------LSSMILWGPPGTGKTTLARIIAGAT--DAPF-----EALSAVTSGVKDL   77 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcCC-------CceEEEECCCCCCHHHHHHHHHHHh--CCCE-----EEEecccccHHHH
Confidence            468888877655   777664433       4568889999999999999998852  2222     2222211111111


Q ss_pred             HHHHHHhhCCCCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEE--EcCChh--HH-
Q 005860          246 KAIIEALEGFVPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILV--TTRKET--VA-  319 (673)
Q Consensus       246 ~~i~~~l~~~~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iiv--Ttr~~~--v~-  319 (673)
                      +.+++                 ..... ..+++.+|++|+++.-...+.+.+...+..   |+.+++  ||.+..  +. 
T Consensus        78 r~ii~-----------------~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI~att~n~~~~l~~  137 (413)
T PRK13342         78 REVIE-----------------EARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLIGATTENPSFEVNP  137 (413)
T ss_pred             HHHHH-----------------HHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEEEeCCCChhhhccH
Confidence            22222                 11111 246788999999976655566666555443   444544  344322  11 


Q ss_pred             HhccccceeecCCCCccccc
Q 005860          320 RMMESIHVISIKELSEQECW  339 (673)
Q Consensus       320 ~~~~~~~~~~l~~L~~~~~~  339 (673)
                      ....-...+.+.+++.++.+
T Consensus       138 aL~SR~~~~~~~~ls~e~i~  157 (413)
T PRK13342        138 ALLSRAQVFELKPLSEEDIE  157 (413)
T ss_pred             HHhccceeeEeCCCCHHHHH
Confidence            11222467888888887754

>PLN03150 hypothetical protein; Provisional

Probab=98.25  E-value=1.3e-06  Score=98.45  Aligned_cols=90  Identities=23%  Similarity=0.404  Sum_probs=72.3

Q ss_pred             cceeeeccccccccccchh-hhccccccccccccceecCCCCc-ccchhhhcCCCccEEEeccCCCCccccccccccccC
Q 005860          545 LRALRIATLMNTWDVNSTN-KILKGIEKLIHLRYLRLVGLGTE-ELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL  622 (673)
Q Consensus       545 L~~L~L~~~~~~~~~~~~~-~lp~~i~~L~~Lr~L~L~~~~i~-~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  622 (673)
                      +..|+|++       +.+. .+|..++.|.+|++|+|++|.+. .+|.+++.|++|++|+|++|..-..+|..+++|++|
T Consensus       420 v~~L~L~~-------n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L  492 (623)
T PLN03150        420 IDGLGLDN-------QGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSL  492 (623)
T ss_pred             EEEEECCC-------CCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCC
Confidence            66777777       6654 57888888899999999988864 788888999999999998877445788888899999


Q ss_pred             Ceeeccccccc-cccccCCC
Q 005860          623 RHLTYDDSCLE-FIPKGIQR  641 (673)
Q Consensus       623 r~L~l~~~~l~-~lP~~i~~  641 (673)
                      ++|++++|.+. .+|..++.
T Consensus       493 ~~L~Ls~N~l~g~iP~~l~~  512 (623)
T PLN03150        493 RILNLNGNSLSGRVPAALGG  512 (623)
T ss_pred             CEEECcCCcccccCChHHhh
Confidence            99998888876 67776664

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=9.8e-06  Score=84.54  Aligned_cols=116  Identities=22%  Similarity=0.233  Sum_probs=85.2

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      |+.+.+||++++++...|..--..   ....-+.|+|..|+|||+.++.|.+..+....=..+++|.+-...++..++..
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~~---~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~   92 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALRG---ERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSK   92 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhcC---CCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHH
Confidence            345999999999999887543211   11223889999999999999999996322211112789988888899999999


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhC--CCeEEEEEcCCC
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLV--GKKFLLILDDMW  286 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~--~kr~LlVLDdvw  286 (673)
                      |+++++..........+....+.+.+.  ++.++||||++-
T Consensus        93 i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid  133 (366)
T COG1474          93 ILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVD  133 (366)
T ss_pred             HHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchh
Confidence            999998544444555666677777764  589999999983

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.23  E-value=9.4e-07  Score=66.87  Aligned_cols=57  Identities=28%  Similarity=0.451  Sum_probs=37.7

Q ss_pred             ccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccc
Q 005860          574 HLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSC  631 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~  631 (673)
                      +|++|++++|.+..+| ..+..+++|++|++++|. +..+|. .+..|++|++|++++|.
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~-l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNN-LTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETSSS-ESEEETTTTTTSTTESEEEETSSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCc-cCccCHHHHcCCCCCCEEeCcCCc
Confidence            5666777777777776 355667777777777654 666654 45777777777766664

...

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=98.22  E-value=1.7e-07  Score=103.36  Aligned_cols=94  Identities=31%  Similarity=0.418  Sum_probs=69.6

Q ss_pred             cceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCe
Q 005860          545 LRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRH  624 (673)
Q Consensus       545 L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~  624 (673)
                      |+.||+++       +.+..+|..|..+.+|+.|+++.|.|.++|.+++++.+|++|+|.+ +.+..+|.++..+++|+.
T Consensus        47 L~~l~lsn-------n~~~~fp~~it~l~~L~~ln~s~n~i~~vp~s~~~~~~l~~lnL~~-n~l~~lP~~~~~lknl~~  118 (1081)
T KOG0618|consen   47 LKSLDLSN-------NQISSFPIQITLLSHLRQLNLSRNYIRSVPSSCSNMRNLQYLNLKN-NRLQSLPASISELKNLQY  118 (1081)
T ss_pred             eEEeeccc-------cccccCCchhhhHHHHhhcccchhhHhhCchhhhhhhcchhheecc-chhhcCchhHHhhhcccc
Confidence            77777777       7777777777777888888887777777887777788888888775 447777877878888888


Q ss_pred             eeccccccccccccCCCCCCCC
Q 005860          625 LTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       625 L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      |+++.|.+..+|.-|..++.+.
T Consensus       119 LdlS~N~f~~~Pl~i~~lt~~~  140 (1081)
T KOG0618|consen  119 LDLSFNHFGPIPLVIEVLTAEE  140 (1081)
T ss_pred             cccchhccCCCchhHHhhhHHH
Confidence            8877777777775554444333

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.22  E-value=6.6e-07  Score=101.65  Aligned_cols=126  Identities=19%  Similarity=0.256  Sum_probs=94.5

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK  571 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~  571 (673)
                      ..++.+.+..+....+|..+.  ++|++|.+++|.+.    . +|..+  ...|..|++++       |.+..+|..+. 
T Consensus       262 s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~Lt----~-LP~~l--p~sL~~L~Ls~-------N~Lt~LP~~l~-  324 (754)
T PRK15370        262 SALQSLDLFHNKISCLPENLP--EELRYLSVYDNSIR----T-LPAHL--PSGITHLNVQS-------NSLTALPETLP-  324 (754)
T ss_pred             CCCCEEECcCCccCccccccC--CCCcEEECCCCccc----c-Ccccc--hhhHHHHHhcC-------CccccCCcccc-
Confidence            467788887776666665443  57888888887631    1 22211  13677888888       88777776554 


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCC
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQ  640 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~  640 (673)
                       .+|++|++++|.+..+|.++.  ++|+.|++++|. +..+|..+.  ++|++|++++|.+..+|+.+.
T Consensus       325 -~sL~~L~Ls~N~Lt~LP~~l~--~sL~~L~Ls~N~-L~~LP~~lp--~~L~~LdLs~N~Lt~LP~~l~  387 (754)
T PRK15370        325 -PGLKTLEAGENALTSLPASLP--PELQVLDVSKNQ-ITVLPETLP--PTITTLDVSRNALTNLPENLP  387 (754)
T ss_pred             -ccceeccccCCccccCChhhc--CcccEEECCCCC-CCcCChhhc--CCcCEEECCCCcCCCCCHhHH
Confidence             689999999999999998775  689999999976 888997663  689999999999999987654

>TIGR00767 rho transcription termination factor Rho

Probab=98.20  E-value=2.4e-06  Score=88.14  Aligned_cols=88  Identities=16%  Similarity=0.084  Sum_probs=62.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc--ccHHHHHHHHHHHhhCCCCCcC--c---H-HHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP--FDELRIAKAIIEALEGFVPTVG--E---L-NSLLES  268 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~l~~~~~~~~--~---~-~~~~~~  268 (673)
                      -..++|+|++|+|||||++.+++.... .+|+..+||.+++.  .++.++++.+...+-....+..  .   . ....+.
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~-nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~  246 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITR-NHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEK  246 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcc-cCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHH
Confidence            457999999999999999999997433 37999999999876  7889999988654433322111  1   0 111122


Q ss_pred             HHHH-hCCCeEEEEEcCC
Q 005860          269 IRAS-LVGKKFLLILDDM  285 (673)
Q Consensus       269 l~~~-l~~kr~LlVLDdv  285 (673)
                      .... -++++++|++|++
T Consensus       247 Ae~~~~~GkdVVLlIDEi  264 (415)
T TIGR00767       247 AKRLVEHKKDVVILLDSI  264 (415)
T ss_pred             HHHHHHcCCCeEEEEECh
Confidence            2222 3689999999999

Members of this family differ in the specificity of RNA binding.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.20  E-value=8.7e-06  Score=90.52  Aligned_cols=118  Identities=15%  Similarity=0.084  Sum_probs=78.2

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc---cccCC--eEEEEEcCCcccH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV---FEYFD--KRMWVCVSDPFDE  241 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~F~--~~~wv~vs~~~~~  241 (673)
                      .|+.+.|||+++++|...|...-.+  .....++.|+|++|.|||++++.|.+....   .....  .+++|.+..-.++
T Consensus       753 VPD~LPhREeEIeeLasfL~paIkg--sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp  830 (1164)
T PTZ00112        753 VPKYLPCREKEIKEVHGFLESGIKQ--SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHP  830 (1164)
T ss_pred             CCCcCCChHHHHHHHHHHHHHHHhc--CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCH
Confidence            3468999999999999888543211  123467889999999999999999875211   11222  2566766666678


Q ss_pred             HHHHHHHHHHhhCCCCC-cCcHHHHHHHHHHHhC---CCeEEEEEcCCC
Q 005860          242 LRIAKAIIEALEGFVPT-VGELNSLLESIRASLV---GKKFLLILDDMW  286 (673)
Q Consensus       242 ~~~~~~i~~~l~~~~~~-~~~~~~~~~~l~~~l~---~kr~LlVLDdvw  286 (673)
                      ..++..|++++....+. .....+....+...+.   ....+||||+|.
T Consensus       831 ~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID  879 (1164)
T PTZ00112        831 NAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEID  879 (1164)
T ss_pred             HHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHh
Confidence            88999999999554332 2233344444554442   234689999993

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.18  E-value=6.9e-06  Score=81.60  Aligned_cols=121  Identities=25%  Similarity=0.326  Sum_probs=78.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      +.+.-+.+||++|+||||||+.+.+..+-..    ..||..|....-..-.++|.++-.               -...+.
T Consensus       160 ~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq---------------~~~~l~  220 (554)
T KOG2028|consen  160 NRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQ---------------NEKSLT  220 (554)
T ss_pred             CCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHH---------------HHHhhh
Confidence            3467788999999999999999999744433    456776665444444444544321               123456


Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEE--EcCChhH---HHhccccceeecCCCCccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILV--TTRKETV---ARMMESIHVISIKELSEQE  337 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iiv--Ttr~~~v---~~~~~~~~~~~l~~L~~~~  337 (673)
                      ++|..|++|.|..-+..+-+.+   +|.-.+|+-++|  ||.+...   +..+.-..++.|+.|+.++
T Consensus       221 krkTilFiDEiHRFNksQQD~f---LP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~  285 (554)
T KOG2028|consen  221 KRKTILFIDEIHRFNKSQQDTF---LPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNA  285 (554)
T ss_pred             cceeEEEeHHhhhhhhhhhhcc---cceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHH
Confidence            7889999999966555554443   555567876666  6665442   2223446788888887554

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.17  E-value=3.8e-07  Score=88.04  Aligned_cols=123  Identities=24%  Similarity=0.278  Sum_probs=100.8

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCC  593 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~  593 (673)
                      -..|.++++++|.+     ..+....+-.+.+++|+++.       +.+..+-. +..|.+|..|||++|.+.++-..-.
T Consensus       283 Wq~LtelDLS~N~I-----~~iDESvKL~Pkir~L~lS~-------N~i~~v~n-La~L~~L~~LDLS~N~Ls~~~Gwh~  349 (490)
T KOG1259|consen  283 WQELTELDLSGNLI-----TQIDESVKLAPKLRRLILSQ-------NRIRTVQN-LAELPQLQLLDLSGNLLAECVGWHL  349 (490)
T ss_pred             Hhhhhhccccccch-----hhhhhhhhhccceeEEeccc-------cceeeehh-hhhcccceEeecccchhHhhhhhHh
Confidence            35688899998864     34555667788999999999       88776544 8889999999999999888877777


Q ss_pred             cCCCccEEEeccCCCCccccccccccccCCeeecccccccccc--ccCCCCCCCCcCCee
Q 005860          594 ELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP--KGIQRLTNLRTLSEF  651 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP--~~i~~L~~L~~L~~~  651 (673)
                      +|-|.++|.|+++. ++.+. ++++|-+|..||+++|++..+-  .+||+|+.|++|...
T Consensus       350 KLGNIKtL~La~N~-iE~LS-GL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~  407 (490)
T KOG1259|consen  350 KLGNIKTLKLAQNK-IETLS-GLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLT  407 (490)
T ss_pred             hhcCEeeeehhhhh-Hhhhh-hhHhhhhheeccccccchhhHHHhcccccccHHHHHhhc
Confidence            88999999999855 77775 8899999999999999988664  578999988887543

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.17  E-value=1.3e-06  Score=98.82  Aligned_cols=79  Identities=22%  Similarity=0.190  Sum_probs=46.0

Q ss_pred             cchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccC
Q 005860          560 NSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       560 ~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i  639 (673)
                      +.+..+|...   ..|+.|+|++|.+..+|...   .+|+.|++++|. +..+|...   .+|+.|++++|.++.+|..+
T Consensus       372 N~L~~LP~l~---~~L~~LdLs~N~Lt~LP~l~---s~L~~LdLS~N~-LssIP~l~---~~L~~L~Ls~NqLt~LP~sl  441 (788)
T PRK15387        372 NRLTSLPALP---SGLKELIVSGNRLTSLPVLP---SELKELMVSGNR-LTSLPMLP---SGLLSLSVYRNQLTRLPESL  441 (788)
T ss_pred             cccccCcccc---cccceEEecCCcccCCCCcc---cCCCEEEccCCc-CCCCCcch---hhhhhhhhccCcccccChHH
Confidence            4444444322   34666666666666666432   456666776654 66666432   34566666667777777666


Q ss_pred             CCCCCCCcC
Q 005860          640 QRLTNLRTL  648 (673)
Q Consensus       640 ~~L~~L~~L  648 (673)
                      +++++|+.|
T Consensus       442 ~~L~~L~~L  450 (788)
T PRK15387        442 IHLSSETTV  450 (788)
T ss_pred             hhccCCCeE
Confidence            666655544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.15  E-value=1e-05  Score=79.48  Aligned_cols=130  Identities=19%  Similarity=0.215  Sum_probs=73.5

Q ss_pred             chhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          174 RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       174 r~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      .+..++.+..++...       ....|.|+|..|+|||+||+.+++.  ........+|++++.-.+      ..     
T Consensus        22 ~~~~~~~l~~~~~~~-------~~~~lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~~~~~~------~~-----   81 (226)
T TIGR03420        22 NAELLAALRQLAAGK-------GDRFLYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPLAELAQ------AD-----   81 (226)
T ss_pred             cHHHHHHHHHHHhcC-------CCCeEEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeHHHHHH------hH-----
Confidence            445667777765432       2467899999999999999999985  222334456665443211      00     


Q ss_pred             CCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCcc-ch-hhhhhhccC-CCCCeEEEEEcCChh---------HHHh
Q 005860          254 GFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYS-KW-EPFHYCLKN-GVRGSKILVTTRKET---------VARM  321 (673)
Q Consensus       254 ~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~-~~-~~l~~~l~~-~~~gs~iivTtr~~~---------v~~~  321 (673)
                                   ..+...+.+. -+|||||+..-... .| +.+...+.. ...+.++|+||+...         +...
T Consensus        82 -------------~~~~~~~~~~-~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r  147 (226)
T TIGR03420        82 -------------PEVLEGLEQA-DLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTR  147 (226)
T ss_pred             -------------HHHHhhcccC-CEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHH
Confidence                         0111122222 38999999543321 22 334433332 123447888887532         2222


Q ss_pred             ccccceeecCCCCccc
Q 005860          322 MESIHVISIKELSEQE  337 (673)
Q Consensus       322 ~~~~~~~~l~~L~~~~  337 (673)
                      +.....+++.++++++
T Consensus       148 ~~~~~~i~l~~l~~~e  163 (226)
T TIGR03420       148 LAWGLVFQLPPLSDEE  163 (226)
T ss_pred             HhcCeeEecCCCCHHH
Confidence            2234578899988865

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.12  E-value=1.5e-05  Score=89.44  Aligned_cols=162  Identities=20%  Similarity=0.243  Sum_probs=96.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC---CeEEEEEcCCc---ccHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF---DKRMWVCVSDP---FDEL  242 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~---~~~~  242 (673)
                      ++++|++..+..+...+....       ...+.|+|++|+||||||+.+++.......+   ...-|+.+...   .+..
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~~-------~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~  226 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASPF-------PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPR  226 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcCC-------CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHH
Confidence            468999999999888774332       4569999999999999999998864333332   12335544321   1222


Q ss_pred             HHHHHH---------------HHHhhCCC----------------CCcCcH-HHHHHHHHHHhCCCeEEEEEcCCCCCCc
Q 005860          243 RIAKAI---------------IEALEGFV----------------PTVGEL-NSLLESIRASLVGKKFLLILDDMWTDDY  290 (673)
Q Consensus       243 ~~~~~i---------------~~~l~~~~----------------~~~~~~-~~~~~~l~~~l~~kr~LlVLDdvw~~~~  290 (673)
                      .+...+               +...+...                ++.+.+ ...+..+.+.+++++++++-|+.|..+.
T Consensus       227 ~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~  306 (615)
T TIGR02903       227 EVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDP  306 (615)
T ss_pred             HHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCc
Confidence            221111               11111100                011112 2357788889999999999888888777


Q ss_pred             cchhhhhhhccCCCCCeEEEE--EcCChhH-HHhc-cccceeecCCCCccc
Q 005860          291 SKWEPFHYCLKNGVRGSKILV--TTRKETV-ARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       291 ~~~~~l~~~l~~~~~gs~iiv--Ttr~~~v-~~~~-~~~~~~~l~~L~~~~  337 (673)
                      ..|+.+...+....+...|++  ||++... ...+ .....+.+.+++.+|
T Consensus       307 ~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~ed  357 (615)
T TIGR02903       307 NVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPED  357 (615)
T ss_pred             ccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHH
Confidence            788888777776666555555  5664321 1111 112345666666554

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.12  E-value=4.4e-06  Score=94.57  Aligned_cols=79  Identities=22%  Similarity=0.124  Sum_probs=44.0

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      +.+++.+.+..+....+|..   .++|++|.+++|..     ..+|..   +..|..|++++       |.+..+|..  
T Consensus       241 p~~Lk~LdLs~N~LtsLP~l---p~sL~~L~Ls~N~L-----~~Lp~l---p~~L~~L~Ls~-------N~Lt~LP~~--  300 (788)
T PRK15387        241 PPELRTLEVSGNQLTSLPVL---PPGLLELSIFSNPL-----THLPAL---PSGLCKLWIFG-------NQLTSLPVL--  300 (788)
T ss_pred             CCCCcEEEecCCccCcccCc---ccccceeeccCCch-----hhhhhc---hhhcCEEECcC-------Ccccccccc--
Confidence            45677888877766655532   35677777776653     112221   23455556665       555555542  


Q ss_pred             cccccccceecCCCCcccch
Q 005860          571 KLIHLRYLRLVGLGTEELPE  590 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~  590 (673)
                       +++|++|+|++|.+..+|.
T Consensus       301 -p~~L~~LdLS~N~L~~Lp~  319 (788)
T PRK15387        301 -PPGLQELSVSDNQLASLPA  319 (788)
T ss_pred             -ccccceeECCCCccccCCC
Confidence             2456666666666555543

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.09  E-value=2.5e-05  Score=80.74  Aligned_cols=147  Identities=20%  Similarity=0.217  Sum_probs=93.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC----ccccccCCeEEEEEc-CCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND----SDVFEYFDKRMWVCV-SDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~----~~~~~~F~~~~wv~v-s~~~~~~~  243 (673)
                      ++++|-+..++.+...+..+.      -...+.++|+.|+||||+|+.+++.    .....|+|...|... +.....++
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~------~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~   77 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR------FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD   77 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC------CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH
Confidence            468899999999999886543      2457789999999999999888773    122356676656542 22223322


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHH-Hh-
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVA-RM-  321 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~-~~-  321 (673)
                       .+++.+.+...                -..+++-++|+|++..-+...++.+...+.....++.+|++|.+.+.. .. 
T Consensus        78 -ir~~~~~~~~~----------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI  140 (313)
T PRK05564         78 -IRNIIEEVNKK----------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTI  140 (313)
T ss_pred             -HHHHHHHHhcC----------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHH
Confidence             22222222111                112445567777775455567889999998888899999888764321 11 


Q ss_pred             ccccceeecCCCCcccc
Q 005860          322 MESIHVISIKELSEQEC  338 (673)
Q Consensus       322 ~~~~~~~~l~~L~~~~~  338 (673)
                      ..-...+++.++++++.
T Consensus       141 ~SRc~~~~~~~~~~~~~  157 (313)
T PRK05564        141 KSRCQIYKLNRLSKEEI  157 (313)
T ss_pred             HhhceeeeCCCcCHHHH
Confidence            12256777887776663

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.09  E-value=2.6e-06  Score=92.73  Aligned_cols=164  Identities=20%  Similarity=0.175  Sum_probs=91.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|-+..++.|..++....      -...+.++|+.|+||||+|+.+.+.......+...+|.|.+... +......-
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~------l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~-i~~~~h~d   86 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR------LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLA-VRRGAHPD   86 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHH-HhcCCCCc
Confidence            478999999999988886554      23567999999999999999988753222223334444322110 00000000


Q ss_pred             HHHhhCC-CCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhHHHhc-cc
Q 005860          249 IEALEGF-VPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETVARMM-ES  324 (673)
Q Consensus       249 ~~~l~~~-~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v~~~~-~~  324 (673)
                      +..+... .....+..++...+.. -..+++-++|+|+++......++.+...+......+.+|++|.. ..+...+ ..
T Consensus        87 v~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SR  166 (504)
T PRK14963         87 VLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSR  166 (504)
T ss_pred             eEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcc
Confidence            0000000 0011111222222221 12356668999999766556677887777765556666665543 3332222 23


Q ss_pred             cceeecCCCCccccc
Q 005860          325 IHVISIKELSEQECW  339 (673)
Q Consensus       325 ~~~~~l~~L~~~~~~  339 (673)
                      ...+++.+++.++..
T Consensus       167 c~~~~f~~ls~~el~  181 (504)
T PRK14963        167 TQHFRFRRLTEEEIA  181 (504)
T ss_pred             eEEEEecCCCHHHHH
Confidence            567899999988854

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.06  E-value=1.6e-05  Score=83.31  Aligned_cols=45  Identities=22%  Similarity=0.304  Sum_probs=37.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|++..++.+..++..+.       .+.+.++|+.|+||||+|+.+.+.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~-------~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPN-------LPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCC-------CceEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999998885433       345789999999999999998875

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=98.06  E-value=2.1e-06  Score=92.22  Aligned_cols=144  Identities=29%  Similarity=0.332  Sum_probs=118.7

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      ++..+.+..+....++..+..+++|+.|.+.++..     ..++.....+..|+.|++++       +.+..+|..+..+
T Consensus       141 nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l-----~~l~~~~~~~~~L~~L~ls~-------N~i~~l~~~~~~~  208 (394)
T COG4886         141 NLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDL-----SDLPKLLSNLSNLNNLDLSG-------NKISDLPPEIELL  208 (394)
T ss_pred             hcccccccccchhhhhhhhhccccccccccCCchh-----hhhhhhhhhhhhhhheeccC-------CccccCchhhhhh
Confidence            68888888888777766778899999999998874     33444444788999999999       9999999988888


Q ss_pred             cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCe
Q 005860          573 IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~  650 (673)
                      .+|.+|.++++.+...|..+.++.++..|.+.++. +..+|..++++.+|+.|++++|.++.++. ++.+.+|+.|..
T Consensus       209 ~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~n~-~~~~~~~~~~l~~l~~L~~s~n~i~~i~~-~~~~~~l~~L~~  284 (394)
T COG4886         209 SALEELDLSNNSIIELLSSLSNLKNLSGLELSNNK-LEDLPESIGNLSNLETLDLSNNQISSISS-LGSLTNLRELDL  284 (394)
T ss_pred             hhhhhhhhcCCcceecchhhhhcccccccccCCce-eeeccchhccccccceecccccccccccc-ccccCccCEEec
Confidence            88999999999888888889999999999977644 77778889999999999999999988876 666666666543

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.03  E-value=3.2e-06  Score=87.87  Aligned_cols=136  Identities=21%  Similarity=0.151  Sum_probs=95.6

Q ss_pred             cCceEEEEEEcCCCCc-cccccccc---cccchhhhccchhhhhhhhhHHHHhhhC-Cccceeeeccccccccccchh--
Q 005860          491 QEKLRHSMLVLGYEAS-FPISIFKA---KNLRSLFINNTLIQVSLTHVLQSLFDQL-KCLRALRIATLMNTWDVNSTN--  563 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~-~~~~~~~~---~~Lr~L~l~~~~~~~~~~~~~~~~~~~l-~~L~~L~L~~~~~~~~~~~~~--  563 (673)
                      ..+++.+.+..+.... .+..+..+   ++|++|.+.++.........+...+..+ +.|+.|++++       +.+.  
T Consensus        80 ~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~-------n~l~~~  152 (319)
T cd00116          80 GCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGR-------NRLEGA  152 (319)
T ss_pred             cCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCC-------CcCCch
Confidence            4578888887766532 22233333   3499999988764322223344556666 8899999998       6644  


Q ss_pred             ---hhccccccccccccceecCCCCc-----ccchhhhcCCCccEEEeccCCCCc-----cccccccccccCCeeecccc
Q 005860          564 ---KILKGIEKLIHLRYLRLVGLGTE-----ELPETCCELLNLQVLEIEQCTSLK-----RLPLGIGKLVNLRHLTYDDS  630 (673)
Q Consensus       564 ---~lp~~i~~L~~Lr~L~L~~~~i~-----~LP~~i~~L~~L~~L~l~~c~~l~-----~lP~~i~~L~~Lr~L~l~~~  630 (673)
                         .++..+..+.+|++|+|++|.+.     .++..+..+++|+.|++++|. +.     .++..+.++++|++|++++|
T Consensus       153 ~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~-i~~~~~~~l~~~~~~~~~L~~L~ls~n  231 (319)
T cd00116         153 SCEALAKALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNG-LTDEGASALAETLASLKSLEVLNLGDN  231 (319)
T ss_pred             HHHHHHHHHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCc-cChHHHHHHHHHhcccCCCCEEecCCC
Confidence               45556777788999999999865     456666777899999999986 43     35556778889999999888


Q ss_pred             cccc
Q 005860          631 CLEF  634 (673)
Q Consensus       631 ~l~~  634 (673)
                      .+..
T Consensus       232 ~l~~  235 (319)
T cd00116         232 NLTD  235 (319)
T ss_pred             cCch
Confidence            7763

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.03  E-value=1.1e-05  Score=91.37  Aligned_cols=137  Identities=20%  Similarity=0.309  Sum_probs=76.8

Q ss_pred             CcceechhhHH---HHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          169 SEIRGRDEEKS---SLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       169 ~~~vGr~~~~~---~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      ++++|.+..+.   .+...+...       ....+.|+|++|+||||||+.+++.  ....|.   .+..+. ....   
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~-------~~~slLL~GPpGtGKTTLA~aIA~~--~~~~f~---~lna~~-~~i~---   91 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD-------RVGSLILYGPPGVGKTTLARIIANH--TRAHFS---SLNAVL-AGVK---   91 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC-------CCceEEEECCCCCCHHHHHHHHHHH--hcCcce---eehhhh-hhhH---
Confidence            46899888764   455555433       2456789999999999999999985  333441   111110 0111   


Q ss_pred             HHHHHHhhCCCCCcCcHHHHHHHHHHHh--CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEE--cCChh--HH
Q 005860          246 KAIIEALEGFVPTVGELNSLLESIRASL--VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVT--TRKET--VA  319 (673)
Q Consensus       246 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivT--tr~~~--v~  319 (673)
                                     +..+......+.+  .+++.+|||||++.-+..+++.+...+.   .|+.++|+  |.+..  +.
T Consensus        92 ---------------dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~aTTenp~~~l~  153 (725)
T PRK13341         92 ---------------DLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIGATTENPYFEVN  153 (725)
T ss_pred             ---------------HHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEEecCCChHhhhh
Confidence                           1111112222222  2467799999996555555666554333   35555553  33321  11


Q ss_pred             Hh-ccccceeecCCCCccccc
Q 005860          320 RM-MESIHVISIKELSEQECW  339 (673)
Q Consensus       320 ~~-~~~~~~~~l~~L~~~~~~  339 (673)
                      .. ..-...+.+++|+.++..
T Consensus       154 ~aL~SR~~v~~l~pLs~edi~  174 (725)
T PRK13341        154 KALVSRSRLFRLKSLSDEDLH  174 (725)
T ss_pred             hHhhccccceecCCCCHHHHH
Confidence            11 122457889999987654

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=98.01  E-value=6.3e-06  Score=57.24  Aligned_cols=39  Identities=23%  Similarity=0.364  Sum_probs=26.1

Q ss_pred             ccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccc
Q 005860          574 HLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLP  613 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP  613 (673)
                      +|++|+|++|.|+.+|+.+++|++|++|++++|+ +..+|
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~-i~~i~   40 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELSNLPNLETLNLSNNP-ISDIS   40 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSC-CSBEG
T ss_pred             cceEEEccCCCCcccCchHhCCCCCCEEEecCCC-CCCCc
Confidence            5677777777777777777777777777777765 65554

...

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.01  E-value=5.8e-06  Score=62.49  Aligned_cols=58  Identities=22%  Similarity=0.330  Sum_probs=51.6

Q ss_pred             Cccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcccch-hhhcCCCccEEEeccCC
Q 005860          543 KCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCT  607 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~  607 (673)
                      ++|+.|++++       +.+..+|+ .+..+++|++|++++|.+..+|+ .+..+++|++|++++|+
T Consensus         1 p~L~~L~l~~-------n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    1 PNLESLDLSN-------NKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEETS-------STESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEECCC-------CCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCc
Confidence            4688999999       99988885 67889999999999999999974 78999999999999975

...

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.01  E-value=3.7e-05  Score=77.34  Aligned_cols=109  Identities=20%  Similarity=0.248  Sum_probs=80.3

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+.+.+|+..+..+..++...+    ..-+..|-|+|-.|.|||.+.+.+++...     -..+|+++-+.++.+.++..
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~----~~~PS~~~iyG~sgTGKT~~~r~~l~~~n-----~~~vw~n~~ecft~~~lle~   75 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNS----CTIPSIVHIYGHSGTGKTYLVRQLLRKLN-----LENVWLNCVECFTYAILLEK   75 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCC----cccceeEEEeccCCCchhHHHHHHHhhcC-----CcceeeehHHhccHHHHHHH
Confidence            4678999999999999886655    22356779999999999999999999642     24589999999999999999


Q ss_pred             HHHHhhCCCCCcC-------cHHHHHHHHHH--HhC--CCeEEEEEcCC
Q 005860          248 IIEALEGFVPTVG-------ELNSLLESIRA--SLV--GKKFLLILDDM  285 (673)
Q Consensus       248 i~~~l~~~~~~~~-------~~~~~~~~l~~--~l~--~kr~LlVLDdv  285 (673)
                      |+.+....+.+..       +.......+.+  ...  ++.++||||++
T Consensus        76 IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDna  124 (438)
T KOG2543|consen   76 ILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNA  124 (438)
T ss_pred             HHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCH
Confidence            9999963322211       12222223333  122  46999999999

>PLN03150 hypothetical protein; Provisional

Probab=97.98  E-value=5.3e-06  Score=93.67  Aligned_cols=104  Identities=19%  Similarity=0.336  Sum_probs=84.5

Q ss_pred             cchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhccccccccccccceecCCCCc-ccchhhhc
Q 005860          517 LRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKGIEKLIHLRYLRLVGLGTE-ELPETCCE  594 (673)
Q Consensus       517 Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~i~~L~~Lr~L~L~~~~i~-~LP~~i~~  594 (673)
                      ++.|.+.++.    +...+|..+..+++|+.|+|++       +.+. .+|..++.+.+|++|+|++|.+. .+|+++++
T Consensus       420 v~~L~L~~n~----L~g~ip~~i~~L~~L~~L~Ls~-------N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~  488 (623)
T PLN03150        420 IDGLGLDNQG----LRGFIPNDISKLRHLQSINLSG-------NSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQ  488 (623)
T ss_pred             EEEEECCCCC----ccccCCHHHhCCCCCCEEECCC-------CcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhc
Confidence            5666777665    3345666788999999999999       8865 68889999999999999999965 78999999


Q ss_pred             CCCccEEEeccCCCCcccccccccc-ccCCeeeccccc
Q 005860          595 LLNLQVLEIEQCTSLKRLPLGIGKL-VNLRHLTYDDSC  631 (673)
Q Consensus       595 L~~L~~L~l~~c~~l~~lP~~i~~L-~~Lr~L~l~~~~  631 (673)
                      |++|++|+|++|..-..+|..++.+ .++..+++.+|.
T Consensus       489 L~~L~~L~Ls~N~l~g~iP~~l~~~~~~~~~l~~~~N~  526 (623)
T PLN03150        489 LTSLRILNLNGNSLSGRVPAALGGRLLHRASFNFTDNA  526 (623)
T ss_pred             CCCCCEEECcCCcccccCChHHhhccccCceEEecCCc
Confidence            9999999999987556899888764 466777776654

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=6e-05  Score=79.45  Aligned_cols=155  Identities=16%  Similarity=0.204  Sum_probs=85.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+..++.+.+.+..+.      -...+.++|+.|+||||+|+.+.+.........       ..++..-....++
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~------~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~-------~~pc~~c~~c~~~   82 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR------IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGIT-------SNPCRKCIICKEI   82 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC------CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCCCHHHHHH
Confidence            578999999999998886543      235678999999999999998887421111100       0000000000111


Q ss_pred             HHHhhC-----CCCCcCcHHHHHHHHHHH-----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-h
Q 005860          249 IEALEG-----FVPTVGELNSLLESIRAS-----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-T  317 (673)
Q Consensus       249 ~~~l~~-----~~~~~~~~~~~~~~l~~~-----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~  317 (673)
                      ......     ........++... +.+.     ..+++-++|+|++..-....++.+...+.......++|++|.+. .
T Consensus        83 ~~~~~~d~~~~~~~~~~~v~~ir~-i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~  161 (363)
T PRK14961         83 EKGLCLDLIEIDAASRTKVEEMRE-ILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEK  161 (363)
T ss_pred             hcCCCCceEEecccccCCHHHHHH-HHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHh
Confidence            000000     0000011122111 1111     12455699999996555446777777777666677777777543 2


Q ss_pred             HHHh-ccccceeecCCCCccc
Q 005860          318 VARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       318 v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      +... .+-...+++.+++.++
T Consensus       162 l~~tI~SRc~~~~~~~l~~~e  182 (363)
T PRK14961        162 IPKTILSRCLQFKLKIISEEK  182 (363)
T ss_pred             hhHHHHhhceEEeCCCCCHHH
Confidence            3222 1224678888887766

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=97.93  E-value=8.3e-06  Score=84.77  Aligned_cols=154  Identities=17%  Similarity=0.188  Sum_probs=104.3

Q ss_pred             CceEEEEEEcCCCCc-----cccccccc-cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh--
Q 005860          492 EKLRHSMLVLGYEAS-----FPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN--  563 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~-----~~~~~~~~-~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~--  563 (673)
                      ++++++.+..+....     +...+..+ ++|+.|.+.++.........+...+..+..|+.|++++       +.+.  
T Consensus       108 ~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~L~~L~l~~-------n~l~~~  180 (319)
T cd00116         108 SSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEALAKALRANRDLKELNLAN-------NGIGDA  180 (319)
T ss_pred             CcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHHHHHHHHhCCCcCEEECcC-------CCCchH
Confidence            458899998776531     12234455 89999999998753323334566677888999999999       6644  


Q ss_pred             ---hhccccccccccccceecCCCCc-----ccchhhhcCCCccEEEeccCCCCcc-cccccc-----ccccCCeeeccc
Q 005860          564 ---KILKGIEKLIHLRYLRLVGLGTE-----ELPETCCELLNLQVLEIEQCTSLKR-LPLGIG-----KLVNLRHLTYDD  629 (673)
Q Consensus       564 ---~lp~~i~~L~~Lr~L~L~~~~i~-----~LP~~i~~L~~L~~L~l~~c~~l~~-lP~~i~-----~L~~Lr~L~l~~  629 (673)
                         .++..+..+.+|++|+|++|.+.     .++..+..+++|++|++++|. +.. -+..+.     ...+|++|++++
T Consensus       181 ~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~-l~~~~~~~l~~~~~~~~~~L~~L~l~~  259 (319)
T cd00116         181 GIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNN-LTDAGAAALASALLSPNISLLTLSLSC  259 (319)
T ss_pred             HHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCc-CchHHHHHHHHHHhccCCCceEEEccC
Confidence               35556666789999999999864     455667788999999999986 543 111221     247999999999


Q ss_pred             cccc-----cccccCCCCCCCCcCCeeEEccC
Q 005860          630 SCLE-----FIPKGIQRLTNLRTLSEFVVVRG  656 (673)
Q Consensus       630 ~~l~-----~lP~~i~~L~~L~~L~~~~~~~~  656 (673)
                      |.+.     .++..+..+   ..|..+.++.+
T Consensus       260 n~i~~~~~~~l~~~~~~~---~~L~~l~l~~N  288 (319)
T cd00116         260 NDITDDGAKDLAEVLAEK---ESLLELDLRGN  288 (319)
T ss_pred             CCCCcHHHHHHHHHHhcC---CCccEEECCCC
Confidence            8775     233333334   44555555443

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.93  E-value=6e-05  Score=83.60  Aligned_cols=157  Identities=13%  Similarity=0.167  Sum_probs=87.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+..++.|.+++..+.      -...+.++|..|+||||+|+.+.+...-...++.       ..+..-...+.|
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR------L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~-------~PCG~C~sCr~I   82 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR------LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTS-------QPCGVCRACREI   82 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCC-------CCCcccHHHHHH
Confidence            579999999999999986543      2346679999999999999877774211111100       001100111111


Q ss_pred             HHH-----hhCCCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-H
Q 005860          249 IEA-----LEGFVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-V  318 (673)
Q Consensus       249 ~~~-----l~~~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v  318 (673)
                      ...     +.....+....+++...+...    ..++.-++|||++..-+...++.+...+.......++|+||.+.. +
T Consensus        83 ~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KI  162 (830)
T PRK07003         83 DEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKI  162 (830)
T ss_pred             hcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhc
Confidence            100     000000011122222222221    134555888999966665668888887776666788888777643 2


Q ss_pred             HH-hccccceeecCCCCcccc
Q 005860          319 AR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      .. ...-...|+++.++.++.
T Consensus       163 p~TIrSRCq~f~Fk~Ls~eeI  183 (830)
T PRK07003        163 PVTVLSRCLQFNLKQMPAGHI  183 (830)
T ss_pred             cchhhhheEEEecCCcCHHHH
Confidence            21 122256778888877664

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.91  E-value=6.6e-05  Score=84.92  Aligned_cols=147  Identities=16%  Similarity=0.196  Sum_probs=89.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-------------------Ce
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-------------------DK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-------------------~~  229 (673)
                      .+++|-+.-++.|.+++..+.      -...+.++|+.|+||||+|+.+.+...-....                   .-
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r------l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~D   89 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR------LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVD   89 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC------CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCce
Confidence            579999999999999886544      13456899999999999999998852211111                   00


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      ++++..+....+                  +++.++...+.. -..+++-++|||++..-.....+.|...+.......+
T Consensus        90 viEidAas~~kV------------------DdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vr  151 (944)
T PRK14949         90 LIEVDAASRTKV------------------DDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVK  151 (944)
T ss_pred             EEEeccccccCH------------------HHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeE
Confidence            111211100111                  111222222211 1246777999999976666677888777776556666


Q ss_pred             EEEEcCC-hhHHHh-ccccceeecCCCCccccc
Q 005860          309 ILVTTRK-ETVARM-MESIHVISIKELSEQECW  339 (673)
Q Consensus       309 iivTtr~-~~v~~~-~~~~~~~~l~~L~~~~~~  339 (673)
                      +|++|.+ ..+... ..-...|++++|+.++..
T Consensus       152 FILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~  184 (944)
T PRK14949        152 FLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIG  184 (944)
T ss_pred             EEEECCCchhchHHHHHhheEEeCCCCCHHHHH
Confidence            6666654 333322 233578899999887753

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.91  E-value=6.1e-05  Score=82.34  Aligned_cols=146  Identities=16%  Similarity=0.216  Sum_probs=88.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc-------------------ccCCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF-------------------EYFDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~F~~  229 (673)
                      .+++|-+..++.|...+....      -...+.++|+.|+||||+|+.+.+...-.                   ..|..
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r------l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~d   89 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK------VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFID   89 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCc
Confidence            578999999999999886543      23567899999999999998887631100                   01112


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      .+++.......+.                  +..++...+.. -..+++-++|+|++..-+...++.+...+......+.
T Consensus        90 lieidaas~~gvd------------------~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~  151 (546)
T PRK14957         90 LIEIDAASRTGVE------------------ETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVK  151 (546)
T ss_pred             eEEeecccccCHH------------------HHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCce
Confidence            2222221111111                  11222222221 1245667999999966555677788888877655666


Q ss_pred             EEEEcCC-hhHHHh-ccccceeecCCCCcccc
Q 005860          309 ILVTTRK-ETVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       309 iivTtr~-~~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      +|++|.+ ..+... ..-...+++++++.++-
T Consensus       152 fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI  183 (546)
T PRK14957        152 FILATTDYHKIPVTILSRCIQLHLKHISQADI  183 (546)
T ss_pred             EEEEECChhhhhhhHHHheeeEEeCCCCHHHH
Confidence            6654443 333322 23367888999987763

>PLN03025 replication factor C subunit; Provisional

Probab=97.90  E-value=6.2e-05  Score=78.03  Aligned_cols=147  Identities=15%  Similarity=0.131  Sum_probs=80.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|.++.++.|..++....       .+.+.++|++|+||||+|+.+.+... ...|. .++-+..++..... ..++
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~-------~~~lll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~eln~sd~~~~~-~vr~   83 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGN-------MPNLILSGPPGTGKTTSILALAHELL-GPNYKEAVLELNASDDRGID-VVRN   83 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC-------CceEEEECCCCCCHHHHHHHHHHHHh-cccCccceeeecccccccHH-HHHH
Confidence            478999988888888775433       34467999999999999999887421 11222 12222333322222 2222


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHh-cccc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARM-MESI  325 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~-~~~~  325 (673)
                      +++.+......             .-.++.-+++||++..-.....+.+...+......+++|+++... .+... ..-.
T Consensus        84 ~i~~~~~~~~~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc  150 (319)
T PLN03025         84 KIKMFAQKKVT-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRC  150 (319)
T ss_pred             HHHHHHhcccc-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhh
Confidence            22222111000             002456689999995544444455655555445567777776542 22111 1113


Q ss_pred             ceeecCCCCccc
Q 005860          326 HVISIKELSEQE  337 (673)
Q Consensus       326 ~~~~l~~L~~~~  337 (673)
                      ..++++++++++
T Consensus       151 ~~i~f~~l~~~~  162 (319)
T PLN03025        151 AIVRFSRLSDQE  162 (319)
T ss_pred             hcccCCCCCHHH
Confidence            466777776655

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.89  E-value=6.7e-05  Score=82.32  Aligned_cols=157  Identities=17%  Similarity=0.174  Sum_probs=88.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+..++.|.+++..+.      -...+.++|+.|+||||+|+.+.+...-..      ++.. ..++.-...+.|
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr------l~HAyLF~GPpGvGKTTlAriLAK~LnC~~------~~~~-~pCg~C~sC~~I   81 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR------LHHAYLFTGTRGVGKTTIARILAKCLNCET------GVTS-TPCEVCATCKAV   81 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhCCCc------CCCC-CCCccCHHHHHH
Confidence            579999999999999987554      246789999999999999998877421111      1000 000000011111


Q ss_pred             HHHhhC-----CCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-H
Q 005860          249 IEALEG-----FVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-V  318 (673)
Q Consensus       249 ~~~l~~-----~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v  318 (673)
                      ...-..     ........++.+..+..    -..++.-++|+|++..-+....+.+...+.....+.++|++|.+.. +
T Consensus        82 ~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kI  161 (702)
T PRK14960         82 NEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKL  161 (702)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhh
Confidence            100000     00001122222222211    1235666899999966555667777777776556677777776532 2


Q ss_pred             H-HhccccceeecCCCCcccc
Q 005860          319 A-RMMESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~-~~~~~~~~~~l~~L~~~~~  338 (673)
                      . ....-...+++++++.++.
T Consensus       162 p~TIlSRCq~feFkpLs~eEI  182 (702)
T PRK14960        162 PITVISRCLQFTLRPLAVDEI  182 (702)
T ss_pred             hHHHHHhhheeeccCCCHHHH
Confidence            2 2223357788888888764

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.88  E-value=4.6e-05  Score=80.22  Aligned_cols=108  Identities=12%  Similarity=0.070  Sum_probs=71.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .++++.+...+.+...|...         +.|.++|++|+|||++|+.+++.......|+.+.||.+++.++..++...+
T Consensus       175 ~d~~i~e~~le~l~~~L~~~---------~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~  245 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK---------KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY  245 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC---------CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhccc
Confidence            46888999999999988643         357889999999999999998864444578889999999988876654322


Q ss_pred             HHHhhCCCCCcC-cHHHHHHHHHHHh--CCCeEEEEEcCCCCCC
Q 005860          249 IEALEGFVPTVG-ELNSLLESIRASL--VGKKFLLILDDMWTDD  289 (673)
Q Consensus       249 ~~~l~~~~~~~~-~~~~~~~~l~~~l--~~kr~LlVLDdvw~~~  289 (673)
                      .    ....... ......+.+....  .++++++|+|++-..+
T Consensus       246 r----P~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRan  285 (459)
T PRK11331        246 R----PNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRAN  285 (459)
T ss_pred             C----CCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccC
Confidence            1    1100000 0011122222222  2478999999994433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.87  E-value=9.2e-05  Score=76.99  Aligned_cols=145  Identities=16%  Similarity=0.142  Sum_probs=78.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc--CCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV--SDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~~~~  246 (673)
                      .+++|+++.++.+..++....       .+.+.|+|..|+||||+|+.+.+... ...+.. .++.+  +...... ...
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~-------~~~~ll~G~~G~GKt~~~~~l~~~l~-~~~~~~-~~i~~~~~~~~~~~-~~~   86 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN-------MPHLLFAGPPGTGKTTAALALARELY-GEDWRE-NFLELNASDERGID-VIR   86 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC-------CCeEEEECCCCCCHHHHHHHHHHHHc-CCcccc-ceEEeccccccchH-HHH
Confidence            468999999999999885433       34579999999999999999988521 111211 12222  2222211 111


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHh-ccc
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARM-MES  324 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~-~~~  324 (673)
                      +.+..+....+              .....+-+|++|++..-.....+.+...+......+++|+++... .+... ...
T Consensus        87 ~~i~~~~~~~~--------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr  152 (319)
T PRK00440         87 NKIKEFARTAP--------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSR  152 (319)
T ss_pred             HHHHHHHhcCC--------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHH
Confidence            22221111100              011235689999984433334555666665555566777776432 11111 111


Q ss_pred             cceeecCCCCccc
Q 005860          325 IHVISIKELSEQE  337 (673)
Q Consensus       325 ~~~~~l~~L~~~~  337 (673)
                      ...+++++++.++
T Consensus       153 ~~~~~~~~l~~~e  165 (319)
T PRK00440        153 CAVFRFSPLKKEA  165 (319)
T ss_pred             hheeeeCCCCHHH
Confidence            3346666666554

>PRK08727 hypothetical protein; Validated

Probab=97.81  E-value=0.0001  Score=72.62  Aligned_cols=36  Identities=19%  Similarity=0.175  Sum_probs=27.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV  235 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  235 (673)
                      ..+.|+|..|+|||+|++++++.  .......+.|+++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~~   77 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLPL   77 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEeH
Confidence            45999999999999999999885  3333345667764

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.81  E-value=0.00016  Score=78.66  Aligned_cols=161  Identities=14%  Similarity=0.177  Sum_probs=89.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCe-EEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDK-RMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|-+.-+..|...+..+.      -...+-++|+.|+||||+|+.+++...-...+.. -.+..+...    .-...
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r------i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C----~~C~~   90 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR------LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQC----TNCIS   90 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCC----hHHHH
Confidence            478999999998888775543      2357889999999999999999875221111100 000000000    00011


Q ss_pred             HHHHhhC-----CCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEE-EcCChh
Q 005860          248 IIEALEG-----FVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILV-TTRKET  317 (673)
Q Consensus       248 i~~~l~~-----~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iiv-Ttr~~~  317 (673)
                      |......     ........+++...+..    -+.+++-++|+|+++.-....++.+...+......+.+|+ ||+...
T Consensus        91 i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~k  170 (507)
T PRK06645         91 FNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQK  170 (507)
T ss_pred             HhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHH
Confidence            1100000     00001112222222221    1345677899999987666778888888876666666665 444444


Q ss_pred             HHHhc-cccceeecCCCCccccc
Q 005860          318 VARMM-ESIHVISIKELSEQECW  339 (673)
Q Consensus       318 v~~~~-~~~~~~~l~~L~~~~~~  339 (673)
                      +...+ .....+++++++.++..
T Consensus       171 I~~tI~SRc~~~ef~~ls~~el~  193 (507)
T PRK06645        171 IPATIISRCQRYDLRRLSFEEIF  193 (507)
T ss_pred             hhHHHHhcceEEEccCCCHHHHH
Confidence            44332 22456888888877643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=0.00013  Score=78.83  Aligned_cols=146  Identities=18%  Similarity=0.202  Sum_probs=81.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccccc--C-----------------Ce
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY--F-----------------DK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F-----------------~~  229 (673)
                      ++++|.+...+.|...+..+.      -...+.++|++|+||||+|+.+.+.......  +                 ..
T Consensus        14 ~divGq~~i~~~L~~~i~~~~------l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~d   87 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS------ISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMD   87 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCc
Confidence            579999988888888776543      2356889999999999999998774211100  0                 01


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      .+.+..+.......+ ++|.+                 .... ...+++-++|+|++..-.....+.+...+........
T Consensus        88 v~el~aa~~~gid~i-R~i~~-----------------~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv  149 (472)
T PRK14962         88 VIELDAASNRGIDEI-RKIRD-----------------AVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVV  149 (472)
T ss_pred             cEEEeCcccCCHHHH-HHHHH-----------------HHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEE
Confidence            112222111111111 11111                 1111 1235667999999954444455666666655444455


Q ss_pred             EEEEcCC-hhHHHhc-cccceeecCCCCcccc
Q 005860          309 ILVTTRK-ETVARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       309 iivTtr~-~~v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      +|++|.+ ..+...+ .....+++.+++.++.
T Consensus       150 ~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el  181 (472)
T PRK14962        150 FVLATTNLEKVPPTIISRCQVIEFRNISDELI  181 (472)
T ss_pred             EEEEeCChHhhhHHHhcCcEEEEECCccHHHH
Confidence            4444433 3333322 2356788888888764

>COG3899 Predicted ATPase [General function prediction only]

Probab=97.79  E-value=6.2e-05  Score=87.41  Aligned_cols=289  Identities=15%  Similarity=0.148  Sum_probs=143.5

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc---CCc--c-cHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV---SDP--F-DELR  243 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~--~-~~~~  243 (673)
                      .++||+.+++.|...+..-.    ...-.++.+.|..|||||+|++.|..-  +...+...+--.+   ..+  + ....
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~----~g~~~~~lv~G~sGIGKsalv~ev~~~--i~~~~~~~i~~~f~q~~~~ipl~~lvq   74 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVS----KGRGEVVLVAGESGIGKSALVNEVHKP--ITQQRGYFIKGKFDQFERNIPLSPLVQ   74 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHh----CCCeEEEEEeecCCCcHHHHHHHHHHH--HhccceeeeHhhcccccCCCchHHHHH
Confidence            37899999999999886655    245679999999999999999999985  3333211111111   111  1 1122


Q ss_pred             HHHHHHHHh-------------------hCCCC-----------------Cc-----CcHHH-----HHHHHHHHh-CCC
Q 005860          244 IAKAIIEAL-------------------EGFVP-----------------TV-----GELNS-----LLESIRASL-VGK  276 (673)
Q Consensus       244 ~~~~i~~~l-------------------~~~~~-----------------~~-----~~~~~-----~~~~l~~~l-~~k  276 (673)
                      .++++..++                   +....                 ..     ...+.     ....+.... +.|
T Consensus        75 ~~r~l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~  154 (849)
T COG3899          75 AFRDLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEH  154 (849)
T ss_pred             HHHHHHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccC
Confidence            333333333                   11100                 00     00011     112223233 456


Q ss_pred             eEEEEEcCCCCCCccchhhhhhhccCCCC----CeEEEEE--cCCh--hHHHhccccceeecCCCCccccc---------
Q 005860          277 KFLLILDDMWTDDYSKWEPFHYCLKNGVR----GSKILVT--TRKE--TVARMMESIHVISIKELSEQECW---------  339 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~~l~~~l~~~~~----gs~iivT--tr~~--~v~~~~~~~~~~~l~~L~~~~~~---------  339 (673)
                      +.++|+||+.-.|....+.+......-..    ...|..+  .+..  .+...-.....+.|.||+..+.-         
T Consensus       155 plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~  234 (849)
T COG3899         155 PLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGC  234 (849)
T ss_pred             CeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCC
Confidence            99999999944444444443333222211    1123333  2222  12222233578999999998864         


Q ss_pred             ---------------cCCchhhHHHHhhhhccC------CCHHHHHHHHhhhcccchhhhhccchhhhhcccCCChhhhh
Q 005860          340 ---------------CKGLPLAAKTIGSLLRFK------RTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKR  398 (673)
Q Consensus       340 ---------------c~GlPLai~~~~~~L~~~------~~~~~w~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~  398 (673)
                                     ..|.|+-+.-+-..+..+      .+...|..-... ....... +.+...+..-.+.||...+.
T Consensus       235 ~~~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~-i~~~~~~-~~vv~~l~~rl~kL~~~t~~  312 (849)
T COG3899         235 TKLLPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIAS-LGILATT-DAVVEFLAARLQKLPGTTRE  312 (849)
T ss_pred             cccccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHh-cCCchhh-HHHHHHHHHHHhcCCHHHHH
Confidence                           678998888877777542      223333322111 1111111 22444577777888887777


Q ss_pred             hhchHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHhcccccccccCCCCcEeE---E-EeChHHHHHHHH
Q 005860          399 CFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVR---C-KMHDIVHDFAQF  466 (673)
Q Consensus       399 cfl~~~l~~~w~a~g~i~~~~~~~~e~~~~~~~~~L~~~sli~~~~~~~~~~~~~---~-~mHdlv~~~a~~  466 (673)
                      ..-..+++..=...+.+..-..+.....+....+.|....++-..+.+..+....   | -.||.+++.+-.
T Consensus       313 Vl~~AA~iG~~F~l~~La~l~~~~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~F~H~~vqqaaY~  384 (849)
T COG3899         313 VLKAAACIGNRFDLDTLAALAEDSPALEAAALLDALQEGLILPLSETYRFGSNVDIATYKFLHDRVQQAAYN  384 (849)
T ss_pred             HHHHHHHhCccCCHHHHHHHHhhchHHHHHHHHHHhHhhceeccccccccccccchhhHHhhHHHHHHHHhc
Confidence            6555333321111111111111133444555555555544443222222221111   1 357777776644

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=97.78  E-value=0.00016  Score=74.84  Aligned_cols=117  Identities=19%  Similarity=0.204  Sum_probs=81.3

Q ss_pred             ccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          166 IDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       166 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      ..+..++||+.+++.+.+++...-+   .+..+-+.|.|-+|.|||.+...++.+..-...=-.++++..-.-..+..++
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle---~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF  223 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLE---LNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIF  223 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhh---cccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHH
Confidence            3567899999999999999866543   2456778999999999999999999974322111245777666556778889


Q ss_pred             HHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC--eEEEEEcCC
Q 005860          246 KAIIEALEGFVPTVGELNSLLESIRASLVGK--KFLLILDDM  285 (673)
Q Consensus       246 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k--r~LlVLDdv  285 (673)
                      ..|...+...........+....+..+....  -+|+|||.+
T Consensus       224 ~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEm  265 (529)
T KOG2227|consen  224 KKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEM  265 (529)
T ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechh
Confidence            9988888332111122244555666666543  689999988

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.77  E-value=2.6e-05  Score=54.13  Aligned_cols=40  Identities=25%  Similarity=0.394  Sum_probs=34.8

Q ss_pred             CCccEEEeccCCCCccccccccccccCCeeecccccccccc
Q 005860          596 LNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       596 ~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      ++|++|+++++. +..+|..+++|++|+.|++++|.++.+|
T Consensus         1 ~~L~~L~l~~N~-i~~l~~~l~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNNQ-ITDLPPELSNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             TT-SEEEETSSS--SSHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred             CcceEEEccCCC-CcccCchHhCCCCCCEEEecCCCCCCCc
Confidence            579999999976 9999988999999999999999988775

...

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.76  E-value=0.00013  Score=79.84  Aligned_cols=162  Identities=13%  Similarity=0.196  Sum_probs=87.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      +++||-+.-++.|.+++..+.-      ...+.++|..|+||||+|+.+.+...-... +..--+. +..+..-...+.|
T Consensus        16 ddVIGQe~vv~~L~~al~~gRL------pHA~LFtGP~GvGKTTLAriLAkaLnC~~p-~~~~g~~-~~PCG~C~sC~~I   87 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQRL------HHAYLFTGTRGVGKTTLSRILAKSLNCTGA-DGEGGIT-AQPCGQCRACTEI   87 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCCC------ceEEEEECCCCCCHHHHHHHHHHHhcCCCc-cccccCC-CCCCcccHHHHHH
Confidence            5799999999999999876542      356789999999999999888764211000 0000000 0000000011111


Q ss_pred             HHH-----hhCCCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEA-----LEGFVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~-----l~~~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      ...     +..........+++.+.+...    ..++.-++|||++..-+...++.|...+.....+.++|++|.+ ..+
T Consensus        88 ~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kL  167 (700)
T PRK12323         88 DAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKI  167 (700)
T ss_pred             HcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhh
Confidence            100     000000011223333222221    2456678999999766666778887777665555665555544 444


Q ss_pred             HHh-ccccceeecCCCCcccc
Q 005860          319 ARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ... ..-...|.++.++.++.
T Consensus       168 lpTIrSRCq~f~f~~ls~eei  188 (700)
T PRK12323        168 PVTVLSRCLQFNLKQMPPGHI  188 (700)
T ss_pred             hhHHHHHHHhcccCCCChHHH
Confidence            332 22356788888877664

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=97.75  E-value=1.9e-06  Score=86.45  Aligned_cols=120  Identities=23%  Similarity=0.295  Sum_probs=92.2

Q ss_pred             chhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceecC-CCCcccch-hhhc
Q 005860          518 RSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVG-LGTEELPE-TCCE  594 (673)
Q Consensus       518 r~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~-~~i~~LP~-~i~~  594 (673)
                      ..+.+..|.    +..+++..|+.+++||.|||++       +.+..+ |..+..|..|..|-+-+ |+|+++|. .+++
T Consensus        70 veirLdqN~----I~~iP~~aF~~l~~LRrLdLS~-------N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~g  138 (498)
T KOG4237|consen   70 VEIRLDQNQ----ISSIPPGAFKTLHRLRRLDLSK-------NNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGG  138 (498)
T ss_pred             eEEEeccCC----cccCChhhccchhhhceecccc-------cchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhh
Confidence            344555554    4466778889999999999999       888776 67788888877777766 66999994 6788


Q ss_pred             CCCccEEEeccCCCCcccc-ccccccccCCeeeccccccccccc-cCCCCCCCCcCC
Q 005860          595 LLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFIPK-GIQRLTNLRTLS  649 (673)
Q Consensus       595 L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~~L~~L~  649 (673)
                      |..||-|.+..|+ +.-++ +.+..|++|+.|.+..|.+..++. .+..+.+++++.
T Consensus       139 L~slqrLllNan~-i~Cir~~al~dL~~l~lLslyDn~~q~i~~~tf~~l~~i~tlh  194 (498)
T KOG4237|consen  139 LSSLQRLLLNANH-INCIRQDALRDLPSLSLLSLYDNKIQSICKGTFQGLAAIKTLH  194 (498)
T ss_pred             HHHHHHHhcChhh-hcchhHHHHHHhhhcchhcccchhhhhhccccccchhccchHh
Confidence            9999999998877 55555 568899999999988888888887 366666666664

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.73  E-value=0.00017  Score=74.90  Aligned_cols=121  Identities=17%  Similarity=0.139  Sum_probs=71.9

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      -++++|.+...+.+..++..+.      -..++.++|++|+||||+|+.+++..  ..   ....++.+. .... ..++
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~~------~~~~lll~G~~G~GKT~la~~l~~~~--~~---~~~~i~~~~-~~~~-~i~~   86 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKGR------IPNMLLHSPSPGTGKTTVAKALCNEV--GA---EVLFVNGSD-CRID-FVRN   86 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCC------CCeEEEeeCcCCCCHHHHHHHHHHHh--Cc---cceEeccCc-ccHH-HHHH
Confidence            3578999999999999886433      24678889999999999999998852  11   223444443 2221 1111


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      .+..+...               ..+.+.+-+||+||+... .....+.+...+.....++++|+||...
T Consensus        87 ~l~~~~~~---------------~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~  141 (316)
T PHA02544         87 RLTRFAST---------------VSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNK  141 (316)
T ss_pred             HHHHHHHh---------------hcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCCh
Confidence            11111000               001234557899999433 2222334544455555677899988653

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.71  E-value=0.00034  Score=73.88  Aligned_cols=149  Identities=9%  Similarity=0.049  Sum_probs=84.5

Q ss_pred             CcceechhhHHHHHHHhccCCccc---ccCCeEEEEEEccCCChHHHHHHHHhcCcccc-------------------cc
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEE---IINDIQIITIVGMGGIGKTTLAQFAYNDSDVF-------------------EY  226 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~---~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~  226 (673)
                      ++++|-+.-++.|.+.+..+..+.   +..-..-+.++|+.|+||||+|+.+.+..--.                   .|
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~h   84 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTH   84 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            468999999999999987643100   00124568899999999999998876521000                   01


Q ss_pred             CCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          227 FDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       227 F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                      .| ..++....                    .....+++...+..    -..+++-++|+|++..-+....+.+...+..
T Consensus        85 pD-~~~i~~~~--------------------~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEe  143 (394)
T PRK07940         85 PD-VRVVAPEG--------------------LSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEE  143 (394)
T ss_pred             CC-EEEecccc--------------------ccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhc
Confidence            11 11111100                    00112222211111    1134555888899965555556667777766


Q ss_pred             CCCCeEEEEEcCCh-hHHHh-ccccceeecCCCCcccc
Q 005860          303 GVRGSKILVTTRKE-TVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       303 ~~~gs~iivTtr~~-~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ...+..+|++|.+. .+... ..-...+.+++++.++.
T Consensus       144 p~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i  181 (394)
T PRK07940        144 PPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAV  181 (394)
T ss_pred             CCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHH
Confidence            56667677666653 33322 22356788888887765

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.71  E-value=0.00032  Score=68.26  Aligned_cols=123  Identities=17%  Similarity=0.267  Sum_probs=70.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccC--CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ...+.|+|..|+|||.|.+++++.  +....  ..++|+      +..++...+...+...     .    ...+++.++
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~--~~~~~~~~~v~y~------~~~~f~~~~~~~~~~~-----~----~~~~~~~~~   96 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANE--AQKQHPGKRVVYL------SAEEFIREFADALRDG-----E----IEEFKDRLR   96 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHH--HHHHCTTS-EEEE------EHHHHHHHHHHHHHTT-----S----HHHHHHHHC
T ss_pred             CCceEEECCCCCCHHHHHHHHHHH--HHhccccccceee------cHHHHHHHHHHHHHcc-----c----chhhhhhhh
Confidence            445789999999999999999996  33322  246677      4556666676666541     1    234555555


Q ss_pred             CCeEEEEEcCCCCCCcc-chhh-hhhhccC-CCCCeEEEEEcCCh---------hHHHhccccceeecCCCCccc
Q 005860          275 GKKFLLILDDMWTDDYS-KWEP-FHYCLKN-GVRGSKILVTTRKE---------TVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~-~~~~-l~~~l~~-~~~gs~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~~  337 (673)
                      +-. +|++||+..-... .|.. +...+.. ...|-+||+|++..         .+...+...-.++++++++++
T Consensus        97 ~~D-lL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~  170 (219)
T PF00308_consen   97 SAD-LLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDED  170 (219)
T ss_dssp             TSS-EEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHH
T ss_pred             cCC-EEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHH
Confidence            443 7889999542221 2332 2222222 23466899998542         233334455677787777665

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.00023  Score=78.96  Aligned_cols=160  Identities=12%  Similarity=0.150  Sum_probs=86.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccccc--CCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY--FDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ++++|-+.-++.|.+++....      -...+.++|..|+||||+|+.+.+...-...  ..+...    ..++.-...+
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r------l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~----~pCg~C~~C~   85 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR------LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA----TPCGVCQACR   85 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC----CCCCccHHHH
Confidence            578999888899999886554      2356789999999999999888553110000  000000    0011111111


Q ss_pred             HHHHHhh-----CCCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-h
Q 005860          247 AIIEALE-----GFVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-E  316 (673)
Q Consensus       247 ~i~~~l~-----~~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~  316 (673)
                      .|-..-.     .........++..+.+...    ..++.-++|||++..-+...++.+...+.......++|++|.+ .
T Consensus        86 ~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~  165 (618)
T PRK14951         86 DIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQ  165 (618)
T ss_pred             HHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCch
Confidence            1100000     0000011122222222111    1244558899999776666778888777765556666655543 3


Q ss_pred             hHHH-hccccceeecCCCCcccc
Q 005860          317 TVAR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       317 ~v~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      .+.. ...-...++++.++.++.
T Consensus       166 kil~TIlSRc~~~~f~~Ls~eei  188 (618)
T PRK14951        166 KVPVTVLSRCLQFNLRPMAPETV  188 (618)
T ss_pred             hhhHHHHHhceeeecCCCCHHHH
Confidence            3332 223367889999988764

>PRK04195 replication factor C large subunit; Provisional

Probab=97.70  E-value=0.00014  Score=79.89  Aligned_cols=146  Identities=17%  Similarity=0.163  Sum_probs=83.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+..++.+..|+..-..   ....+.+.|+|++|+||||+|++++++.    .|+ .+-++.++..+.. ....+
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~---g~~~~~lLL~GppG~GKTtla~ala~el----~~~-~ielnasd~r~~~-~i~~~   84 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLK---GKPKKALLLYGPPGVGKTSLAHALANDY----GWE-VIELNASDQRTAD-VIERV   84 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhc---CCCCCeEEEECCCCCCHHHHHHHHHHHc----CCC-EEEEcccccccHH-HHHHH
Confidence            5799999999999999854321   1226789999999999999999999963    222 3344555433222 22333


Q ss_pred             HHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCc----cchhhhhhhccCCCCCeEEEEEcCChh-HHH--h
Q 005860          249 IEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDY----SKWEPFHYCLKNGVRGSKILVTTRKET-VAR--M  321 (673)
Q Consensus       249 ~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~----~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~--~  321 (673)
                      +.......              .....++-+||+|++..-..    ..+..+...+..  .+..||+|+.+.. ...  .
T Consensus        85 i~~~~~~~--------------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~~~~~~~k~L  148 (482)
T PRK04195         85 AGEAATSG--------------SLFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTANDPYDPSLREL  148 (482)
T ss_pred             HHHhhccC--------------cccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEeccCccccchhhH
Confidence            32221110              01113677999999954221    224455554443  2345666664421 111  1


Q ss_pred             ccccceeecCCCCccccc
Q 005860          322 MESIHVISIKELSEQECW  339 (673)
Q Consensus       322 ~~~~~~~~l~~L~~~~~~  339 (673)
                      -.....+.+.+++.++..
T Consensus       149 rsr~~~I~f~~~~~~~i~  166 (482)
T PRK04195        149 RNACLMIEFKRLSTRSIV  166 (482)
T ss_pred             hccceEEEecCCCHHHHH
Confidence            122456778888776643

>PRK09087 hypothetical protein; Validated

Probab=97.70  E-value=9.7e-05  Score=72.11  Aligned_cols=104  Identities=18%  Similarity=0.271  Sum_probs=58.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      .+.+.|+|..|+|||+|++.+++...       ..|++..      .+..+++..+                     .+ 
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~~-------~~~i~~~------~~~~~~~~~~---------------------~~-   88 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKSD-------ALLIHPN------EIGSDAANAA---------------------AE-   88 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhcC-------CEEecHH------HcchHHHHhh---------------------hc-
Confidence            35689999999999999999987521       2244321      1111111111                     11 


Q ss_pred             eEEEEEcCCCCCCccchhhhhhhccC-CCCCeEEEEEcCC---------hhHHHhccccceeecCCCCccc
Q 005860          277 KFLLILDDMWTDDYSKWEPFHYCLKN-GVRGSKILVTTRK---------ETVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~~l~~~l~~-~~~gs~iivTtr~---------~~v~~~~~~~~~~~l~~L~~~~  337 (673)
                       -+|++||+..... .-+.+...+.. ...|..||+|++.         .++...+.....+++++++.++
T Consensus        89 -~~l~iDDi~~~~~-~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~  157 (226)
T PRK09087         89 -GPVLIEDIDAGGF-DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDAL  157 (226)
T ss_pred             -CeEEEECCCCCCC-CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHH
Confidence             2788899943211 11223333322 2346679998873         3334444556677888777654

>PRK08116 hypothetical protein; Validated

Probab=97.70  E-value=0.00011  Score=73.68  Aligned_cols=103  Identities=25%  Similarity=0.259  Sum_probs=61.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ..+.++|..|+|||.||.++++.  +...-..++|++      ..+++..+.........  ..    ...+.+.+.+-.
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~------~~~ll~~i~~~~~~~~~--~~----~~~~~~~l~~~d  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVN------FPQLLNRIKSTYKSSGK--ED----ENEIIRSLVNAD  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEE------HHHHHHHHHHHHhcccc--cc----HHHHHHHhcCCC
Confidence            35889999999999999999996  333334566774      34455555554432211  11    223334444444


Q ss_pred             EEEEEcCCCCCCccchhh--hhhhccC-CCCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDYSKWEP--FHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~--l~~~l~~-~~~gs~iivTtr~  315 (673)
                       ||||||+-.+....|..  +...+.. -..|..+|+||..
T Consensus       181 -lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        181 -LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             -EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence             89999995444444533  3333332 2346679999874

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.69  E-value=0.00019  Score=79.73  Aligned_cols=158  Identities=16%  Similarity=0.238  Sum_probs=89.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .++||-+..++.|.+.+..+.      -...+.++|..|+||||+|+.+.+...-...+.       +..+..-...+.|
T Consensus        16 ~divGQe~vv~~L~~~l~~~r------l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~-------~~pCg~C~~C~~i   82 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR------LHHAYLFSGTRGVGKTTIARLLAKGLNCETGIT-------ATPCGECDNCREI   82 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCC-------CCCCCCCHHHHHH
Confidence            579999999999998886543      134578999999999999999877521111000       0011111111111


Q ss_pred             HHH-------hhCCC-CCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEA-------LEGFV-PTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~-------l~~~~-~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      ...       +.... ...++..++...+.. -..+++-++|+|++..-+....+.|...+.......++|++|.+ ..+
T Consensus        83 ~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kL  162 (647)
T PRK07994         83 EQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  162 (647)
T ss_pred             HcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCcccc
Confidence            110       00000 011112222222211 13466779999999766666778887777765556666665554 434


Q ss_pred             HH-hccccceeecCCCCccccc
Q 005860          319 AR-MMESIHVISIKELSEQECW  339 (673)
Q Consensus       319 ~~-~~~~~~~~~l~~L~~~~~~  339 (673)
                      .. ...-...|.+++++.++..
T Consensus       163 l~TI~SRC~~~~f~~Ls~~ei~  184 (647)
T PRK07994        163 PVTILSRCLQFHLKALDVEQIR  184 (647)
T ss_pred             chHHHhhheEeeCCCCCHHHHH
Confidence            32 2233678899999887753

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.69  E-value=0.00012  Score=78.08  Aligned_cols=159  Identities=14%  Similarity=0.191  Sum_probs=87.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|-+..+..|..++....      -...+.++|+.|+||||+|+.+.+...-..... ..+..|    ..-..+...
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~r------i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C----~sC~~i~~g   87 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSGK------IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNEC----TSCLEITKG   87 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCC----cHHHHHHcc
Confidence            578999999999998886543      124688999999999999999988521111000 001111    011111111


Q ss_pred             HHHHh---hC-CCCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhHHHh
Q 005860          248 IIEAL---EG-FVPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETVARM  321 (673)
Q Consensus       248 i~~~l---~~-~~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v~~~  321 (673)
                      +...+   .. .....++..++.+.+... ..++.-++|+|++..-+...++.+...+.........|++|.. ..+...
T Consensus        88 ~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~T  167 (484)
T PRK14956         88 ISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPET  167 (484)
T ss_pred             CCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHH
Confidence            10000   00 001111222222233221 2456679999999766666788887777654445555545443 444322


Q ss_pred             -ccccceeecCCCCccc
Q 005860          322 -MESIHVISIKELSEQE  337 (673)
Q Consensus       322 -~~~~~~~~l~~L~~~~  337 (673)
                       ..-...|.+.+++.++
T Consensus       168 I~SRCq~~~f~~ls~~~  184 (484)
T PRK14956        168 ILSRCQDFIFKKVPLSV  184 (484)
T ss_pred             HHhhhheeeecCCCHHH
Confidence             2235678888887655

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.68  E-value=0.00022  Score=78.02  Aligned_cols=146  Identities=13%  Similarity=0.148  Sum_probs=85.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccccc-------------------CCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY-------------------FDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~  229 (673)
                      +++||-+.-++.|.+++....      -...+.++|+.|+||||+|+.+.+...-...                   |.-
T Consensus        16 ~divGq~~v~~~L~~~~~~~~------l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d   89 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY------LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPD   89 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC------CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCce
Confidence            579999999999999996554      2346789999999999999888774211111                   111


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKI  309 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~i  309 (673)
                      ++.+..+....++++ +++++.+..                .-..++.-++|+|++..-+....+.+...+......+++
T Consensus        90 ~~eidaas~~~v~~i-R~l~~~~~~----------------~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~f  152 (509)
T PRK14958         90 LFEVDAASRTKVEDT-RELLDNIPY----------------APTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKF  152 (509)
T ss_pred             EEEEcccccCCHHHH-HHHHHHHhh----------------ccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEE
Confidence            222222211112111 112211110                011356668999999665556777777777766666777


Q ss_pred             EEEcCC-hhHHHh-ccccceeecCCCCccc
Q 005860          310 LVTTRK-ETVARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       310 ivTtr~-~~v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      |++|.+ ..+... ..-...+++++++.++
T Consensus       153 Ilattd~~kl~~tI~SRc~~~~f~~l~~~~  182 (509)
T PRK14958        153 ILATTDHHKLPVTVLSRCLQFHLAQLPPLQ  182 (509)
T ss_pred             EEEECChHhchHHHHHHhhhhhcCCCCHHH
Confidence            766544 333222 2224567788877665

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=97.68  E-value=1.7e-05  Score=80.91  Aligned_cols=133  Identities=22%  Similarity=0.212  Sum_probs=69.8

Q ss_pred             CceEEEEEEcCCCCcccc--ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          492 EKLRHSMLVLGYEASFPI--SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~--~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      +++|.+++..+.....+.  ....++++|.|+++.+.++.  ....-.+..+|++|++|+++.       +.+....++ 
T Consensus       121 kkL~~IsLdn~~V~~~~~~~~~k~~~~v~~LdLS~NL~~n--w~~v~~i~eqLp~Le~LNls~-------Nrl~~~~~s~  191 (505)
T KOG3207|consen  121 KKLREISLDNYRVEDAGIEEYSKILPNVRDLDLSRNLFHN--WFPVLKIAEQLPSLENLNLSS-------NRLSNFISSN  191 (505)
T ss_pred             HhhhheeecCccccccchhhhhhhCCcceeecchhhhHHh--HHHHHHHHHhcccchhccccc-------ccccCCcccc
Confidence            445555555544432221  23456777777777665321  122334556677777777766       443322111 


Q ss_pred             -cccccccccceecCCCCc--------------------------ccchhhhcCCCccEEEeccCCCCcccc--cccccc
Q 005860          569 -IEKLIHLRYLRLVGLGTE--------------------------ELPETCCELLNLQVLEIEQCTSLKRLP--LGIGKL  619 (673)
Q Consensus       569 -i~~L~~Lr~L~L~~~~i~--------------------------~LP~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~L  619 (673)
                       -..+.||+.|.|++|.+.                          .--.+...++.|+.|||++++ +..+|  ..++.|
T Consensus       192 ~~~~l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~-li~~~~~~~~~~l  270 (505)
T KOG3207|consen  192 TTLLLSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNN-LIDFDQGYKVGTL  270 (505)
T ss_pred             chhhhhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCc-ccccccccccccc
Confidence             123455555555555542                          111112235667777777755 55566  346777


Q ss_pred             ccCCeeecccccccc
Q 005860          620 VNLRHLTYDDSCLEF  634 (673)
Q Consensus       620 ~~Lr~L~l~~~~l~~  634 (673)
                      +.|+.|+++.|.+..
T Consensus       271 ~~L~~Lnls~tgi~s  285 (505)
T KOG3207|consen  271 PGLNQLNLSSTGIAS  285 (505)
T ss_pred             cchhhhhccccCcch
Confidence            777777776666553

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.67  E-value=1.8e-05  Score=89.20  Aligned_cols=130  Identities=23%  Similarity=0.242  Sum_probs=92.8

Q ss_pred             CceEEEEEEcCCC--Cccccccc-cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc
Q 005860          492 EKLRHSMLVLGYE--ASFPISIF-KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       492 ~~~r~l~l~~~~~--~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      .+++++.+.+...  ...+..++ .+|.|++|.+.+-..   ....+...+.++++|+.||+++       +.+..+ ..
T Consensus       122 ~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~---~~~dF~~lc~sFpNL~sLDIS~-------TnI~nl-~G  190 (699)
T KOG3665|consen  122 QNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQF---DNDDFSQLCASFPNLRSLDISG-------TNISNL-SG  190 (699)
T ss_pred             HhhhhcCccccchhhccHHHHHhhhCcccceEEecCcee---cchhHHHHhhccCccceeecCC-------CCccCc-HH
Confidence            4566666655332  12222333 479999999988653   1233566788999999999999       888877 78


Q ss_pred             cccccccccceecCCCCcccc--hhhhcCCCccEEEeccCCCCccccc-------cccccccCCeeeccccccc
Q 005860          569 IEKLIHLRYLRLVGLGTEELP--ETCCELLNLQVLEIEQCTSLKRLPL-------GIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP--~~i~~L~~L~~L~l~~c~~l~~lP~-------~i~~L~~Lr~L~l~~~~l~  633 (673)
                      |++|++|+.|.+++-.+..-+  ..+.+|++|++||+|...+. .-|.       .-..|++||+||.+++.+.
T Consensus       191 IS~LknLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~-~~~~ii~qYlec~~~LpeLrfLDcSgTdi~  263 (699)
T KOG3665|consen  191 ISRLKNLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNN-DDTKIIEQYLECGMVLPELRFLDCSGTDIN  263 (699)
T ss_pred             HhccccHHHHhccCCCCCchhhHHHHhcccCCCeeeccccccc-cchHHHHHHHHhcccCccccEEecCCcchh
Confidence            999999999999987766543  46789999999999985532 2221       1234889999998887654

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.67  E-value=0.00029  Score=70.16  Aligned_cols=115  Identities=21%  Similarity=0.138  Sum_probs=82.5

Q ss_pred             Ccceech---hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccH
Q 005860          169 SEIRGRD---EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDE  241 (673)
Q Consensus       169 ~~~vGr~---~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~  241 (673)
                      +.++|-.   +-++++.++|..+.    .....-+.|||.+|.|||+++++..+.--...    .--.++.|.....++.
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~P~----~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~  109 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEYPK----RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDE  109 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhCCc----ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCCh
Confidence            4556643   34566666666554    34567799999999999999988886421110    1125778888899999


Q ss_pred             HHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC-CeEEEEEcCCCC
Q 005860          242 LRIAKAIIEALEGFVPTVGELNSLLESIRASLVG-KKFLLILDDMWT  287 (673)
Q Consensus       242 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~-kr~LlVLDdvw~  287 (673)
                      ..+...|+++++.+.........+.......++. +-=+||+|.+.+
T Consensus       110 ~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~  156 (302)
T PF05621_consen  110 RRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHN  156 (302)
T ss_pred             HHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHH
Confidence            9999999999999877666766666666666654 445899999943

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=0.00018  Score=76.78  Aligned_cols=162  Identities=14%  Similarity=0.211  Sum_probs=84.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE-cCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC-VSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~~~~~  247 (673)
                      .+++|.+..++.|..++..+.      -...+.++|+.|+||||+|+.+.+...-...+....|.. +..++..-...+.
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~~------~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~   89 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMGR------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRD   89 (397)
T ss_pred             hhccChHHHHHHHHHHHHhCC------cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHH
Confidence            578999999999988886543      134588999999999999988776421111110000100 0011110011111


Q ss_pred             HHHHhhC-----CCCCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC-Ch
Q 005860          248 IIEALEG-----FVPTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR-KE  316 (673)
Q Consensus       248 i~~~l~~-----~~~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr-~~  316 (673)
                      +......     ........+++.+ +.+.+     .+++-++|+|++..-....++.+...+......+.+|++|. ..
T Consensus        90 ~~~~~~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~  168 (397)
T PRK14955         90 FDAGTSLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELH  168 (397)
T ss_pred             HhcCCCCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChH
Confidence            1110000     0001111233322 22222     34566889999955454567788888876666777666553 33


Q ss_pred             hHHHhc-cccceeecCCCCccc
Q 005860          317 TVARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       317 ~v~~~~-~~~~~~~l~~L~~~~  337 (673)
                      .+.... .....++++++++++
T Consensus       169 kl~~tl~sR~~~v~f~~l~~~e  190 (397)
T PRK14955        169 KIPATIASRCQRFNFKRIPLEE  190 (397)
T ss_pred             HhHHHHHHHHHHhhcCCCCHHH
Confidence            333221 123466777776655

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.65  E-value=2.2e-05  Score=88.55  Aligned_cols=108  Identities=22%  Similarity=0.220  Sum_probs=79.9

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc--hhhhccccccccccccceecCCCCcccchh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS--TNKILKGIEKLIHLRYLRLVGLGTEELPET  591 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~--~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~  591 (673)
                      -.+|++|++.+...  -....+...-..||+|+.|.+.+       -.  ..++-.-..++++|+.||+++|+++.+ ..
T Consensus       121 r~nL~~LdI~G~~~--~s~~W~~kig~~LPsL~sL~i~~-------~~~~~~dF~~lc~sFpNL~sLDIS~TnI~nl-~G  190 (699)
T KOG3665|consen  121 RQNLQHLDISGSEL--FSNGWPKKIGTMLPSLRSLVISG-------RQFDNDDFSQLCASFPNLRSLDISGTNISNL-SG  190 (699)
T ss_pred             HHhhhhcCccccch--hhccHHHHHhhhCcccceEEecC-------ceecchhHHHHhhccCccceeecCCCCccCc-HH
Confidence            46899999988653  12223334455788999999988       33  223444456778999999999999999 88


Q ss_pred             hhcCCCccEEEeccCCCCccccc--cccccccCCeeecccccc
Q 005860          592 CCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCL  632 (673)
Q Consensus       592 i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l  632 (673)
                      |++|+|||+|.+++.. ++.-+.  ++-+|++|++||++....
T Consensus       191 IS~LknLq~L~mrnLe-~e~~~~l~~LF~L~~L~vLDIS~~~~  232 (699)
T KOG3665|consen  191 ISRLKNLQVLSMRNLE-FESYQDLIDLFNLKKLRVLDISRDKN  232 (699)
T ss_pred             HhccccHHHHhccCCC-CCchhhHHHHhcccCCCeeecccccc
Confidence            9999999999998754 554442  578999999999876543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.64  E-value=0.00021  Score=75.52  Aligned_cols=53  Identities=21%  Similarity=0.253  Sum_probs=39.4

Q ss_pred             CCcceechhhHHHHHHHhccCCccc------ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEE------IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~------~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++.|+++.++++.+.+...-...      +....+-+.++|++|+|||++|+++++.
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~  179 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  179 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            3578999999999998774321100      0123456899999999999999999985

Many proteins may score above the trusted cutoff because an internal

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.63  E-value=0.00028  Score=78.29  Aligned_cols=143  Identities=15%  Similarity=0.229  Sum_probs=82.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccccc-------------------CCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY-------------------FDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~  229 (673)
                      ++++|.+..++.|.+++....      -...+.++|+.|+||||+|+.+.+...-...                   |..
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r------l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~D   89 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR------LHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVD   89 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccc
Confidence            579999999999999987543      2356899999999999999888774111100                   100


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCC
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVR  305 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~  305 (673)
                      .+.+..+..                     ...+.+...+..    -..+++-++|+|++..-+....+.+...+.....
T Consensus        90 vlEidaAs~---------------------~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~  148 (709)
T PRK08691         90 LLEIDAASN---------------------TGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPE  148 (709)
T ss_pred             eEEEecccc---------------------CCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCC
Confidence            111211111                     111222222211    1235667899999955444446666666765445


Q ss_pred             CeEEEEEcCCh-hHHH-hccccceeecCCCCcccc
Q 005860          306 GSKILVTTRKE-TVAR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       306 gs~iivTtr~~-~v~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      ..++|++|.+. .+.. ..+-...+.++.++.++.
T Consensus       149 ~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI  183 (709)
T PRK08691        149 HVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQV  183 (709)
T ss_pred             CcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHH
Confidence            56677666543 2221 122245567777777663

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.61  E-value=0.0003  Score=69.32  Aligned_cols=114  Identities=16%  Similarity=0.175  Sum_probs=62.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ...+.|+|+.|+|||+|++.+++.  ....-..+.|+++.....                    ...+..    +.+.. 
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~~~~~~--------------------~~~~~~----~~~~~-   97 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPLDKRAW--------------------FVPEVL----EGMEQ-   97 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEHHHHhh--------------------hhHHHH----HHhhh-
Confidence            357899999999999999999985  222334566776543110                    001111    11111 


Q ss_pred             eEEEEEcCCCCCC-ccchhh-hhhhccC-CCCC-eEEEEEcCCh---------hHHHhccccceeecCCCCccc
Q 005860          277 KFLLILDDMWTDD-YSKWEP-FHYCLKN-GVRG-SKILVTTRKE---------TVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       277 r~LlVLDdvw~~~-~~~~~~-l~~~l~~-~~~g-s~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~~  337 (673)
                      --+|++||+.... ...|+. +...+.. ...| .++|+||+..         .+...+....+++++++++++
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~  171 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEE  171 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHH
Confidence            1378999994321 124443 2222222 1233 3789998743         233334445677777776544

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.61  E-value=0.00016  Score=64.09  Aligned_cols=21  Identities=43%  Similarity=0.430  Sum_probs=19.6

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|++|+||||+|+.+.+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            579999999999999999996

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.61  E-value=0.00027  Score=63.21  Aligned_cols=87  Identities=24%  Similarity=0.117  Sum_probs=46.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC-
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK-  276 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k-  276 (673)
                      ..+.|+|++|+||||+|+.+....  ......++++..+...........  ...................+.+..+.. 
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAREL--GPPGGGVIYIDGEDILEEVLDQLL--LIIVGGKKASGSGELRLRLALALARKLK   78 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcc--CCCCCCEEEECCEEccccCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHHhcC
Confidence            578999999999999999998862  222224555554433222111111  111111111122222233444444443 


Q ss_pred             eEEEEEcCCCCC
Q 005860          277 KFLLILDDMWTD  288 (673)
Q Consensus       277 r~LlVLDdvw~~  288 (673)
                      ..+|++|++...
T Consensus        79 ~~viiiDei~~~   90 (148)
T smart00382       79 PDVLILDEITSL   90 (148)
T ss_pred             CCEEEEECCccc
Confidence            489999999553

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.60  E-value=0.00035  Score=76.62  Aligned_cols=157  Identities=16%  Similarity=0.187  Sum_probs=84.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|.+..++.+.+.+..+.      -...+.++|+.|+||||+|+.+.+...-..      |... ..++.-...+.+
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r------l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~------~~~~-~~Cg~C~sCr~i   82 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK------LTHAYIFSGPRGIGKTSIAKIFAKAINCLN------PKDG-DCCNSCSVCESI   82 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCceEEEECCCCCCHHHHHHHHHHHhcCCC------CCCC-CCCcccHHHHHH
Confidence            578999999999999886543      235688999999999999988877421101      1110 011111111111


Q ss_pred             HHHhhCC-----CCCcCcHHHH---HHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEALEGF-----VPTVGELNSL---LESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~l~~~-----~~~~~~~~~~---~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      .......     .......+++   ...+... ..+++-++|+|++..-+...++.+...+........+|++|.. ..+
T Consensus        83 ~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KL  162 (605)
T PRK05896         83 NTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKI  162 (605)
T ss_pred             HcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhh
Confidence            1110000     0000112222   2111111 1233446999999655555677777777765556666655543 333


Q ss_pred             HHh-ccccceeecCCCCcccc
Q 005860          319 ARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ... ......+++.+++.++.
T Consensus       163 l~TI~SRcq~ieF~~Ls~~eL  183 (605)
T PRK05896        163 PLTIISRCQRYNFKKLNNSEL  183 (605)
T ss_pred             hHHHHhhhhhcccCCCCHHHH
Confidence            322 22356788888887764

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.60  E-value=0.0008  Score=70.49  Aligned_cols=161  Identities=15%  Similarity=0.090  Sum_probs=90.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc--cCCe----EEEEEcCCcccHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE--YFDK----RMWVCVSDPFDEL  242 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~----~~wv~vs~~~~~~  242 (673)
                      .+++|-+..++.+.+.+..+.-      ...+.++|+.|+||+|+|..+.+..--..  ..+.    ..=..+...+   
T Consensus        19 ~~iiGq~~~~~~L~~~~~~~rl------~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c---   89 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRSGRL------HHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDH---   89 (365)
T ss_pred             hhccChHHHHHHHHHHHHcCCC------CceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCC---
Confidence            5799999999999998876542      34688999999999999966655311000  0000    0000000000   


Q ss_pred             HHHHHHHHHhhCC---------C-----CCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCC
Q 005860          243 RIAKAIIEALEGF---------V-----PTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNG  303 (673)
Q Consensus       243 ~~~~~i~~~l~~~---------~-----~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~  303 (673)
                      ...+.|...-...         .     .....+++.. .+.+.+     .+.+-++|+|++..-+....+.+...+...
T Consensus        90 ~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR-~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEep  168 (365)
T PRK07471         90 PVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVR-ELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP  168 (365)
T ss_pred             hHHHHHHccCCCCeEEEecccccccccccccccHHHHH-HHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcC
Confidence            0111111100000         0     0111234422 333333     256678999999766667777888777766


Q ss_pred             CCCeEEEEEcCChh-HHHh-ccccceeecCCCCccccc
Q 005860          304 VRGSKILVTTRKET-VARM-MESIHVISIKELSEQECW  339 (673)
Q Consensus       304 ~~gs~iivTtr~~~-v~~~-~~~~~~~~l~~L~~~~~~  339 (673)
                      ..++.+|++|.+.+ +... ..-...+.+.+++.++..
T Consensus       169 p~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~  206 (365)
T PRK07471        169 PARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVI  206 (365)
T ss_pred             CCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHH
Confidence            56777777777653 3222 233667889988887753

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.58  E-value=0.00042  Score=74.77  Aligned_cols=146  Identities=16%  Similarity=0.179  Sum_probs=86.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc------------------cc-ccCCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD------------------VF-EYFDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~------------------~~-~~F~~  229 (673)
                      .+++|-+.-++.|.+.+..+.      -...+-++|+.|+||||+|+.+.+...                  +. ..+.-
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r------i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~D   86 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK------IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPD   86 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCC
Confidence            578999999988888876543      134788999999999999988865210                  00 01112


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKI  309 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~i  309 (673)
                      ++.+..+....+.+ .++|++....                .-+.+++-++|+|++..-.....+.+...+....+.+++
T Consensus        87 v~eidaas~~~vdd-IR~Iie~~~~----------------~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~f  149 (491)
T PRK14964         87 VIEIDAASNTSVDD-IKVILENSCY----------------LPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKF  149 (491)
T ss_pred             EEEEecccCCCHHH-HHHHHHHHHh----------------ccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEE
Confidence            23333332222222 1122221110                012345668999999655555677788888776667777


Q ss_pred             EEEcCC-hhHHHhc-cccceeecCCCCccc
Q 005860          310 LVTTRK-ETVARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       310 ivTtr~-~~v~~~~-~~~~~~~l~~L~~~~  337 (673)
                      |++|.+ ..+...+ .-...+++++++.++
T Consensus       150 Ilatte~~Kl~~tI~SRc~~~~f~~l~~~e  179 (491)
T PRK14964        150 ILATTEVKKIPVTIISRCQRFDLQKIPTDK  179 (491)
T ss_pred             EEEeCChHHHHHHHHHhheeeecccccHHH
Confidence            766643 3443322 235677788777665

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=97.57  E-value=0.00015  Score=68.77  Aligned_cols=51  Identities=27%  Similarity=0.395  Sum_probs=34.9

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++|||.+.-++.+.-++......  .+.+.-+-+||++|+||||||..+.+.
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~r--~~~l~h~lf~GPPG~GKTTLA~IIA~e   73 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKKR--GEALDHMLFYGPPGLGKTTLARIIANE   73 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHCT--TS---EEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHHccCcHHHHhhhHHHHHHHHhc--CCCcceEEEECCCccchhHHHHHHHhc
Confidence            368999999888876655322100  134778999999999999999999996

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.56  E-value=0.00034  Score=68.71  Aligned_cols=110  Identities=18%  Similarity=0.191  Sum_probs=59.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ...+.|+|..|+|||+||+++++... ... ....+++......      .    +                  ... ..
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~~~-~~~-~~~~~i~~~~~~~------~----~------------------~~~-~~   90 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVADAS-YGG-RNARYLDAASPLL------A----F------------------DFD-PE   90 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-hCC-CcEEEEehHHhHH------H----H------------------hhc-cc
Confidence            45788999999999999999998521 112 2345554433110      0    0                  011 22


Q ss_pred             eEEEEEcCCCCCCccchhhhhhhccC-CCCCe-EEEEEcCChhHHH--------hccccceeecCCCCccc
Q 005860          277 KFLLILDDMWTDDYSKWEPFHYCLKN-GVRGS-KILVTTRKETVAR--------MMESIHVISIKELSEQE  337 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~~l~~~l~~-~~~gs-~iivTtr~~~v~~--------~~~~~~~~~l~~L~~~~  337 (673)
                      .-+||+||+..-+...-+.+...+.. ...|. .||+|++......        .+.....++++++++++
T Consensus        91 ~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~  161 (227)
T PRK08903         91 AELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDAD  161 (227)
T ss_pred             CCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHH
Confidence            34788999943222222334443432 12344 3666666432111        22224678899999765

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.55  E-value=0.00075  Score=71.32  Aligned_cols=145  Identities=13%  Similarity=0.166  Sum_probs=80.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc--------------------ccCC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF--------------------EYFD  228 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~F~  228 (673)
                      .+++|.+..++.+.+.+..+.      -...+-++|+.|+||||+|+.+.+...-.                    .+++
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~------~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~   87 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR------IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLD   87 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCC
Confidence            478999999999999886543      24578899999999999997776531100                    1222


Q ss_pred             eEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          229 KRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       229 ~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      . +++.-+...... -.+++++.+...                -..+++-++|+|++..-.....+.+...+......+.
T Consensus        88 ~-~~~~~~~~~~~~-~~~~l~~~~~~~----------------p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~  149 (355)
T TIGR02397        88 V-IEIDAASNNGVD-DIREILDNVKYA----------------PSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVV  149 (355)
T ss_pred             E-EEeeccccCCHH-HHHHHHHHHhcC----------------cccCCceEEEEeChhhcCHHHHHHHHHHHhCCcccee
Confidence            2 222211111111 111222221110                1224455888999843333456667777765555677


Q ss_pred             EEEEcCChh-HHHh-ccccceeecCCCCccc
Q 005860          309 ILVTTRKET-VARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       309 iivTtr~~~-v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      +|++|.+.. +... ......+++.+++.++
T Consensus       150 lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~  180 (355)
T TIGR02397       150 FILATTEPHKIPATILSRCQRFDFKRIPLED  180 (355)
T ss_pred             EEEEeCCHHHHHHHHHhheeEEEcCCCCHHH
Confidence            777765543 2222 1224566777766655

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.55  E-value=8.8e-05  Score=77.22  Aligned_cols=113  Identities=17%  Similarity=0.225  Sum_probs=61.2

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecccccccccc-chhhhcccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVN-STNKILKGIEK  571 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~-~~~~lp~~i~~  571 (673)
                      .+.++.+..+....+| .  -..+|++|.+.++...    ..+|..+  ..+|+.|++++       | .+..+|+++. 
T Consensus        53 ~l~~L~Is~c~L~sLP-~--LP~sLtsL~Lsnc~nL----tsLP~~L--P~nLe~L~Ls~-------Cs~L~sLP~sLe-  115 (426)
T PRK15386         53 ASGRLYIKDCDIESLP-V--LPNELTEITIENCNNL----TTLPGSI--PEGLEKLTVCH-------CPEISGLPESVR-  115 (426)
T ss_pred             CCCEEEeCCCCCcccC-C--CCCCCcEEEccCCCCc----ccCCchh--hhhhhheEccC-------cccccccccccc-
Confidence            3455666655444444 1  1235666666654321    1122222  13566677766       5 3555655433 


Q ss_pred             ccccccceecCCC---CcccchhhhcC------------------CCccEEEeccCCCCccccccccccccCCeeecccc
Q 005860          572 LIHLRYLRLVGLG---TEELPETCCEL------------------LNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDS  630 (673)
Q Consensus       572 L~~Lr~L~L~~~~---i~~LP~~i~~L------------------~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~  630 (673)
                           .|++.++.   +..||+++..|                  .+|++|++++|..+ .+|..+-  .+|++|.++.+
T Consensus       116 -----~L~L~~n~~~~L~~LPssLk~L~I~~~n~~~~~~lp~~LPsSLk~L~Is~c~~i-~LP~~LP--~SLk~L~ls~n  187 (426)
T PRK15386        116 -----SLEIKGSATDSIKNVPNGLTSLSINSYNPENQARIDNLISPSLKTLSLTGCSNI-ILPEKLP--ESLQSITLHIE  187 (426)
T ss_pred             -----eEEeCCCCCcccccCcchHhheeccccccccccccccccCCcccEEEecCCCcc-cCccccc--ccCcEEEeccc
Confidence                 33333322   56666666555                  37899999998844 4565443  47888886554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.51  E-value=0.00054  Score=71.35  Aligned_cols=162  Identities=16%  Similarity=0.141  Sum_probs=90.8

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc--ccCCeEEEEEcCCcccHHHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF--EYFDKRMWVCVSDPFDELRI  244 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~~~~~~~~  244 (673)
                      ....++|-+...+.+...+..+.      -...+.|+|+.|+||||+|..+.+..--.  ..+....   ....+.....
T Consensus        21 ~~~~l~Gh~~a~~~L~~a~~~gr------l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~---~~~~~~~c~~   91 (351)
T PRK09112         21 ENTRLFGHEEAEAFLAQAYREGK------LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPET---LADPDPASPV   91 (351)
T ss_pred             chhhccCcHHHHHHHHHHHHcCC------CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccc---cCCCCCCCHH
Confidence            34679999999999999986554      24568899999999999998777642110  0011110   0001111112


Q ss_pred             HHHHHHH-------hhCC--C-----CCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCC
Q 005860          245 AKAIIEA-------LEGF--V-----PTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVR  305 (673)
Q Consensus       245 ~~~i~~~-------l~~~--~-----~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~  305 (673)
                      .+.|...       +..+  .     ......++.. .+.+.+     .+++-++|+|++..-+....+.+...+.....
T Consensus        92 c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR-~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~  170 (351)
T PRK09112         92 WRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIR-RVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPA  170 (351)
T ss_pred             HHHHHcCCCCCEEEeecccccccccccccCCHHHHH-HHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCC
Confidence            2222221       1000  0     0112234433 333333     35667999999966666667777777766545


Q ss_pred             CeEEEEEcCCh-hHHHhc-cccceeecCCCCcccc
Q 005860          306 GSKILVTTRKE-TVARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       306 gs~iivTtr~~-~v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      ...+|++|... .+.... .-...+++.+++.++.
T Consensus       171 ~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~  205 (351)
T PRK09112        171 RALFILISHSSGRLLPTIRSRCQPISLKPLDDDEL  205 (351)
T ss_pred             CceEEEEECChhhccHHHHhhccEEEecCCCHHHH
Confidence            55555555433 332222 2256888888888764

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.51  E-value=0.001  Score=63.17  Aligned_cols=63  Identities=13%  Similarity=0.168  Sum_probs=38.3

Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHhc-cccceeecCCCCccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~~-~~~~~~~l~~L~~~~  337 (673)
                      +.+-++|+||+..-.....+.+...+......+.+|++|++. .+...+ .....+++.+++.++
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~  159 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEA  159 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHH
Confidence            456689999995555556777887777666667777777643 222211 123456666665443

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08118 topology modulation protein; Reviewed

Probab=97.49  E-value=5.7e-05  Score=70.10  Aligned_cols=34  Identities=32%  Similarity=0.556  Sum_probs=28.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcCcccc-ccCCeEEE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVF-EYFDKRMW  232 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~w  232 (673)
                      .|.|+|++|+||||||+.+++...+. -+||..+|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58999999999999999999975543 46777775

>COG3903 Predicted ATPase [General function prediction only]

Probab=97.48  E-value=8.5e-05  Score=76.04  Aligned_cols=194  Identities=23%  Similarity=0.239  Sum_probs=126.8

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ..+.+.++|.|||||||++-.+..   +...| +.++++....-.++..+.-.+...++....+.   +.....+.....
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g---~~~~~~~~~~~~   86 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQPG---DSAVDTLVRRIG   86 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccccccc---hHHHHHHHHHHh
Confidence            468899999999999999987776   45667 66778877777777777777777777654332   223456677778


Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeecCCCCccccc---------------
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIKELSEQECW---------------  339 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l~~L~~~~~~---------------  339 (673)
                      ++|.++|+||.-+- ..+-..+...+..+...-.|+.|+|....   ......+.+.+|+..+.-               
T Consensus        87 ~rr~llvldncehl-~~~~a~~i~all~~~~~~~~~atsre~~l---~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f  162 (414)
T COG3903          87 DRRALLVLDNCEHL-LDACAALIVALLGACPRLAILATSREAIL---VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSF  162 (414)
T ss_pred             hhhHHHHhcCcHHH-HHHHHHHHHHHHccchhhhhHHHhHhhhc---ccccccccCCccccCCchhHHHHHHHHHhccce
Confidence            89999999998211 11222333444455556678888886432   244566777777776511               


Q ss_pred             ----------------cCCchhhHHHHhhhhccCCCHHHHHHHHhhhcccch-------hhhhccchhhhhcccCCChhh
Q 005860          340 ----------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELWQLE-------EFEKGLLAPLLLSYNDLPPMI  396 (673)
Q Consensus       340 ----------------c~GlPLai~~~~~~L~~~~~~~~w~~~l~~~~~~~~-------~~~~~i~~~l~~sy~~L~~~~  396 (673)
                                      .+|.|++|...++..+.- ...+-.+.++.....+.       .-.....+.+.+||.-|....
T Consensus       163 ~l~~~~~a~v~~icr~ldg~~laielaaarv~sl-~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe  241 (414)
T COG3903         163 WLTDDNAAAVAEICRRLDGIPLAIELAAARVRSL-SPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWE  241 (414)
T ss_pred             eecCCchHHHHHHHHHhhcchHHHHHHHHHHHhc-CHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHH
Confidence                            689999999999888644 34444444433221111       122456778889998887655


Q ss_pred             hhhh
Q 005860          397 KRCF  400 (673)
Q Consensus       397 k~cf  400 (673)
                      +--|
T Consensus       242 ~~~~  245 (414)
T COG3903         242 RALF  245 (414)
T ss_pred             HHHh
Confidence            4444

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.47  E-value=0.00069  Score=75.36  Aligned_cols=160  Identities=13%  Similarity=0.126  Sum_probs=87.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC--eEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD--KRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~  246 (673)
                      .+++|.+..++.|.+.+..+.      -..-+-++|+.|+||||+|+.+.+...-.....  ...+-    .+..-.-.+
T Consensus        24 ~dliGq~~~v~~L~~~~~~gr------i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~----~cg~c~~C~   93 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETGR------IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTID----LCGVGEHCQ   93 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccc----cCcccHHHH
Confidence            579999999999999886554      234688999999999999998887421111110  00000    000001111


Q ss_pred             HHHHHhhCC-----CCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc-CCh
Q 005860          247 AIIEALEGF-----VPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT-RKE  316 (673)
Q Consensus       247 ~i~~~l~~~-----~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt-r~~  316 (673)
                      .|...-...     .......+++.+.+...    ..+++-++|+|++..-+....+.|...+.....++++|++| ...
T Consensus        94 ~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~  173 (598)
T PRK09111         94 AIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIR  173 (598)
T ss_pred             HHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChh
Confidence            111111000     00111223322221111    23455579999996555556777777777666677776655 333


Q ss_pred             hHHHhc-cccceeecCCCCcccc
Q 005860          317 TVARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       317 ~v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      .+...+ .-...+++..++.++.
T Consensus       174 kll~tI~SRcq~~~f~~l~~~el  196 (598)
T PRK09111        174 KVPVTVLSRCQRFDLRRIEADVL  196 (598)
T ss_pred             hhhHHHHhheeEEEecCCCHHHH
Confidence            333222 2356788888887663

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.0009  Score=73.77  Aligned_cols=142  Identities=17%  Similarity=0.219  Sum_probs=82.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc-------------------cCCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE-------------------YFDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~  229 (673)
                      .+++|-+.-++.+.+++....      -...+.++|+.|+||||+|+.+.+...-..                   .|.-
T Consensus        16 ~divGq~~v~~~L~~~i~~~~------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d   89 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR------LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVD   89 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCc
Confidence            478999999999999887544      134678999999999999988876421110                   0111


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCC
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVR  305 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~  305 (673)
                      .+++..+..                     ...+++...+..    -..+++-++|+|++..-.....+.+...+.....
T Consensus        90 ~~ei~~~~~---------------------~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~  148 (527)
T PRK14969         90 LIEVDAASN---------------------TQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPE  148 (527)
T ss_pred             eeEeecccc---------------------CCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCC
Confidence            122221111                     112222211111    1235667899999965554556777777776556


Q ss_pred             CeEEEEEcCCh-hHHH-hccccceeecCCCCccc
Q 005860          306 GSKILVTTRKE-TVAR-MMESIHVISIKELSEQE  337 (673)
Q Consensus       306 gs~iivTtr~~-~v~~-~~~~~~~~~l~~L~~~~  337 (673)
                      .+.+|++|.+. .+.. ...-...+++++++.++
T Consensus       149 ~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~  182 (527)
T PRK14969        149 HVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPL  182 (527)
T ss_pred             CEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHH
Confidence            66666666443 2221 11224566777776655

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=97.46  E-value=3.9e-05  Score=78.33  Aligned_cols=82  Identities=22%  Similarity=0.314  Sum_probs=37.5

Q ss_pred             CCccceeeeccccccccccchhhhc--cccccccccccceecCCCCccc--chh-----hhcCCCccEEEeccCCCCccc
Q 005860          542 LKCLRALRIATLMNTWDVNSTNKIL--KGIEKLIHLRYLRLVGLGTEEL--PET-----CCELLNLQVLEIEQCTSLKRL  612 (673)
Q Consensus       542 l~~L~~L~L~~~~~~~~~~~~~~lp--~~i~~L~~Lr~L~L~~~~i~~L--P~~-----i~~L~~L~~L~l~~c~~l~~l  612 (673)
                      ++.|+.|||++       +.+-.++  ..++.|+.|+-|+++.|.+.++  |+.     ...+++|++|+++.++ +.+.
T Consensus       245 ~~~L~~LdLs~-------N~li~~~~~~~~~~l~~L~~Lnls~tgi~si~~~d~~s~~kt~~f~kL~~L~i~~N~-I~~w  316 (505)
T KOG3207|consen  245 LQTLQELDLSN-------NNLIDFDQGYKVGTLPGLNQLNLSSTGIASIAEPDVESLDKTHTFPKLEYLNISENN-IRDW  316 (505)
T ss_pred             hhHHhhccccC-------CcccccccccccccccchhhhhccccCcchhcCCCccchhhhcccccceeeecccCc-cccc
Confidence            34455555555       4443333  3455555555555555554333  221     1234555555555533 4444


Q ss_pred             cc--cccccccCCeeeccccc
Q 005860          613 PL--GIGKLVNLRHLTYDDSC  631 (673)
Q Consensus       613 P~--~i~~L~~Lr~L~l~~~~  631 (673)
                      |.  .+..+.+|++|...++.
T Consensus       317 ~sl~~l~~l~nlk~l~~~~n~  337 (505)
T KOG3207|consen  317 RSLNHLRTLENLKHLRITLNY  337 (505)
T ss_pred             cccchhhccchhhhhhccccc
Confidence            42  23344444555444433

>PRK05642 DNA replication initiation factor; Validated

Probab=97.44  E-value=0.00055  Score=67.36  Aligned_cols=92  Identities=18%  Similarity=0.286  Sum_probs=53.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ...+.|+|..|+|||.|++++++.  ....-..++|++..+      +...                  ...+.+.+.+-
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~--~~~~~~~v~y~~~~~------~~~~------------------~~~~~~~~~~~   98 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLR--FEQRGEPAVYLPLAE------LLDR------------------GPELLDNLEQY   98 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHhCCCcEEEeeHHH------HHhh------------------hHHHHHhhhhC
Confidence            356899999999999999999874  222224567776432      2111                  01222223322


Q ss_pred             eEEEEEcCCCCC-Cccchhh-hhhhccC-CCCCeEEEEEcCC
Q 005860          277 KFLLILDDMWTD-DYSKWEP-FHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       277 r~LlVLDdvw~~-~~~~~~~-l~~~l~~-~~~gs~iivTtr~  315 (673)
                      . +||+||+... ....|.. +...+.. ...|..||+||+.
T Consensus        99 d-~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~  139 (234)
T PRK05642         99 E-LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASK  139 (234)
T ss_pred             C-EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCC
Confidence            2 6789999432 1234543 4333332 2346678888874

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.43  E-value=0.001  Score=74.13  Aligned_cols=164  Identities=13%  Similarity=0.190  Sum_probs=86.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE-cCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC-VSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~~~~~  247 (673)
                      .+++|-+..+..|.+.+..+.      -...+.++|+.|+||||+|+.+.+...-...++.-.|.. +...+..-...+.
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r------i~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~   89 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRD   89 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHH
Confidence            578999999999999886543      134588999999999999987776421111110000110 0011111111111


Q ss_pred             HHHHhhCC-----CCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc-CChh
Q 005860          248 IIEALEGF-----VPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT-RKET  317 (673)
Q Consensus       248 i~~~l~~~-----~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt-r~~~  317 (673)
                      +...-...     .......+++...+...    ..+.+-++|+|++..-.....+.|...+......+.+|++| +...
T Consensus        90 ~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~k  169 (620)
T PRK14954         90 FDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHK  169 (620)
T ss_pred             HhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhh
Confidence            11100000     00111123333222221    23455578999996555556777887777665566665555 4344


Q ss_pred             HHHh-ccccceeecCCCCcccc
Q 005860          318 VARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       318 v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      +... ......+++.+++.++.
T Consensus       170 Ll~TI~SRc~~vef~~l~~~ei  191 (620)
T PRK14954        170 IPATIASRCQRFNFKRIPLDEI  191 (620)
T ss_pred             hhHHHHhhceEEecCCCCHHHH
Confidence            4332 23367788888887763

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.42  E-value=0.00085  Score=77.26  Aligned_cols=157  Identities=15%  Similarity=0.147  Sum_probs=87.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|.+..++.|..++....      -...+.++|+.|+||||+|+.+.+...-......       ..+..-.-.+.|
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r------i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~-------~pCg~C~sC~~~   81 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR------INHAYLFSGPRGCGKTSSARILARSLNCVEGPTS-------TPCGECDSCVAL   81 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC------CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCC-------CCCcccHHHHHH
Confidence            478999999999999987544      2346789999999999999888774211111100       000000001111


Q ss_pred             HHH-------hhCCCCCcCcHHHHHH---HHH-HHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-h
Q 005860          249 IEA-------LEGFVPTVGELNSLLE---SIR-ASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-E  316 (673)
Q Consensus       249 ~~~-------l~~~~~~~~~~~~~~~---~l~-~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~  316 (673)
                      ...       +.........++++..   .+. .-..++.-++|||++..-....++.|...+......+.+|++|.+ .
T Consensus        82 ~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~  161 (824)
T PRK07764         82 APGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPD  161 (824)
T ss_pred             HcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChh
Confidence            100       0000000111222222   111 112355567889999766666788888888876666666665543 3


Q ss_pred             hHHHhc-cccceeecCCCCcccc
Q 005860          317 TVARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       317 ~v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      .+...+ .-...|++..++.++-
T Consensus       162 kLl~TIrSRc~~v~F~~l~~~~l  184 (824)
T PRK07764        162 KVIGTIRSRTHHYPFRLVPPEVM  184 (824)
T ss_pred             hhhHHHHhheeEEEeeCCCHHHH
Confidence            444332 3367788888877664

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.41  E-value=0.00098  Score=73.59  Aligned_cols=157  Identities=14%  Similarity=0.175  Sum_probs=84.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|-+..++.|.+.+....      -...+.++|+.|+||||+|+.+.+..--....+.       ..++.-...+.|
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r------i~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~-------~pCg~C~sC~~i   82 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR------VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTG-------EPCNTCEQCRKV   82 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC------CCceEEEECCCCCCHHHHHHHHHHhccccCCCCC-------CCCcccHHHHHH
Confidence            478999988888888886543      2357889999999999999888875221110000       001110111111


Q ss_pred             HHHhhCC-----CCCcCcHHHHH---HHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEALEGF-----VPTVGELNSLL---ESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~l~~~-----~~~~~~~~~~~---~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      .......     ......+++..   ..+.. -..+++-+||+|++..-.....+.|...+........+|++|.+ ..+
T Consensus        83 ~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kl  162 (624)
T PRK14959         83 TQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKF  162 (624)
T ss_pred             hcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhh
Confidence            1100000     00001112211   11111 12456678999999555555667777777654445666665554 333


Q ss_pred             HHh-ccccceeecCCCCcccc
Q 005860          319 ARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ... ..-...+++++++.++.
T Consensus       163 l~TI~SRcq~i~F~pLs~~eL  183 (624)
T PRK14959        163 PVTIVSRCQHFTFTRLSEAGL  183 (624)
T ss_pred             hHHHHhhhhccccCCCCHHHH
Confidence            322 22245778888887764

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.41  E-value=0.0013  Score=72.71  Aligned_cols=157  Identities=15%  Similarity=0.123  Sum_probs=87.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+.-++.|.+++..+.      -...+.++|+.|+||||+|+.+.+...-....+.       ..++.-...+.|
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~-------~pCg~C~~C~~i   79 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR------INHAYLFSGPRGCGKTSSARILARSLNCAQGPTA-------TPCGVCESCVAL   79 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCC-------CcccccHHHHHh
Confidence            579999999999999986543      2346789999999999999888874211111000       000000011111


Q ss_pred             HHH---------hhC-CCCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc-CCh
Q 005860          249 IEA---------LEG-FVPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT-RKE  316 (673)
Q Consensus       249 ~~~---------l~~-~~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt-r~~  316 (673)
                      ...         +.. .....++..++.+.+... ..+++-++|+|++..-.....+.|...+........+|++| ...
T Consensus        80 ~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~  159 (584)
T PRK14952         80 APNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPE  159 (584)
T ss_pred             hcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChH
Confidence            100         000 000111222222222211 23455688999997666667788888887665566666555 444


Q ss_pred             hHHHh-ccccceeecCCCCcccc
Q 005860          317 TVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       317 ~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      .+... ..-...+++..++.++.
T Consensus       160 kll~TI~SRc~~~~F~~l~~~~i  182 (584)
T PRK14952        160 KVLPTIRSRTHHYPFRLLPPRTM  182 (584)
T ss_pred             hhHHHHHHhceEEEeeCCCHHHH
Confidence            44432 22356788888887663

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.41  E-value=1.1e-05  Score=69.21  Aligned_cols=113  Identities=17%  Similarity=0.155  Sum_probs=84.8

Q ss_pred             ccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccccc-ccccceecCCCCcccchhhhc
Q 005860          516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLI-HLRYLRLVGLGTEELPETCCE  594 (673)
Q Consensus       516 ~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~-~Lr~L~L~~~~i~~LP~~i~~  594 (673)
                      .+..+.++++..  .........+.....|...+|++       +.+..+|+.+.... .+..|+|.+|.|.++|..+..
T Consensus        28 E~h~ldLssc~l--m~i~davy~l~~~~el~~i~ls~-------N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aa   98 (177)
T KOG4579|consen   28 ELHFLDLSSCQL--MYIADAVYMLSKGYELTKISLSD-------NGFKKFPKKFTIKFPTATTLNLANNEISDVPEELAA   98 (177)
T ss_pred             Hhhhcccccchh--hHHHHHHHHHhCCceEEEEeccc-------chhhhCCHHHhhccchhhhhhcchhhhhhchHHHhh
Confidence            344556666542  11112233345556777788888       88888888776554 788999999999999998999


Q ss_pred             CCCccEEEeccCCCCccccccccccccCCeeecccccccccccc
Q 005860          595 LLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG  638 (673)
Q Consensus       595 L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~  638 (673)
                      ++.|+.|+++.++ +...|.-|..|.+|-.|+..++.+..+|-.
T Consensus        99 m~aLr~lNl~~N~-l~~~p~vi~~L~~l~~Lds~~na~~eid~d  141 (177)
T KOG4579|consen   99 MPALRSLNLRFNP-LNAEPRVIAPLIKLDMLDSPENARAEIDVD  141 (177)
T ss_pred             hHHhhhcccccCc-cccchHHHHHHHhHHHhcCCCCccccCcHH
Confidence            9999999999866 888998888899999999888887777744

>PRK10536 hypothetical protein; Provisional

Probab=97.41  E-value=0.00091  Score=65.32  Aligned_cols=133  Identities=18%  Similarity=0.216  Sum_probs=73.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE--c--CC-----cc
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC--V--SD-----PF  239 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~--v--s~-----~~  239 (673)
                      ..+.++......++.+|..         ..+|.+.|.+|.|||+||.++..+.-....|+.++.+.  +  .+     +.
T Consensus        55 ~~i~p~n~~Q~~~l~al~~---------~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG  125 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES---------KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPG  125 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc---------CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCC
Confidence            4577888888888888853         23899999999999999988766421123454433331  1  11     11


Q ss_pred             cHH----HHHHHHHHHhhCCCCCcCcHHHHHH--------HHHHHhCCCeE---EEEEcCCCCCCccchhhhhhhccCCC
Q 005860          240 DEL----RIAKAIIEALEGFVPTVGELNSLLE--------SIRASLVGKKF---LLILDDMWTDDYSKWEPFHYCLKNGV  304 (673)
Q Consensus       240 ~~~----~~~~~i~~~l~~~~~~~~~~~~~~~--------~l~~~l~~kr~---LlVLDdvw~~~~~~~~~l~~~l~~~~  304 (673)
                      +..    ..+..+.+.+..--. ....+....        .-..+++++.+   +||+|...+-+..+   +...+...+
T Consensus       126 ~~~eK~~p~~~pi~D~L~~~~~-~~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~---~k~~ltR~g  201 (262)
T PRK10536        126 DIAEKFAPYFRPVYDVLVRRLG-ASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQ---MKMFLTRLG  201 (262)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhC-hHHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHH---HHHHHhhcC
Confidence            221    122223332221100 011111100        01235566655   99999996655433   444455557


Q ss_pred             CCeEEEEEcC
Q 005860          305 RGSKILVTTR  314 (673)
Q Consensus       305 ~gs~iivTtr  314 (673)
                      .+|++|+|=-
T Consensus       202 ~~sk~v~~GD  211 (262)
T PRK10536        202 ENVTVIVNGD  211 (262)
T ss_pred             CCCEEEEeCC
Confidence            8999998754

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.39  E-value=0.00069  Score=78.22  Aligned_cols=45  Identities=24%  Similarity=0.248  Sum_probs=37.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++++++..|....       ..-+.++|++|+|||++|+.+.+.
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~-------~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRK-------KNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCC-------CCceEEECCCCCCHHHHHHHHHHH
Confidence            479999999999999886554       223568999999999999988874

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.38  E-value=0.00049  Score=74.32  Aligned_cols=104  Identities=22%  Similarity=0.232  Sum_probs=59.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .-+.|+|..|+|||+|++++.+.......-..++++      +..++...+...+....       .....+++.++. .
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv------~~~~f~~~~~~~l~~~~-------~~~~~~~~~~~~-~  207 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYM------SGDEFARKAVDILQKTH-------KEIEQFKNEICQ-N  207 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEE------EHHHHHHHHHHHHHHhh-------hHHHHHHHHhcc-C
Confidence            458899999999999999999842111111234555      34557777777665311       112334444443 3


Q ss_pred             EEEEEcCCCCCCc-cch-hhhhhhccC-CCCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDY-SKW-EPFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~-~~~-~~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      -+|||||+..... ..+ +.+...+.. ...|..||+|+..
T Consensus       208 dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~  248 (450)
T PRK14087        208 DVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDK  248 (450)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCC
Confidence            4788999944221 122 334333332 2345578888763

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.36  E-value=0.00014  Score=75.77  Aligned_cols=64  Identities=16%  Similarity=0.235  Sum_probs=37.2

Q ss_pred             hhCCccceeeeccccccccccchhhhccccccccccccceecCCC-CcccchhhhcCCCccEEEeccCCCCcccccc
Q 005860          540 DQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG-TEELPETCCELLNLQVLEIEQCTSLKRLPLG  615 (673)
Q Consensus       540 ~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~-i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~  615 (673)
                      ..++.++.|++++       |.+..+|. +  ..+|+.|.+++|. ++.+|..+.  .+|++|++++|+++..+|.+
T Consensus        49 ~~~~~l~~L~Is~-------c~L~sLP~-L--P~sLtsL~Lsnc~nLtsLP~~LP--~nLe~L~Ls~Cs~L~sLP~s  113 (426)
T PRK15386         49 EEARASGRLYIKD-------CDIESLPV-L--PNELTEITIENCNNLTTLPGSIP--EGLEKLTVCHCPEISGLPES  113 (426)
T ss_pred             HHhcCCCEEEeCC-------CCCcccCC-C--CCCCcEEEccCCCCcccCCchhh--hhhhheEccCcccccccccc
Confidence            3446666666666       55555552 1  1246666666655 666665442  46666667666556666643

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.35  E-value=5.8e-05  Score=64.99  Aligned_cols=90  Identities=13%  Similarity=0.185  Sum_probs=68.2

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCC  593 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~  593 (673)
                      ...|....+++|.+    ..+++++-..++.+..|++++       +.+..+|..+..++.||.|+++.|.+...|.-|.
T Consensus        52 ~~el~~i~ls~N~f----k~fp~kft~kf~t~t~lNl~~-------neisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~  120 (177)
T KOG4579|consen   52 GYELTKISLSDNGF----KKFPKKFTIKFPTATTLNLAN-------NEISDVPEELAAMPALRSLNLRFNPLNAEPRVIA  120 (177)
T ss_pred             CceEEEEecccchh----hhCCHHHhhccchhhhhhcch-------hhhhhchHHHhhhHHhhhcccccCccccchHHHH
Confidence            34555667777763    344445555666788888888       8888888888888888888888888888888888


Q ss_pred             cCCCccEEEeccCCCCcccccc
Q 005860          594 ELLNLQVLEIEQCTSLKRLPLG  615 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~~lP~~  615 (673)
                      .|.+|-.|+..++. +.++|-+
T Consensus       121 ~L~~l~~Lds~~na-~~eid~d  141 (177)
T KOG4579|consen  121 PLIKLDMLDSPENA-RAEIDVD  141 (177)
T ss_pred             HHHhHHHhcCCCCc-cccCcHH
Confidence            88888888888754 7777765

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.35  E-value=0.0003  Score=68.32  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=28.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV  235 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  235 (673)
                      -.++|+|..|+|||||+..+..+  ....|+.+++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~--~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYY--LRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHh--hcccCCEEEEEec
Confidence            35789999999999999888875  6778877666643

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.35  E-value=0.0014  Score=69.44  Aligned_cols=146  Identities=15%  Similarity=0.218  Sum_probs=79.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc------cccCCeEE-EEEcCCcccH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV------FEYFDKRM-WVCVSDPFDE  241 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~------~~~F~~~~-wv~vs~~~~~  241 (673)
                      ++++|.+..++.+...+..+.      -...+.++|+.|+||||+|+.+.+...-      ...|...+ -+........
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~------~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~   90 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH------LAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSV   90 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCH
Confidence            578999999999999886543      2458889999999999999888774211      01121111 1111111111


Q ss_pred             HHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC-ChhHHH
Q 005860          242 LRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR-KETVAR  320 (673)
Q Consensus       242 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr-~~~v~~  320 (673)
                      . ..+++++.+..                .-..+++-+|++|++..-....++.+...+......+.+|++|. ...+..
T Consensus        91 ~-~i~~l~~~~~~----------------~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~  153 (367)
T PRK14970         91 D-DIRNLIDQVRI----------------PPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIP  153 (367)
T ss_pred             H-HHHHHHHHHhh----------------ccccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCH
Confidence            1 11111211110                01124455799999844333456666666655444555655553 322222


Q ss_pred             -hccccceeecCCCCccc
Q 005860          321 -MMESIHVISIKELSEQE  337 (673)
Q Consensus       321 -~~~~~~~~~l~~L~~~~  337 (673)
                       .......++.+++++++
T Consensus       154 ~l~sr~~~v~~~~~~~~~  171 (367)
T PRK14970        154 TILSRCQIFDFKRITIKD  171 (367)
T ss_pred             HHHhcceeEecCCccHHH
Confidence             12224467777776655

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.34  E-value=0.0013  Score=69.89  Aligned_cols=115  Identities=20%  Similarity=0.220  Sum_probs=71.2

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKF  278 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~  278 (673)
                      ++.|+|+-++||||+++.+....  .+.   .+++..-+......-+.+.                 ...+.+.-..++.
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~--~~~---~iy~~~~d~~~~~~~l~d~-----------------~~~~~~~~~~~~~   96 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGL--LEE---IIYINFDDLRLDRIELLDL-----------------LRAYIELKEREKS   96 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhC--Ccc---eEEEEecchhcchhhHHHH-----------------HHHHHHhhccCCc
Confidence            99999999999999997766642  111   5565433321111111111                 1111111122788


Q ss_pred             EEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHh-----c-cccceeecCCCCcccc
Q 005860          279 LLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARM-----M-ESIHVISIKELSEQEC  338 (673)
Q Consensus       279 LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~-----~-~~~~~~~l~~L~~~~~  338 (673)
                      +|+||.|  .....|+.....+.+.++. +|++|+-+..+...     . |-...+++-||+-.|.
T Consensus        97 yifLDEI--q~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Ef  159 (398)
T COG1373          97 YIFLDEI--QNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREF  159 (398)
T ss_pred             eEEEecc--cCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHH
Confidence            9999999  4456798877777776665 88888876554332     1 2256778888887776

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.32  E-value=0.00079  Score=72.49  Aligned_cols=123  Identities=20%  Similarity=0.200  Sum_probs=66.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ..-+.|+|+.|+|||+|++++.+.  +......+++++      ...+...+...+...     .    ...++..+.. 
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi~------~~~f~~~~~~~l~~~-----~----~~~f~~~~~~-  202 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHA--LRESGGKILYVR------SELFTEHLVSAIRSG-----E----MQRFRQFYRN-  202 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEee------HHHHHHHHHHHHhcc-----h----HHHHHHHccc-
Confidence            346789999999999999999995  322233456664      334445555554321     1    1234444433 


Q ss_pred             eEEEEEcCCCCCCccch--hhhhhhccC-CCCCeEEEEEcCC-hh--------HHHhccccceeecCCCCccc
Q 005860          277 KFLLILDDMWTDDYSKW--EPFHYCLKN-GVRGSKILVTTRK-ET--------VARMMESIHVISIKELSEQE  337 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~--~~l~~~l~~-~~~gs~iivTtr~-~~--------v~~~~~~~~~~~l~~L~~~~  337 (673)
                      .-+|++||+.......+  +.+...+.. ...|..||+||.. ..        +...+.....+++++++.++
T Consensus       203 ~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~  275 (445)
T PRK12422        203 VDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEG  275 (445)
T ss_pred             CCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHH
Confidence            44788899844221111  223322221 1235578888754 21        12222334566777766554

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.31  E-value=0.001  Score=77.42  Aligned_cols=45  Identities=24%  Similarity=0.307  Sum_probs=37.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++.+++..|....       ..-+.++|.+|+||||+|+.+.+.
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~-------~~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRR-------QNNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCC-------cCceeEECCCCCCHHHHHHHHHHH
Confidence            578999999999999886654       223469999999999999988874

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=97.31  E-value=0.0099  Score=66.93  Aligned_cols=123  Identities=17%  Similarity=0.258  Sum_probs=76.6

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccC---CeEEEEEcCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF---DKRMWVCVSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~~~~~~  243 (673)
                      ..++|-+..++.+.+.+.....+  ..+.++.+...+|+.|||||-||+++...     -|   +..+-+      |+.+
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~-----Lfg~e~aliR~------DMSE  559 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA-----LFGDEQALIRI------DMSE  559 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH-----hcCCCccceee------chHH
Confidence            46899999988888877433210  01345778889999999999999888773     34   233333      3333


Q ss_pred             HHH-HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeE-EEEEcCCCCCCccchhhhhhhccCC
Q 005860          244 IAK-AIIEALEGFVPTVGELNSLLESIRASLVGKKF-LLILDDMWTDDYSKWEPFHYCLKNG  303 (673)
Q Consensus       244 ~~~-~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~-LlVLDdvw~~~~~~~~~l~~~l~~~  303 (673)
                      ... .=...|-+..+.--..++ -..+-+..+.++| +|.||+|...+++..+.+...+.++
T Consensus       560 y~EkHsVSrLIGaPPGYVGyee-GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         560 YMEKHSVSRLIGAPPGYVGYEE-GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             HHHHHHHHHHhCCCCCCceecc-ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence            222 222333333222111111 2345666777888 7889999777777788887777754

>PRK08181 transposase; Validated

Probab=97.26  E-value=0.0007  Score=67.60  Aligned_cols=99  Identities=23%  Similarity=0.153  Sum_probs=54.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKF  278 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~  278 (673)
                      -+.|+|++|+|||.||.++.+.  .......++|+++      .+++..+......     ......    .+.+. +-=
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~~------~~L~~~l~~a~~~-----~~~~~~----l~~l~-~~d  169 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRT------TDLVQKLQVARRE-----LQLESA----IAKLD-KFD  169 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHH--HHHcCCceeeeeH------HHHHHHHHHHHhC-----CcHHHH----HHHHh-cCC
Confidence            4899999999999999999885  3233345666643      3455555333211     122221    22222 334


Q ss_pred             EEEEcCCCCCCccchh--hhhhhccCCCCCeEEEEEcCC
Q 005860          279 LLILDDMWTDDYSKWE--PFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       279 LlVLDdvw~~~~~~~~--~l~~~l~~~~~gs~iivTtr~  315 (673)
                      ||||||+-......|.  .+...+.....+..+||||..
T Consensus       170 LLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~  208 (269)
T PRK08181        170 LLILDDLAYVTKDQAETSVLFELISARYERRSILITANQ  208 (269)
T ss_pred             EEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCC
Confidence            9999999543333332  233333321112358888874

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0021  Score=72.05  Aligned_cols=146  Identities=14%  Similarity=0.209  Sum_probs=86.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc---------------------ccccC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD---------------------VFEYF  227 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~---------------------~~~~F  227 (673)
                      ++++|.+..++.|...+..+.      -...+.++|+.|+||||+|+.+.+...                     ...+|
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~------l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~   90 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK------LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSY   90 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCC
Confidence            579999999999999986543      245688999999999999977666311                     01133


Q ss_pred             CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCe
Q 005860          228 DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGS  307 (673)
Q Consensus       228 ~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs  307 (673)
                      +.. .+..+....+.++ +++++++...                -..+++=++|+|++..-+...++.|...+.....++
T Consensus        91 n~~-~ld~~~~~~vd~I-r~li~~~~~~----------------P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~t  152 (614)
T PRK14971         91 NIH-ELDAASNNSVDDI-RNLIEQVRIP----------------PQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYA  152 (614)
T ss_pred             ceE-EecccccCCHHHH-HHHHHHHhhC----------------cccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCe
Confidence            321 2222211111111 1111111110                012345578999986555566788888887766667


Q ss_pred             EEEEEc-CChhHHHh-ccccceeecCCCCcccc
Q 005860          308 KILVTT-RKETVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       308 ~iivTt-r~~~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      .+|++| ....+... ..-...+++++++.++.
T Consensus       153 ifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei  185 (614)
T PRK14971        153 IFILATTEKHKILPTILSRCQIFDFNRIQVADI  185 (614)
T ss_pred             EEEEEeCCchhchHHHHhhhheeecCCCCHHHH
Confidence            766555 44444432 23367788888888764

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.22  E-value=0.002  Score=69.19  Aligned_cols=101  Identities=22%  Similarity=0.308  Sum_probs=55.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccC--CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ...+.|+|..|+|||+|++++++.  +....  ..++|++      ..++...+...+...     ..+    .+.+.++
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~------~~~~~~~~~~~~~~~-----~~~----~~~~~~~  198 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVS------SEKFTNDFVNALRNN-----KME----EFKEKYR  198 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEE------HHHHHHHHHHHHHcC-----CHH----HHHHHHH
Confidence            346889999999999999999996  33332  2356664      334455555555432     122    2333333


Q ss_pred             CCeEEEEEcCCCCCCcc-ch-hhhhhhccC-CCCCeEEEEEcCC
Q 005860          275 GKKFLLILDDMWTDDYS-KW-EPFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~-~~-~~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      + .-+|||||+...... .+ +.+...+.. ...|..+|+||..
T Consensus       199 ~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       199 S-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             h-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence            3 238889999532111 11 223333322 1235567787764

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>CHL00181 cbbX CbbX; Provisional

Probab=97.20  E-value=0.0041  Score=63.10  Aligned_cols=23  Identities=30%  Similarity=0.297  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.++|++|+||||+|+.+++.
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            45889999999999999999774

>PRK09183 transposase/IS protein; Provisional

Probab=97.19  E-value=0.00098  Score=66.55  Aligned_cols=100  Identities=21%  Similarity=0.230  Sum_probs=52.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ..+.|+|++|+|||+||..+..... ... ..+.|+.      ..++...+......     ..   +...+...+ .+.
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~-~~G-~~v~~~~------~~~l~~~l~~a~~~-----~~---~~~~~~~~~-~~~  165 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAV-RAG-IKVRFTT------AADLLLQLSTAQRQ-----GR---YKTTLQRGV-MAP  165 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHH-HcC-CeEEEEe------HHHHHHHHHHHHHC-----Cc---HHHHHHHHh-cCC
Confidence            4577999999999999999976421 122 2344553      23343333322111     11   112222222 345


Q ss_pred             EEEEEcCCCCCCccchh--hhhhhccC-CCCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDYSKWE--PFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~--~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      -++|+||+.......+.  .+...+.. -..++ +|+||..
T Consensus       166 dlLiiDdlg~~~~~~~~~~~lf~li~~r~~~~s-~iiTsn~  205 (259)
T PRK09183        166 RLLIIDEIGYLPFSQEEANLFFQVIAKRYEKGS-MILTSNL  205 (259)
T ss_pred             CEEEEcccccCCCChHHHHHHHHHHHHHHhcCc-EEEecCC
Confidence            69999999643333332  23333322 12354 7888863

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.18  E-value=0.0016  Score=64.00  Aligned_cols=103  Identities=18%  Similarity=0.200  Sum_probs=57.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ...+.++|.+|+|||+||.++.+.  ....-..++++++      .+++..+-......   ...    ...+.+.+. +
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it~------~~l~~~l~~~~~~~---~~~----~~~~l~~l~-~  162 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNE--LLLRGKSVLIITV------ADIMSAMKDTFSNS---ETS----EEQLLNDLS-N  162 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEH------HHHHHHHHHHHhhc---ccc----HHHHHHHhc-c
Confidence            347899999999999999999996  3233345666643      44544444433211   111    122333344 3


Q ss_pred             eEEEEEcCCCCCCccchhh--hhhhccCC-CCCeEEEEEcCC
Q 005860          277 KFLLILDDMWTDDYSKWEP--FHYCLKNG-VRGSKILVTTRK  315 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~~--l~~~l~~~-~~gs~iivTtr~  315 (673)
                      .=+|||||+-......|..  +...+... ...-.+||||.-
T Consensus       163 ~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        163 VDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             CCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence            4488889996655455653  22222211 223347777763

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.18  E-value=0.0052  Score=56.66  Aligned_cols=137  Identities=17%  Similarity=0.122  Sum_probs=74.9

Q ss_pred             echhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC----cccc--------------ccCCeEEEEE
Q 005860          173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND----SDVF--------------EYFDKRMWVC  234 (673)
Q Consensus       173 Gr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~----~~~~--------------~~F~~~~wv~  234 (673)
                      |-+...+.|.+.+..+.      -...+.++|..|+||+|+|..+.+.    ....              ....-..|+.
T Consensus         1 gq~~~~~~L~~~~~~~~------l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~   74 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR------LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIK   74 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--------SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEE
T ss_pred             CcHHHHHHHHHHHHcCC------cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEe
Confidence            44566677777775543      2346889999999999999666553    1110              1111222332


Q ss_pred             cCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEE
Q 005860          235 VSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKI  309 (673)
Q Consensus       235 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~i  309 (673)
                      -....                  .....++.. .+.+.+     .+++=++|+||+..-.....+.|...+.....++.+
T Consensus        75 ~~~~~------------------~~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~f  135 (162)
T PF13177_consen   75 PDKKK------------------KSIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYF  135 (162)
T ss_dssp             TTTSS------------------SSBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEE
T ss_pred             ccccc------------------chhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEE
Confidence            22110                  011223322 222222     235568899999776777888899888888889999


Q ss_pred             EEEcCChh-HHHh-ccccceeecCCCC
Q 005860          310 LVTTRKET-VARM-MESIHVISIKELS  334 (673)
Q Consensus       310 ivTtr~~~-v~~~-~~~~~~~~l~~L~  334 (673)
                      |++|.+.. +... ..-...+.+++++
T Consensus       136 iL~t~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  136 ILITNNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             EEEES-GGGS-HHHHTTSEEEEE----
T ss_pred             EEEECChHHChHHHHhhceEEecCCCC
Confidence            99988754 3322 2224556665543

...

>PRK07261 topology modulation protein; Provisional

Probab=97.18  E-value=0.00093  Score=62.30  Aligned_cols=65  Identities=22%  Similarity=0.262  Sum_probs=39.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcCcccc-ccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVF-EYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .|.|+|++|+||||||+.+.....+. -+.|...|-....                     ..+.++....+.+.+.+.+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~   60 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQ---------------------ERDDDDMIADISNFLLKHD   60 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccccc---------------------cCCHHHHHHHHHHHHhCCC
Confidence            48999999999999999987643221 2345555521111                     1123344555566666666


Q ss_pred             EEEEEcCCC
Q 005860          278 FLLILDDMW  286 (673)
Q Consensus       278 ~LlVLDdvw  286 (673)
                        .|+|+..
T Consensus        61 --wIidg~~   67 (171)
T PRK07261         61 --WIIDGNY   67 (171)
T ss_pred             --EEEcCcc
Confidence              6788874

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.17  E-value=0.00076  Score=65.03  Aligned_cols=124  Identities=22%  Similarity=0.329  Sum_probs=71.0

Q ss_pred             cccCCcceechhhHHHHHHHh---ccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH
Q 005860          165 LIDVSEIRGRDEEKSSLKSKL---LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE  241 (673)
Q Consensus       165 ~~~~~~~vGr~~~~~~l~~~L---~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  241 (673)
                      ++..++++|.|..++.|++--   ..+.      ...-+.+||..|.|||+|++++.+...-..    .--|.|...   
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~------pannvLL~G~rGtGKSSlVkall~~y~~~G----LRlIev~k~---   89 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGL------PANNVLLWGARGTGKSSLVKALLNEYADQG----LRLIEVSKE---   89 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCC------CCcceEEecCCCCCHHHHHHHHHHHHhhcC----ceEEEECHH---
Confidence            344568999999888776532   2222      245677899999999999999988422111    112333221   


Q ss_pred             HHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCC---CCCe-EEEEEcCCh
Q 005860          242 LRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNG---VRGS-KILVTTRKE  316 (673)
Q Consensus       242 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~---~~gs-~iivTtr~~  316 (673)
                                      +..++..+...++.  ...||+|++||+-.+ +...+..++..+..+   .+.. .|.+||-.+
T Consensus        90 ----------------~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRR  151 (249)
T PF05673_consen   90 ----------------DLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRR  151 (249)
T ss_pred             ----------------HhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchh
Confidence                            12233333334432  357999999998432 233466676666532   2233 344455445


Q ss_pred             hHH
Q 005860          317 TVA  319 (673)
Q Consensus       317 ~v~  319 (673)
                      ++.
T Consensus       152 HLv  154 (249)
T PF05673_consen  152 HLV  154 (249)
T ss_pred             hcc
Confidence            443

>PRK12377 putative replication protein; Provisional

Probab=97.17  E-value=0.0013  Score=64.91  Aligned_cols=100  Identities=19%  Similarity=0.147  Sum_probs=56.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ..+.|+|..|+|||+||.++.+.  +......++++++.      +++..|-......    ....    .+.+.+ .+-
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~~------~l~~~l~~~~~~~----~~~~----~~l~~l-~~~  164 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTVP------DVMSRLHESYDNG----QSGE----KFLQEL-CKV  164 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEHH------HHHHHHHHHHhcc----chHH----HHHHHh-cCC
Confidence            56899999999999999999996  33444456777543      3444444333211    1111    222233 345


Q ss_pred             EEEEEcCCCCCCccchhh--hhhhccCC-CCCeEEEEEcC
Q 005860          278 FLLILDDMWTDDYSKWEP--FHYCLKNG-VRGSKILVTTR  314 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~--l~~~l~~~-~~gs~iivTtr  314 (673)
                      =||||||+-......|..  +...+... .+.--+||||-
T Consensus       165 dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSN  204 (248)
T PRK12377        165 DLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTN  204 (248)
T ss_pred             CEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcC
Confidence            689999995443334532  33333321 22234677775

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.17  E-value=0.0045  Score=67.50  Aligned_cols=145  Identities=14%  Similarity=0.184  Sum_probs=80.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc---cc----------------cCCe
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV---FE----------------YFDK  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~----------------~F~~  229 (673)
                      .+++|-+..+..+.+.+....      -...+.++|+.|+||||+|+.+.....-   ..                .|..
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~------i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d   89 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR------VSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPD   89 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCc
Confidence            478999999999999986543      2346778999999999999887663110   00                0111


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      .+++..+.....                  ++...+...+.. -..+++-++|+|++..-.....+.+...+........
T Consensus        90 ~~eidaas~~gv------------------d~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v  151 (486)
T PRK14953         90 LIEIDAASNRGI------------------DDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTI  151 (486)
T ss_pred             EEEEeCccCCCH------------------HHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeE
Confidence            112211111111                  111122222211 1235667999999955444456677777766555555


Q ss_pred             EEEEc-CChhHHHh-ccccceeecCCCCccc
Q 005860          309 ILVTT-RKETVARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       309 iivTt-r~~~v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      +|++| +...+... ......+.+.+++.++
T Consensus       152 ~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~e  182 (486)
T PRK14953        152 FILCTTEYDKIPPTILSRCQRFIFSKPTKEQ  182 (486)
T ss_pred             EEEEECCHHHHHHHHHHhceEEEcCCCCHHH
Confidence            55555 33333322 2224567777776655

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.00095  Score=74.86  Aligned_cols=157  Identities=13%  Similarity=0.171  Sum_probs=84.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|-+.-++.|..++....      -...+.++|+.|+||||+|+.+.+.......+.      -...++.-...+.|
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~------i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~i   83 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGR------VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRAI   83 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC------CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHHH
Confidence            579999999999988886543      235678999999999999998887421100000      00111111222333


Q ss_pred             HHHhhCC-----CCCcCcHHHHHHHH---HH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEALEGF-----VPTVGELNSLLESI---RA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~l~~~-----~~~~~~~~~~~~~l---~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      .......     .......+++.+.+   .. -..+++-++|+|++..-.....+.|...+......+.+|++|.+ ..+
T Consensus        84 ~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kl  163 (585)
T PRK14950         84 AEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKV  163 (585)
T ss_pred             hcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhh
Confidence            2211110     00111222222211   11 11345668999999544445567777777665556677766644 333


Q ss_pred             HHhc-cccceeecCCCCccc
Q 005860          319 ARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       319 ~~~~-~~~~~~~l~~L~~~~  337 (673)
                      .... .....+.++.++..+
T Consensus       164 l~tI~SR~~~i~f~~l~~~e  183 (585)
T PRK14950        164 PATILSRCQRFDFHRHSVAD  183 (585)
T ss_pred             hHHHHhccceeeCCCCCHHH
Confidence            3221 224566677666654

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.16  E-value=0.001  Score=71.74  Aligned_cols=100  Identities=21%  Similarity=0.251  Sum_probs=57.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcccccc-CC-eEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEY-FD-KRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG  275 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~-~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  275 (673)
                      .-+.|+|..|+|||+||+++++.  +... .. .++|++.      .++..++...+...     ..+    .+++.+..
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~--l~~~~~~~~v~yi~~------~~f~~~~~~~~~~~-----~~~----~f~~~~~~  193 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYITS------EKFLNDLVDSMKEG-----KLN----EFREKYRK  193 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEEH------HHHHHHHHHHHhcc-----cHH----HHHHHHHh
Confidence            34899999999999999999996  3333 23 4567743      45666666665422     122    23333334


Q ss_pred             CeEEEEEcCCCCCC-ccch-hhhhhhccC-CCCCeEEEEEcC
Q 005860          276 KKFLLILDDMWTDD-YSKW-EPFHYCLKN-GVRGSKILVTTR  314 (673)
Q Consensus       276 kr~LlVLDdvw~~~-~~~~-~~l~~~l~~-~~~gs~iivTtr  314 (673)
                      +.-+|++||+.... ...+ +.+...+.. ...|..||+||.
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd  235 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSD  235 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECC
Confidence            45589999995321 1111 123222221 123446888874

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.16  E-value=0.0034  Score=70.55  Aligned_cols=156  Identities=18%  Similarity=0.252  Sum_probs=84.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccccc-CCe-EEEEE---cCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY-FDK-RMWVC---VSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~-~~wv~---vs~~~~~~~  243 (673)
                      .+++|.+..++.|...+..+.      -...+.++|+.|+||||+|+.+.+..--... ... -|-.|   ....++.- 
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r------l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvi-   90 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK------ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDII-   90 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEE-
Confidence            478999999999999886543      2456789999999999999888763111000 000 00000   00000000 


Q ss_pred             HHHHHHHHhhCC-CCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc-CChhHHH
Q 005860          244 IAKAIIEALEGF-VPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT-RKETVAR  320 (673)
Q Consensus       244 ~~~~i~~~l~~~-~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt-r~~~v~~  320 (673)
                             .+... .....++.++...+... ..+++-++|+|++..-....++.+...+........+|++| ....+..
T Consensus        91 -------eidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~  163 (725)
T PRK07133         91 -------EMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPL  163 (725)
T ss_pred             -------EEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhH
Confidence                   00000 00011122222222211 23566689999996555566777877776655555555444 4444433


Q ss_pred             h-ccccceeecCCCCcccc
Q 005860          321 M-MESIHVISIKELSEQEC  338 (673)
Q Consensus       321 ~-~~~~~~~~l~~L~~~~~  338 (673)
                      . ..-...+++.+++.++.
T Consensus       164 TI~SRcq~ieF~~L~~eeI  182 (725)
T PRK07133        164 TILSRVQRFNFRRISEDEI  182 (725)
T ss_pred             HHHhhceeEEccCCCHHHH
Confidence            2 23356788888887764

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.16  E-value=0.0021  Score=64.54  Aligned_cols=51  Identities=24%  Similarity=0.223  Sum_probs=33.6

Q ss_pred             cceechhhHHHHHHHhccC--------CcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKLLCE--------SSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~--------~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|.+..++.|.+.....        ..-...+...-+.++|++|+||||+|+.+++.
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~   65 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKL   65 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHH
Confidence            5889887776665432110        00000234567889999999999999999764

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.15  E-value=0.0028  Score=70.87  Aligned_cols=156  Identities=15%  Similarity=0.225  Sum_probs=83.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+.-++.|.+.+..+.      -...+.++|+.|+||||+|+.+.+..--....+.       ..++.-.....|
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~------~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~-------~~c~~c~~c~~i   82 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGR------VAHAFLFTGARGVGKTSTARILAKALNCEQGLTA-------EPCNVCPPCVEI   82 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC-------CCCCccHHHHHH
Confidence            579999999999999886543      2356789999999999999888774211111000       000000111111


Q ss_pred             HHHh-------hCC-CCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC-ChhH
Q 005860          249 IEAL-------EGF-VPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR-KETV  318 (673)
Q Consensus       249 ~~~l-------~~~-~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr-~~~v  318 (673)
                      ...-       ... ....++..++...+... ..+++-++|+|++..-+....+.|...+......+.+|++|. ...+
T Consensus        83 ~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl  162 (576)
T PRK14965         83 TEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKV  162 (576)
T ss_pred             hcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhh
Confidence            1000       000 00111122222222111 134555788999965555567778777776555666665554 3444


Q ss_pred             HHh-ccccceeecCCCCccc
Q 005860          319 ARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~  337 (673)
                      ... ..-...+++++++.++
T Consensus       163 ~~tI~SRc~~~~f~~l~~~~  182 (576)
T PRK14965        163 PITILSRCQRFDFRRIPLQK  182 (576)
T ss_pred             hHHHHHhhhhhhcCCCCHHH
Confidence            332 2224566777776655

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.14  E-value=0.004  Score=67.98  Aligned_cols=143  Identities=13%  Similarity=0.137  Sum_probs=85.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc--ccc----------------CCe-
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV--FEY----------------FDK-  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~----------------F~~-  229 (673)
                      ++++|-+..++.+...+..+.      -..++.++|+.|+||||+|+.+.+..--  ...                ++. 
T Consensus        14 deiiGqe~v~~~L~~~I~~gr------l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~d   87 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR------LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHID   87 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCe
Confidence            579999999999999886543      2456789999999999999876653100  000                100 


Q ss_pred             EEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH----HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCC
Q 005860          230 RMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA----SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVR  305 (673)
Q Consensus       230 ~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~----~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~  305 (673)
                      ++.+..+...                     ..+++...+..    -..+++-++|+|++..-+....+.+...+.....
T Consensus        88 v~eldaas~~---------------------gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~  146 (535)
T PRK08451         88 IIEMDAASNR---------------------GIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPS  146 (535)
T ss_pred             EEEecccccc---------------------CHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCC
Confidence            1111111111                     12222222221    1124566889999966665667778777776666


Q ss_pred             CeEEEEEcCCh-hHHH-hccccceeecCCCCcccc
Q 005860          306 GSKILVTTRKE-TVAR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       306 gs~iivTtr~~-~v~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      .+++|++|.+. .+.. ...-...+++.+++.++.
T Consensus       147 ~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei  181 (535)
T PRK08451        147 YVKFILATTDPLKLPATILSRTQHFRFKQIPQNSI  181 (535)
T ss_pred             ceEEEEEECChhhCchHHHhhceeEEcCCCCHHHH
Confidence            77777777653 2221 112256788888887764

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.13  E-value=0.0019  Score=65.54  Aligned_cols=123  Identities=20%  Similarity=0.229  Sum_probs=60.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKF  278 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~  278 (673)
                      -+.++|++|+||||+|+.+.+...-.......-|+.++.    .+    ++..+.+..     .......+.+.   ..-
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~~----l~~~~~g~~-----~~~~~~~~~~a---~~g  123 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DD----LVGQYIGHT-----APKTKEILKRA---MGG  123 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----HH----HhHhhcccc-----hHHHHHHHHHc---cCc
Confidence            578999999999999977666321111111112444442    12    222222211     11122222222   235


Q ss_pred             EEEEcCCCCC---------CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccc--------cceeecCCCCccc
Q 005860          279 LLILDDMWTD---------DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMES--------IHVISIKELSEQE  337 (673)
Q Consensus       279 LlVLDdvw~~---------~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~--------~~~~~l~~L~~~~  337 (673)
                      +|+||++..-         ....++.+...+.....+-+||+++.....-.....        ...+++++++.+|
T Consensus       124 vL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~ed  199 (284)
T TIGR02880       124 VLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAE  199 (284)
T ss_pred             EEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHH
Confidence            8899999421         011234444555455456677777654322221111        3457777777554

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=97.12  E-value=3.9e-05  Score=77.29  Aligned_cols=103  Identities=22%  Similarity=0.298  Sum_probs=85.4

Q ss_pred             cceeeeccccccccccchhhhcc-ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccc-ccccccc
Q 005860          545 LRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVN  621 (673)
Q Consensus       545 L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~  621 (673)
                      -..++|..       +.+..+|+ .++.+.+||.|||+.|.|+.+ |..+..|.+|-+|-+-+.++|..+|. .|+.|..
T Consensus        69 tveirLdq-------N~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~s  141 (498)
T KOG4237|consen   69 TVEIRLDQ-------NQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSS  141 (498)
T ss_pred             ceEEEecc-------CCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHH
Confidence            45567777       88999976 588999999999999999888 78899999998888888677999997 4899999


Q ss_pred             CCeeecccccccccccc-CCCCCCCCcCCeeEEc
Q 005860          622 LRHLTYDDSCLEFIPKG-IQRLTNLRTLSEFVVV  654 (673)
Q Consensus       622 Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~~~~~~  654 (673)
                      |+-|.+.-+.+.-++.. +..|++|..|..++-.
T Consensus       142 lqrLllNan~i~Cir~~al~dL~~l~lLslyDn~  175 (498)
T KOG4237|consen  142 LQRLLLNANHINCIRQDALRDLPSLSLLSLYDNK  175 (498)
T ss_pred             HHHHhcChhhhcchhHHHHHHhhhcchhcccchh
Confidence            99999887777766654 6778888777766653

>PRK06921 hypothetical protein; Provisional

Probab=97.09  E-value=0.0017  Score=65.02  Aligned_cols=99  Identities=18%  Similarity=0.242  Sum_probs=55.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccccc-CCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEY-FDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG  275 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  275 (673)
                      ..-+.++|..|+|||+||.++.+.  +... -..++|++..      +++..+...+          +.... ..+.+. 
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~~------~l~~~l~~~~----------~~~~~-~~~~~~-  176 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPFV------EGFGDLKDDF----------DLLEA-KLNRMK-  176 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEHH------HHHHHHHHHH----------HHHHH-HHHHhc-
Confidence            456899999999999999999996  3333 3456777642      2333332221          11111 222232 


Q ss_pred             CeEEEEEcCCCC-----CCccchhh--hhhhccCC-CCCeEEEEEcCC
Q 005860          276 KKFLLILDDMWT-----DDYSKWEP--FHYCLKNG-VRGSKILVTTRK  315 (673)
Q Consensus       276 kr~LlVLDdvw~-----~~~~~~~~--l~~~l~~~-~~gs~iivTtr~  315 (673)
                      +-=||||||+..     +....|..  +...+... ..+..+||||..
T Consensus       177 ~~dlLiIDDl~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~  224 (266)
T PRK06921        177 KVEVLFIDDLFKPVNGKPRATEWQIEQMYSVLNYRYLNHKPILISSEL  224 (266)
T ss_pred             CCCEEEEeccccccCCCccCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            345999999932     22234442  33333321 234457888863

>PRK06620 hypothetical protein; Validated

Probab=97.09  E-value=0.0012  Score=63.81  Aligned_cols=23  Identities=30%  Similarity=0.231  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.+.|+|++|+|||+|++.+++.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            57899999999999999998885

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.07  E-value=0.004  Score=71.24  Aligned_cols=45  Identities=24%  Similarity=0.262  Sum_probs=36.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++.+++..|.....       .-+.++|.+|+|||++|+.+.+.
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~-------~n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRK-------NNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCC-------CCeEEECCCCCCHHHHHHHHHHH
Confidence            4699999999999998876431       22357999999999999998864

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.06  E-value=0.0029  Score=68.40  Aligned_cols=144  Identities=17%  Similarity=0.229  Sum_probs=80.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc---------------------ccC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF---------------------EYF  227 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---------------------~~F  227 (673)
                      ++++|.+..++.+.+.+..+.      -...+.++|+.|+||||+|+.+.+...-.                     .++
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~------i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~   90 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNR------AAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSL   90 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC------CceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCC
Confidence            579999999999999886543      13567889999999999998876631100                     011


Q ss_pred             CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCC
Q 005860          228 DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRG  306 (673)
Q Consensus       228 ~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~g  306 (673)
                      + .+++.-......                  ++..++.+.+.. ...+++-++|+|++..-.....+.+...+......
T Consensus        91 d-~~~i~g~~~~gi------------------d~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~  151 (451)
T PRK06305         91 D-VLEIDGASHRGI------------------EDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQH  151 (451)
T ss_pred             c-eEEeeccccCCH------------------HHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCC
Confidence            1 111111011011                  111111111111 12356668899998443444556677677665556


Q ss_pred             eEEEEEcCC-hhHHHh-ccccceeecCCCCccc
Q 005860          307 SKILVTTRK-ETVARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       307 s~iivTtr~-~~v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      ..+|++|.+ ..+... ......++++++++++
T Consensus       152 ~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~e  184 (451)
T PRK06305        152 VKFFLATTEIHKIPGTILSRCQKMHLKRIPEET  184 (451)
T ss_pred             ceEEEEeCChHhcchHHHHhceEEeCCCCCHHH
Confidence            666666643 323222 2225567888887765

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.05  E-value=0.00013  Score=79.01  Aligned_cols=86  Identities=24%  Similarity=0.313  Sum_probs=53.2

Q ss_pred             HhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccccc
Q 005860          538 LFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLGI  616 (673)
Q Consensus       538 ~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~i  616 (673)
                      .+.-++.|+.|+|+.       |.+...- .+..+.+|+.|||+.|.+..+|. +.... .|+.|+++++. +.+|- +|
T Consensus       182 SLqll~ale~LnLsh-------Nk~~~v~-~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc-~L~~L~lrnN~-l~tL~-gi  250 (1096)
T KOG1859|consen  182 SLQLLPALESLNLSH-------NKFTKVD-NLRRLPKLKHLDLSYNCLRHVPQLSMVGC-KLQLLNLRNNA-LTTLR-GI  250 (1096)
T ss_pred             HHHHHHHhhhhccch-------hhhhhhH-HHHhcccccccccccchhccccccchhhh-hheeeeecccH-HHhhh-hH
Confidence            344456666777777       6655544 56666777777777777666663 22222 37777777644 66554 66


Q ss_pred             cccccCCeeecccccccc
Q 005860          617 GKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       617 ~~L~~Lr~L~l~~~~l~~  634 (673)
                      .+|.+|++||++.|.+..
T Consensus       251 e~LksL~~LDlsyNll~~  268 (1096)
T KOG1859|consen  251 ENLKSLYGLDLSYNLLSE  268 (1096)
T ss_pred             HhhhhhhccchhHhhhhc
Confidence            777777777776665543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.05  E-value=0.0029  Score=68.99  Aligned_cols=101  Identities=22%  Similarity=0.271  Sum_probs=55.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccC--CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ..-+.|+|..|+|||+|++++.+.  +...+  ..++|++.      .++...+...+...     ..    ..+.+.++
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~-----~~----~~~~~~~~  210 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYVTS------EKFTNDFVNALRNN-----TM----EEFKEKYR  210 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEEEH------HHHHHHHHHHHHcC-----cH----HHHHHHHh
Confidence            356899999999999999999996  43443  23556643      33444455544321     11    23333444


Q ss_pred             CCeEEEEEcCCCCCCccc-h-hhhhhhccC-CCCCeEEEEEcCC
Q 005860          275 GKKFLLILDDMWTDDYSK-W-EPFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~-~-~~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      + .-+|||||+....... + +.+...+.. ...|..||+||..
T Consensus       211 ~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~  253 (450)
T PRK00149        211 S-VDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDR  253 (450)
T ss_pred             c-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCC
Confidence            2 4489999994321111 1 223332221 1234568887764

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.04  E-value=0.0014  Score=69.61  Aligned_cols=52  Identities=21%  Similarity=0.254  Sum_probs=38.8

Q ss_pred             CcceechhhHHHHHHHhccCCcc------cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE------EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|+++.++++.+.+...-..      -+....+-|.++|++|+|||++|+++++.
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            57899999999998876332100      00133566899999999999999999985

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.04  E-value=0.0027  Score=74.49  Aligned_cols=139  Identities=17%  Similarity=0.225  Sum_probs=77.1

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|.+..++.+...+.....+  .......++.++|+.|+|||++|+.+...  ....-...+.+..+.-.+...   
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~~~~---  639 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYMEKHS---  639 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhcccch---
Confidence            46899999999999888653210  00123467889999999999999999874  211122344444443222111   


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCC-CeEEEEEcCCCCCCccchhhhhhhccCC----C-------CCeEEEEEcC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVG-KKFLLILDDMWTDDYSKWEPFHYCLKNG----V-------RGSKILVTTR  314 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~-kr~LlVLDdvw~~~~~~~~~l~~~l~~~----~-------~gs~iivTtr  314 (673)
                        ...+.+..+.....++ ...+.+.++. ...+|+||++..-+...++.+...+..+    +       ..+-||+||.
T Consensus       640 --~~~l~g~~~g~~g~~~-~g~l~~~v~~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn  716 (852)
T TIGR03346       640 --VARLIGAPPGYVGYEE-GGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSN  716 (852)
T ss_pred             --HHHhcCCCCCccCccc-ccHHHHHHHcCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCC
Confidence              1122121111111100 1122233322 3348999999777777777777776543    1       2334777776


Q ss_pred             C
Q 005860          315 K  315 (673)
Q Consensus       315 ~  315 (673)
                      -
T Consensus       717 ~  717 (852)
T TIGR03346       717 L  717 (852)
T ss_pred             c
Confidence            3

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK06526 transposase; Provisional

Probab=97.02  E-value=0.00092  Score=66.36  Aligned_cols=99  Identities=22%  Similarity=0.241  Sum_probs=51.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .-+.|+|++|+|||+||.++.... ....+ .+.|+      +..++...+.....     ....   ...+.. + .+.
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a-~~~g~-~v~f~------t~~~l~~~l~~~~~-----~~~~---~~~l~~-l-~~~  160 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRA-CQAGH-RVLFA------TAAQWVARLAAAHH-----AGRL---QAELVK-L-GRY  160 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHH-HHCCC-chhhh------hHHHHHHHHHHHHh-----cCcH---HHHHHH-h-ccC
Confidence            458999999999999999988752 12222 33443      33344444433211     1111   122322 2 234


Q ss_pred             EEEEEcCCCCCCccchh--hhhhhccC-CCCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDYSKWE--PFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~--~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      -+|||||+.......+.  .+...+.. ...++ +|+||..
T Consensus       161 dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s-~IitSn~  200 (254)
T PRK06526        161 PLLIVDEVGYIPFEPEAANLFFQLVSSRYERAS-LIVTSNK  200 (254)
T ss_pred             CEEEEcccccCCCCHHHHHHHHHHHHHHHhcCC-EEEEcCC
Confidence            58999999533222222  23333322 22344 8888874

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.01  E-value=0.0015  Score=76.51  Aligned_cols=45  Identities=22%  Similarity=0.278  Sum_probs=37.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||++++++++..|....       ..-+.++|++|+|||++|+.+...
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~-------~~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT-------KNNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc-------cCCeEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999997654       223469999999999999888774

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.99  E-value=0.005  Score=67.84  Aligned_cols=122  Identities=14%  Similarity=0.178  Sum_probs=67.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccC--CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG  275 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  275 (673)
                      ..+.|+|..|+|||.|++++++.  ....+  -.++|++      ..++..++...+...     .    ...+++.+++
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~--a~~~~~g~~V~Yit------aeef~~el~~al~~~-----~----~~~f~~~y~~  377 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHY--ARRLYPGTRVRYVS------SEEFTNEFINSIRDG-----K----GDSFRRRYRE  377 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEee------HHHHHHHHHHHHHhc-----c----HHHHHHHhhc
Confidence            34899999999999999999995  33222  2456664      334455555444321     1    1223334433


Q ss_pred             CeEEEEEcCCCCCCc-cchh-hhhhhccC-CCCCeEEEEEcCCh---------hHHHhccccceeecCCCCccc
Q 005860          276 KKFLLILDDMWTDDY-SKWE-PFHYCLKN-GVRGSKILVTTRKE---------TVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       276 kr~LlVLDdvw~~~~-~~~~-~l~~~l~~-~~~gs~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~~  337 (673)
                       -=+|||||+..... ..|. .+...+.. ...|..|||||...         .+...+...-+++++..+.+.
T Consensus       378 -~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~Et  450 (617)
T PRK14086        378 -MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELET  450 (617)
T ss_pred             -CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHH
Confidence             24788999954322 1222 23333322 13355688888752         222333445667777776554

>PF14516 AAA_35: AAA-like domain

Probab=96.98  E-value=0.0063  Score=63.24  Aligned_cols=183  Identities=14%  Similarity=0.121  Sum_probs=105.6

Q ss_pred             cccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-----c
Q 005860          165 LIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-----F  239 (673)
Q Consensus       165 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~  239 (673)
                      +.+.+.+|+|...-+++.+.|..+.        ..+.|.|+-.+|||||...+.+..+- ..+ .++++++..-     .
T Consensus         7 ~~~~~~Yi~R~~~e~~~~~~i~~~G--------~~~~I~apRq~GKTSll~~l~~~l~~-~~~-~~v~id~~~~~~~~~~   76 (331)
T PF14516_consen    7 PLDSPFYIERPPAEQECYQEIVQPG--------SYIRIKAPRQMGKTSLLLRLLERLQQ-QGY-RCVYIDLQQLGSAIFS   76 (331)
T ss_pred             CCCCCcccCchHHHHHHHHHHhcCC--------CEEEEECcccCCHHHHHHHHHHHHHH-CCC-EEEEEEeecCCCcccC
Confidence            3455678899977777777775533        57999999999999999888875322 233 4567776542     2


Q ss_pred             cHHHHHHHHHHHhhCC----CC-------CcCcHHHHHHHHHHHh---CCCeEEEEEcCCCCCC--ccchhhhhhhccC-
Q 005860          240 DELRIAKAIIEALEGF----VP-------TVGELNSLLESIRASL---VGKKFLLILDDMWTDD--YSKWEPFHYCLKN-  302 (673)
Q Consensus       240 ~~~~~~~~i~~~l~~~----~~-------~~~~~~~~~~~l~~~l---~~kr~LlVLDdvw~~~--~~~~~~l~~~l~~-  302 (673)
                      +...+++.++..+...    ..       ...........+.+.+   .+++.+|+||+|..--  ....+++...+.. 
T Consensus        77 ~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~  156 (331)
T PF14516_consen   77 DLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSW  156 (331)
T ss_pred             CHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHH
Confidence            4555565555555432    11       1112223344454433   2689999999983211  1111223332221 


Q ss_pred             ---C----CCCeEEEEEcCChhH--H-Hh----ccccceeecCCCCccccc---------------------cCCchhhH
Q 005860          303 ---G----VRGSKILVTTRKETV--A-RM----MESIHVISIKELSEQECW---------------------CKGLPLAA  347 (673)
Q Consensus       303 ---~----~~gs~iivTtr~~~v--~-~~----~~~~~~~~l~~L~~~~~~---------------------c~GlPLai  347 (673)
                         .    ...+-.+|...+...  . ..    .+....++|++++.+|..                     ++|+|.-+
T Consensus       157 ~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~~~~~~~~l~~~tgGhP~Lv  236 (331)
T PF14516_consen  157 YEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEFSQEQLEQLMDWTGGHPYLV  236 (331)
T ss_pred             HHhcccCcccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccCCHHHHHHHHHHHCCCHHHH
Confidence               0    011222222222111  1 11    122456788888888864                     99999999


Q ss_pred             HHHhhhhccC
Q 005860          348 KTIGSLLRFK  357 (673)
Q Consensus       348 ~~~~~~L~~~  357 (673)
                      ..++..+...
T Consensus       237 ~~~~~~l~~~  246 (331)
T PF14516_consen  237 QKACYLLVEE  246 (331)
T ss_pred             HHHHHHHHHc
Confidence            9999999653

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.97  E-value=0.014  Score=67.38  Aligned_cols=52  Identities=25%  Similarity=0.272  Sum_probs=39.8

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.+.+|.+.-+++|+++|....... .....++.++|++|+||||+|+.+...
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~-~~~g~~i~l~GppG~GKTtl~~~ia~~  372 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVN-KIKGPILCLVGPPGVGKTSLGQSIAKA  372 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcc-cCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999998886322100 123457999999999999999999974

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.96  E-value=0.003  Score=61.97  Aligned_cols=47  Identities=19%  Similarity=0.164  Sum_probs=34.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRI  244 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~  244 (673)
                      ..-.++.|+|.+|+|||++|.++...  ....-..++|++.. .++...+
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC-CCCHHHH
Confidence            34679999999999999999777764  32334678899887 5555443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.95  E-value=0.0038  Score=73.09  Aligned_cols=126  Identities=16%  Similarity=0.198  Sum_probs=68.6

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|.+..++.+...+.....+  ..+....++.++|+.|+|||+||+.+.+.  ....-...+.+..+.-..     .
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~--l~~~~~~~i~id~se~~~-----~  640 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANF--MFDSDDAMVRIDMSEFME-----K  640 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHH--hhcCCCcEEEEEhHHhhh-----h
Confidence            46899999998888887542100  00123457899999999999999999874  211112334444432111     1


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCC-CeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVG-KKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~-kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                      .....+.+..+.....+. ...+.+.++. ..-+|+||++..-+...++.+...+..
T Consensus       641 ~~~~~LiG~~pgy~g~~~-~g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll~ile~  696 (857)
T PRK10865        641 HSVSRLVGAPPGYVGYEE-GGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDD  696 (857)
T ss_pred             hhHHHHhCCCCcccccch-hHHHHHHHHhCCCCeEEEeehhhCCHHHHHHHHHHHhh
Confidence            112222222211111111 1122333322 235899999966666677777766654

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=96.95  E-value=0.00028  Score=76.06  Aligned_cols=109  Identities=21%  Similarity=0.327  Sum_probs=60.9

Q ss_pred             cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccch
Q 005860          511 IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE  590 (673)
Q Consensus       511 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~  590 (673)
                      +..+.+|..|.+.++.+     ..+...+..+.+|++|++++       +.+..+. .+..+..|+.|++++|.|..++.
T Consensus        91 l~~~~~l~~l~l~~n~i-----~~i~~~l~~~~~L~~L~ls~-------N~I~~i~-~l~~l~~L~~L~l~~N~i~~~~~  157 (414)
T KOG0531|consen   91 LSKLKSLEALDLYDNKI-----EKIENLLSSLVNLQVLDLSF-------NKITKLE-GLSTLTLLKELNLSGNLISDISG  157 (414)
T ss_pred             cccccceeeeeccccch-----hhcccchhhhhcchheeccc-------ccccccc-chhhccchhhheeccCcchhccC
Confidence            34455666666666542     11222244566666666666       6555542 35555556666666666665543


Q ss_pred             hhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccc
Q 005860          591 TCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       591 ~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~  634 (673)
                       +..|++|+.++++++. +..++.. ...+.+|+.+++..|.+..
T Consensus       158 -~~~l~~L~~l~l~~n~-i~~ie~~~~~~~~~l~~l~l~~n~i~~  200 (414)
T KOG0531|consen  158 -LESLKSLKLLDLSYNR-IVDIENDELSELISLEELDLGGNSIRE  200 (414)
T ss_pred             -CccchhhhcccCCcch-hhhhhhhhhhhccchHHHhccCCchhc
Confidence             3446666666666655 5555432 3556666666666655443

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.94  E-value=0.0022  Score=65.49  Aligned_cols=121  Identities=13%  Similarity=0.129  Sum_probs=69.4

Q ss_pred             echhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       173 Gr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      ++....+...+++..-..   ....+-+.|+|..|+|||.||.++++..  ...-..+.|++++      .++.++-...
T Consensus       135 ~~~~~~~~~~~fi~~~~~---~~~~~gl~L~G~~G~GKThLa~Aia~~l--~~~g~~v~~~~~~------~l~~~lk~~~  203 (306)
T PRK08939        135 DRLDALMAALDFLEAYPP---GEKVKGLYLYGDFGVGKSYLLAAIANEL--AKKGVSSTLLHFP------EFIRELKNSI  203 (306)
T ss_pred             HHHHHHHHHHHHHHHhhc---cCCCCeEEEECCCCCCHHHHHHHHHHHH--HHcCCCEEEEEHH------HHHHHHHHHH
Confidence            444444455555542211   0124568999999999999999999963  2222345677553      4555555554


Q ss_pred             hCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhh--hhhhc-cCC-CCCeEEEEEcC
Q 005860          253 EGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEP--FHYCL-KNG-VRGSKILVTTR  314 (673)
Q Consensus       253 ~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~--l~~~l-~~~-~~gs~iivTtr  314 (673)
                      ...     +..+   .+ +.+. +-=||||||+-.+....|..  +...+ ... ..+-.+|+||-
T Consensus       204 ~~~-----~~~~---~l-~~l~-~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        204 SDG-----SVKE---KI-DAVK-EAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             hcC-----cHHH---HH-HHhc-CCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence            321     1222   22 2232 45589999997666667753  44443 322 24556888886

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.94  E-value=0.007  Score=67.92  Aligned_cols=158  Identities=14%  Similarity=0.206  Sum_probs=84.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|.+..++.|..++....      -...+.++|..|+||||+|+.+.+..--. .++..    ....+..-...+.+
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r------l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~-~~~~~----~~~~Cg~C~~C~~i   84 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR------IAPAYLFTGPRGTGKTSSARILAKSLNCL-NSDKP----TPEPCGKCELCRAI   84 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC------CCceEEEECCCCCChHHHHHHHHHHhcCC-CcCCC----CCCCCcccHHHHHH
Confidence            478999999999999886543      13467899999999999999888752111 11000    00111111222222


Q ss_pred             HHHhhCC-----CCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEALEGF-----VPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~l~~~-----~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      .......     .......+.+.+.+...    ..+++-++|+|++..-....++.|...+........+|++|.+ ..+
T Consensus        85 ~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~l  164 (620)
T PRK14948         85 AAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRV  164 (620)
T ss_pred             hcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhh
Confidence            2211110     00111222222222111    1345568899999655555677787777765555655555544 333


Q ss_pred             HHh-ccccceeecCCCCccc
Q 005860          319 ARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~  337 (673)
                      ... ..-...+++..++.++
T Consensus       165 lpTIrSRc~~~~f~~l~~~e  184 (620)
T PRK14948        165 LPTIISRCQRFDFRRIPLEA  184 (620)
T ss_pred             hHHHHhheeEEEecCCCHHH
Confidence            322 2224566677776654

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.94  E-value=0.0024  Score=61.77  Aligned_cols=49  Identities=18%  Similarity=0.188  Sum_probs=36.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..-.++.|+|.+|+|||++|.++...  .......++|++... +++..+.+
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHHHHH
Confidence            44689999999999999999776654  323456789998865 56555443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.93  E-value=0.0015  Score=72.72  Aligned_cols=52  Identities=19%  Similarity=0.245  Sum_probs=41.0

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++++|-+..++++..++.....+  ....+++.|+|++|+||||+++.+...
T Consensus        82 ~ldel~~~~~ki~~l~~~l~~~~~~--~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        82 TQHELAVHKKKIEEVETWLKAQVLE--NAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             CHHHhcCcHHHHHHHHHHHHhcccc--cCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3458999999999999998654321  123468999999999999999999985

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.90  E-value=0.0051  Score=60.33  Aligned_cols=88  Identities=18%  Similarity=0.098  Sum_probs=53.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccC------CeEEEEEcCCcccHHHHHHHHHHHhhCCC---------CCc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF------DKRMWVCVSDPFDELRIAKAIIEALEGFV---------PTV  259 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F------~~~~wv~vs~~~~~~~~~~~i~~~l~~~~---------~~~  259 (673)
                      ..-.++.|+|.+|+|||+||.++.-.  ....-      ..++|++....++...+. ++.+......         ...
T Consensus        17 ~~g~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~   93 (226)
T cd01393          17 PTGRITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARP   93 (226)
T ss_pred             cCCcEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeC
Confidence            34579999999999999999777653  11222      567899887777765543 3333322110         011


Q ss_pred             CcHHHHHHHHHHHhC----CCeEEEEEcCC
Q 005860          260 GELNSLLESIRASLV----GKKFLLILDDM  285 (673)
Q Consensus       260 ~~~~~~~~~l~~~l~----~kr~LlVLDdv  285 (673)
                      .+.+++...+.+...    .+.-|||+|.+
T Consensus        94 ~~~~~~~~~l~~~~~~~~~~~~~lvVIDsi  123 (226)
T cd01393          94 YNGEQQLEIVEELERIMSSGRVDLVVVDSV  123 (226)
T ss_pred             CCHHHHHHHHHHHHHHhhcCCeeEEEEcCc
Confidence            334444444444432    34558999987

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=96.90  E-value=7.2e-05  Score=80.93  Aligned_cols=131  Identities=18%  Similarity=0.101  Sum_probs=92.5

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      +.++-..+..++.......++.-++.|++|+++.|.+    .. . ..+..+..|+.|||+.       |.+..+|..-.
T Consensus       163 Wn~L~~a~fsyN~L~~mD~SLqll~ale~LnLshNk~----~~-v-~~Lr~l~~LkhLDlsy-------N~L~~vp~l~~  229 (1096)
T KOG1859|consen  163 WNKLATASFSYNRLVLMDESLQLLPALESLNLSHNKF----TK-V-DNLRRLPKLKHLDLSY-------NCLRHVPQLSM  229 (1096)
T ss_pred             hhhHhhhhcchhhHHhHHHHHHHHHHhhhhccchhhh----hh-h-HHHHhccccccccccc-------chhccccccch
Confidence            3445555555555444444555577889999988863    11 1 2567888999999999       88877776433


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccc--cccccccCCeeecccccccccc
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      .=.+|..|+|++|.++.|- .|.+|++|+.||++++- +...-+  -+|.|..|+.|++.+|.+-.-|
T Consensus       230 ~gc~L~~L~lrnN~l~tL~-gie~LksL~~LDlsyNl-l~~hseL~pLwsLs~L~~L~LeGNPl~c~p  295 (1096)
T KOG1859|consen  230 VGCKLQLLNLRNNALTTLR-GIENLKSLYGLDLSYNL-LSEHSELEPLWSLSSLIVLWLEGNPLCCAP  295 (1096)
T ss_pred             hhhhheeeeecccHHHhhh-hHHhhhhhhccchhHhh-hhcchhhhHHHHHHHHHHHhhcCCccccCH
Confidence            3345899999999888885 48899999999999853 544321  3688888999999988876555

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.88  E-value=0.0033  Score=64.92  Aligned_cols=101  Identities=16%  Similarity=0.049  Sum_probs=63.5

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc-cCCe-EEEEEcCCc-ccHHHHHHHHHHHhh
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE-YFDK-RMWVCVSDP-FDELRIAKAIIEALE  253 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~-~~wv~vs~~-~~~~~~~~~i~~~l~  253 (673)
                      -..++++.+..-.      .-.-+.|+|..|+|||||++.+.+.  +.. +-+. ++|+.+.+. .++.++.+.+...+.
T Consensus       119 ~~~RvID~l~PiG------kGQR~LIvG~pGtGKTTLl~~la~~--i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vv  190 (380)
T PRK12608        119 LSMRVVDLVAPIG------KGQRGLIVAPPRAGKTVLLQQIAAA--VAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVY  190 (380)
T ss_pred             hhHhhhhheeecC------CCceEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEE
Confidence            3455777765322      2345799999999999999998885  322 2244 466666654 467788888887776


Q ss_pred             CCCCCcCcHH-----HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          254 GFVPTVGELN-----SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       254 ~~~~~~~~~~-----~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      ....+.....     .....+.+++  ++++++||+|++
T Consensus       191 ast~de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsl  229 (380)
T PRK12608        191 ASTFDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSL  229 (380)
T ss_pred             eecCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCc
Confidence            5432222111     1122222222  589999999999

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.87  E-value=0.0071  Score=56.95  Aligned_cols=120  Identities=15%  Similarity=0.118  Sum_probs=66.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE---cCCcccHHHH------HHHHHHHhhCCC------CCcCc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC---VSDPFDELRI------AKAIIEALEGFV------PTVGE  261 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---vs~~~~~~~~------~~~i~~~l~~~~------~~~~~  261 (673)
                      -.+++|+|..|.|||||++.+....   ....+.+++.   +.. .+....      ..++++.++...      .....
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~---~~~~G~v~~~g~~~~~-~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLL---KPSSGEILLDGKDLAS-LSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCCcEEEECCEECCc-CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            3589999999999999999999852   3344555542   221 122111      112444444321      11112


Q ss_pred             HHHHHHHHHHHhCCCeEEEEEcCCCC-CCccchhhhhhhccCC-CC-CeEEEEEcCChhHHH
Q 005860          262 LNSLLESIRASLVGKKFLLILDDMWT-DDYSKWEPFHYCLKNG-VR-GSKILVTTRKETVAR  320 (673)
Q Consensus       262 ~~~~~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~~l~~~l~~~-~~-gs~iivTtr~~~v~~  320 (673)
                      -+...-.+...+-..+-++++|+--. -|....+.+...+... .. |..||++|.+.....
T Consensus       101 G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~  162 (180)
T cd03214         101 GERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            22333445566677778999998732 1222333344444322 22 668899998876553

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.87  E-value=0.00075  Score=63.22  Aligned_cols=99  Identities=21%  Similarity=0.278  Sum_probs=50.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .-+.|+|..|+|||.||.++.+.  ...+=..+.|+.+      .+++..+    ..... ......    +.+.+.+ -
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~--~~~~g~~v~f~~~------~~L~~~l----~~~~~-~~~~~~----~~~~l~~-~  109 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANE--AIRKGYSVLFITA------SDLLDEL----KQSRS-DGSYEE----LLKRLKR-V  109 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEH------HHHHHHH----HCCHC-CTTHCH----HHHHHHT-S
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHH--hccCCcceeEeec------Cceeccc----ccccc-ccchhh----hcCcccc-c
Confidence            45999999999999999999885  2222234667743      3344443    32211 112222    2223332 3


Q ss_pred             EEEEEcCCCCCCccchhh--hhhhccCC-CCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDYSKWEP--FHYCLKNG-VRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~--l~~~l~~~-~~gs~iivTtr~  315 (673)
                      =||||||+-......|..  +...+... .++ .+||||.-
T Consensus       110 dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~-~tIiTSN~  149 (178)
T PF01695_consen  110 DLLILDDLGYEPLSEWEAELLFEIIDERYERK-PTIITSNL  149 (178)
T ss_dssp             SCEEEETCTSS---HHHHHCTHHHHHHHHHT--EEEEEESS
T ss_pred             cEecccccceeeecccccccchhhhhHhhccc-CeEeeCCC
Confidence            478899996554444432  22222211 233 57778864

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.87  E-value=0.0052  Score=71.07  Aligned_cols=123  Identities=15%  Similarity=0.125  Sum_probs=69.1

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|.+..++.+.+.+......  .......++.++|+.|+|||+||+.+...  .   +...+.++.++-.+..    
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l---~~~~~~~d~se~~~~~----  524 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEA--L---GVHLERFDMSEYMEKH----  524 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHH--h---cCCeEEEeCchhhhcc----
Confidence            46788888888888877532100  00123567899999999999999999884  2   2334555544422111    


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCC-CeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVG-KKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~-kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                      .+...++... .....++ ...+.+.++. ..-+|+||++..-+...++.+...+..
T Consensus       525 ~~~~lig~~~-gyvg~~~-~~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld~  579 (731)
T TIGR02639       525 TVSRLIGAPP-GYVGFEQ-GGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDY  579 (731)
T ss_pred             cHHHHhcCCC-CCcccch-hhHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhcc
Confidence            1122222221 1101111 1123333333 345999999977666667777666654

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.87  E-value=0.00045  Score=62.07  Aligned_cols=89  Identities=22%  Similarity=0.177  Sum_probs=48.0

Q ss_pred             EEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEE
Q 005860          200 ITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFL  279 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~L  279 (673)
                      |.++|.+|+|||+||+.++..  .   =....-+.++...+..++....--. ... .. .....+...++     +..+
T Consensus         2 vlL~G~~G~GKt~l~~~la~~--~---~~~~~~i~~~~~~~~~dl~g~~~~~-~~~-~~-~~~~~l~~a~~-----~~~i   68 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAAL--L---GRPVIRINCSSDTTEEDLIGSYDPS-NGQ-FE-FKDGPLVRAMR-----KGGI   68 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH--H---TCEEEEEE-TTTSTHHHHHCEEET--TTT-TC-EEE-CCCTTHH-----EEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH--h---hcceEEEEeccccccccceeeeeec-ccc-cc-ccccccccccc-----ceeE
Confidence            679999999999999999884  2   1233456777777777655422211 000 00 00000000011     7889


Q ss_pred             EEEcCCCCCCccchhhhhhhcc
Q 005860          280 LILDDMWTDDYSKWEPFHYCLK  301 (673)
Q Consensus       280 lVLDdvw~~~~~~~~~l~~~l~  301 (673)
                      +|||++...+...+..+...+.
T Consensus        69 l~lDEin~a~~~v~~~L~~ll~   90 (139)
T PF07728_consen   69 LVLDEINRAPPEVLESLLSLLE   90 (139)
T ss_dssp             EEESSCGG--HHHHHTTHHHHS
T ss_pred             EEECCcccCCHHHHHHHHHHHh
Confidence            9999995444444445544443

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.86  E-value=0.00087  Score=68.85  Aligned_cols=51  Identities=18%  Similarity=0.212  Sum_probs=41.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.++.++++++++....... ...-++++++|++|+||||||+.+.+.
T Consensus        51 ~~~~G~~~~i~~lv~~l~~~a~g~-~~~r~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       51 HDFFGMEEAIERFVNYFKSAAQGL-EERKQILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             hhccCcHHHHHHHHHHHHHHHhcC-CCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            379999999999999986543211 234689999999999999999999885

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.85  E-value=0.0066  Score=55.71  Aligned_cols=124  Identities=18%  Similarity=0.226  Sum_probs=73.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE---c------------------CCc-----------------
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC---V------------------SDP-----------------  238 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---v------------------s~~-----------------  238 (673)
                      -..+.++|++|.|||||.+.+|..++.   =.+.+|+.   +                  -++                 
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~p---t~G~i~~~~~dl~~l~~~~iP~LRR~IGvVFQD~rLL~~~tvyeNVA~pL  104 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERP---TRGKILVNGHDLSRLKGREIPFLRRQIGVVFQDFRLLPDRTVYENVALPL  104 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcC---CCceEEECCeecccccccccchhhheeeeEeeeccccccchHhhhhhhhh
Confidence            468999999999999999999996443   22344431   0                  011                 


Q ss_pred             ----ccHHHHHHHHHHHh---hCCC------CCcCcHHHHHHHHHHHhCCCeEEEEEcCCC-C-CCccchhhhhhhccCC
Q 005860          239 ----FDELRIAKAIIEAL---EGFV------PTVGELNSLLESIRASLVGKKFLLILDDMW-T-DDYSKWEPFHYCLKNG  303 (673)
Q Consensus       239 ----~~~~~~~~~i~~~l---~~~~------~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw-~-~~~~~~~~l~~~l~~~  303 (673)
                          ....++.+...+.+   +...      .+...-++-.-.|.+.+-+++-+++=|.-- + +....|+-+.-.-.-+
T Consensus       105 ~v~G~~~~~i~~rV~~~L~~VgL~~k~~~lP~~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeein  184 (223)
T COG2884         105 RVIGKPPREIRRRVSEVLDLVGLKHKARALPSQLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEIN  184 (223)
T ss_pred             hccCCCHHHHHHHHHHHHHHhccchhhhcCccccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHh
Confidence                11223333333332   2211      112222344556777788888899988431 1 2333565544333346


Q ss_pred             CCCeEEEEEcCChhHHHhcc
Q 005860          304 VRGSKILVTTRKETVARMME  323 (673)
Q Consensus       304 ~~gs~iivTtr~~~v~~~~~  323 (673)
                      ..|+.||+.|.+.++.+.+.
T Consensus       185 r~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         185 RLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             hcCcEEEEEeccHHHHHhcc
Confidence            77999999999999887764

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.84  E-value=0.0022  Score=63.70  Aligned_cols=81  Identities=25%  Similarity=0.276  Sum_probs=50.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ..-+.++|.+|+|||.||.++.+.  +...--.+.|+++      .+++.++.......        .....+.+.+. +
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~--l~~~g~sv~f~~~------~el~~~Lk~~~~~~--------~~~~~l~~~l~-~  167 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNE--LLKAGISVLFITA------PDLLSKLKAAFDEG--------RLEEKLLRELK-K  167 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEEEH------HHHHHHHHHHHhcC--------chHHHHHHHhh-c
Confidence            345899999999999999999996  3333345667754      34555555554331        11222333222 2


Q ss_pred             eEEEEEcCCCCCCccchh
Q 005860          277 KFLLILDDMWTDDYSKWE  294 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~  294 (673)
                      -=||||||+-......|.
T Consensus       168 ~dlLIiDDlG~~~~~~~~  185 (254)
T COG1484         168 VDLLIIDDIGYEPFSQEE  185 (254)
T ss_pred             CCEEEEecccCccCCHHH
Confidence            238999999665555554

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.84  E-value=0.0035  Score=73.11  Aligned_cols=137  Identities=18%  Similarity=0.227  Sum_probs=74.0

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|.+..++.+.+.+......  .......++.++|+.|+|||.||+.+...  .-......+-++++.-.+.    .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~~----~  639 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQEA----H  639 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhhh----h
Confidence            47899999999998887432100  00234568999999999999999887663  2111112222222221110    1


Q ss_pred             HHHHHhhCCCC--CcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCC-----------CCeEEEEEc
Q 005860          247 AIIEALEGFVP--TVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGV-----------RGSKILVTT  313 (673)
Q Consensus       247 ~i~~~l~~~~~--~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~-----------~gs~iivTt  313 (673)
                      .+.+-++....  ...+...+...++   +...-+|+||++..-+...++.+...+..+.           ..+-||+||
T Consensus       640 ~~~~l~g~~~gyvg~~~~g~L~~~v~---~~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TS  716 (852)
T TIGR03345       640 TVSRLKGSPPGYVGYGEGGVLTEAVR---RKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTS  716 (852)
T ss_pred             hhccccCCCCCcccccccchHHHHHH---hCCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeC
Confidence            11111222111  1111122233333   2455699999996666666777766665442           345566676


Q ss_pred             C
Q 005860          314 R  314 (673)
Q Consensus       314 r  314 (673)
                      .
T Consensus       717 N  717 (852)
T TIGR03345       717 N  717 (852)
T ss_pred             C
Confidence            5

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.84  E-value=0.0033  Score=65.75  Aligned_cols=123  Identities=19%  Similarity=0.229  Sum_probs=72.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCC--eEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD--KRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      ....+.|||..|.|||.|++++.+.  ......  .++++      +.+....+++..+...         -...+++..
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~--~~~~~~~a~v~y~------~se~f~~~~v~a~~~~---------~~~~Fk~~y  174 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNE--ALANGPNARVVYL------TSEDFTNDFVKALRDN---------EMEKFKEKY  174 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHH--HHhhCCCceEEec------cHHHHHHHHHHHHHhh---------hHHHHHHhh
Confidence            3568999999999999999999996  444454  34444      3344455555544331         134455555


Q ss_pred             CCCeEEEEEcCCCCCCc-cchh-hhhhhccC-CCCCeEEEEEcCCh---------hHHHhccccceeecCCCCccc
Q 005860          274 VGKKFLLILDDMWTDDY-SKWE-PFHYCLKN-GVRGSKILVTTRKE---------TVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~-~~~~-~l~~~l~~-~~~gs~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~~  337 (673)
                        .-=++++||++.-.. +.|+ .+...+.. ...|-.||+|++..         .+...++..-++++.+++.+.
T Consensus       175 --~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~  248 (408)
T COG0593         175 --SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDET  248 (408)
T ss_pred             --ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHH
Confidence              333888999954211 1222 23333332 23344899998632         233344556677777777654

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.83  E-value=0.00077  Score=58.84  Aligned_cols=22  Identities=41%  Similarity=0.484  Sum_probs=20.4

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ||+|+|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999884

...

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.80  E-value=0.0041  Score=61.76  Aligned_cols=87  Identities=16%  Similarity=0.108  Sum_probs=53.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----  262 (673)
                      -.-++|+|..|+||||||+.+++.  ++.+| +.++++-+.+... +.++...+.+.=...       ..+..-.     
T Consensus        69 GQr~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~  146 (274)
T cd01133          69 GGKIGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARV  146 (274)
T ss_pred             CCEEEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            357899999999999999999996  55556 4566666766543 344555544321110       1111101     


Q ss_pred             HHHHHHHHHHh---CCCeEEEEEcCC
Q 005860          263 NSLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       263 ~~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      -...-.+.+++   +++.+|+++||+
T Consensus       147 ~~~a~~~AEyfr~~~g~~Vl~~~Dsl  172 (274)
T cd01133         147 ALTGLTMAEYFRDEEGQDVLLFIDNI  172 (274)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeCh
Confidence            11223344555   389999999999

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.80  E-value=0.0035  Score=73.60  Aligned_cols=45  Identities=24%  Similarity=0.292  Sum_probs=36.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++.+++..|....       -.-+.++|.+|+|||++|+.+...
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~-------~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRT-------KNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCC-------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            469999999999999986644       233458999999999999888774

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.79  E-value=0.0032  Score=59.05  Aligned_cols=36  Identities=28%  Similarity=0.474  Sum_probs=28.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      ...+|.|+|+.|+||||+|+.+++.  ....+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~--l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYER--LKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HHHcCCcEEEE
Confidence            4569999999999999999999985  44556666665

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.79  E-value=0.012  Score=65.18  Aligned_cols=157  Identities=11%  Similarity=0.049  Sum_probs=86.1

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|-+..++.|...+....      -...+.++|+.|+||||+|+.+.+..--......   ..+....+-    +.|
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~------i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~---~pC~~C~~C----~~i   82 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK------IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP---MPCGECSSC----KSI   82 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC---CCCccchHH----HHH
Confidence            579999999999999986543      2457889999999999999998875211111000   000000000    111


Q ss_pred             HHHhhC-----CCCCcCcHHHHHHHH---HH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEALEG-----FVPTVGELNSLLESI---RA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~l~~-----~~~~~~~~~~~~~~l---~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      ...-..     ........+++....   .. -..+++-++|+|++..-+...++.+...+......+.+|++|.+ ..+
T Consensus        83 ~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL  162 (563)
T PRK06647         83 DNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKL  162 (563)
T ss_pred             HcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHh
Confidence            110000     000011222222221   11 12356668999999665555677787777765566676666643 333


Q ss_pred             HHh-ccccceeecCCCCcccc
Q 005860          319 ARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ... ..-...++..+++.++-
T Consensus       163 ~~tI~SRc~~~~f~~l~~~el  183 (563)
T PRK06647        163 PATIKSRCQHFNFRLLSLEKI  183 (563)
T ss_pred             HHHHHHhceEEEecCCCHHHH
Confidence            322 22245677887776653

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=96.79  E-value=0.00031  Score=75.71  Aligned_cols=120  Identities=23%  Similarity=0.298  Sum_probs=89.8

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCC  593 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~  593 (673)
                      +..+..+.+..+..     ......+..++.|..|++.+       +.+..+...+..+.+|++|+|++|.|..+.. +.
T Consensus        71 l~~l~~l~l~~n~i-----~~~~~~l~~~~~l~~l~l~~-------n~i~~i~~~l~~~~~L~~L~ls~N~I~~i~~-l~  137 (414)
T KOG0531|consen   71 LTSLKELNLRQNLI-----AKILNHLSKLKSLEALDLYD-------NKIEKIENLLSSLVNLQVLDLSFNKITKLEG-LS  137 (414)
T ss_pred             hHhHHhhccchhhh-----hhhhcccccccceeeeeccc-------cchhhcccchhhhhcchheeccccccccccc-hh
Confidence            44455555444432     11223356788999999999       8888887778999999999999999998864 78


Q ss_pred             cCCCccEEEeccCCCCccccccccccccCCeeecccccccccccc-CCCCCCCCcC
Q 005860          594 ELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTL  648 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L  648 (673)
                      .|..|+.|+++++. +..++ .+..+.+|+.++++.|.+..++.. ...+.+|..+
T Consensus       138 ~l~~L~~L~l~~N~-i~~~~-~~~~l~~L~~l~l~~n~i~~ie~~~~~~~~~l~~l  191 (414)
T KOG0531|consen  138 TLTLLKELNLSGNL-ISDIS-GLESLKSLKLLDLSYNRIVDIENDELSELISLEEL  191 (414)
T ss_pred             hccchhhheeccCc-chhcc-CCccchhhhcccCCcchhhhhhhhhhhhccchHHH
Confidence            88889999999976 87776 666789999999999988887643 3455555544

>cd01394 radB RadB

Probab=96.78  E-value=0.0055  Score=59.71  Aligned_cols=44  Identities=16%  Similarity=0.082  Sum_probs=32.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD  240 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  240 (673)
                      ..-.++.|.|.+|+||||+|.++...  ....-..++|++....+.
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e~~~~   60 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTEGLSS   60 (218)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCCCCH
Confidence            34689999999999999999777764  222334677887655544

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.77  E-value=0.0022  Score=66.04  Aligned_cols=102  Identities=20%  Similarity=0.264  Sum_probs=55.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .-+.++|..|+|||+||.++.+..  ...-..++|+++.      +++..+...-...   ..+..   .. .+.+.+ -
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l--~~~g~~V~y~t~~------~l~~~l~~~~~~~---~~~~~---~~-~~~l~~-~  247 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKEL--LDRGKSVIYRTAD------ELIEILREIRFNN---DKELE---EV-YDLLIN-C  247 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHH--HHCCCeEEEEEHH------HHHHHHHHHHhcc---chhHH---HH-HHHhcc-C
Confidence            569999999999999999999963  2223356777543      3333333211111   01111   11 222322 2


Q ss_pred             EEEEEcCCCCCCccchh--hhhhhccCC-CCCeEEEEEcCC
Q 005860          278 FLLILDDMWTDDYSKWE--PFHYCLKNG-VRGSKILVTTRK  315 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~--~l~~~l~~~-~~gs~iivTtr~  315 (673)
                      =||||||+-......|.  .+...+... ..+-.+||||..
T Consensus       248 DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        248 DLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             CEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            48999999554434442  233333321 234568888863

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.75  E-value=0.0093  Score=56.04  Aligned_cols=126  Identities=13%  Similarity=0.061  Sum_probs=65.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC--CC-------------CCcCc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG--FV-------------PTVGE  261 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~--~~-------------~~~~~  261 (673)
                      -.+++|+|..|.|||||++.+.....   .-.+.+++.-.   +.......+-+.++-  +.             .....
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~---~~~G~i~~~g~---~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~LS~  101 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDLK---PQQGEITLDGV---PVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRRFSG  101 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC---CCCCEEEECCE---EHHHHHHHHHhhEEEEccCCeeecccHHHhhcccCCH
Confidence            35899999999999999999998532   22344443211   111111111111110  00             00111


Q ss_pred             HHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeec
Q 005860          262 LNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       262 ~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                      -+...-.+...+-.++=+++||+..+. |....+.+...+.....|..||++|.+......  ..+.+.+
T Consensus       102 G~~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~--~d~~~~l  169 (178)
T cd03247         102 GERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIEH--MDKILFL  169 (178)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHHh--CCEEEEE
Confidence            122233455566677788999987432 222223333333322246779999998776653  3444444

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=96.73  E-value=0.011  Score=53.42  Aligned_cols=106  Identities=16%  Similarity=0.138  Sum_probs=58.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      -.+++|+|..|.|||||++.+.....   ...+.+++.-..             .+.- ..+...-+...-.+...+..+
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~---~~~G~i~~~~~~-------------~i~~-~~~lS~G~~~rv~laral~~~   88 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELE---PDEGIVTWGSTV-------------KIGY-FEQLSGGEKMRLALAKLLLEN   88 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCC---CCceEEEECCeE-------------EEEE-EccCCHHHHHHHHHHHHHhcC
Confidence            35899999999999999999988532   234444432100             0000 000111122233455556667


Q ss_pred             eEEEEEcCCCC-CCccchhhhhhhccCCCCCeEEEEEcCChhHHHh
Q 005860          277 KFLLILDDMWT-DDYSKWEPFHYCLKNGVRGSKILVTTRKETVARM  321 (673)
Q Consensus       277 r~LlVLDdvw~-~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~  321 (673)
                      +-++++|+.-. -|......+...+...  +..||++|.+......
T Consensus        89 p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~~  132 (144)
T cd03221          89 PNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLDQ  132 (144)
T ss_pred             CCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHHH
Confidence            77899998632 1222333344444332  2468888888665543

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.72  E-value=0.011  Score=60.96  Aligned_cols=64  Identities=8%  Similarity=0.093  Sum_probs=43.1

Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHHh-ccccceeecCCCCcccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      +++-++|+|++..-+....+.+...+.....++.+|+||.+.. +... .+-...+.+.+++.++.
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~  170 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEES  170 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHH
Confidence            3344556799976666778888888877666778888877643 3322 23356788888877764

>PRK04296 thymidine kinase; Provisional

Probab=96.72  E-value=0.0025  Score=60.56  Aligned_cols=113  Identities=14%  Similarity=-0.002  Sum_probs=62.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCC--cCcHHHHHHHHHHHhCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPT--VGELNSLLESIRASLVG  275 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~~  275 (673)
                      .++.|+|..|.||||+|..+...  ...+-..++.+.  ..++.+.....++++++.....  ....+++...+.+ ..+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~--~~~~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~   77 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYN--YEERGMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGE   77 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHHcCCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCC
Confidence            47889999999999999766664  222333333331  1122222233455555432221  2234455555555 334


Q ss_pred             CeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh
Q 005860          276 KKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET  317 (673)
Q Consensus       276 kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~  317 (673)
                      +.-+||+|.+..-+.++...+...+  ...|-.||+|.++.+
T Consensus        78 ~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~  117 (190)
T PRK04296         78 KIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTD  117 (190)
T ss_pred             CCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCcc
Confidence            5558999999432222233333332  245778999988743

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.71  E-value=0.004  Score=59.14  Aligned_cols=129  Identities=24%  Similarity=0.234  Sum_probs=62.0

Q ss_pred             echhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc----CCc-----ccHHH
Q 005860          173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV----SDP-----FDELR  243 (673)
Q Consensus       173 Gr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v----s~~-----~~~~~  243 (673)
                      .+..+....++.|..         ..++.+.|++|.|||.||.+..-+.-....|+..+++.-    .+.     .+..+
T Consensus         4 p~~~~Q~~~~~al~~---------~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~e   74 (205)
T PF02562_consen    4 PKNEEQKFALDALLN---------NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEE   74 (205)
T ss_dssp             --SHHHHHHHHHHHH----------SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS------
T ss_pred             CCCHHHHHHHHHHHh---------CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHH
Confidence            455666677777762         358999999999999999666554333477888877641    111     01110


Q ss_pred             ----HHHHHHHHhhCCCCCcCcHHHHHHH------HHHHhCCC---eEEEEEcCCCCCCccchhhhhhhccCCCCCeEEE
Q 005860          244 ----IAKAIIEALEGFVPTVGELNSLLES------IRASLVGK---KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKIL  310 (673)
Q Consensus       244 ----~~~~i~~~l~~~~~~~~~~~~~~~~------l~~~l~~k---r~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~ii  310 (673)
                          .+..+.+.+..-. .....+.+...      -..+++|+   ..+||+|++.+-...++..   .+...+.|||||
T Consensus        75 K~~p~~~p~~d~l~~~~-~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~---ilTR~g~~skii  150 (205)
T PF02562_consen   75 KMEPYLRPIYDALEELF-GKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKM---ILTRIGEGSKII  150 (205)
T ss_dssp             ---TTTHHHHHHHTTTS--TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHH---HHTTB-TT-EEE
T ss_pred             HHHHHHHHHHHHHHHHh-ChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHH---HHcccCCCcEEE
Confidence                1122222222211 11112221110      01234553   4699999996655555544   455567899999


Q ss_pred             EEcC
Q 005860          311 VTTR  314 (673)
Q Consensus       311 vTtr  314 (673)
                      ++=-
T Consensus       151 ~~GD  154 (205)
T PF02562_consen  151 ITGD  154 (205)
T ss_dssp             EEE-
T ss_pred             EecC
Confidence            9854

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.71  E-value=0.0044  Score=61.07  Aligned_cols=153  Identities=16%  Similarity=0.168  Sum_probs=92.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeE-EEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKR-MWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~-~wv~vs~~~~~~~~~~~  247 (673)
                      ++++|-+..++-|.+.+...       .......+|++|.|||+-|.+.....--.+.|.++ +=.++|+.-...-+-.+
T Consensus        36 de~~gQe~vV~~L~~a~~~~-------~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~K  108 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLRR-------ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREK  108 (346)
T ss_pred             HhhcchHHHHHHHHHHHhhc-------CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhh
Confidence            57899999999999988762       36789999999999999998777743223456443 33455554322200000


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHh--CCCe-EEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhH-HH-hc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASL--VGKK-FLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETV-AR-MM  322 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l--~~kr-~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v-~~-~~  322 (673)
                                 ..+...+........  .-++ -.||||++.+-..+.|..+.....+....++.|+++..-+. .. ..
T Consensus       109 -----------ik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~  177 (346)
T KOG0989|consen  109 -----------IKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLV  177 (346)
T ss_pred             -----------hcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHH
Confidence                       011111111110000  0123 37889999776777899999988887777777666654321 11 11


Q ss_pred             cccceeecCCCCccccc
Q 005860          323 ESIHVISIKELSEQECW  339 (673)
Q Consensus       323 ~~~~~~~l~~L~~~~~~  339 (673)
                      .-...|..++|.+++..
T Consensus       178 SRC~KfrFk~L~d~~iv  194 (346)
T KOG0989|consen  178 SRCQKFRFKKLKDEDIV  194 (346)
T ss_pred             hhHHHhcCCCcchHHHH
Confidence            22456777888776654

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.70  E-value=0.01  Score=59.53  Aligned_cols=42  Identities=21%  Similarity=0.199  Sum_probs=28.6

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      -|.+.|.+|+|||+||+.+.+.  ..   ...+.++.+...+..+++
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~--lg---~~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARK--RD---RPVMLINGDAELTTSDLV   64 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH--hC---CCEEEEeCCccCCHHHHh
Confidence            3568999999999999999872  21   234556665555555443

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.70  E-value=0.0076  Score=56.24  Aligned_cols=125  Identities=18%  Similarity=0.181  Sum_probs=64.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC--cccHHHHHHHHHHHhhC--CCCC----------cCcH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD--PFDELRIAKAIIEALEG--FVPT----------VGEL  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~l~~--~~~~----------~~~~  262 (673)
                      -.+++|+|..|.|||||.+.+..-.   ....+.+++.-..  .......    ...++-  +...          ...-
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~~---~~~~G~i~~~g~~~~~~~~~~~----~~~i~~~~~~~~~~~~t~~e~lLS~G  100 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRLY---DPTSGEILIDGVDLRDLDLESL----RKNIAYVPQDPFLFSGTIRENILSGG  100 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCC---CCCCCEEEECCEEhhhcCHHHH----HhhEEEEcCCchhccchHHHHhhCHH
Confidence            3589999999999999999999852   2334444432110  0011111    111110  0000          0011


Q ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeec
Q 005860          263 NSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       263 ~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                      +...-.+...+-.++=+++||+-... |....+.+...+.....+..||++|.+......  ..+++.+
T Consensus       101 ~~~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~--~d~~~~l  167 (171)
T cd03228         101 QRQRIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIRD--ADRIIVL  167 (171)
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHHHh--CCEEEEE
Confidence            12223355566667789999987432 222233343434332235678999998776654  3344443

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.70  E-value=0.016  Score=56.57  Aligned_cols=122  Identities=17%  Similarity=0.151  Sum_probs=67.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcc-----cc------ccC---CeEEEEEc----CCc--ccH----------------
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSD-----VF------EYF---DKRMWVCV----SDP--FDE----------------  241 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~-----~~------~~F---~~~~wv~v----s~~--~~~----------------  241 (673)
                      .+++|+|+.|.|||||.+.+..-.+     +.      ..+   ..+.||.=    ...  .++                
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~~  110 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWFR  110 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccccc
Confidence            6899999999999999999998311     10      011   13445421    111  111                


Q ss_pred             ------HHHHHHHHHHhhCC---CCCcCc---HHHHHHHHHHHhCCCeEEEEEcCCCC----CCccchhhhhhhccCCCC
Q 005860          242 ------LRIAKAIIEALEGF---VPTVGE---LNSLLESIRASLVGKKFLLILDDMWT----DDYSKWEPFHYCLKNGVR  305 (673)
Q Consensus       242 ------~~~~~~i~~~l~~~---~~~~~~---~~~~~~~l~~~l~~kr~LlVLDdvw~----~~~~~~~~l~~~l~~~~~  305 (673)
                            ++...+.++.++..   .....+   -+.-+-.+.+.|..++=|+|||.--.    ......-.+...+..  .
T Consensus       111 ~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~--e  188 (254)
T COG1121         111 RLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQ--E  188 (254)
T ss_pred             cccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHH--C
Confidence                  13333444444432   122222   23334557788889999999996422    111223333333333  3


Q ss_pred             CeEEEEEcCChhHHHh
Q 005860          306 GSKILVTTRKETVARM  321 (673)
Q Consensus       306 gs~iivTtr~~~v~~~  321 (673)
                      |..|+++|.+-+....
T Consensus       189 g~tIl~vtHDL~~v~~  204 (254)
T COG1121         189 GKTVLMVTHDLGLVMA  204 (254)
T ss_pred             CCEEEEEeCCcHHhHh
Confidence            8899999998665443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.69  E-value=0.0035  Score=73.31  Aligned_cols=45  Identities=24%  Similarity=0.296  Sum_probs=37.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++.+++..|....       ..-+.++|.+|+||||+|+.+...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~-------~~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRT-------KNNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCC-------cCceEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999986654       233558999999999999888874

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.67  E-value=0.019  Score=63.89  Aligned_cols=157  Identities=15%  Similarity=0.201  Sum_probs=82.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.+..++.+.+.+....      -...+.++|+.|+||||+|+.+.+..--...-+       ..+++.-...+.|
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~------~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~-------~~pC~~C~~C~~i   82 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGK------ISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPD-------GEPCNECEICKAI   82 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCccHHHHHH
Confidence            579999999999999987654      245677899999999999988766311100000       0011111111111


Q ss_pred             HHHhhCC-----CCCcCcHHH---HHHHHHH-HhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc-CChhH
Q 005860          249 IEALEGF-----VPTVGELNS---LLESIRA-SLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT-RKETV  318 (673)
Q Consensus       249 ~~~l~~~-----~~~~~~~~~---~~~~l~~-~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt-r~~~v  318 (673)
                      .......     .......++   +...+.. -..+++-++|+|++..-....++.|...+........+|++| ....+
T Consensus        83 ~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki  162 (559)
T PRK05563         83 TNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKI  162 (559)
T ss_pred             hcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhC
Confidence            1110000     000011222   2222211 124566688999996555556777777776554455555544 33333


Q ss_pred             HHh-ccccceeecCCCCcccc
Q 005860          319 ARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      ... ......++..+++.++.
T Consensus       163 ~~tI~SRc~~~~f~~~~~~ei  183 (559)
T PRK05563        163 PATILSRCQRFDFKRISVEDI  183 (559)
T ss_pred             cHHHHhHheEEecCCCCHHHH
Confidence            222 22245677777776553

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.67  E-value=0.0099  Score=58.68  Aligned_cols=90  Identities=23%  Similarity=0.208  Sum_probs=53.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccccc----CCeEEEEEcCCcccHHHHHHHHHHHhhCCC------------CC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY----FDKRMWVCVSDPFDELRIAKAIIEALEGFV------------PT  258 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------------~~  258 (673)
                      ..-.++.|+|.+|+|||+||.+++-.......    ...++|++....++...+.. +++..+...            .+
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~-~~~~~~~~~~~~~~~i~~~~~~~   95 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ-IAERFGLDPEEVLDNIYVARAYN   95 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH-HHHHhccChHhHhcCEEEEecCC
Confidence            34579999999999999999887643212121    36789999888777654433 333332211            01


Q ss_pred             cCcHHHHHHHHHHHhC-C-CeEEEEEcCC
Q 005860          259 VGELNSLLESIRASLV-G-KKFLLILDDM  285 (673)
Q Consensus       259 ~~~~~~~~~~l~~~l~-~-kr~LlVLDdv  285 (673)
                      ..++......+.+.+. . +.-+||+|.+
T Consensus        96 ~~~l~~~l~~l~~~l~~~~~~~liVIDSi  124 (235)
T cd01123          96 SDHQLQLLEELEAILIESSRIKLVIVDSV  124 (235)
T ss_pred             HHHHHHHHHHHHHHHhhcCCeeEEEEeCc
Confidence            1122233344444443 3 5668888887

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK06696 uridine kinase; Validated

Probab=96.65  E-value=0.002  Score=62.98  Aligned_cols=44  Identities=23%  Similarity=0.273  Sum_probs=34.9

Q ss_pred             echhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       173 Gr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.+-+++|.+.+....    .....+|+|.|.+|+||||||+.+.+.
T Consensus         2 ~~~~~~~~la~~~~~~~----~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          2 SRKQLIKELAEHILTLN----LTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             cHHHHHHHHHHHHHHhC----CCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            35667777777776543    245789999999999999999999874

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.62  E-value=0.014  Score=60.54  Aligned_cols=142  Identities=12%  Similarity=0.092  Sum_probs=81.6

Q ss_pred             ccee-chhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc--------------------cCC
Q 005860          170 EIRG-RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE--------------------YFD  228 (673)
Q Consensus       170 ~~vG-r~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~  228 (673)
                      .++| -+.-++.+...+..+.      -...+.++|+.|+||||+|+.+.+..--..                    |.|
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~------l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD   79 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR------LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPD   79 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC------CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCC
Confidence            4566 5666777777775443      245779999999999999977755311000                    112


Q ss_pred             eEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCC
Q 005860          229 KRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGV  304 (673)
Q Consensus       229 ~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~  304 (673)
                      .. ++....                    .....+++.+.+...    ..+.+=++|+|++..-+....+.+...+....
T Consensus        80 ~~-~i~~~~--------------------~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp  138 (329)
T PRK08058         80 VH-LVAPDG--------------------QSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPS  138 (329)
T ss_pred             EE-Eecccc--------------------ccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCC
Confidence            11 111000                    011123322222211    23455578999985555556777888887766


Q ss_pred             CCeEEEEEcCChh-HHHh-ccccceeecCCCCcccc
Q 005860          305 RGSKILVTTRKET-VARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       305 ~gs~iivTtr~~~-v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      .++.+|++|.+.. +... -.-...+++.+++.++.
T Consensus       139 ~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~  174 (329)
T PRK08058        139 GGTTAILLTENKHQILPTILSRCQVVEFRPLPPESL  174 (329)
T ss_pred             CCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHH
Confidence            7787887776533 3322 22366788888877663

>PRK13695 putative NTPase; Provisional

Probab=96.62  E-value=0.00082  Score=62.98  Aligned_cols=22  Identities=41%  Similarity=0.380  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|+|.+|+|||||++.+++.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999998875

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.60  E-value=0.011  Score=57.76  Aligned_cols=125  Identities=18%  Similarity=0.142  Sum_probs=73.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-----cccHHHHHHHHHHHhhCCC------C-CcCcHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-----PFDELRIAKAIIEALEGFV------P-TVGELNS  264 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-----~~~~~~~~~~i~~~l~~~~------~-~~~~~~~  264 (673)
                      -.+++|||..|.|||||++.+..-   ...-.+.+++.-.+     .....+-..++++.++...      + +...-+.
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L---~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGL---EEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcC---cCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            468999999999999999999984   33344455543211     1123344555666655432      1 1122222


Q ss_pred             HHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccC--CCCCeEEEEEcCChhHHHhccc
Q 005860          265 LLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKN--GVRGSKILVTTRKETVARMMES  324 (673)
Q Consensus       265 ~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~--~~~gs~iivTtr~~~v~~~~~~  324 (673)
                      -.-.+.+.|.-++=+||.|..-+. |...-..+...+..  ...|-..+.+|.+-.++..+..
T Consensus       116 QRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~isd  178 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYISD  178 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhcc
Confidence            334567788889999999976321 11111112222221  2346678999999888887644

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.59  E-value=0.012  Score=61.19  Aligned_cols=125  Identities=16%  Similarity=0.078  Sum_probs=73.9

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc-------------------cCCeE
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE-------------------YFDKR  230 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~  230 (673)
                      .++|-+....++..+.....     .....+-++|+.|+||||+|..+.+..--..                   ....+
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~-----~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~   76 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESG-----RLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDF   76 (325)
T ss_pred             CcccchhHHHHHHHHHHhcC-----CCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCce
Confidence            46677778888888876433     1223599999999999999988877411000                   11233


Q ss_pred             EEEEcCCccc---HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCe
Q 005860          231 MWVCVSDPFD---ELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGS  307 (673)
Q Consensus       231 ~wv~vs~~~~---~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs  307 (673)
                      ..+..++...   ..+..+++.+.......                .++.-++++|++..-..+.-+.+...+......+
T Consensus        77 lel~~s~~~~~~i~~~~vr~~~~~~~~~~~----------------~~~~kviiidead~mt~~A~nallk~lEep~~~~  140 (325)
T COG0470          77 LELNPSDLRKIDIIVEQVRELAEFLSESPL----------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNT  140 (325)
T ss_pred             EEecccccCCCcchHHHHHHHHHHhccCCC----------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCe
Confidence            3444443333   12222222222211110                3567789999995544445566666666667778


Q ss_pred             EEEEEcCC
Q 005860          308 KILVTTRK  315 (673)
Q Consensus       308 ~iivTtr~  315 (673)
                      .+|++|.+
T Consensus       141 ~~il~~n~  148 (325)
T COG0470         141 RFILITND  148 (325)
T ss_pred             EEEEEcCC
Confidence            88888874

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.58  E-value=0.01  Score=55.45  Aligned_cols=104  Identities=17%  Similarity=0.079  Sum_probs=58.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE------cCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC------VSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIR  270 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~------vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~  270 (673)
                      -.+++|+|..|+|||||++.+..-.   ....+.+++.      +.+...                  ...-+...-.+.
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~---~p~~G~i~~~g~~i~~~~q~~~------------------LSgGq~qrv~la   83 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQL---IPNGDNDEWDGITPVYKPQYID------------------LSGGELQRVAIA   83 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC---CCCCcEEEECCEEEEEEcccCC------------------CCHHHHHHHHHH
Confidence            3589999999999999999998842   2233333331      111111                  111222334455


Q ss_pred             HHhCCCeEEEEEcCCCCC-CccchhhhhhhccCC-CC-CeEEEEEcCChhHHHh
Q 005860          271 ASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNG-VR-GSKILVTTRKETVARM  321 (673)
Q Consensus       271 ~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~-~~-gs~iivTtr~~~v~~~  321 (673)
                      ..+..++-+++||+--+. |....+.+...+... .. +..||++|.+......
T Consensus        84 ral~~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~~~  137 (177)
T cd03222          84 AALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLDY  137 (177)
T ss_pred             HHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHHHH
Confidence            666667788999986321 222222233333221 12 3568888888765553

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.57  E-value=0.0098  Score=69.68  Aligned_cols=139  Identities=16%  Similarity=0.203  Sum_probs=75.3

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|-+..++.+...+......  ..+.....+.++|+.|+|||+||+.+.+.  .-..-...+-+..+.-.+..    
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~--l~~~~~~~~~~d~s~~~~~~----  582 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASY--FFGSEDAMIRLDMSEYMEKH----  582 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHH--hcCCccceEEEEchhccccc----
Confidence            46899999999998877532110  00123456779999999999999888763  11111223334433321111    


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe-EEEEEcCCCCCCccchhhhhhhccCC-----------CCCeEEEEEcC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKK-FLLILDDMWTDDYSKWEPFHYCLKNG-----------VRGSKILVTTR  314 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr-~LlVLDdvw~~~~~~~~~l~~~l~~~-----------~~gs~iivTtr  314 (673)
                      .+..-++.+ +.....++ ...+.+.++.++ .+|+||++..-+...++.+...+..+           ...+-||+||.
T Consensus       583 ~~~~l~g~~-~gyvg~~~-~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn  660 (821)
T CHL00095        583 TVSKLIGSP-PGYVGYNE-GGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSN  660 (821)
T ss_pred             cHHHhcCCC-CcccCcCc-cchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCC
Confidence            111112221 11100111 112344444444 58889999766666777777766643           13455666766


Q ss_pred             C
Q 005860          315 K  315 (673)
Q Consensus       315 ~  315 (673)
                      .
T Consensus       661 ~  661 (821)
T CHL00095        661 L  661 (821)
T ss_pred             c
Confidence            3

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.54  E-value=0.0078  Score=59.98  Aligned_cols=56  Identities=27%  Similarity=0.286  Sum_probs=39.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      -.+.=|+|.+|+|||.|+.+++-...+..    .=..++|++-...|+++.+. +|++...
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~   97 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFG   97 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTT
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccc
Confidence            45999999999999999966653322221    22458999999889887764 5666543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PHA00729 NTP-binding motif containing protein

Probab=96.52  E-value=0.0084  Score=57.68  Aligned_cols=25  Identities=36%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +...|.|+|.+|+||||||..+.+.
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHH
Confidence            3567899999999999999998874

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.52  E-value=0.02  Score=53.11  Aligned_cols=124  Identities=14%  Similarity=0.091  Sum_probs=64.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE-------EcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV-------CVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLE  267 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv-------~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~  267 (673)
                      -.+++|+|..|.|||||++.+......   ..+.+++       .+.+...  ...+...+.-.   .......-+..+-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~---~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~---~~~~LS~G~~~rv  100 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPW---GSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP---WDDVLSGGEQQRL  100 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC---CCceEEECCCceEEEECCCCccccccHHHHhhcc---CCCCCCHHHHHHH
Confidence            358999999999999999999985322   1222221       1222221  11222332210   1112222233344


Q ss_pred             HHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeec
Q 005860          268 SIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       268 ~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                      .+.+.+-.++=++++|+--+. |......+...+...  +..||++|.+......  ..+++.+
T Consensus       101 ~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~~~--~d~i~~l  160 (166)
T cd03223         101 AFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLWKF--HDRVLDL  160 (166)
T ss_pred             HHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHHhh--CCEEEEE
Confidence            455666667778889976321 222223333333332  4568888888766542  3344444

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.51  E-value=0.01  Score=60.80  Aligned_cols=59  Identities=22%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccc----ccCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVF----EYFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      ..-.++-|+|.+|+|||+|+.+++-.....    ..=..++||+....|+++.+. ++++.++.
T Consensus        94 ~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~  156 (313)
T TIGR02238        94 ESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGV  156 (313)
T ss_pred             cCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCC
Confidence            346799999999999999996654321111    112468999999888888765 45666654

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.50  E-value=0.022  Score=54.75  Aligned_cols=61  Identities=16%  Similarity=0.221  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHhCCCeEEEEEcCCC-CCCccchhhhhhhccC--CCCCeEEEEEcCChhHHHhcc
Q 005860          263 NSLLESIRASLVGKKFLLILDDMW-TDDYSKWEPFHYCLKN--GVRGSKILVTTRKETVARMME  323 (673)
Q Consensus       263 ~~~~~~l~~~l~~kr~LlVLDdvw-~~~~~~~~~l~~~l~~--~~~gs~iivTtr~~~v~~~~~  323 (673)
                      ++-+-.+.+.|-..+-+|+-|+-- +-|...=+.+...+..  ...|..||+.|.+..+|..+.
T Consensus       147 qqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~~d  210 (226)
T COG1136         147 QQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKYAD  210 (226)
T ss_pred             HHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhCC
Confidence            444556777888888899999641 1111222223333332  245788999999999999653

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=96.50  E-value=0.018  Score=63.07  Aligned_cols=141  Identities=18%  Similarity=0.144  Sum_probs=89.5

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc---cc---ccCCeEEEEEcCCccc
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD---VF---EYFDKRMWVCVSDPFD  240 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~---~~---~~F~~~~wv~vs~~~~  240 (673)
                      .+..+-+|+.+..+|..++..--+++  ..-+.+.|.|.+|.|||..+..|.+...   .+   ..|+ .+.|..-.-..
T Consensus       394 vp~sLpcRe~E~~~I~~f~~~~i~~~--~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~  470 (767)
T KOG1514|consen  394 VPESLPCRENEFSEIEDFLRSFISDQ--GLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLAS  470 (767)
T ss_pred             ccccccchhHHHHHHHHHHHhhcCCC--CCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecC
Confidence            34567799999999988875433211  2345999999999999999999988422   11   2332 23344344456


Q ss_pred             HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC-----CCeEEEEEcCCCCCCccchhhhhhhccC-CCCCeEEEEEc
Q 005860          241 ELRIAKAIIEALEGFVPTVGELNSLLESIRASLV-----GKKFLLILDDMWTDDYSKWEPFHYCLKN-GVRGSKILVTT  313 (673)
Q Consensus       241 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-----~kr~LlVLDdvw~~~~~~~~~l~~~l~~-~~~gs~iivTt  313 (673)
                      +.++...|++++.+....   +....+.+..++.     .+.++|++|++..--...-+-+...+.| ..++||++|.+
T Consensus       471 ~~~~Y~~I~~~lsg~~~~---~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~  546 (767)
T KOG1514|consen  471 PREIYEKIWEALSGERVT---WDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIA  546 (767)
T ss_pred             HHHHHHHHHHhcccCccc---HHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEE
Confidence            889999999999876432   2333444555543     4678888888711000112335555666 46788887765

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.48  E-value=0.022  Score=58.59  Aligned_cols=162  Identities=13%  Similarity=0.133  Sum_probs=87.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc------------c-cccCCeEEEEEc
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD------------V-FEYFDKRMWVCV  235 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~------------~-~~~F~~~~wv~v  235 (673)
                      ++++|-+..++.+...+..+.      -....-++|+.|+||+++|..+.+..-            + .....-..|+.-
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r------l~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p   77 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR------IAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEP   77 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC------CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEec
Confidence            468999999999999886554      246899999999999999866654310            0 011112233321


Q ss_pred             CCcccHHHHHHHHHHHhhC--CCCCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeE
Q 005860          236 SDPFDELRIAKAIIEALEG--FVPTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSK  308 (673)
Q Consensus       236 s~~~~~~~~~~~i~~~l~~--~~~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~  308 (673)
                      ....+-..+-.+-++..+.  ........++.. .+.+.+     .+++-++|+|++..-+....+.+...+....+ +.
T Consensus        78 ~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir-~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~-~~  155 (314)
T PRK07399         78 TYQHQGKLITASEAEEAGLKRKAPPQIRLEQIR-EIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPGN-GT  155 (314)
T ss_pred             cccccccccchhhhhhccccccccccCcHHHHH-HHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCCC-Ce
Confidence            0000000000111111110  111112223322 233333     35667899999855555667777777765544 45


Q ss_pred             EEEEcCC-hhHHHhc-cccceeecCCCCcccc
Q 005860          309 ILVTTRK-ETVARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       309 iivTtr~-~~v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      +|++|.+ ..+...+ .-...+++.++++++.
T Consensus       156 fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~  187 (314)
T PRK07399        156 LILIAPSPESLLPTIVSRCQIIPFYRLSDEQL  187 (314)
T ss_pred             EEEEECChHhCcHHHHhhceEEecCCCCHHHH
Confidence            5555543 3333332 3367788888887764

>TIGR00763 lon ATP-dependent protease La

Probab=96.46  E-value=0.06  Score=62.80  Aligned_cols=51  Identities=22%  Similarity=0.250  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++++.+++....... .....++.++|++|+|||++|+.+.+.
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~-~~~~~~lll~GppG~GKT~lAk~iA~~  370 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRG-KMKGPILCLVGPPGVGKTSLGKSIAKA  370 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhc-CCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999988764221000 122357999999999999999999985

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.45  E-value=0.0054  Score=61.85  Aligned_cols=131  Identities=25%  Similarity=0.256  Sum_probs=70.0

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC-ccccccCCeEEE----EEcCCcc-----cH
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND-SDVFEYFDKRMW----VCVSDPF-----DE  241 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~-~~~~~~F~~~~w----v~vs~~~-----~~  241 (673)
                      -+|..+..--+++|+.++       +..|.+.|.+|.|||.||-+..=. .-.+..|..++-    +.+.++.     ..
T Consensus       227 ~prn~eQ~~ALdlLld~d-------I~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~e  299 (436)
T COG1875         227 RPRNAEQRVALDLLLDDD-------IDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTE  299 (436)
T ss_pred             CcccHHHHHHHHHhcCCC-------CCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCch
Confidence            346666666677777654       899999999999999998433221 122344443332    1233221     11


Q ss_pred             ----HHHHHHHHHHh---hCCCCCcCcHHHHHHHH---------HHHhCCC---eEEEEEcCCCCCCccchhhhhhhccC
Q 005860          242 ----LRIAKAIIEAL---EGFVPTVGELNSLLESI---------RASLVGK---KFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       242 ----~~~~~~i~~~l---~~~~~~~~~~~~~~~~l---------~~~l~~k---r~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                          .--++.|..-+   ...... . ...+...+         ..+.+++   +-+|++|...+-...   .++..+..
T Consensus       300 EeKm~PWmq~i~DnLE~L~~~~~~-~-~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTph---eikTiltR  374 (436)
T COG1875         300 EEKMGPWMQAIFDNLEVLFSPNEP-G-DRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPH---ELKTILTR  374 (436)
T ss_pred             hhhccchHHHHHhHHHHHhccccc-c-hHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHH---HHHHHHHh
Confidence                11223333322   222111 1 11111111         1123443   459999999654433   34555667


Q ss_pred             CCCCeEEEEEcC
Q 005860          303 GVRGSKILVTTR  314 (673)
Q Consensus       303 ~~~gs~iivTtr  314 (673)
                      .+.||||+.|--
T Consensus       375 ~G~GsKIVl~gd  386 (436)
T COG1875         375 AGEGSKIVLTGD  386 (436)
T ss_pred             ccCCCEEEEcCC
Confidence            789999999864

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.45  E-value=0.0036  Score=59.90  Aligned_cols=112  Identities=13%  Similarity=0.165  Sum_probs=59.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ++|.|+|+.|+||||++..+...  +.......+++- .++..  ...... ..+-....-..+.......++..+....
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t~-e~~~E--~~~~~~-~~~i~q~~vg~~~~~~~~~i~~aLr~~p   75 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILTI-EDPIE--FVHESK-RSLINQREVGLDTLSFENALKAALRQDP   75 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEEE-cCCcc--ccccCc-cceeeecccCCCccCHHHHHHHHhcCCc
Confidence            47899999999999999887774  333334444432 22111  000000 0000000000111234556777777777


Q ss_pred             EEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHH
Q 005860          278 FLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR  320 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~  320 (673)
                      =.|++|++.+  .+.......   ....|..++.|+...++..
T Consensus        76 d~ii~gEird--~e~~~~~l~---~a~~G~~v~~t~Ha~~~~~  113 (198)
T cd01131          76 DVILVGEMRD--LETIRLALT---AAETGHLVMSTLHTNSAAK  113 (198)
T ss_pred             CEEEEcCCCC--HHHHHHHHH---HHHcCCEEEEEecCCcHHH
Confidence            7999999943  333333222   2234666888888766544

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.45  E-value=0.0097  Score=60.31  Aligned_cols=88  Identities=18%  Similarity=0.124  Sum_probs=45.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ..++|+|+|++|+||||++..+......+..-..+..|+.... ....+.+....+.++.......+..++...+... .
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~-~  271 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRL-R  271 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHc-c
Confidence            4579999999999999999887764222211124555654321 1122333333333333322223334444444433 3


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      + .=+|++|..
T Consensus       272 ~-~d~vliDt~  281 (282)
T TIGR03499       272 D-KDLILIDTA  281 (282)
T ss_pred             C-CCEEEEeCC
Confidence            3 346777753

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.44  E-value=0.015  Score=54.30  Aligned_cols=122  Identities=16%  Similarity=0.204  Sum_probs=65.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCc-cc--cc---cCC--eEEEEEcCCcccHHHHHHHHHHHhhCCCC----CcCcH--
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDS-DV--FE---YFD--KRMWVCVSDPFDELRIAKAIIEALEGFVP----TVGEL--  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~-~~--~~---~F~--~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----~~~~~--  262 (673)
                      -.+++|+|+.|+|||||.+.+..+. .+  ..   .|.  .+.|+  .+        .+.++.++....    ....+  
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~--~q--------~~~l~~~~L~~~~~~~~~~~LSg   90 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFI--DQ--------LQFLIDVGLGYLTLGQKLSTLSG   90 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEE--hH--------HHHHHHcCCCccccCCCcCcCCH
Confidence            4689999999999999999885321 11  11   110  12232  21        345566654311    11111  


Q ss_pred             -HHHHHHHHHHhCCC--eEEEEEcCCCCC-CccchhhhhhhccC-CCCCeEEEEEcCChhHHHhccccceeec
Q 005860          263 -NSLLESIRASLVGK--KFLLILDDMWTD-DYSKWEPFHYCLKN-GVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       263 -~~~~~~l~~~l~~k--r~LlVLDdvw~~-~~~~~~~l~~~l~~-~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                       +...-.+...+-.+  +=++++|+.-.. +....+.+...+.. ...|..||++|.+.+....  ...++.+
T Consensus        91 Gq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~~--~d~i~~l  161 (176)
T cd03238          91 GELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLSS--ADWIIDF  161 (176)
T ss_pred             HHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh--CCEEEEE
Confidence             22233344555556  668888976321 22223334343332 1246779999998876643  4455554

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.43  E-value=0.0074  Score=65.58  Aligned_cols=52  Identities=19%  Similarity=0.221  Sum_probs=37.9

Q ss_pred             CcceechhhHHHHHHHhccCCcc------cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE------EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|.+..++++.+.+..+-..      .+-...+-+.++|++|+|||++|+++++.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            46788999999888876421100      00123456899999999999999999996

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.41  E-value=0.0074  Score=55.80  Aligned_cols=117  Identities=15%  Similarity=0.118  Sum_probs=63.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC--cccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD--PFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      -.+++|+|..|.|||||.+.+....   ....+.+++.-..  ..+..+..+   +.++- ..+...-+...-.+...+-
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~---~~~~G~v~~~g~~~~~~~~~~~~~---~~i~~-~~qLS~G~~qrl~laral~   98 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLY---KPDSGEILVDGKEVSFASPRDARR---AGIAM-VYQLSVGERQMVEIARALA   98 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEECCcCCHHHHHh---cCeEE-EEecCHHHHHHHHHHHHHh
Confidence            3589999999999999999999842   3445555553111  111111110   01110 0011222233344556666


Q ss_pred             CCeEEEEEcCCCCC-CccchhhhhhhccCC-CCCeEEEEEcCChhHHH
Q 005860          275 GKKFLLILDDMWTD-DYSKWEPFHYCLKNG-VRGSKILVTTRKETVAR  320 (673)
Q Consensus       275 ~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~-~~gs~iivTtr~~~v~~  320 (673)
                      .++-++++|+.-+. |......+...+... ..|..||++|.+.....
T Consensus        99 ~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~  146 (163)
T cd03216          99 RNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVF  146 (163)
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            67788999987331 222233344444321 34667899998876444

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.38  E-value=0.013  Score=61.61  Aligned_cols=24  Identities=29%  Similarity=0.288  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++.++|++|+||||++..+...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999887753

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.35  E-value=0.017  Score=57.04  Aligned_cols=86  Identities=21%  Similarity=0.164  Sum_probs=53.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCC------------------
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFV------------------  256 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------------------  256 (673)
                      +.-.++.|+|.+|+||||||.++.... .+ .=..++|++..+.  +.++.+++ ++++...                  
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~-~~-~g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~   97 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGA-LK-QGKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEG   97 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHH-Hh-CCCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEeccccc
Confidence            446799999999999999998874321 22 2356888988664  44555543 2232110                  


Q ss_pred             --CCcCcHHHHHHHHHHHhCC-CeEEEEEcCC
Q 005860          257 --PTVGELNSLLESIRASLVG-KKFLLILDDM  285 (673)
Q Consensus       257 --~~~~~~~~~~~~l~~~l~~-kr~LlVLDdv  285 (673)
                        ....+.+.+...+.+.+.. +.-++|+|.+
T Consensus        98 ~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~  129 (234)
T PRK06067         98 FEWNSTLANKLLELIIEFIKSKREDVIIIDSL  129 (234)
T ss_pred             cccCcchHHHHHHHHHHHHHhcCCCEEEEecH
Confidence              0112335566666666653 5558999987

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.34  E-value=0.062  Score=55.07  Aligned_cols=64  Identities=9%  Similarity=0.079  Sum_probs=44.8

Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHH-hccccceeecCCCCcccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVAR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      +++=++|+|++..-+....+.+...+.....++.+|++|.+. .+.. ..+-...+.+.+++.++.
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~  172 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQA  172 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHH
Confidence            445588899986666667888888888777778777776654 3433 333366788888887765

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.34  E-value=0.01  Score=60.72  Aligned_cols=84  Identities=21%  Similarity=0.202  Sum_probs=54.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCC-----CCCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGF-----VPTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~-----~~~~~~~~~~~~~l  269 (673)
                      +.-+++-|+|++|+||||||.+++-.  ....-..++||+....+++.     .++.++..     ..+..+.++....+
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~  125 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIA  125 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHH
Confidence            44679999999999999999776653  33344568899887766653     23333332     11223445555555


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      ...++ +..-+||+|-|
T Consensus       126 ~~li~s~~~~lIVIDSv  142 (325)
T cd00983         126 DSLVRSGAVDLIVVDSV  142 (325)
T ss_pred             HHHHhccCCCEEEEcch
Confidence            55543 45669999987

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.33  E-value=0.013  Score=67.12  Aligned_cols=122  Identities=11%  Similarity=0.130  Sum_probs=66.8

Q ss_pred             cceechhhHHHHHHHhccCCc--ccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESS--EEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .++|-++.++.+...+.....  .........+.++|+.|+|||++|+.+....  .   ...+.++.++-....    .
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l--~---~~~i~id~se~~~~~----~  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL--G---IELLRFDMSEYMERH----T  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh--C---CCcEEeechhhcccc----c
Confidence            578999998888888753210  0001235678999999999999999988742  1   122334433321111    1


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhC-CCeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLV-GKKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~-~kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                      +.+-++.+ +.....+ ....+.+.++ ....+|+||++..-+...++.+...+..
T Consensus       530 ~~~LiG~~-~gyvg~~-~~g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~ld~  583 (758)
T PRK11034        530 VSRLIGAP-PGYVGFD-QGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDN  583 (758)
T ss_pred             HHHHcCCC-CCccccc-ccchHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHHhc
Confidence            22222222 1110000 0112333333 3346999999966666667777666553

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.31  E-value=0.011  Score=56.33  Aligned_cols=56  Identities=21%  Similarity=0.142  Sum_probs=36.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcC-CcccHHHHHHHHHHHhhCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS-DPFDELRIAKAIIEALEGF  255 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~~~~~i~~~l~~~  255 (673)
                      +||.+||+.|+||||.+-++.....  ..-..+..++.. ......+-++...+.++.+
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~--~~~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLK--LKGKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHH--HTT--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHh--hccccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            6999999999999999866655422  223345666643 2234556667777777654

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.31  E-value=0.015  Score=54.33  Aligned_cols=125  Identities=15%  Similarity=0.175  Sum_probs=63.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC--cccHHHHHHHHHHHhhC--CCCC----------cCcH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD--PFDELRIAKAIIEALEG--FVPT----------VGEL  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~l~~--~~~~----------~~~~  262 (673)
                      -.+++|+|..|.|||||.+.+....   ....+.+++.-..  .......    ...++-  +...          ...-
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~~~~~----~~~i~~~~q~~~~~~~tv~~~lLS~G  100 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLL---RPTSGRVRLDGADISQWDPNEL----GDHVGYLPQDDELFSGSIAENILSGG  100 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcc---CCCCCeEEECCEEcccCCHHHH----HhheEEECCCCccccCcHHHHCcCHH
Confidence            3589999999999999999999842   2233444432100  0111111    111111  1100          0111


Q ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccC-CCCCeEEEEEcCChhHHHhccccceeec
Q 005860          263 NSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKN-GVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       263 ~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~-~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                      +...-.+...+-.++=+++||+.... |......+...+.. ...|..||++|.+......  ..+++.+
T Consensus       101 ~~qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~--~d~v~~l  168 (173)
T cd03246         101 QRQRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPETLAS--ADRILVL  168 (173)
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh--CCEEEEE
Confidence            22233455556666778899987431 22222233333322 1246779999998776643  3444444

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PRK09354 recA recombinase A; Provisional

Probab=96.29  E-value=0.016  Score=59.73  Aligned_cols=84  Identities=21%  Similarity=0.191  Sum_probs=55.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCC-----CCCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGF-----VPTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~-----~~~~~~~~~~~~~l  269 (673)
                      +.-+++-|+|++|+||||||.++...  ....-..++||+.-..+++.     .+++++..     ..+....++....+
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~  130 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIA  130 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            44689999999999999999776653  33344678899888777753     34444332     11223345555555


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      ...++ +..-+||+|-|
T Consensus       131 ~~li~s~~~~lIVIDSv  147 (349)
T PRK09354        131 DTLVRSGAVDLIVVDSV  147 (349)
T ss_pred             HHHhhcCCCCEEEEeCh
Confidence            55553 45669999988

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.29  E-value=0.019  Score=52.22  Aligned_cols=117  Identities=16%  Similarity=0.092  Sum_probs=59.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc---CCcccHHHHHHHHHHHh-----hCC----CCC-cCc---
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV---SDPFDELRIAKAIIEAL-----EGF----VPT-VGE---  261 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~~~~~~~~~~i~~~l-----~~~----~~~-~~~---  261 (673)
                      ..|-|++..|.||||+|..+.-.. ....+ .+.++-+   ........++..+ ..+     +..    ..+ ..+   
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra-~~~g~-~v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRA-LGHGY-RVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-HHCCC-eEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            478888999999999995544421 12222 3333322   2223333333332 000     000    000 011   


Q ss_pred             HHHHHHHHHHHhCC-CeEEEEEcCCCCC---CccchhhhhhhccCCCCCeEEEEEcCChh
Q 005860          262 LNSLLESIRASLVG-KKFLLILDDMWTD---DYSKWEPFHYCLKNGVRGSKILVTTRKET  317 (673)
Q Consensus       262 ~~~~~~~l~~~l~~-kr~LlVLDdvw~~---~~~~~~~l~~~l~~~~~gs~iivTtr~~~  317 (673)
                      ..+.....++.+.. .-=|||||++-..   ..-..+.+...+.....+.-||+|.|+..
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            11223334445544 4459999998221   12234566666666667778999999843

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.26  E-value=0.016  Score=59.91  Aligned_cols=59  Identities=22%  Similarity=0.120  Sum_probs=41.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccc---c-cCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVF---E-YFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      ..-.++-|+|.+|+|||+|+.+++-.....   . .-..++||+....|+++.+.+ +++.++.
T Consensus       124 ~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~  186 (344)
T PLN03187        124 ETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGM  186 (344)
T ss_pred             CCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            345789999999999999997665321121   1 124689999999999887654 5666554

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.25  E-value=0.058  Score=55.32  Aligned_cols=64  Identities=11%  Similarity=0.117  Sum_probs=41.9

Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhHHHh-ccccceeecCCCCcccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      +++-++|+|++..-+...-+.+...+.....++.+|++|.+ ..+... .+-...+.+.+++.++.
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~  177 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEA  177 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHH
Confidence            45668999999555555566777777766667777777765 333332 23356677777777664

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.24  E-value=0.015  Score=63.78  Aligned_cols=90  Identities=18%  Similarity=0.180  Sum_probs=60.0

Q ss_pred             cCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          194 INDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       194 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      .+.-+|.-++|++|+||||||..|..+    ..| .++=|.+|+.-++..+-..|...+....-...             
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkq----aGY-sVvEINASDeRt~~~v~~kI~~avq~~s~l~a-------------  384 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQ----AGY-SVVEINASDERTAPMVKEKIENAVQNHSVLDA-------------  384 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHh----cCc-eEEEecccccccHHHHHHHHHHHHhhcccccc-------------
Confidence            356689999999999999999999985    233 46678888888877777766666543321100             


Q ss_pred             CCCeEEEEEcCCCCCCccchhhhhhhcc
Q 005860          274 VGKKFLLILDDMWTDDYSKWEPFHYCLK  301 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~~~~~~l~~~l~  301 (673)
                      .+++.-+|+|.+.-......+.+...+.
T Consensus       385 dsrP~CLViDEIDGa~~~~Vdvilslv~  412 (877)
T KOG1969|consen  385 DSRPVCLVIDEIDGAPRAAVDVILSLVK  412 (877)
T ss_pred             CCCcceEEEecccCCcHHHHHHHHHHHH
Confidence            1567788999883333223444544443

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.23  E-value=0.021  Score=58.67  Aligned_cols=58  Identities=22%  Similarity=0.157  Sum_probs=39.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ..-.++.|+|.+|+|||||+..++-......    .-..++|++....+++..+ .++.+.++
T Consensus        94 ~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~  155 (316)
T TIGR02239        94 ETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYG  155 (316)
T ss_pred             CCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcC
Confidence            4468999999999999999987764321211    1235799998887777763 44555543

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.22  E-value=0.019  Score=62.78  Aligned_cols=71  Identities=23%  Similarity=0.188  Sum_probs=47.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ..-|.|.|..|+|||+||+++++... +.+.-.+.+|+++.-..  .+.+++                 .+...+.+.+.
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk-----------------~l~~vfse~~~  492 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQK-----------------FLNNVFSEALW  492 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHH-----------------HHHHHHHHHHh
Confidence            45689999999999999999999743 33444455665554211  122211                 12334555667


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      ..+-+|||||+
T Consensus       493 ~~PSiIvLDdl  503 (952)
T KOG0735|consen  493 YAPSIIVLDDL  503 (952)
T ss_pred             hCCcEEEEcch
Confidence            78999999998

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.21  E-value=0.014  Score=55.61  Aligned_cols=81  Identities=22%  Similarity=0.192  Sum_probs=45.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCC---eEEEEEcCCcccHHHHHHHHHHHh----hCCCCCcCcHHHHHHHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFD---KRMWVCVSDPFDELRIAKAIIEAL----EGFVPTVGELNSLLESIRA  271 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~vs~~~~~~~~~~~i~~~l----~~~~~~~~~~~~~~~~l~~  271 (673)
                      ||+|.|.+|+||||+|+.+...... ....   ....+....-........ .-...    ....+...+.+.+.+.+..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~-~~~~~~~~~~~~~~d~~~~~~~~~~-~~~~~~~~~~~~~p~a~d~~~l~~~l~~   78 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK-RGIPAMEMDIILSLDDFYDDYHLRD-RKGRGENRYNFDHPDAFDFDLLKEDLKA   78 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT-CTTTCCCSEEEEEGGGGBHHHHHHH-HHHHCTTTSSTTSGGGBSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc-cCcCccceeEEEeecccccccchhh-HhhccccccCCCCccccCHHHHHHHHHH
Confidence            7999999999999999998874211 1222   233443333222222211 11111    1112345667777888877


Q ss_pred             HhCCCeEEEE
Q 005860          272 SLVGKKFLLI  281 (673)
Q Consensus       272 ~l~~kr~LlV  281 (673)
                      ..+++.+-+-
T Consensus        79 L~~g~~i~~p   88 (194)
T PF00485_consen   79 LKNGGSIEIP   88 (194)
T ss_dssp             HHTTSCEEEE
T ss_pred             HhCCCccccc
Confidence            7777765443

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.21  E-value=0.041  Score=57.26  Aligned_cols=113  Identities=12%  Similarity=0.072  Sum_probs=56.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      ..++|+|+|++|+||||++..+...  ....=..+.+++. +.+.  ..+-++...+.++.+-....+.+.+...+...-
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~--L~~~GkkVglI~a-Dt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk  316 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQ--FHGKKKTVGFITT-DHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFK  316 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHH--HHHcCCcEEEEec-CCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHH
Confidence            4589999999999999999888763  2222123444443 2333  223333333444433222234445554444432


Q ss_pred             CC-CeEEEEEcCCCCCC--ccchhhhhhhccCCCCCeEEEE
Q 005860          274 VG-KKFLLILDDMWTDD--YSKWEPFHYCLKNGVRGSKILV  311 (673)
Q Consensus       274 ~~-kr~LlVLDdvw~~~--~~~~~~l~~~l~~~~~gs~iiv  311 (673)
                      .. +.=+|++|-.-...  ......+...+....+...++|
T Consensus       317 ~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLV  357 (436)
T PRK11889        317 EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLT  357 (436)
T ss_pred             hccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEE
Confidence            21 23477788663321  2234444444433333333444

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.21  E-value=0.042  Score=57.88  Aligned_cols=89  Identities=16%  Similarity=0.134  Sum_probs=51.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCcccc--ccCCeEEEEEcCCcccH--HHHHHHHHHHhhCCCCCcCcHHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVF--EYFDKRMWVCVSDPFDE--LRIAKAIIEALEGFVPTVGELNSLLESIRA  271 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~  271 (673)
                      ..++|.++|+.|+||||.+..+.......  .+-..+..+++. ++..  ...++...+.++.+-......+++...+.+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~D-t~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~  251 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID-NYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ  251 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEecc-CccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH
Confidence            35799999999999999997776542221  112245555543 3333  233555555555543333344555555544


Q ss_pred             HhCCCeEEEEEcCCCC
Q 005860          272 SLVGKKFLLILDDMWT  287 (673)
Q Consensus       272 ~l~~kr~LlVLDdvw~  287 (673)
                      .  .+.-+|++|..-.
T Consensus       252 ~--~~~DlVLIDTaGr  265 (388)
T PRK12723        252 S--KDFDLVLVDTIGK  265 (388)
T ss_pred             h--CCCCEEEEcCCCC
Confidence            3  3456888998743

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.20  E-value=0.031  Score=57.81  Aligned_cols=58  Identities=24%  Similarity=0.263  Sum_probs=40.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccccc----CCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY----FDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ..-.++-|+|.+|+|||+++.+++-.......    =..++||+....+++..+.+ +++.++
T Consensus       100 ~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g  161 (317)
T PRK04301        100 ETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALG  161 (317)
T ss_pred             cCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcC
Confidence            34679999999999999999766543211111    14789999988888876554 444443

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.20  E-value=0.015  Score=56.59  Aligned_cols=22  Identities=36%  Similarity=0.392  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|||.|.+|+||||+|+.+...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHH
Confidence            5899999999999999998874

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.17  E-value=0.013  Score=62.83  Aligned_cols=97  Identities=21%  Similarity=0.290  Sum_probs=62.7

Q ss_pred             CcceechhhHHHHHHHhccCCccc-----ccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEE-----IINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      .++=|.+..+.++.+++..-..+.     +-...+=|.++|++|.|||.||+++.++.  .-.|     +.++.+     
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel--~vPf-----~~isAp-----  257 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL--GVPF-----LSISAP-----  257 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc--CCce-----Eeecch-----
Confidence            467789999998888875432111     12345678899999999999999999963  3333     333322     


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                         +|+..+.+     .+.+.+.+.+.+.-..-++++++|++
T Consensus       258 ---eivSGvSG-----ESEkkiRelF~~A~~~aPcivFiDeI  291 (802)
T KOG0733|consen  258 ---EIVSGVSG-----ESEKKIRELFDQAKSNAPCIVFIDEI  291 (802)
T ss_pred             ---hhhcccCc-----ccHHHHHHHHHHHhccCCeEEEeecc
Confidence               12222222     22234445555556778999999998

>PHA02244 ATPase-like protein

Probab=96.17  E-value=0.031  Score=57.75  Aligned_cols=21  Identities=24%  Similarity=0.355  Sum_probs=19.3

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|+.|+|||+||+++...
T Consensus       122 VLL~GppGtGKTtLA~aLA~~  142 (383)
T PHA02244        122 VFLKGGAGSGKNHIAEQIAEA  142 (383)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999884

>CHL00176 ftsH cell division protein; Validated

Probab=96.16  E-value=0.016  Score=65.29  Aligned_cols=97  Identities=16%  Similarity=0.210  Sum_probs=54.6

Q ss_pred             CcceechhhHHHHHHHh---ccCCc--ccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKL---LCESS--EEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L---~~~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      .++.|.++.++++.+.+   .....  .-+....+-|.++|++|+|||+||+++.+..  ...     |+.++..    +
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~--~~p-----~i~is~s----~  251 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA--EVP-----FFSISGS----E  251 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh--CCC-----eeeccHH----H
Confidence            46889887766665543   22210  0001224568999999999999999998852  112     2333221    1


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                      +.    ....+     .....+...+.......+++|+|||+
T Consensus       252 f~----~~~~g-----~~~~~vr~lF~~A~~~~P~ILfIDEI  284 (638)
T CHL00176        252 FV----EMFVG-----VGAARVRDLFKKAKENSPCIVFIDEI  284 (638)
T ss_pred             HH----HHhhh-----hhHHHHHHHHHHHhcCCCcEEEEecc
Confidence            11    00000     01122334455555678899999999

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=96.15  E-value=0.0037  Score=60.96  Aligned_cols=50  Identities=26%  Similarity=0.400  Sum_probs=40.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|.+.-++.+.-++......  +..+--|.++|++|.||||||.-+.+.
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r--~e~lDHvLl~GPPGlGKTTLA~IIA~E   75 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKR--GEALDHVLLFGPPGLGKTTLAHIIANE   75 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhc--CCCcCeEEeeCCCCCcHHHHHHHHHHH
Confidence            58999999998888777543321  245778999999999999999999996

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.13  E-value=0.022  Score=52.19  Aligned_cols=40  Identities=28%  Similarity=0.328  Sum_probs=29.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD  240 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  240 (673)
                      ++.|+|.+|+||||+++.+...  ....-..++|+.......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECCcchH
Confidence            4789999999999999988775  222335677887765543

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.12  E-value=0.016  Score=59.18  Aligned_cols=84  Identities=20%  Similarity=0.188  Sum_probs=54.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCC-----CCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFV-----PTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~-----~~~~~~~~~~~~l  269 (673)
                      +.-+++-|+|++|+||||||.++...  ....-..++||+....++..     .+++++...     .+....++....+
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~  125 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIA  125 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            45689999999999999999776654  22334567899877666653     344443321     1223445555555


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      ...++ +..-+||+|.|
T Consensus       126 ~~li~~~~~~lIVIDSv  142 (321)
T TIGR02012       126 ETLVRSGAVDIIVVDSV  142 (321)
T ss_pred             HHHhhccCCcEEEEcch
Confidence            55553 45679999987

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=96.12  E-value=0.014  Score=61.95  Aligned_cols=52  Identities=25%  Similarity=0.287  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccCCc------ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS------EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~------~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|.+..+++|.+.+...-.      .-+-...+-|.++|++|+|||+||+++.+.
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            4688999988888876632110      001134567889999999999999999985

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.12  E-value=0.0018  Score=62.35  Aligned_cols=85  Identities=25%  Similarity=0.232  Sum_probs=50.8

Q ss_pred             cccccccccceecCC--C-CcccchhhhcCCCccEEEeccCCCCcc---ccccccccccCCeeecccccccccc----cc
Q 005860          569 IEKLIHLRYLRLVGL--G-TEELPETCCELLNLQVLEIEQCTSLKR---LPLGIGKLVNLRHLTYDDSCLEFIP----KG  638 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~--~-i~~LP~~i~~L~~L~~L~l~~c~~l~~---lP~~i~~L~~Lr~L~l~~~~l~~lP----~~  638 (673)
                      +..|++|++|.++.|  . ...++....++++|++|+++++. +..   ++ ....+.+|..|++..|....+-    .-
T Consensus        61 ~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nk-i~~lstl~-pl~~l~nL~~Ldl~n~~~~~l~dyre~v  138 (260)
T KOG2739|consen   61 FPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNK-IKDLSTLR-PLKELENLKSLDLFNCSVTNLDDYREKV  138 (260)
T ss_pred             CCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCc-cccccccc-hhhhhcchhhhhcccCCccccccHHHHH
Confidence            344667777777777  3 44566556666777777777754 332   22 2345566666666555443321    11


Q ss_pred             CCCCCCCCcCCeeEEcc
Q 005860          639 IQRLTNLRTLSEFVVVR  655 (673)
Q Consensus       639 i~~L~~L~~L~~~~~~~  655 (673)
                      +.-|++|..|+++.+..
T Consensus       139 f~ll~~L~~LD~~dv~~  155 (260)
T KOG2739|consen  139 FLLLPSLKYLDGCDVDG  155 (260)
T ss_pred             HHHhhhhccccccccCC
Confidence            34467888888887764

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.11  E-value=0.0051  Score=66.62  Aligned_cols=50  Identities=24%  Similarity=0.220  Sum_probs=39.5

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++|.++.+++|++.|......- ...-+++.++|++|+||||||+.+.+-
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl-~~~~~IL~LvGPpG~GKSsLa~~la~~  126 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGL-EEKKQILYLLGPVGGGKSSLAERLKSL  126 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhc-CCCCceEEEecCCCCCchHHHHHHHHH
Confidence            68999999999999993221100 134579999999999999999999883

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.09  E-value=0.082  Score=51.15  Aligned_cols=97  Identities=22%  Similarity=0.302  Sum_probs=59.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc-CCcccHHHHHHHHHHHhhCCCCCcCcHH----HHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV-SDPFDELRIAKAIIEALEGFVPTVGELN----SLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v-s~~~~~~~~~~~i~~~l~~~~~~~~~~~----~~~~~l~  270 (673)
                      +-+++.++|.-|.|||++.+++.....    =+.++-|.+ ....+...+...|...+..+  ...+..    .....+.
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~~----~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~--p~~~~~~~~e~~~~~L~  123 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASLN----EDQVAVVVIDKPTLSDATLLEAIVADLESQ--PKVNVNAVLEQIDRELA  123 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhcC----CCceEEEEecCcchhHHHHHHHHHHHhccC--ccchhHHHHHHHHHHHH
Confidence            357999999999999999995444211    122222333 33456677888888888773  223333    3333343


Q ss_pred             HHh-CCCe-EEEEEcCCCCCCccchhhhhh
Q 005860          271 ASL-VGKK-FLLILDDMWTDDYSKWEPFHY  298 (673)
Q Consensus       271 ~~l-~~kr-~LlVLDdvw~~~~~~~~~l~~  298 (673)
                      +.. +++| ..+++|+.........+.++-
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrl  153 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRL  153 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHH
Confidence            333 5677 899999986655555555443

>PRK07667 uridine kinase; Provisional

Probab=96.09  E-value=0.0066  Score=57.85  Aligned_cols=38  Identities=21%  Similarity=0.226  Sum_probs=29.3

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++.+.+....     +...+|+|.|.+|+||||+|+.+...
T Consensus         3 ~~~~~~~~~~~~-----~~~~iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667          3 TNELINIMKKHK-----ENRFILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             HHHHHHHHHhcC-----CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            455666664444     34589999999999999999998874

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.08  E-value=0.073  Score=50.22  Aligned_cols=124  Identities=17%  Similarity=0.166  Sum_probs=71.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc-------------------CCcc------------------
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV-------------------SDPF------------------  239 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v-------------------s~~~------------------  239 (673)
                      -.|+.|+|++|+|||||.+.+..-+.+   =.+.+||.-                   -+.|                  
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~LE~~---~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~~  104 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGLEEP---DSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVK  104 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCcCC---CCceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhHH
Confidence            459999999999999999999874332   234555531                   0111                  


Q ss_pred             -------cHHHHHHHHHHHhhCCC-----C-CcCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccC-CC
Q 005860          240 -------DELRIAKAIIEALEGFV-----P-TVGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKN-GV  304 (673)
Q Consensus       240 -------~~~~~~~~i~~~l~~~~-----~-~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~-~~  304 (673)
                             .+++...++++.++..+     + +...-++-+-.|.+.|.-++-++.+|..-+. |++....+...... ..
T Consensus       105 v~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~  184 (240)
T COG1126         105 VKKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAE  184 (240)
T ss_pred             HcCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHH
Confidence                   12233344444444331     1 1222344455677888888889999998432 22222222222222 34


Q ss_pred             CCeEEEEEcCChhHHHhcc
Q 005860          305 RGSKILVTTRKETVARMME  323 (673)
Q Consensus       305 ~gs~iivTtr~~~v~~~~~  323 (673)
                      .|-..|+.|..-..|..+.
T Consensus       185 eGmTMivVTHEM~FAr~Va  203 (240)
T COG1126         185 EGMTMIIVTHEMGFAREVA  203 (240)
T ss_pred             cCCeEEEEechhHHHHHhh
Confidence            5777888888877777643

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.08  E-value=0.033  Score=52.02  Aligned_cols=119  Identities=21%  Similarity=0.153  Sum_probs=62.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC--CCCC------------cCcH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG--FVPT------------VGEL  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~--~~~~------------~~~~  262 (673)
                      -.+++|+|..|.|||||++.+....   ....+.+++.-....+..   ..+...++-  +...            ...-
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~---~~~~~~i~~~~q~~~~~~~~tv~~~~~LS~G   99 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL---KPDSGEIKVLGKDIKKEP---EEVKRRIGYLPEEPSLYENLTVRENLKLSGG   99 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEEcccch---HhhhccEEEEecCCccccCCcHHHHhhcCHH
Confidence            3589999999999999999998852   223444444210000000   011111110  0000            0111


Q ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCC-CCCeEEEEEcCChhHHHh
Q 005860          263 NSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNG-VRGSKILVTTRKETVARM  321 (673)
Q Consensus       263 ~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~-~~gs~iivTtr~~~v~~~  321 (673)
                      +...-.+...+..++=++++|+.-.. |......+...+... ..|..||++|.+......
T Consensus       100 ~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~~~~~  160 (173)
T cd03230         100 MKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILEEAER  160 (173)
T ss_pred             HHHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHH
Confidence            22233456666778889999987331 222223333333321 236779999998776553

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=96.08  E-value=0.0023  Score=36.93  Aligned_cols=18  Identities=33%  Similarity=0.612  Sum_probs=8.3

Q ss_pred             cccceecCCCCcccchhh
Q 005860          575 LRYLRLVGLGTEELPETC  592 (673)
Q Consensus       575 Lr~L~L~~~~i~~LP~~i  592 (673)
                      |++|+|++|.++.+|+++
T Consensus         2 L~~Ldls~n~l~~ip~~~   19 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSSF   19 (22)
T ss_dssp             ESEEEETSSEESEEGTTT
T ss_pred             ccEEECCCCcCEeCChhh
Confidence            444444444444444443

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.07  E-value=0.0097  Score=57.58  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=20.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            48899999999999999988874

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=96.06  E-value=0.021  Score=60.34  Aligned_cols=56  Identities=18%  Similarity=0.300  Sum_probs=33.2

Q ss_pred             HHHHHHhCCCeEEEEEcCCCCCCccch-hhhhhhccC-CCCCeEEEEEcCChhHHHhc
Q 005860          267 ESIRASLVGKKFLLILDDMWTDDYSKW-EPFHYCLKN-GVRGSKILVTTRKETVARMM  322 (673)
Q Consensus       267 ~~l~~~l~~kr~LlVLDdvw~~~~~~~-~~l~~~l~~-~~~gs~iivTtr~~~v~~~~  322 (673)
                      --+.+.+-+.++|+|||.--+.-..+= ..+...+.. ...|..+|++|....+...+
T Consensus       481 IaLARAlYG~P~lvVLDEPNsNLD~~GE~AL~~Ai~~~k~rG~~vvviaHRPs~L~~~  538 (580)
T COG4618         481 IALARALYGDPFLVVLDEPNSNLDSEGEAALAAAILAAKARGGTVVVIAHRPSALASV  538 (580)
T ss_pred             HHHHHHHcCCCcEEEecCCCCCcchhHHHHHHHHHHHHHHcCCEEEEEecCHHHHhhc
Confidence            346788899999999996522111111 123333332 34577777777777766643

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.05  E-value=0.061  Score=56.98  Aligned_cols=119  Identities=18%  Similarity=0.201  Sum_probs=67.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      .++.-+.+.|++|+|||+||..+...    ..|..+=-++      ++++       ++.+  .......+.......-+
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiS------pe~m-------iG~s--EsaKc~~i~k~F~DAYk  596 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIIS------PEDM-------IGLS--ESAKCAHIKKIFEDAYK  596 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeC------hHHc-------cCcc--HHHHHHHHHHHHHHhhc
Confidence            45778889999999999999888875    4565433332      1110       0000  00011122334444556


Q ss_pred             CCeEEEEEcCCCCCCccchh------------hhhhhccC-CCCCeE--EEEEcCChhHHHhccc----cceeecCCCC
Q 005860          275 GKKFLLILDDMWTDDYSKWE------------PFHYCLKN-GVRGSK--ILVTTRKETVARMMES----IHVISIKELS  334 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~------------~l~~~l~~-~~~gs~--iivTtr~~~v~~~~~~----~~~~~l~~L~  334 (673)
                      +.=-.||+||+  +..-+|-            .+...+.. ...|-|  |+-||....+...|+-    ...|+++.++
T Consensus       597 S~lsiivvDdi--ErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~  673 (744)
T KOG0741|consen  597 SPLSIIVVDDI--ERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLT  673 (744)
T ss_pred             CcceEEEEcch--hhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccC
Confidence            66779999999  3333443            23333332 223444  5557777888888865    4456666655

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.05  E-value=0.071  Score=53.37  Aligned_cols=116  Identities=14%  Similarity=0.062  Sum_probs=61.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC-CCCC-------cCcHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG-FVPT-------VGELNSLLE  267 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~-~~~~-------~~~~~~~~~  267 (673)
                      +..-++|+|..|.|||||.+.+....   ....+.+++.- ......+-..++...... ....       .++... ..
T Consensus       110 ~~~~~~i~g~~g~GKttl~~~l~~~~---~~~~G~i~~~g-~~v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k-~~  184 (270)
T TIGR02858       110 RVLNTLIISPPQCGKTTLLRDLARIL---STGISQLGLRG-KKVGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPK-AE  184 (270)
T ss_pred             CeeEEEEEcCCCCCHHHHHHHHhCcc---CCCCceEEECC-EEeecchhHHHHHHHhcccccccccccccccccchH-HH
Confidence            35789999999999999999999852   22333444310 011000011223222211 1110       111111 11


Q ss_pred             HHHHHhC-CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHHh
Q 005860          268 SIRASLV-GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARM  321 (673)
Q Consensus       268 ~l~~~l~-~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~  321 (673)
                      -+...+. ..+-++++|.+-  ....+..+...+.   .|..||+||.+..+...
T Consensus       185 ~~~~~i~~~~P~villDE~~--~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~~  234 (270)
T TIGR02858       185 GMMMLIRSMSPDVIVVDEIG--REEDVEALLEALH---AGVSIIATAHGRDVEDL  234 (270)
T ss_pred             HHHHHHHhCCCCEEEEeCCC--cHHHHHHHHHHHh---CCCEEEEEechhHHHHH
Confidence            2333332 578899999983  3344555544442   47789999998766443

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=96.04  E-value=0.015  Score=54.62  Aligned_cols=117  Identities=16%  Similarity=0.092  Sum_probs=60.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE---cCCcc-cHHHHHHHHHHHhhC--CCCC------------
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC---VSDPF-DELRIAKAIIEALEG--FVPT------------  258 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---vs~~~-~~~~~~~~i~~~l~~--~~~~------------  258 (673)
                      -.+++|+|..|.|||||++.+....   ....+.+.+.   ++... ....    ..+.+.-  +.+.            
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~---~~~~G~i~~~g~~~~~~~~~~~~----~~~~i~~~~q~~~~~~~~t~~~~l~   98 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGLE---EPDSGSILIDGEDLTDLEDELPP----LRRRIGMVFQDFALFPHLTVLENIA   98 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCceEEEECCEEccccchhHHH----HhhcEEEEecCCccCCCCCHHHhee
Confidence            3589999999999999999998742   2334444442   11100 0111    1111110  0000            


Q ss_pred             --cCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCC-C-CCeEEEEEcCChhHHH
Q 005860          259 --VGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNG-V-RGSKILVTTRKETVAR  320 (673)
Q Consensus       259 --~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~-~-~gs~iivTtr~~~v~~  320 (673)
                        ...-+..+-.+...+..++=++++|+--.. |......+...+... . .|..||++|.+.....
T Consensus        99 ~~lS~G~~qr~~la~al~~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~~  165 (178)
T cd03229          99 LGLSGGQQQRVALARALAMDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDLDEAA  165 (178)
T ss_pred             ecCCHHHHHHHHHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence              000122233355566667778999976321 222233343333321 2 2567888988876555

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.04  E-value=0.03  Score=57.97  Aligned_cols=59  Identities=22%  Similarity=0.143  Sum_probs=42.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      ..-.++-|+|.+|+|||+|+..++-......    .-..++||+....|+++.+ .+|++.++.
T Consensus       121 ~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~  183 (342)
T PLN03186        121 ETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGL  183 (342)
T ss_pred             cCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCC
Confidence            3467899999999999999977664322211    1136899999999888775 456666544

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.03  E-value=0.017  Score=60.19  Aligned_cols=88  Identities=17%  Similarity=0.116  Sum_probs=49.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG  275 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  275 (673)
                      -.++.++|+.|+||||++.++......+.....+.+++... .....+-++...+.++.......+..++...+ ..+.+
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l-~~l~~  215 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLAL-AELRN  215 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHH-HHhcC
Confidence            46899999999999999988877421111123455554322 22344555555666655432222222333333 33445


Q ss_pred             CeEEEEEcCCC
Q 005860          276 KKFLLILDDMW  286 (673)
Q Consensus       276 kr~LlVLDdvw  286 (673)
                      + -+|++|..-
T Consensus       216 ~-DlVLIDTaG  225 (374)
T PRK14722        216 K-HMVLIDTIG  225 (374)
T ss_pred             C-CEEEEcCCC
Confidence            5 456699873

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.01  E-value=0.054  Score=58.05  Aligned_cols=86  Identities=21%  Similarity=0.137  Sum_probs=49.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH--HHHHHHHHHHhhCCC---CCcCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE--LRIAKAIIEALEGFV---PTVGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~---~~~~~~~~~~~~l~  270 (673)
                      ...+|.++|.+|+||||+|..+...  ....-..+..|++ +.+.+  .+.+..+.++++.+.   ....+.........
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~--L~~~g~kV~lV~~-D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al  170 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARY--FKKKGLKVGLVAA-DTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGL  170 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEecC-CCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            4689999999999999999888764  2222123444443 23333  445666666665431   11223333333333


Q ss_pred             HHhCCCeEEEEEcCC
Q 005860          271 ASLVGKKFLLILDDM  285 (673)
Q Consensus       271 ~~l~~kr~LlVLDdv  285 (673)
                      +.+.+. -+||+|..
T Consensus       171 ~~~~~~-DvVIIDTA  184 (437)
T PRK00771        171 EKFKKA-DVIIVDTA  184 (437)
T ss_pred             HHhhcC-CEEEEECC
Confidence            344444 57889987

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.01  E-value=0.048  Score=58.47  Aligned_cols=86  Identities=16%  Similarity=0.170  Sum_probs=46.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      .+++.++|++|+||||++..+.........-..+..|+... +.  ..+.+....+.++.......+.+++...+.+ +.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~-~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~-~~  298 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT-YRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ-LR  298 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc-cHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH-hC
Confidence            46999999999999999876655321012223566666532 22  1222333333344332222333444445543 23


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                       ..=+|++|..
T Consensus       299 -~~DlVlIDt~  308 (424)
T PRK05703        299 -DCDVILIDTA  308 (424)
T ss_pred             -CCCEEEEeCC
Confidence             3457888965

>PRK14974 cell division protein FtsY; Provisional

Probab=95.98  E-value=0.043  Score=56.67  Aligned_cols=114  Identities=17%  Similarity=0.123  Sum_probs=56.0

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCC---CCcCcHHHH-HHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFV---PTVGELNSL-LESI  269 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~---~~~~~~~~~-~~~l  269 (673)
                      +..+|.++|++|+||||++..+..... ...+ .++.+. .+.+.  ..+.++...+.++...   ....+.... ...+
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~-~~g~-~V~li~-~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai  215 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLK-KNGF-SVVIAA-GDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAI  215 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCC-eEEEec-CCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHH
Confidence            468999999999999998777665321 1223 233343 33333  2334555666665431   111222222 2222


Q ss_pred             HHHhCCCeEEEEEcCCCCC--CccchhhhhhhccCCCCCeEEEEE
Q 005860          270 RASLVGKKFLLILDDMWTD--DYSKWEPFHYCLKNGVRGSKILVT  312 (673)
Q Consensus       270 ~~~l~~kr~LlVLDdvw~~--~~~~~~~l~~~l~~~~~gs~iivT  312 (673)
                      ........=+|++|-.-..  +...++.+........+.-.++|.
T Consensus       216 ~~~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl  260 (336)
T PRK14974        216 EHAKARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVG  260 (336)
T ss_pred             HHHHhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEee
Confidence            2222222238889987432  222344443333223334445554

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.97  E-value=0.0098  Score=57.06  Aligned_cols=120  Identities=14%  Similarity=0.134  Sum_probs=60.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCc---CcHHHHHHHHHHH-
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTV---GELNSLLESIRAS-  272 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~---~~~~~~~~~l~~~-  272 (673)
                      .+++.|.|+.|.||||+.+.+.... +..  ..-++|.... .. -.+...|...++..+...   .....-...+... 
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~-~la--~~G~~vpa~~-~~-l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~il  103 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLA-IMA--QIGCFVPAEY-AT-LPIFNRLLSRLSNDDSMERNLSTFASEMSETAYIL  103 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHH--HcCCCcchhh-cC-ccChhheeEecCCccccchhhhHHHHHHHHHHHHH
Confidence            4789999999999999998887531 111  1112221111 01 122333333333321111   1111101112222 


Q ss_pred             -hCCCeEEEEEcCCCCCC-ccc----hhhhhhhccCCCCCeEEEEEcCChhHHHhcc
Q 005860          273 -LVGKKFLLILDDMWTDD-YSK----WEPFHYCLKNGVRGSKILVTTRKETVARMME  323 (673)
Q Consensus       273 -l~~kr~LlVLDdvw~~~-~~~----~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~  323 (673)
                       +..++-|+++|.....- ..+    ...+...+..  .|+.+|++|.+.+++..+.
T Consensus       104 ~~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~--~~~~~i~~TH~~~l~~~~~  158 (204)
T cd03282         104 DYADGDSLVLIDELGRGTSSADGFAISLAILECLIK--KESTVFFATHFRDIAAILG  158 (204)
T ss_pred             HhcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHh--cCCEEEEECChHHHHHHhh
Confidence             23567899999974321 111    1122222322  3789999999998887654

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PTZ00035 Rad51 protein; Provisional

Probab=95.94  E-value=0.042  Score=57.05  Aligned_cols=58  Identities=21%  Similarity=0.168  Sum_probs=39.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccc---c-cCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVF---E-YFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ..-.++.|+|.+|+|||||+..++-.....   . .=..++|++....++++.+ .++.+.++
T Consensus       116 ~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g  177 (337)
T PTZ00035        116 ETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFG  177 (337)
T ss_pred             CCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhC
Confidence            446899999999999999998776432211   1 1235679988877777763 44455544

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.94  E-value=0.11  Score=53.55  Aligned_cols=65  Identities=9%  Similarity=0.028  Sum_probs=45.7

Q ss_pred             CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHh-ccccceeecCCCCcccc
Q 005860          274 VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      .+++=++|+|++..-+....+.+...+.....++.+|++|.+. .+... .+-...+.+.+++.++.
T Consensus       105 ~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~  171 (325)
T PRK06871        105 QGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQA  171 (325)
T ss_pred             cCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHH
Confidence            3556678899996666667788888888777778888777764 34322 23366788888877764

>TIGR00235 udk uridine kinase

Probab=95.92  E-value=0.0063  Score=58.78  Aligned_cols=26  Identities=42%  Similarity=0.451  Sum_probs=23.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +...+|+|+|++|+||||||+.+...
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34689999999999999999999874

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.91  E-value=0.034  Score=54.63  Aligned_cols=26  Identities=38%  Similarity=0.478  Sum_probs=23.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|+|.|++|+|||||++.+...
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998884

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=95.89  E-value=0.013  Score=62.81  Aligned_cols=52  Identities=23%  Similarity=0.279  Sum_probs=37.8

Q ss_pred             CcceechhhHHHHHHHhccCCcc------cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE------EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|.+..++++.+.+...-..      -+-...+-|.++|++|+|||++|+++++.
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~e  240 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE  240 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            46789999999888877422100      00123456789999999999999999995

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=95.89  E-value=0.09  Score=50.69  Aligned_cols=24  Identities=38%  Similarity=0.387  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        34 G~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          34 GEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999764

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.88  E-value=0.048  Score=56.29  Aligned_cols=58  Identities=22%  Similarity=0.251  Sum_probs=40.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ..-.++-|+|.+|+||||++.+++-......    .=..++||+....++++.+. ++++.++
T Consensus        93 ~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~g  154 (310)
T TIGR02236        93 ETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARG  154 (310)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcC
Confidence            3468999999999999999977765422211    11378999998888887654 4444443

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=95.87  E-value=0.0054  Score=53.96  Aligned_cols=21  Identities=43%  Similarity=0.525  Sum_probs=19.4

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|.|..|+||||+|+.+.+.
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            789999999999999998885

...

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.86  E-value=0.0065  Score=58.79  Aligned_cols=25  Identities=44%  Similarity=0.573  Sum_probs=22.8

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|.+|+||||||+.+...
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999999885

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.85  E-value=0.0056  Score=54.58  Aligned_cols=24  Identities=38%  Similarity=0.380  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .--|+|.||+|+||||+++.+.+.
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~   28 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEK   28 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHH
Confidence            346899999999999999999875

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=95.84  E-value=0.018  Score=52.90  Aligned_cols=116  Identities=17%  Similarity=0.173  Sum_probs=62.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc--cHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF--DELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG  275 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  275 (673)
                      .+++|+|..|.|||||++.+....   ....+.+++.-....  ....    ....+.-.. +...-+...-.+...+..
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~---~~~~G~i~~~~~~~~~~~~~~----~~~~i~~~~-qlS~G~~~r~~l~~~l~~   97 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLL---KPTSGEILIDGKDIAKLPLEE----LRRRIGYVP-QLSGGQRQRVALARALLL   97 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCccEEEECCEEcccCCHHH----HHhceEEEe-eCCHHHHHHHHHHHHHhc
Confidence            689999999999999999999852   234555555321110  1111    111111100 011112233345566666


Q ss_pred             CeEEEEEcCCCCC-CccchhhhhhhccC-CCCCeEEEEEcCChhHHHh
Q 005860          276 KKFLLILDDMWTD-DYSKWEPFHYCLKN-GVRGSKILVTTRKETVARM  321 (673)
Q Consensus       276 kr~LlVLDdvw~~-~~~~~~~l~~~l~~-~~~gs~iivTtr~~~v~~~  321 (673)
                      .+-++++|+.-.. |......+...+.. ...+..++++|.+......
T Consensus        98 ~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~  145 (157)
T cd00267          98 NPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAEL  145 (157)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            7789999987431 12223333333332 1225678999988776654

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.76  E-value=0.019  Score=54.88  Aligned_cols=102  Identities=20%  Similarity=0.152  Sum_probs=49.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh----
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL----  273 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----  273 (673)
                      +++.|.|.+|.||||+++.+.+.  .... ...+.+......-...    +.+..+...   ..+..   .+...-    
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~--~~~~-g~~v~~~apT~~Aa~~----L~~~~~~~a---~Ti~~---~l~~~~~~~~   85 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEA--LEAA-GKRVIGLAPTNKAAKE----LREKTGIEA---QTIHS---FLYRIPNGDD   85 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHH--HHHT-T--EEEEESSHHHHHH----HHHHHTS-E---EEHHH---HTTEECCEEC
T ss_pred             eEEEEEECCCCCHHHHHHHHHHH--HHhC-CCeEEEECCcHHHHHH----HHHhhCcch---hhHHH---HHhcCCcccc
Confidence            57888999999999999888774  2222 2233333322222222    222222110   00000   000000    


Q ss_pred             -----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC
Q 005860          274 -----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       274 -----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                           ..++-+||+|+..--+...+..+......  .|+|+|+.=-
T Consensus        86 ~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD  129 (196)
T PF13604_consen   86 EGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGD  129 (196)
T ss_dssp             CSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-
T ss_pred             cccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECC
Confidence                 12334999999965555556665555443  5778887643

>PRK08233 hypothetical protein; Provisional

Probab=95.75  E-value=0.0076  Score=56.77  Aligned_cols=24  Identities=42%  Similarity=0.509  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            479999999999999999999874

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.72  E-value=0.076  Score=50.05  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          26 GEIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999985

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.72  E-value=0.097  Score=54.22  Aligned_cols=64  Identities=8%  Similarity=0.113  Sum_probs=44.5

Q ss_pred             CCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhHHHh-ccccceeecCCCCcccc
Q 005860          275 GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      +++=++|+|++..-+....+.+...+....+++.+|++|.+ ..+... ..-...+.+.+++.++.
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~  196 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAA  196 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHH
Confidence            45558889999776777888888888877777776666665 444333 23356788888877654

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=95.70  E-value=0.074  Score=50.68  Aligned_cols=118  Identities=19%  Similarity=0.142  Sum_probs=59.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE---------------cCCccc---HHHHHHHHHHHhhCCCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC---------------VSDPFD---ELRIAKAIIEALEGFVPT  258 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---------------vs~~~~---~~~~~~~i~~~l~~~~~~  258 (673)
                      -.+++|.|..|.|||||.+.+..-.. .....+.+++.               +.+...   ...+...+.-.....  .
T Consensus        35 Ge~~~l~G~nGsGKStLl~~i~Gl~~-~~~~~G~i~~~g~~~~~~~~~~~i~~~~q~~~~~~~~t~~~~i~~~~~~~--~  111 (194)
T cd03213          35 GELTAIMGPSGAGKSTLLNALAGRRT-GLGVSGEVLINGRPLDKRSFRKIIGYVPQDDILHPTLTVRETLMFAAKLR--G  111 (194)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC-CCCCceEEEECCEeCchHhhhheEEEccCcccCCCCCcHHHHHHHHHHhc--c
Confidence            46899999999999999999988430 02222322221               111110   011222221100000  1


Q ss_pred             cCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccC-CCCCeEEEEEcCChh
Q 005860          259 VGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKN-GVRGSKILVTTRKET  317 (673)
Q Consensus       259 ~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~-~~~gs~iivTtr~~~  317 (673)
                      ...-+...-.+...+-.++-++++|+.-+. |......+...+.. ...|..||++|.+..
T Consensus       112 LS~G~~qrv~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  172 (194)
T cd03213         112 LSGGERKRVSIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLADTGRTIICSIHQPS  172 (194)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEecCch
Confidence            111122233455566667779999987331 22223334333432 223777888988864

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=95.70  E-value=0.038  Score=55.15  Aligned_cols=88  Identities=23%  Similarity=0.152  Sum_probs=56.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHH-hhC---C-CCCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEA-LEG---F-VPTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~-l~~---~-~~~~~~~~~~~~~l  269 (673)
                      +.-+++=|+|+.|+||||+|.+++-.  ....-..++|++.-..+++..+.. +... +..   . ..+..+..++.+.+
T Consensus        58 ~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~-l~~~~~d~l~v~~~~~~e~q~~i~~~~  134 (279)
T COG0468          58 PRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQ-LGVDLLDNLLVSQPDTGEQQLEIAEKL  134 (279)
T ss_pred             ccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHH-HHHhhhcceeEecCCCHHHHHHHHHHH
Confidence            45689999999999999999665553  444455899999998888876433 3333 221   1 11222222344444


Q ss_pred             HHHhCCCeEEEEEcCC
Q 005860          270 RASLVGKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~~kr~LlVLDdv  285 (673)
                      ......+--|||+|.+
T Consensus       135 ~~~~~~~i~LvVVDSv  150 (279)
T COG0468         135 ARSGAEKIDLLVVDSV  150 (279)
T ss_pred             HHhccCCCCEEEEecC
Confidence            4444445669999988

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.70  E-value=0.022  Score=53.86  Aligned_cols=46  Identities=22%  Similarity=0.251  Sum_probs=36.8

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.++||-++.++++.-.-.++.       .+-+.|.||+|+||||-+..+.+.
T Consensus        26 l~dIVGNe~tv~rl~via~~gn-------mP~liisGpPG~GKTTsi~~LAr~   71 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGN-------MPNLIISGPPGTGKTTSILCLARE   71 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCC-------CCceEeeCCCCCchhhHHHHHHHH
Confidence            3589999999999877665443       667889999999999987776663

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.69  E-value=0.049  Score=52.02  Aligned_cols=104  Identities=21%  Similarity=0.299  Sum_probs=63.4

Q ss_pred             ccCCcceechhhHHHHHHHh---ccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHH
Q 005860          166 IDVSEIRGRDEEKSSLKSKL---LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDEL  242 (673)
Q Consensus       166 ~~~~~~vGr~~~~~~l~~~L---~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  242 (673)
                      ++-..++|.|...+.+++--   ..+.      ...-|.+||.-|.||++|++++.+.  +....-.  -|.|...    
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~------pANnVLLwGaRGtGKSSLVKA~~~e--~~~~glr--LVEV~k~----  122 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGL------PANNVLLWGARGTGKSSLVKALLNE--YADEGLR--LVEVDKE----  122 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCC------cccceEEecCCCCChHHHHHHHHHH--HHhcCCe--EEEEcHH----
Confidence            34457899988877776432   2221      2445789999999999999999995  3333322  3333321    


Q ss_pred             HHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh--CCCeEEEEEcCCCC-CCccchhhhhhhccC
Q 005860          243 RIAKAIIEALEGFVPTVGELNSLLESIRASL--VGKKFLLILDDMWT-DDYSKWEPFHYCLKN  302 (673)
Q Consensus       243 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~-~~~~~~~~l~~~l~~  302 (673)
                      ++               .+    ...+.+.|  ...||.|..||+-. ++...+..++..+..
T Consensus       123 dl---------------~~----Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG  166 (287)
T COG2607         123 DL---------------AT----LPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEG  166 (287)
T ss_pred             HH---------------hh----HHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcC
Confidence            11               11    12222333  35799999999843 233456777777764

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.69  E-value=0.023  Score=54.68  Aligned_cols=82  Identities=24%  Similarity=0.255  Sum_probs=50.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhC-------CCCCcCcH-------
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEG-------FVPTVGEL-------  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~-------~~~~~~~~-------  262 (673)
                      .-++|+|..|+|||+|+..+.+..    .-+..+++.+.+.. .+.++.+++...-..       ...+..-.       
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~----~~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~   91 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQ----DADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPY   91 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHC----TTTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhcc----cccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhc
Confidence            468999999999999999888753    23445888887653 444555555332100       01111100       


Q ss_pred             --HHHHHHHHHHhCCCeEEEEEcCC
Q 005860          263 --NSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       263 --~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                        -...+.++.  +++++|+++||+
T Consensus        92 ~a~t~AEyfrd--~G~dVlli~Dsl  114 (215)
T PF00006_consen   92 TALTIAEYFRD--QGKDVLLIIDSL  114 (215)
T ss_dssp             HHHHHHHHHHH--TTSEEEEEEETH
T ss_pred             cchhhhHHHhh--cCCceeehhhhh
Confidence              122233333  799999999999

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=95.69  E-value=0.0056  Score=54.82  Aligned_cols=107  Identities=17%  Similarity=0.104  Sum_probs=58.2

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc-cccCCeEEEEEcCCcccHHHHHHHHHH
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV-FEYFDKRMWVCVSDPFDELRIAKAIIE  250 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~~~~~~~~~i~~  250 (673)
                      ||.-..++++.+.+..-.     ..-.-|.|+|..|+||+++|+.++..... ...|..+   ..... .     .++++
T Consensus         1 vG~S~~~~~l~~~l~~~a-----~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~---~~~~~-~-----~~~l~   66 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLA-----KSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVI---DCASL-P-----AELLE   66 (138)
T ss_dssp             --SCHHHHHHHHHHHHHH-----CSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCC---CHHCT-C-----HHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh-----CCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEe---chhhC-c-----HHHHH
Confidence            455566666666664332     12245789999999999999999986322 1122111   00010 0     11111


Q ss_pred             HhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccC-CCCCeEEEEEcCC
Q 005860          251 ALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       251 ~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      +                     .  +.--|+|+|+..-+......+...+.. .....|+|.||..
T Consensus        67 ~---------------------a--~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~  109 (138)
T PF14532_consen   67 Q---------------------A--KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQ  109 (138)
T ss_dssp             H---------------------C--TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC
T ss_pred             H---------------------c--CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence            1                     1  334577888855444455556655553 2567799999875

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.67  E-value=0.031  Score=52.17  Aligned_cols=22  Identities=41%  Similarity=0.505  Sum_probs=19.6

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++.++|++|+||||++..+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999888764

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.66  E-value=0.11  Score=49.48  Aligned_cols=63  Identities=16%  Similarity=0.101  Sum_probs=40.3

Q ss_pred             HHHHHHHHhCCCeEEEEEcCCCCCCccchhhh---hhhccC-CCCCeEEEEEcCChhHHHhccccceee
Q 005860          265 LLESIRASLVGKKFLLILDDMWTDDYSKWEPF---HYCLKN-GVRGSKILVTTRKETVARMMESIHVIS  329 (673)
Q Consensus       265 ~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l---~~~l~~-~~~gs~iivTtr~~~v~~~~~~~~~~~  329 (673)
                      .+..+.+.+-=++=|.|||...+  --+.+.+   ...+.. ...|+-++++|..+.++....++.+|-
T Consensus       151 KR~EilQ~~~lePkl~ILDE~DS--GLDIdalk~V~~~i~~lr~~~~~~liITHy~rll~~i~pD~vhv  217 (251)
T COG0396         151 KRNEILQLLLLEPKLAILDEPDS--GLDIDALKIVAEGINALREEGRGVLIITHYQRLLDYIKPDKVHV  217 (251)
T ss_pred             HHHHHHHHHhcCCCEEEecCCCc--CccHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHhhcCCCEEEE
Confidence            34556666666777999998833  2334333   222222 345778999999999999876655443

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.65  E-value=0.054  Score=57.71  Aligned_cols=86  Identities=16%  Similarity=0.130  Sum_probs=47.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCC------CCCcCcH-----HHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGF------VPTVGEL-----NSL  265 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~------~~~~~~~-----~~~  265 (673)
                      -..++|+|..|+|||||++.+.....   ....++++.--..-++.++....+......      +.+..-.     ...
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~  241 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLT  241 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHH
Confidence            45799999999999999999987532   222344443222334444444343332111      1111101     111


Q ss_pred             HHHHHHHh--CCCeEEEEEcCC
Q 005860          266 LESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       266 ~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      ...+.+++  +++.+|+++||+
T Consensus       242 a~~iAEyfrd~G~~Vll~~Dsl  263 (450)
T PRK06002        242 ATAIAEYFRDRGENVLLIVDSV  263 (450)
T ss_pred             HHHHHHHHHHcCCCEEEeccch
Confidence            22233333  589999999999

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.64  E-value=0.028  Score=60.77  Aligned_cols=87  Identities=20%  Similarity=0.096  Sum_probs=44.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      ...+|+|+|.+|+||||++..+......+.....+..++.. .+.  ..+.+....+.++.......+...+...+.+ +
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtD-tyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~-l  426 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTD-TQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLER-L  426 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecc-cccccHHHHHHHhhcccCceeEecCcHHHHHHHHHH-h
Confidence            35799999999999999997776532111112345555432 222  2222332233333222222233344444433 3


Q ss_pred             CCCeEEEEEcCC
Q 005860          274 VGKKFLLILDDM  285 (673)
Q Consensus       274 ~~kr~LlVLDdv  285 (673)
                      .+ .=+|++|..
T Consensus       427 ~~-~DLVLIDTa  437 (559)
T PRK12727        427 RD-YKLVLIDTA  437 (559)
T ss_pred             cc-CCEEEecCC
Confidence            33 458888877

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.64  E-value=0.044  Score=55.31  Aligned_cols=25  Identities=32%  Similarity=0.348  Sum_probs=21.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....+|||.|..|+||||+|+.+..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999987755

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=95.63  E-value=0.045  Score=58.05  Aligned_cols=85  Identities=18%  Similarity=0.171  Sum_probs=51.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH-HHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE-LRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+..    ..+.++++-+.+.... .++..+++..-+..       ..+..-.     .
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~~----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRGT----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGC  237 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccCC----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHH
Confidence            4579999999999999999998742    2256666777765443 44555544331111       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       238 ~~A~tiAEyfrd~G~~VLl~~Dsl  261 (444)
T PRK08972        238 ETATTIAEYFRDQGLNVLLLMDSL  261 (444)
T ss_pred             HHHHHHHHHHHHcCCCEEEEEcCh
Confidence            1122244444  689999999999

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=95.62  E-value=0.077  Score=52.35  Aligned_cols=62  Identities=15%  Similarity=0.233  Sum_probs=36.4

Q ss_pred             HHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeec
Q 005860          267 ESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISI  330 (673)
Q Consensus       267 ~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l  330 (673)
                      -.+...+-.++-+++||+..+. |....+.+...+.....|..||++|.+......  ..+.+.+
T Consensus       146 l~la~aL~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sh~~~~~~~--~d~~~~l  208 (236)
T cd03253         146 VAIARAILKNPPILLLDEATSALDTHTEREIQAALRDVSKGRTTIVIAHRLSTIVN--ADKIIVL  208 (236)
T ss_pred             HHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHHHHh--CCEEEEE
Confidence            3455666777889999987432 222233344444332226678898888776653  4445444

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00301 uridine kinase; Provisional

Probab=95.62  E-value=0.0085  Score=57.61  Aligned_cols=24  Identities=29%  Similarity=0.494  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|.+|+||||||+.+.+.
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHH
Confidence            479999999999999999988763

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.61  E-value=0.064  Score=52.93  Aligned_cols=49  Identities=14%  Similarity=0.402  Sum_probs=34.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHH-hcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFA-YNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v-~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      +.-.++.|.|.+|+|||++|.++ ++.  . ..-..++||+..+  ++.++.+.+
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~--~-~~ge~~lyvs~ee--~~~~i~~~~   68 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNG--L-QMGEPGIYVALEE--HPVQVRRNM   68 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHH--H-HcCCcEEEEEeeC--CHHHHHHHH
Confidence            44689999999999999999654 442  2 2345788888765  455555543

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=95.61  E-value=0.13  Score=56.55  Aligned_cols=105  Identities=15%  Similarity=0.177  Sum_probs=62.4

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      +.+=.|+++-+++|++++.-..-. +..+-+++..+|++|||||++|+.|...  ....|   +-++|+.-.|..+|-..
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLr-gs~qGkIlCf~GPPGVGKTSI~kSIA~A--LnRkF---fRfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLR-GSVQGKILCFVGPPGVGKTSIAKSIARA--LNRKF---FRFSVGGMTDVAEIKGH  483 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhc-ccCCCcEEEEeCCCCCCcccHHHHHHHH--hCCce---EEEeccccccHHhhccc
Confidence            356689999999999998433210 0234689999999999999999999885  33333   12456665555443211


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                      =-..+      ..-...+.+.++.. +..+-|+.||.|
T Consensus       484 RRTYV------GAMPGkiIq~LK~v-~t~NPliLiDEv  514 (906)
T KOG2004|consen  484 RRTYV------GAMPGKIIQCLKKV-KTENPLILIDEV  514 (906)
T ss_pred             ceeee------ccCChHHHHHHHhh-CCCCceEEeehh
Confidence            00000      01112233333322 345668888988

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=95.60  E-value=0.0081  Score=46.44  Aligned_cols=22  Identities=41%  Similarity=0.539  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|..|+||||+|+.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999988875

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>TIGR00959 ffh signal recognition particle protein

Probab=95.59  E-value=0.041  Score=58.80  Aligned_cols=88  Identities=18%  Similarity=0.113  Sum_probs=45.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH--HHHHHHHHHHhhCCC---CCcCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE--LRIAKAIIEALEGFV---PTVGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~---~~~~~~~~~~~~l~  270 (673)
                      ...++.++|.+|+||||+|..+......+..+ .+..|++ +.+.+  .+.+....+.++.+.   ....+..++.....
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~-kV~lV~~-D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLKKKQGK-KVLLVAC-DLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhCCC-eEEEEec-cccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHH
Confidence            36799999999999999986666531111122 2333433 22332  233344444444331   11223334443333


Q ss_pred             HHhCCCeE-EEEEcCC
Q 005860          271 ASLVGKKF-LLILDDM  285 (673)
Q Consensus       271 ~~l~~kr~-LlVLDdv  285 (673)
                      +....+.| +||+|-.
T Consensus       176 ~~~~~~~~DvVIIDTa  191 (428)
T TIGR00959       176 EYAKENGFDVVIVDTA  191 (428)
T ss_pred             HHHHhcCCCEEEEeCC
Confidence            33434444 7777765

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK05439 pantothenate kinase; Provisional

Probab=95.59  E-value=0.058  Score=54.92  Aligned_cols=79  Identities=20%  Similarity=0.165  Sum_probs=43.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcccccc--CCeEEEEEcCCcccHHHHHHHHHHHhh--CCCCCcCcHHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEY--FDKRMWVCVSDPFDELRIAKAIIEALE--GFVPTVGELNSLLESIR  270 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~~~~~i~~~l~--~~~~~~~~~~~~~~~l~  270 (673)
                      ....+|||.|.+|+||||+|+.+..-  ....  -..+.-++..+=+...+.+..  ..+.  ...+..-+.+.+...+.
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~--l~~~~~~~~v~vi~~DdFy~~~~~l~~--~~l~~~kg~Pes~D~~~l~~~L~  159 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQAL--LSRWPEHPKVELVTTDGFLYPNAVLEE--RGLMKRKGFPESYDMRALLRFLS  159 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHhhCCCCceEEEeccccccCHHHHhh--hhccccCCCcccccHHHHHHHHH
Confidence            45789999999999999999888763  2221  122334443332222222211  0111  11233456666666666


Q ss_pred             HHhCCCe
Q 005860          271 ASLVGKK  277 (673)
Q Consensus       271 ~~l~~kr  277 (673)
                      ....++.
T Consensus       160 ~Lk~G~~  166 (311)
T PRK05439        160 DVKSGKP  166 (311)
T ss_pred             HHHcCCC
Confidence            6666654

>PRK10867 signal recognition particle protein; Provisional

Probab=95.58  E-value=0.043  Score=58.64  Aligned_cols=87  Identities=18%  Similarity=0.166  Sum_probs=45.4

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHH--HHHHHHHHHhhCC---CCCcCcHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDEL--RIAKAIIEALEGF---VPTVGELNSLLESI  269 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~--~~~~~i~~~l~~~---~~~~~~~~~~~~~l  269 (673)
                      ...+|.++|.+|+||||+|..+...  ..... ..+..|+. +.+.+.  +-++...+..+.+   .....+..++....
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~--l~~~~G~kV~lV~~-D~~R~aa~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a  175 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKY--LKKKKKKKVLLVAA-DVYRPAAIEQLKTLGEQIGVPVFPSGDGQDPVDIAKAA  175 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH--HHHhcCCcEEEEEc-cccchHHHHHHHHHHhhcCCeEEecCCCCCHHHHHHHH
Confidence            3689999999999999987666553  22221 22334433 333332  2334445554432   11122344444434


Q ss_pred             HHHhCCCeE-EEEEcCC
Q 005860          270 RASLVGKKF-LLILDDM  285 (673)
Q Consensus       270 ~~~l~~kr~-LlVLDdv  285 (673)
                      .+..+.+.| +||+|-.
T Consensus       176 ~~~a~~~~~DvVIIDTa  192 (433)
T PRK10867        176 LEEAKENGYDVVIVDTA  192 (433)
T ss_pred             HHHHHhcCCCEEEEeCC
Confidence            344444444 6777765

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=95.57  E-value=0.027  Score=58.40  Aligned_cols=47  Identities=15%  Similarity=0.090  Sum_probs=37.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|....+.++.+.+..-.     ..-.-|.|+|..|+||+++|+.++..
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a-----~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLA-----PLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHh-----CCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            358999998888888775543     12235789999999999999999874

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=95.57  E-value=0.013  Score=64.48  Aligned_cols=102  Identities=20%  Similarity=0.263  Sum_probs=61.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+=.|.++-+++|+++|.-..-.. .-.-.++.+||++|+|||+|++.|.+.  ....|   +-++++.--|..+|    
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~-~~kGpILcLVGPPGVGKTSLgkSIA~a--l~Rkf---vR~sLGGvrDEAEI----  392 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTK-KLKGPILCLVGPPGVGKTSLGKSIAKA--LGRKF---VRISLGGVRDEAEI----  392 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhc-cCCCcEEEEECCCCCCchhHHHHHHHH--hCCCE---EEEecCccccHHHh----
Confidence            456899999999999984322100 134579999999999999999999984  44455   22344444343332    


Q ss_pred             HHHhhCCCCC--cCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          249 IEALEGFVPT--VGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       249 ~~~l~~~~~~--~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                          .++...  ..-...+.+.+++ .+.++-+++||.+
T Consensus       393 ----RGHRRTYIGamPGrIiQ~mkk-a~~~NPv~LLDEI  426 (782)
T COG0466         393 ----RGHRRTYIGAMPGKIIQGMKK-AGVKNPVFLLDEI  426 (782)
T ss_pred             ----ccccccccccCChHHHHHHHH-hCCcCCeEEeech
Confidence                111100  0111222233332 2456778999988

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.57  E-value=0.023  Score=62.69  Aligned_cols=52  Identities=27%  Similarity=0.249  Sum_probs=34.7

Q ss_pred             CcceechhhHHHHHHHhc---cCCc--ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLL---CESS--EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~---~~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.++.++++.+.+.   ....  ..+....+-+.++|++|+|||+||+++.+.
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            478898887766655443   1110  000122345889999999999999999985

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK06547 hypothetical protein; Provisional

Probab=95.56  E-value=0.015  Score=54.04  Aligned_cols=25  Identities=36%  Similarity=0.361  Sum_probs=22.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|.|++|+||||+|+.+.+.
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999999774

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.56  E-value=0.01  Score=56.35  Aligned_cols=26  Identities=38%  Similarity=0.478  Sum_probs=23.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.+|||.|.+|+||||+|+.+++.
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~   31 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            35789999999999999999999985

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.56  E-value=0.06  Score=55.60  Aligned_cols=63  Identities=8%  Similarity=0.066  Sum_probs=38.1

Q ss_pred             CeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHHhc-cccceeecCCCCcccc
Q 005860          276 KKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VARMM-ESIHVISIKELSEQEC  338 (673)
Q Consensus       276 kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~~~-~~~~~~~l~~L~~~~~  338 (673)
                      ++=++|+|++..-+...-+.+...+.....+..+|++|.+.. +...+ .-...+.+.+++.++.
T Consensus       113 ~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~  177 (325)
T PRK08699        113 GLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEA  177 (325)
T ss_pred             CceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHH
Confidence            334456688855555556666666665445666777777644 33332 2256777888877664

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.54  E-value=0.0063  Score=35.10  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=13.2

Q ss_pred             CccEEEeccCCCCccccccccc
Q 005860          597 NLQVLEIEQCTSLKRLPLGIGK  618 (673)
Q Consensus       597 ~L~~L~l~~c~~l~~lP~~i~~  618 (673)
                      +|++|+|++|. +..+|.+|++
T Consensus         1 ~L~~Ldls~n~-l~~ip~~~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNN-LTSIPSSFSN   21 (22)
T ss_dssp             TESEEEETSSE-ESEEGTTTTT
T ss_pred             CccEEECCCCc-CEeCChhhcC
Confidence            46677777663 6666666554

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=95.53  E-value=0.13  Score=53.58  Aligned_cols=41  Identities=17%  Similarity=0.225  Sum_probs=31.9

Q ss_pred             hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          176 EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       176 ~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-.+.|.+.+....    .....+|+|.|.=|+||||+.+.+.+.
T Consensus         3 ~~a~~la~~I~~~~----~~~~~~IgL~G~WGsGKSs~l~~l~~~   43 (325)
T PF07693_consen    3 PYAKALAEIIKNPD----SDDPFVIGLYGEWGSGKSSFLNMLKEE   43 (325)
T ss_pred             HHHHHHHHHHhccC----CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34566667776553    245789999999999999999998885

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=95.53  E-value=0.097  Score=51.05  Aligned_cols=24  Identities=29%  Similarity=0.349  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        30 Ge~~~i~G~nGsGKSTLl~~l~G~   53 (221)
T cd03244          30 GEKVGIVGRTGSGKSSLLLALFRL   53 (221)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            358999999999999999999874

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.51  E-value=0.015  Score=62.10  Aligned_cols=43  Identities=16%  Similarity=0.115  Sum_probs=37.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++||++.++.+...+..+.         -|.|.|++|+|||+||+.+...
T Consensus        20 ~~i~gre~vI~lll~aalag~---------hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE---------SVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC---------CEEEECCCChhHHHHHHHHHHH
Confidence            468999999999998887665         4889999999999999999984

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=95.49  E-value=0.028  Score=57.69  Aligned_cols=26  Identities=23%  Similarity=0.331  Sum_probs=24.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++.++|||++|.|||.+|+++++.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999996

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.48  E-value=0.062  Score=51.49  Aligned_cols=120  Identities=15%  Similarity=0.081  Sum_probs=60.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE-------------------cCCcccH--HHHHHHHHHHhhCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC-------------------VSDPFDE--LRIAKAIIEALEGF  255 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-------------------vs~~~~~--~~~~~~i~~~l~~~  255 (673)
                      -.+++|+|..|.|||||.+.+....... .-.+.+.+.                   +.+....  .....+++...   
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~~-p~~G~i~~~g~~~~~~~~~~~~~~~i~~v~q~~~~~~~~~~~~~l~~~---  101 (200)
T cd03217          26 GEVHALMGPNGSGKSTLAKTIMGHPKYE-VTEGEILFKGEDITDLPPEERARLGIFLAFQYPPEIPGVKNADFLRYV---  101 (200)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCcCC-CCccEEEECCEECCcCCHHHHhhCcEEEeecChhhccCccHHHHHhhc---
Confidence            3689999999999999999988852100 001111110                   1111100  00111111111   


Q ss_pred             CCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCC-CCCeEEEEEcCChhHHH
Q 005860          256 VPTVGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNG-VRGSKILVTTRKETVAR  320 (673)
Q Consensus       256 ~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~-~~gs~iivTtr~~~v~~  320 (673)
                      ......-+...-.+...+-..+=++++|+.-.. |....+.+...+... ..|..||++|.+.....
T Consensus       102 ~~~LS~G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~L~~~~~~~~tiii~sh~~~~~~  168 (200)
T cd03217         102 NEGFSGGEKKRNEILQLLLLEPDLAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQRLLD  168 (200)
T ss_pred             cccCCHHHHHHHHHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCHHHHH
Confidence            011122223334456666677789999987321 222233333333321 23667899998877665

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=95.44  E-value=0.19  Score=48.26  Aligned_cols=131  Identities=18%  Similarity=0.188  Sum_probs=66.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccc---cCCe-EEEEEcCC---------------cccHHHHHHHHHHH------
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFE---YFDK-RMWVCVSD---------------PFDELRIAKAIIEA------  251 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~-~~wv~vs~---------------~~~~~~~~~~i~~~------  251 (673)
                      -.+++|+|..|.|||||++.+........   .|+. +.++.-..               .++... .....+.      
T Consensus        31 G~~~~i~G~nG~GKSTLl~~i~G~~~~~~G~i~~~g~i~~~~q~~~l~~~t~~enl~~~~~~~~~~-~~~~~~~~~l~~~  109 (204)
T cd03250          31 GELVAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGSIAYVSQEPWIQNGTIRENILFGKPFDEER-YEKVIKACALEPD  109 (204)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCcCCCCCCeEEEcCEEEEEecCchhccCcHHHHhccCCCcCHHH-HHHHHHHcCcHHH
Confidence            45899999999999999999988532211   1222 23331110               111111 1111111      


Q ss_pred             hhCC-----------CCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-Cccchhhhhhh-cc-CCCCCeEEEEEcCChh
Q 005860          252 LEGF-----------VPTVGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYC-LK-NGVRGSKILVTTRKET  317 (673)
Q Consensus       252 l~~~-----------~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~-l~-~~~~gs~iivTtr~~~  317 (673)
                      +...           ......-+...-.+...+..++=++++|+--+. |....+.+... +. ....|..||++|.+..
T Consensus       110 ~~~~~~~~~~~~~~~~~~lS~G~~qrv~laral~~~p~llllDEP~~~LD~~~~~~l~~~ll~~~~~~~~tvi~~sh~~~  189 (204)
T cd03250         110 LEILPDGDLTEIGEKGINLSGGQKQRISLARAVYSDADIYLLDDPLSAVDAHVGRHIFENCILGLLLNNKTRILVTHQLQ  189 (204)
T ss_pred             HHhccCcccceecCCCCcCCHHHHHHHHHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHHhccCCCEEEEEeCCHH
Confidence            1110           011112233344566677778889999986332 22222334332 22 2234778899998876


Q ss_pred             HHHhccccceeec
Q 005860          318 VARMMESIHVISI  330 (673)
Q Consensus       318 v~~~~~~~~~~~l  330 (673)
                      ....  ..+++.+
T Consensus       190 ~~~~--~d~i~~l  200 (204)
T cd03250         190 LLPH--ADQIVVL  200 (204)
T ss_pred             HHhh--CCEEEEE
Confidence            6654  3444443

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=95.43  E-value=0.098  Score=52.12  Aligned_cols=24  Identities=33%  Similarity=0.519  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.++..
T Consensus        30 Ge~~~I~G~NGsGKSTLl~~i~Gl   53 (251)
T PRK09544         30 GKILTLLGPNGAGKSTLVRVVLGL   53 (251)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999975

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=95.42  E-value=0.08  Score=60.30  Aligned_cols=24  Identities=33%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..|+|+|..|+|||||+|.+..-
T Consensus       499 Ge~vaIvG~SGsGKSTL~KLL~gl  522 (709)
T COG2274         499 GEKVAIVGRSGSGKSTLLKLLLGL  522 (709)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999998873

>PRK06762 hypothetical protein; Provisional

Probab=95.42  E-value=0.011  Score=54.80  Aligned_cols=23  Identities=39%  Similarity=0.499  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999874

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=95.41  E-value=0.012  Score=52.92  Aligned_cols=21  Identities=38%  Similarity=0.513  Sum_probs=19.4

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +|.++|++|+||||+|+.+..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999999886

...

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.40  E-value=0.12  Score=56.20  Aligned_cols=129  Identities=24%  Similarity=0.294  Sum_probs=73.1

Q ss_pred             eEEEEEEccCCChHHH-HHHHHhcCccccccC--CeEEEEEcCCcccHHHHHHHHHHHhhCCCC----------Cc----
Q 005860          197 IQIITIVGMGGIGKTT-LAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAKAIIEALEGFVP----------TV----  259 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTt-La~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----------~~----  259 (673)
                      ..||.|||-.|+|||| |||.+|.+     .|  .+.+-++-....-+-.+.+.+.+.++..-.          +.    
T Consensus       371 n~vvvivgETGSGKTTQl~QyL~ed-----GY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~~  445 (1042)
T KOG0924|consen  371 NQVVVIVGETGSGKTTQLAQYLYED-----GYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSED  445 (1042)
T ss_pred             CcEEEEEecCCCCchhhhHHHHHhc-----ccccCCeeeecCchHHHHHHHHHHHHHHhCCccccccceEEEeeecCCCc
Confidence            4699999999999998 56999986     23  233333333333344567777777754311          10    


Q ss_pred             ------CcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhcc---CCCCCeEEEEEcCChh---HHHhccccce
Q 005860          260 ------GELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLK---NGVRGSKILVTTRKET---VARMMESIHV  327 (673)
Q Consensus       260 ------~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~---~~~~gs~iivTtr~~~---v~~~~~~~~~  327 (673)
                            .+---+.+.+....-.|=-.||+|...... ..-+.+.+.+.   .....-|+||||-..+   .++..+....
T Consensus       446 T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERs-lNtDilfGllk~~larRrdlKliVtSATm~a~kf~nfFgn~p~  524 (1042)
T KOG0924|consen  446 TKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERS-LNTDILFGLLKKVLARRRDLKLIVTSATMDAQKFSNFFGNCPQ  524 (1042)
T ss_pred             eeEEEeccchHHHHHhhhhhhhheeEEEechhhhcc-cchHHHHHHHHHHHHhhccceEEEeeccccHHHHHHHhCCCce
Confidence                  111223344444444555689999985432 23333444333   2345679999987544   4455554444


Q ss_pred             eecC
Q 005860          328 ISIK  331 (673)
Q Consensus       328 ~~l~  331 (673)
                      +.++
T Consensus       525 f~Ip  528 (1042)
T KOG0924|consen  525 FTIP  528 (1042)
T ss_pred             eeec
Confidence            4443

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.40  E-value=0.082  Score=50.30  Aligned_cols=24  Identities=29%  Similarity=0.401  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        33 Ge~~~l~G~nGsGKSTLl~~l~G~   56 (192)
T cd03232          33 GTLTALMGESGAGKTTLLDVLAGR   56 (192)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999863

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=95.37  E-value=0.14  Score=50.28  Aligned_cols=23  Identities=39%  Similarity=0.525  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|..|.|||||.+.+...
T Consensus        30 ~~~~i~G~nGsGKSTLl~~l~G~   52 (229)
T cd03254          30 ETVAIVGPTGAGKTTLINLLMRF   52 (229)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999875

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.36  E-value=0.1  Score=54.15  Aligned_cols=89  Identities=15%  Similarity=0.154  Sum_probs=52.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRAS  272 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~  272 (673)
                      ...+++.|+|+.|+||||++..+...  ....-..+.+|+.. ++.  ..+-++...+.++.......+.+++...+...
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA~~--l~~~g~~V~lItaD-tyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l  280 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQ--LLKQNRTVGFITTD-TFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYM  280 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEeCC-ccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHH
Confidence            34689999999999999999777754  22222345566543 332  24455555555554322234455555555443


Q ss_pred             hC-CCeEEEEEcCCC
Q 005860          273 LV-GKKFLLILDDMW  286 (673)
Q Consensus       273 l~-~kr~LlVLDdvw  286 (673)
                      -. +..=+|++|-.-
T Consensus       281 ~~~~~~D~VLIDTAG  295 (407)
T PRK12726        281 TYVNCVDHILIDTVG  295 (407)
T ss_pred             HhcCCCCEEEEECCC
Confidence            21 345678888773

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.36  E-value=0.074  Score=55.90  Aligned_cols=82  Identities=27%  Similarity=0.233  Sum_probs=48.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCC-----cCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPT-----VGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  270 (673)
                      .-.++.|.|.+|+|||||+.++...  ....-..++|++..+.  ...+ ..-++.++...+.     ..+++.+...+.
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~EEs--~~qi-~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~  155 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGEES--PEQI-KLRADRLGISTENLYLLAETNLEDILASIE  155 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCcC--HHHH-HHHHHHcCCCcccEEEEccCcHHHHHHHHH
Confidence            3579999999999999999877764  2233356778876543  3332 2223444432211     123444444432


Q ss_pred             HHhCCCeEEEEEcCC
Q 005860          271 ASLVGKKFLLILDDM  285 (673)
Q Consensus       271 ~~l~~kr~LlVLDdv  285 (673)
                         ..+.-+||+|.+
T Consensus       156 ---~~~~~lVVIDSI  167 (372)
T cd01121         156 ---ELKPDLVIIDSI  167 (372)
T ss_pred             ---hcCCcEEEEcch
Confidence               235668899987

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.33  E-value=0.024  Score=52.98  Aligned_cols=22  Identities=41%  Similarity=0.468  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|.|.+|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999886

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.31  E-value=0.028  Score=52.57  Aligned_cols=24  Identities=29%  Similarity=0.374  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|++|+||||+|+.+...
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999999885

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.29  E-value=0.031  Score=49.95  Aligned_cols=44  Identities=27%  Similarity=0.253  Sum_probs=33.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCC
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGF  255 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~  255 (673)
                      +|.|-|++|+||||+|+.+.++.-.  .     +|      +.-.++++|++..+..
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl--~-----~v------saG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGL--K-----LV------SAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCC--c-----ee------eccHHHHHHHHHcCCC
Confidence            6899999999999999999985322  1     12      3345888898887654

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.29  E-value=0.057  Score=62.22  Aligned_cols=47  Identities=28%  Similarity=0.301  Sum_probs=37.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|....+.++.+.+..-.     ..-.-|.|+|..|+|||++|+.+++.
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a-----~~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVA-----QSDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHh-----CCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            479999988888877664332     12245889999999999999999985

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.25  E-value=0.1  Score=58.27  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=22.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-..++|+|+.|+|||||++.+...
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3468999999999999999999874

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.25  E-value=0.08  Score=53.25  Aligned_cols=87  Identities=15%  Similarity=0.145  Sum_probs=46.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHH--HHHHHHHHHhhCC---CCCcCcHHH-HHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDEL--RIAKAIIEALEGF---VPTVGELNS-LLESI  269 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~~~~~i~~~l~~~---~~~~~~~~~-~~~~l  269 (673)
                      ..++|.++|++|+||||++..+...  ....-..+..++.. .+...  +-+....+..+..   .....+... ....+
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~--l~~~g~~V~li~~D-~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l  147 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANK--LKKQGKSVLLAAGD-TFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAI  147 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEeCC-CCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHH
Confidence            4689999999999999998777653  22222345555433 33332  3333344444422   111122222 22334


Q ss_pred             HHHhCCCeEEEEEcCC
Q 005860          270 RASLVGKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~~kr~LlVLDdv  285 (673)
                      ........=+|++|-.
T Consensus       148 ~~~~~~~~D~ViIDT~  163 (272)
T TIGR00064       148 QKAKARNIDVVLIDTA  163 (272)
T ss_pred             HHHHHCCCCEEEEeCC
Confidence            4434444557888866

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed

Probab=95.20  E-value=0.15  Score=50.80  Aligned_cols=24  Identities=29%  Similarity=0.375  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (248)
T PRK09580         27 GEVHAIMGPNGSGKSTLSATLAGR   50 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            358999999999999999999985

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.19  E-value=0.085  Score=52.96  Aligned_cols=142  Identities=21%  Similarity=0.193  Sum_probs=76.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC-ccccccCCeEEEEEcCCcccH-HHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND-SDVFEYFDKRMWVCVSDPFDE-LRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~-~~~~~~F~~~~wv~vs~~~~~-~~~~~  246 (673)
                      ..++|-.++.+++..++....-.   ++-.-|.|+|+.|.|||+|.-.+..+ .++.++   .+-|........ +-.++
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~---gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~---~l~v~Lng~~~~dk~al~   97 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILH---GESNSVIIIGPRGSGKTILIDTRLSDIQENGEN---FLLVRLNGELQTDKIALK   97 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHh---cCCCceEEEccCCCCceEeeHHHHhhHHhcCCe---EEEEEECccchhhHHHHH
Confidence            46889888888888877443210   12235788999999999998777665 123333   344455444332 22444


Q ss_pred             HHHHHhhC----CCCCcCcHHHHHHHHHHHhC------CCeEEEEEcCCCCCCcc-chhhhhhhcc----CCCCCeEEEE
Q 005860          247 AIIEALEG----FVPTVGELNSLLESIRASLV------GKKFLLILDDMWTDDYS-KWEPFHYCLK----NGVRGSKILV  311 (673)
Q Consensus       247 ~i~~~l~~----~~~~~~~~~~~~~~l~~~l~------~kr~LlVLDdvw~~~~~-~~~~l~~~l~----~~~~gs~iiv  311 (673)
                      .|.+++..    ......+..+....+-..|+      +-++..|+|.+.-.-.. .-..+...+.    ...+=+-|-+
T Consensus        98 ~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~  177 (408)
T KOG2228|consen   98 GITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGV  177 (408)
T ss_pred             HHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEe
Confidence            55555433    22333334444445555553      34688888876111000 0011222222    2355677888


Q ss_pred             EcCCh
Q 005860          312 TTRKE  316 (673)
Q Consensus       312 Ttr~~  316 (673)
                      |||-.
T Consensus       178 Ttrld  182 (408)
T KOG2228|consen  178 TTRLD  182 (408)
T ss_pred             ecccc
Confidence            99853

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.18  E-value=0.034  Score=50.45  Aligned_cols=22  Identities=32%  Similarity=0.557  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ||.|+|.+|+||||+|+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            5789999999999999998884

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.16  E-value=0.079  Score=60.15  Aligned_cols=86  Identities=23%  Similarity=0.230  Sum_probs=50.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      .+||+++|+.|+||||++.++.........-..+..++. +.+.  ..+.++...+.++.......+.+++...+. .++
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~-Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~-~~~  262 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTT-DSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALA-ALG  262 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecC-cccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHH-Hhc
Confidence            479999999999999999888764221111124445543 3333  345555666666554433345555555554 344


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      ++. +|++|-.
T Consensus       263 ~~D-~VLIDTA  272 (767)
T PRK14723        263 DKH-LVLIDTV  272 (767)
T ss_pred             CCC-EEEEeCC
Confidence            443 7777866

>PRK03839 putative kinase; Provisional

Probab=95.16  E-value=0.014  Score=54.98  Aligned_cols=22  Identities=41%  Similarity=0.696  Sum_probs=20.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|+|++|+||||+|+.+.+.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999985

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.16  E-value=0.012  Score=56.46  Aligned_cols=22  Identities=45%  Similarity=0.552  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998774

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.14  E-value=0.015  Score=54.99  Aligned_cols=25  Identities=36%  Similarity=0.380  Sum_probs=22.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +..+|.|+|++|+||||+|+.+...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3679999999999999999998863

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=95.13  E-value=0.086  Score=53.41  Aligned_cols=95  Identities=18%  Similarity=0.222  Sum_probs=58.3

Q ss_pred             cceechhhHHHHHHHhccCCccc------ccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEE------IINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      ++=|-++.+++|.+...-+-.+.      +-..++=|.++|++|.|||-||++|.+.  ....     |+.|..+     
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~--T~At-----FIrvvgS-----  219 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ--TDAT-----FIRVVGS-----  219 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhc--cCce-----EEEeccH-----
Confidence            56678988988888764432100      2345677899999999999999999996  3233     4444432     


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC-CCeEEEEEcCC
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASLV-GKKFLLILDDM  285 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~kr~LlVLDdv  285 (673)
                         ++.+..-+.      -..+...+.+.-+ ..+..|.+|.+
T Consensus       220 ---ElVqKYiGE------GaRlVRelF~lArekaPsIIFiDEI  253 (406)
T COG1222         220 ---ELVQKYIGE------GARLVRELFELAREKAPSIIFIDEI  253 (406)
T ss_pred             ---HHHHHHhcc------chHHHHHHHHHHhhcCCeEEEEech
Confidence               122222111      1223334444433 56889999988

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.11  E-value=0.032  Score=52.41  Aligned_cols=22  Identities=41%  Similarity=0.570  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998874

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.10  E-value=0.09  Score=55.87  Aligned_cols=88  Identities=17%  Similarity=0.197  Sum_probs=44.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ...+|+++|..|+||||++..+..........+.+..+.... .....+-+....+.++.......+..+....+ ..+.
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al-~~l~  268 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLML-HELR  268 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHHHHHHH-HHhc
Confidence            357999999999999999976655311111223334443222 12223334444455544433333333333222 2344


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      ++ -++++|-.
T Consensus       269 ~~-d~VLIDTa  278 (420)
T PRK14721        269 GK-HMVLIDTV  278 (420)
T ss_pred             CC-CEEEecCC
Confidence            44 34666655

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.10  E-value=0.19  Score=50.76  Aligned_cols=53  Identities=17%  Similarity=0.169  Sum_probs=36.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      -.++.|.|.+|+||||++.++.... ...+=..++|+++..  ...++...+...+
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~-~~~~g~~vl~iS~E~--~~~~~~~r~~~~~   82 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDL-ITQHGVRVGTISLEE--PVVRTARRLLGQY   82 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH-HHhcCceEEEEEccc--CHHHHHHHHHHHH
Confidence            4588899999999999998776642 122134678887765  4455666665554

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=95.07  E-value=0.048  Score=56.54  Aligned_cols=45  Identities=16%  Similarity=0.083  Sum_probs=32.9

Q ss_pred             ceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          171 IRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       171 ~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|....++++.+.+..-.     ..-.-|.|+|..|+||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a-----~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLA-----PLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHh-----CCCCCEEEECCCCChHHHHHHHHHHh
Confidence            4677777777776664433     12234789999999999999999874

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=95.06  E-value=0.0037  Score=61.13  Aligned_cols=37  Identities=22%  Similarity=0.127  Sum_probs=16.6

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecc
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIAT  552 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~  552 (673)
                      -.+|+.|+++.+..  -......-.+.+++.|..|+|++
T Consensus       233 N~~L~~lnlsm~sG--~t~n~~~ll~~scs~L~~LNlsW  269 (419)
T KOG2120|consen  233 NSNLVRLNLSMCSG--FTENALQLLLSSCSRLDELNLSW  269 (419)
T ss_pred             cccceeeccccccc--cchhHHHHHHHhhhhHhhcCchH
Confidence            34455555544431  01122333455555555555555

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.03  E-value=0.083  Score=52.87  Aligned_cols=41  Identities=17%  Similarity=0.244  Sum_probs=29.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      +.-.++.|.|.+|+||||+|.++.... . ..=..++|++...
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~-a-~~Ge~vlyis~Ee   74 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQ-A-SRGNPVLFVTVES   74 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHH-H-hCCCcEEEEEecC
Confidence            345799999999999999997654321 1 2234678888764

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.03  E-value=0.033  Score=64.69  Aligned_cols=52  Identities=27%  Similarity=0.316  Sum_probs=37.7

Q ss_pred             CcceechhhHHHHHHHhccCCcc-c-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE-E-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~-~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.+..++++.+++...-.. +     +-...+-|.++|++|+||||||+++.+.
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            45889999999988876432100 0     0123456889999999999999999885

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.02  E-value=0.12  Score=53.11  Aligned_cols=85  Identities=18%  Similarity=0.182  Sum_probs=48.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+...    -+..++..+... -++.++.......-...       ..+....     .
T Consensus        69 Gqri~I~G~sG~GKTtLl~~Ia~~~~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~  144 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARGTT----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAA  144 (326)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHH
Confidence            35789999999999999999998532    233444444432 34444444444432111       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  ++|.+|+++||+
T Consensus       145 ~~a~~~AEyfr~~g~~Vll~~Dsl  168 (326)
T cd01136         145 YTATAIAEYFRDQGKDVLLLMDSL  168 (326)
T ss_pred             HHHHHHHHHHHHcCCCeEEEeccc
Confidence            1122233333  589999999998

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.02  E-value=0.04  Score=52.75  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=22.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|++|+||||||+.+...
T Consensus        23 ~~~~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         23 KGVVLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999884

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=95.02  E-value=0.022  Score=57.32  Aligned_cols=88  Identities=30%  Similarity=0.348  Sum_probs=47.6

Q ss_pred             HHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHH-hhCCCC
Q 005860          179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEA-LEGFVP  257 (673)
Q Consensus       179 ~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~-l~~~~~  257 (673)
                      ..+++.+....        +-+.++|+.|+|||++++...+...- ..| ...-++.|...+...++. +++. +.....
T Consensus        23 ~~ll~~l~~~~--------~pvLl~G~~GtGKT~li~~~l~~l~~-~~~-~~~~~~~s~~Tts~~~q~-~ie~~l~k~~~   91 (272)
T PF12775_consen   23 SYLLDLLLSNG--------RPVLLVGPSGTGKTSLIQNFLSSLDS-DKY-LVITINFSAQTTSNQLQK-IIESKLEKRRG   91 (272)
T ss_dssp             HHHHHHHHHCT--------EEEEEESSTTSSHHHHHHHHHHCSTT-CCE-EEEEEES-TTHHHHHHHH-CCCTTECECTT
T ss_pred             HHHHHHHHHcC--------CcEEEECCCCCchhHHHHhhhccCCc-ccc-ceeEeeccCCCCHHHHHH-HHhhcEEcCCC
Confidence            45555555443        45689999999999999887764221 111 234456666555544432 2221 111000


Q ss_pred             CcCcHHHHHHHHHHHhCCCeEEEEEcCCCC
Q 005860          258 TVGELNSLLESIRASLVGKKFLLILDDMWT  287 (673)
Q Consensus       258 ~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~  287 (673)
                        .        ...--.+|+.++.+||+--
T Consensus        92 --~--------~~gP~~~k~lv~fiDDlN~  111 (272)
T PF12775_consen   92 --R--------VYGPPGGKKLVLFIDDLNM  111 (272)
T ss_dssp             --E--------EEEEESSSEEEEEEETTT-
T ss_pred             --C--------CCCCCCCcEEEEEecccCC
Confidence              0        0000146899999999933

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.00  E-value=0.022  Score=55.61  Aligned_cols=21  Identities=33%  Similarity=0.594  Sum_probs=19.4

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|++|+||||+|+.+.+.
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            889999999999999998774

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=94.98  E-value=0.11  Score=55.25  Aligned_cols=85  Identities=19%  Similarity=0.216  Sum_probs=49.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCC-------CCCcCcHH-----
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGF-------VPTVGELN-----  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~-----  263 (673)
                      -..++|+|..|+|||||++.+.+..    +.+..+++.+.+.. .+.+++.+....=...       ..+..-..     
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~  230 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAP----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRAL  230 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCC----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHH
Confidence            4589999999999999999999853    34455666555543 3334444443210000       01111111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       231 ~~a~tiAEyfrd~G~~VLl~~Dsl  254 (433)
T PRK07594        231 FVATTIAEFFRDNGKRVVLLADSL  254 (433)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCH
Confidence            1122234444  589999999999

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=94.94  E-value=0.03  Score=50.67  Aligned_cols=36  Identities=31%  Similarity=0.254  Sum_probs=27.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC  234 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  234 (673)
                      ..||-|.|.+|+||||||+++.+.  ....-..+.++.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~--L~~~g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERR--LFARGIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHH--HHHTTS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEec
Confidence            368999999999999999999985  444444556653

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PRK04040 adenylate kinase; Provisional

Probab=94.94  E-value=0.018  Score=54.43  Aligned_cols=23  Identities=30%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|+|++|+||||+++.+.+.
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~   25 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEK   25 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            68999999999999999998884

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.94  E-value=0.091  Score=52.38  Aligned_cols=79  Identities=13%  Similarity=0.251  Sum_probs=47.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccc--ccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVF--EYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      .++|.++|++|.|||+|.+++++...++  ..+.....+.++.    ..++.+-...      .......+.+.+.+.+.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins----hsLFSKWFsE------SgKlV~kmF~kI~ELv~  246 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS----HSLFSKWFSE------SGKLVAKMFQKIQELVE  246 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh----hHHHHHHHhh------hhhHHHHHHHHHHHHHh
Confidence            5899999999999999999999975443  3343333343322    1222222111      11233455566666666


Q ss_pred             CCe--EEEEEcCC
Q 005860          275 GKK--FLLILDDM  285 (673)
Q Consensus       275 ~kr--~LlVLDdv  285 (673)
                      ++.  +++.+|.|
T Consensus       247 d~~~lVfvLIDEV  259 (423)
T KOG0744|consen  247 DRGNLVFVLIDEV  259 (423)
T ss_pred             CCCcEEEEEeHHH
Confidence            554  45568888

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.91  E-value=0.055  Score=56.80  Aligned_cols=82  Identities=21%  Similarity=0.182  Sum_probs=49.0

Q ss_pred             CcceechhhHHHHHHHhccC-------CcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC---CeEEEEEcCCc
Q 005860          169 SEIRGRDEEKSSLKSKLLCE-------SSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF---DKRMWVCVSDP  238 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~-------~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~  238 (673)
                      ..++|.++.++.+...+...       ..-......+-|.++|++|+|||++|+.+....  ...|   +..-|+..+..
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l--~~~fi~vdat~~~e~g~v   89 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLA--NAPFIKVEATKFTEVGYV   89 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHh--CCeEEEeecceeecCCcc
Confidence            46888888888776665432       000001224678999999999999999998853  2333   33323322222


Q ss_pred             -ccHHHHHHHHHHHh
Q 005860          239 -FDELRIAKAIIEAL  252 (673)
Q Consensus       239 -~~~~~~~~~i~~~l  252 (673)
                       .+...+++.+.+..
T Consensus        90 G~dvE~i~r~l~e~A  104 (441)
T TIGR00390        90 GRDVESMVRDLTDAA  104 (441)
T ss_pred             cCCHHHHHHHHHHHH
Confidence             25556666655543

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=94.91  E-value=0.031  Score=49.16  Aligned_cols=25  Identities=32%  Similarity=0.274  Sum_probs=22.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      -.+|.+.|.-|+||||+++.+.+..
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3589999999999999999999863

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=94.89  E-value=0.019  Score=53.98  Aligned_cols=23  Identities=39%  Similarity=0.644  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|+|+.|+|||||++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999998774

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=94.89  E-value=0.015  Score=54.61  Aligned_cols=22  Identities=41%  Similarity=0.501  Sum_probs=20.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|.+|+||||+|+.+.+.
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999885

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=94.86  E-value=0.12  Score=55.01  Aligned_cols=85  Identities=20%  Similarity=0.191  Sum_probs=47.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCC-------CCCcCcHH-----
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGF-------VPTVGELN-----  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~~-----  263 (673)
                      -..++|+|..|+|||||++.+....+   . +..+.+.+.+. -.+.++..+.+..-+..       ..+..-..     
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~~~---~-~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~  215 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARNTD---A-DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAA  215 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCC---C-CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHH
Confidence            35799999999999999999998532   1 23333333332 23444444443332111       11111111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       216 ~~a~~iAEyfrd~G~~Vll~~Dsl  239 (418)
T TIGR03498       216 YTATAIAEYFRDQGKDVLLLMDSV  239 (418)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccch
Confidence            1222344444  589999999999

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=94.86  E-value=0.1  Score=55.95  Aligned_cols=88  Identities=18%  Similarity=0.087  Sum_probs=52.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -.-++|.|..|+|||||+..+...... .+=+.++++-+.+... +.++..++...=...       ..+..-.     .
T Consensus       144 GQR~gIfa~~GvGKt~Ll~~i~~~~~~-~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~  222 (463)
T PRK09280        144 GGKIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVA  222 (463)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHh-cCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            357899999999999999877654221 1114577787776543 445555555431111       1111111     1


Q ss_pred             HHHHHHHHHh---CCCeEEEEEcCC
Q 005860          264 SLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      .....+.+++   +++++||++|++
T Consensus       223 ~~a~tiAEyfrd~~G~~VLll~Dsl  247 (463)
T PRK09280        223 LTGLTMAEYFRDVEGQDVLLFIDNI  247 (463)
T ss_pred             HHHHHHHHHHHHhcCCceEEEecch
Confidence            2233355555   689999999999

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=94.86  E-value=0.026  Score=52.17  Aligned_cols=25  Identities=32%  Similarity=0.397  Sum_probs=22.4

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++|+|..|+|||||++.+...
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHH
Confidence            4679999999999999999988875

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.84  E-value=0.016  Score=53.78  Aligned_cols=40  Identities=23%  Similarity=0.225  Sum_probs=29.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccc-ccCCeEEEEEcCCc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVF-EYFDKRMWVCVSDP  238 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~  238 (673)
                      ..++.+.|+.|+|||.||+.+.+.  +. ......+-+..+.-
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~--l~~~~~~~~~~~d~s~~   43 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAEL--LFVGSERPLIRIDMSEY   43 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHH--HT-SSCCEEEEEEGGGH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHH--hccCCccchHHHhhhcc
Confidence            568899999999999999998884  22 23345555665543

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.84  E-value=0.096  Score=56.60  Aligned_cols=86  Identities=17%  Similarity=0.182  Sum_probs=44.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc--cHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF--DELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      .+|++++|+.|+||||++.++......+..-..+..++. +.+  ...+-++...+.++.......+..+....+ ..+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~-Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL-~~L~  333 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTT-DSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLAL-SELR  333 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeC-CccchhHHHHHHHHHHHhCCCeeccCCchhHHHHH-Hhcc
Confidence            479999999999999999888864222221223445543 233  233334444454443322112222222222 2334


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      ++ -.+++|-.
T Consensus       334 d~-d~VLIDTa  343 (484)
T PRK06995        334 NK-HIVLIDTI  343 (484)
T ss_pred             CC-CeEEeCCC
Confidence            44 36677766

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.83  E-value=0.053  Score=56.70  Aligned_cols=112  Identities=18%  Similarity=0.221  Sum_probs=61.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ..|.|.|+.|+||||+++.+.+.  +..+...+++. +.++...  ..... ..+-.......+.......++..++..+
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~--i~~~~~~~i~t-iEdp~E~--~~~~~-~~~i~q~evg~~~~~~~~~l~~~lr~~p  196 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDY--INKNAAGHIIT-IEDPIEY--VHRNK-RSLINQREVGLDTLSFANALRAALREDP  196 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh--hCcCCCCEEEE-EcCChhh--hccCc-cceEEccccCCCCcCHHHHHHHhhccCC
Confidence            68999999999999999988874  33344455543 2222111  10000 0000000000111234566777888889


Q ss_pred             EEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHH
Q 005860          278 FLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR  320 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~  320 (673)
                      =.|++|.+.  +...+...   +.....|..|+.|+...++..
T Consensus       197 d~i~vgEir--d~~~~~~~---l~aa~tGh~v~~T~Ha~~~~~  234 (343)
T TIGR01420       197 DVILIGEMR--DLETVELA---LTAAETGHLVFGTLHTNSAAQ  234 (343)
T ss_pred             CEEEEeCCC--CHHHHHHH---HHHHHcCCcEEEEEcCCCHHH
Confidence            999999994  33334332   222234656777776655443

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=94.83  E-value=0.13  Score=54.80  Aligned_cols=85  Identities=19%  Similarity=0.171  Sum_probs=50.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH-HHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE-LRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+...    .+.++++-+.+.... .++..+.+..-+..       ..+..-.     .
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~  233 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAA  233 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHH
Confidence            46789999999999999999998532    245666767665443 34444443321111       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       234 ~~a~tiAEyfrd~G~~Vll~~Dsl  257 (442)
T PRK08927        234 YLTLAIAEYFRDQGKDVLCLMDSV  257 (442)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCc
Confidence            1222344444  589999999999

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=94.81  E-value=0.023  Score=52.71  Aligned_cols=81  Identities=21%  Similarity=0.260  Sum_probs=38.3

Q ss_pred             hhhCCccceeeeccccccccccchhhhccccccc-cccccceecCCCCcccc--hhhhcCCCccEEEeccCCCCccccc-
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL-IHLRYLRLVGLGTEELP--ETCCELLNLQVLEIEQCTSLKRLPL-  614 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L-~~Lr~L~L~~~~i~~LP--~~i~~L~~L~~L~l~~c~~l~~lP~-  614 (673)
                      |..++.|..|.|.+       +.+..+-+.+..+ ++|..|.|.+|+|.+|-  ..+..++.|++|.+-+++ ++..+. 
T Consensus        60 lp~l~rL~tLll~n-------NrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll~Np-v~~k~~Y  131 (233)
T KOG1644|consen   60 LPHLPRLHTLLLNN-------NRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLLGNP-VEHKKNY  131 (233)
T ss_pred             CCCccccceEEecC-------CcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceeeecCCc-hhcccCc
Confidence            34455555555555       5555554444433 33555555555544432  123344455555555433 333322 


Q ss_pred             ---cccccccCCeeec
Q 005860          615 ---GIGKLVNLRHLTY  627 (673)
Q Consensus       615 ---~i~~L~~Lr~L~l  627 (673)
                         -+.++++|+.||.
T Consensus       132 R~yvl~klp~l~~LDF  147 (233)
T KOG1644|consen  132 RLYVLYKLPSLRTLDF  147 (233)
T ss_pred             eeEEEEecCcceEeeh
Confidence               2455555555554

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=94.80  E-value=0.24  Score=55.39  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|+|||||++.+...
T Consensus        27 Ge~~~liG~NGsGKSTLl~~l~Gl   50 (530)
T PRK15064         27 GNRYGLIGANGCGKSTFMKILGGD   50 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999975

>PRK00625 shikimate kinase; Provisional

Probab=94.80  E-value=0.019  Score=53.44  Aligned_cols=22  Identities=23%  Similarity=0.318  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.++||+|+||||+++.+.+.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999999774

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=94.79  E-value=0.12  Score=58.51  Aligned_cols=150  Identities=24%  Similarity=0.280  Sum_probs=79.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc---cccccC-CeEEEEEcCCcccHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS---DVFEYF-DKRMWVCVSDPFDELRI  244 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~---~~~~~F-~~~~wv~vs~~~~~~~~  244 (673)
                      +.++||++++.+++..|.....    + .+  .++|.+|||||++|.-+....   .+-... +..++.-     |    
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~K----N-NP--vLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sL-----D----  233 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTK----N-NP--VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSL-----D----  233 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCC----C-CC--eEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEe-----c----
Confidence            4689999999999999976652    2 22  357999999999875444420   121111 2222210     1    


Q ss_pred             HHHHHHHhhCCCCCcCcHHHHHHHHHHHh-CCCeEEEEEcCCCCC----C-----ccchhhhhhhccCCCCCeEEEEEcC
Q 005860          245 AKAIIEALEGFVPTVGELNSLLESIRASL-VGKKFLLILDDMWTD----D-----YSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       245 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-~~kr~LlVLDdvw~~----~-----~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                         |..-+.+ ..-..+.++....+.+.+ +.++..+++|.++.-    .     .+.-+.++..|..+ .--.|=.||-
T Consensus       234 ---~g~LvAG-akyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLARG-eL~~IGATT~  308 (786)
T COG0542         234 ---LGSLVAG-AKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARG-ELRCIGATTL  308 (786)
T ss_pred             ---HHHHhcc-ccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhcC-CeEEEEeccH
Confidence               1111111 122344555444444444 345899999998431    0     11222233333332 2334666776


Q ss_pred             ChhHHH------hccccceeecCCCCccccc
Q 005860          315 KETVAR------MMESIHVISIKELSEQECW  339 (673)
Q Consensus       315 ~~~v~~------~~~~~~~~~l~~L~~~~~~  339 (673)
                      ++.---      ..--...+.++..+.+++.
T Consensus       309 ~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti  339 (786)
T COG0542         309 DEYRKYIEKDAALERRFQKVLVDEPSVEDTI  339 (786)
T ss_pred             HHHHHHhhhchHHHhcCceeeCCCCCHHHHH
Confidence            543211      0112467788888888875

>PTZ00185 ATPase alpha subunit; Provisional

Probab=94.78  E-value=0.15  Score=54.69  Aligned_cols=89  Identities=19%  Similarity=0.214  Sum_probs=51.8

Q ss_pred             eEEEEEEccCCChHHHHH-HHHhcCccc-----cccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC------CcCc---
Q 005860          197 IQIITIVGMGGIGKTTLA-QFAYNDSDV-----FEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP------TVGE---  261 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa-~~v~~~~~~-----~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~---  261 (673)
                      -.-++|.|-.|+|||||| -.+.|...+     ..+-+.++++.+.+..+.-.-+.+.+++-+.-..      ..++   
T Consensus       189 GQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~  268 (574)
T PTZ00185        189 GQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAG  268 (574)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHH
Confidence            356899999999999997 666665322     1244678899998876543323333333321100      0111   


Q ss_pred             HH----HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          262 LN----SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       262 ~~----~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      ..    -....+.+++  +++.+|||+||+
T Consensus       269 ~r~~Apy~a~tiAEYFrd~GkdVLiv~DDL  298 (574)
T PTZ00185        269 LQYLAPYSGVTMGEYFMNRGRHCLCVYDDL  298 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEcCc
Confidence            00    0112233333  589999999999

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=94.77  E-value=0.22  Score=50.80  Aligned_cols=24  Identities=33%  Similarity=0.407  Sum_probs=22.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.++++.|+.|+|||||.+.+..-
T Consensus        31 Gei~gllG~NGAGKTTllk~l~gl   54 (293)
T COG1131          31 GEIFGLLGPNGAGKTTLLKILAGL   54 (293)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999985

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=94.76  E-value=0.019  Score=53.86  Aligned_cols=24  Identities=46%  Similarity=0.530  Sum_probs=22.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|-||=|+||||||+.+.+.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~   27 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEH   27 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHH
Confidence            478999999999999999999995

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.75  E-value=0.037  Score=56.41  Aligned_cols=83  Identities=19%  Similarity=0.113  Sum_probs=50.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  270 (673)
                      .-+++-|+|..|+||||||..+...  ....-..++||.....+++.     .++.++...+     ..+..++....+.
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e  124 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAE  124 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHH
T ss_pred             cCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHH
Confidence            4579999999999999999777764  44445668999988877664     3344443311     1233344455555


Q ss_pred             HHhCC-CeEEEEEcCC
Q 005860          271 ASLVG-KKFLLILDDM  285 (673)
Q Consensus       271 ~~l~~-kr~LlVLDdv  285 (673)
                      ..++. .--+||+|-|
T Consensus       125 ~lirsg~~~lVVvDSv  140 (322)
T PF00154_consen  125 QLIRSGAVDLVVVDSV  140 (322)
T ss_dssp             HHHHTTSESEEEEE-C
T ss_pred             HHhhcccccEEEEecC
Confidence            55543 4458899987

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=94.74  E-value=0.23  Score=47.55  Aligned_cols=21  Identities=24%  Similarity=0.254  Sum_probs=19.9

Q ss_pred             EEEEEEccCCChHHHHHHHHh
Q 005860          198 QIITIVGMGGIGKTTLAQFAY  218 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~  218 (673)
                      +++.|.|+.|.|||||.+.+.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            789999999999999999887

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=94.74  E-value=0.019  Score=55.89  Aligned_cols=120  Identities=16%  Similarity=0.139  Sum_probs=59.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC---CcCcHHHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP---TVGELNSLLESIRAS  272 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~~  272 (673)
                      +.+++.|+|+.|.||||+.+.+...   .-.+..-++|..... . -.+...++..++..+.   .......-...+...
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~---~~la~~g~~vpa~~~-~-~~~~~~il~~~~l~d~~~~~lS~~~~e~~~~a~i  103 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVI---VLMAQIGCFVPCDSA-D-IPIVDCILARVGASDSQLKGVSTFMAEMLETAAI  103 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHH---HHHHHhCCCcCcccE-E-EeccceeEeeeccccchhcCcChHHHHHHHHHHH
Confidence            3579999999999999998887642   111111123322210 0 0122223333322211   111111112223333


Q ss_pred             h--CCCeEEEEEcCCCCC----Ccc--chhhhhhhccCCCCCeEEEEEcCChhHHHhc
Q 005860          273 L--VGKKFLLILDDMWTD----DYS--KWEPFHYCLKNGVRGSKILVTTRKETVARMM  322 (673)
Q Consensus       273 l--~~kr~LlVLDdvw~~----~~~--~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~  322 (673)
                      +  -..+-|++||.....    |..  .|. +...+.. ..|+.+|+||...++...+
T Consensus       104 l~~~~~~sLvLLDEp~~gT~~lD~~~~~~~-il~~l~~-~~~~~vlisTH~~el~~~~  159 (222)
T cd03285         104 LKSATENSLIIIDELGRGTSTYDGFGLAWA-IAEYIAT-QIKCFCLFATHFHELTALA  159 (222)
T ss_pred             HHhCCCCeEEEEecCcCCCChHHHHHHHHH-HHHHHHh-cCCCeEEEEechHHHHHHh
Confidence            3  356889999998321    111  121 1122322 3478899999987776654

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=94.72  E-value=0.18  Score=58.00  Aligned_cols=122  Identities=12%  Similarity=0.141  Sum_probs=70.8

Q ss_pred             cceechhhHHHHHHHhccCCccccc-CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEII-NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .++|-++.+..|-+.+.....+-.+ .......+.|+.|+|||-||+++...  +....+..+-++      ..+... +
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~--~Fgse~~~IriD------mse~~e-v  633 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEY--VFGSEENFIRLD------MSEFQE-V  633 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHH--HcCCccceEEec------hhhhhh-h
Confidence            5778888888888777654421111 25678899999999999999988873  222223333333      333333 3


Q ss_pred             HHHhhCCCCCcCcHHHHHHHHHHHhCCCeE-EEEEcCCCCCCccchhhhhhhccC
Q 005860          249 IEALEGFVPTVGELNSLLESIRASLVGKKF-LLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       249 ~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~-LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                      .+.++.+ +..-. .+--..+.+.++.++| +|+||||...+......+...+..
T Consensus       634 skligsp-~gyvG-~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~lD~  686 (898)
T KOG1051|consen  634 SKLIGSP-PGYVG-KEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLDR  686 (898)
T ss_pred             hhccCCC-ccccc-chhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHHHhc
Confidence            3333332 21111 1123467777888776 556899965555555544455543

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.72  E-value=0.07  Score=59.59  Aligned_cols=49  Identities=14%  Similarity=0.147  Sum_probs=38.8

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....++|....++++.+.+..-.     ..-.-|.|+|..|+|||++|+.+++.
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a-----~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVA-----RSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHh-----CcCCCEEEECCCCccHHHHHHHHHHh
Confidence            44689999999999888775443     11234679999999999999999985

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.71  E-value=0.16  Score=49.87  Aligned_cols=41  Identities=17%  Similarity=0.213  Sum_probs=29.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP  238 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  238 (673)
                      .-.++.|.|.+|+||||||.++.... . ..-..++|++....
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~-~-~~g~~~~~is~e~~   59 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKG-L-RDGDPVIYVTTEES   59 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHH-H-hcCCeEEEEEccCC
Confidence            45799999999999999997755421 1 22356788876543

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR03263 guanyl_kin guanylate kinase

Probab=94.71  E-value=0.023  Score=53.40  Aligned_cols=23  Identities=35%  Similarity=0.609  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|+|+|+.|+||||||+.+.+.
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            47999999999999999999984

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=94.70  E-value=0.41  Score=49.73  Aligned_cols=65  Identities=11%  Similarity=0.040  Sum_probs=44.5

Q ss_pred             CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHh-ccccceeecCCCCcccc
Q 005860          274 VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARM-MESIHVISIKELSEQEC  338 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~-~~~~~~~~l~~L~~~~~  338 (673)
                      .+++=++|+|++..-+...-+.+...+.....++.+|++|.+. .+... .+-...+.+.+++.++.
T Consensus       106 ~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~  172 (334)
T PRK07993        106 LGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYA  172 (334)
T ss_pred             cCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHH
Confidence            3566689999986656667788888888777778777777763 34433 33356677777776653

>cd04159 Arl10_like Arl10-like subfamily

Probab=94.70  E-value=0.13  Score=46.57  Aligned_cols=21  Identities=43%  Similarity=0.586  Sum_probs=19.6

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|+|..|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            789999999999999999886

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=94.69  E-value=0.26  Score=53.75  Aligned_cols=24  Identities=33%  Similarity=0.570  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|+|||||++.+...
T Consensus        50 GEivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         50 GEIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            358999999999999999999885

>PRK00131 aroK shikimate kinase; Reviewed

Probab=94.69  E-value=0.022  Score=53.18  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|+|++|+||||+|+.+.+.
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999885

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=94.67  E-value=0.036  Score=49.36  Aligned_cols=23  Identities=39%  Similarity=0.508  Sum_probs=21.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|..|+|||||.+.+...
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEEccCCCccccceeeeccc
Confidence            48999999999999999999985

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=94.66  E-value=0.016  Score=49.23  Aligned_cols=21  Identities=52%  Similarity=0.580  Sum_probs=18.7

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |-|+|.+|+|||+||+.+..+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998875

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=94.65  E-value=0.18  Score=47.66  Aligned_cols=21  Identities=24%  Similarity=0.173  Sum_probs=18.7

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ++.|.|..|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            478999999999999998884

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=94.65  E-value=0.13  Score=51.01  Aligned_cols=89  Identities=19%  Similarity=0.114  Sum_probs=54.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccc--cccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH----
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDV--FEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL----  262 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~----  262 (673)
                      -..++|.|-.|+|||||+..+.++...  +.+-+.++++-+.+... ..++..++.+.=...       ..+..-.    
T Consensus        69 GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~  148 (276)
T cd01135          69 GQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERII  148 (276)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHH
Confidence            356899999999999999888875321  12347789998888654 445555544431111       0111101    


Q ss_pred             -HHHHHHHHHHh---CCCeEEEEEcCC
Q 005860          263 -NSLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       263 -~~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                       --....+.+++   +++++|+++||+
T Consensus       149 a~~~a~aiAEyfrd~~g~~VLl~~D~l  175 (276)
T cd01135         149 TPRMALTTAEYLAYEKGKHVLVILTDM  175 (276)
T ss_pred             HHHHHHHHHHHHHhccCCeEEEEEcCh
Confidence             11222344554   378999999999

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=94.64  E-value=0.2  Score=51.40  Aligned_cols=48  Identities=21%  Similarity=0.121  Sum_probs=36.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAI  248 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i  248 (673)
                      -..++|.|..|+|||+|++++.+..    +-+.++++-+.+..+ +.+++.++
T Consensus       157 Gqr~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         157 GGTAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             CCEEEEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHH
Confidence            3579999999999999999999963    335788888877543 34455554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=94.64  E-value=0.16  Score=50.42  Aligned_cols=82  Identities=22%  Similarity=0.187  Sum_probs=48.3

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccccccCCeE-EEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDVFEYFDKR-MWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----  262 (673)
                      .-++|+|..|+|||+|| ..+.+..    +-+.+ +++-+.+..+ +.++...+.+.-...       ..+..-.     
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~~----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a  145 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQK----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLA  145 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHhc----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHH
Confidence            56899999999999996 6676631    23444 6777777643 445555554321110       1111101     


Q ss_pred             ----HHHHHHHHHHhCCCeEEEEEcCC
Q 005860          263 ----NSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       263 ----~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                          -...+.++.  +++.+|||+||+
T Consensus       146 ~~~a~aiAE~fr~--~G~~Vlvl~Dsl  170 (274)
T cd01132         146 PYTGCAMGEYFMD--NGKHALIIYDDL  170 (274)
T ss_pred             HHHHHHHHHHHHH--CCCCEEEEEcCh
Confidence                122333333  589999999999

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK04328 hypothetical protein; Provisional

Probab=94.63  E-value=0.12  Score=51.38  Aligned_cols=41  Identities=15%  Similarity=0.310  Sum_probs=29.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP  238 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  238 (673)
                      .-.++.|.|.+|+|||+||.++... .. ..-..++|++..+.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~-~~-~~ge~~lyis~ee~   62 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWN-GL-QMGEPGVYVALEEH   62 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH-HH-hcCCcEEEEEeeCC
Confidence            4579999999999999999664432 12 23456788887663

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.62  E-value=0.18  Score=46.45  Aligned_cols=117  Identities=17%  Similarity=0.083  Sum_probs=60.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEE--EEEcCCcccHHHHHHHHHHHhh-----CC----CCCc-Cc---
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRM--WVCVSDPFDELRIAKAIIEALE-----GF----VPTV-GE---  261 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~--wv~vs~~~~~~~~~~~i~~~l~-----~~----~~~~-~~---  261 (673)
                      -..|-|++..|.||||.|..+.-.. ....+...+  |+.-.........+..+  .+.     ..    ..+. .+   
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra-~~~g~~v~ivQFlKg~~~~GE~~~l~~~--~~~~~~~g~g~~~~~~~~~~~~~~   81 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRA-LGHGKKVGVIQFIKGAWPNGERAAFEPH--GVEFQVMGTGFTWETQNREADTAI   81 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHH-HHCCCeEEEEEEecCCcccChHHHHHhc--CcEEEECCCCCeecCCCcHHHHHH
Confidence            4678888999999999994444321 222222211  22222222333343332  111     00    0011 11   


Q ss_pred             HHHHHHHHHHHhCCCe-EEEEEcCCCC---CCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          262 LNSLLESIRASLVGKK-FLLILDDMWT---DDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       262 ~~~~~~~l~~~l~~kr-~LlVLDdvw~---~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      ..+.....++.+...+ =|||||.+-.   -..-..+.+...+.....+.-||+|-|+.
T Consensus        82 ~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        82 AKAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            1223344555555544 4999998821   11123456666666666778999999975

Alternate name: corrinoid adenosyltransferase.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=94.61  E-value=0.096  Score=58.03  Aligned_cols=48  Identities=21%  Similarity=0.266  Sum_probs=39.2

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...++|....++++.+.+..-.     ..-.-|.|+|..|+|||++|+.+++.
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a-----~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVA-----ASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHh-----CCCCcEEEECCCCccHHHHHHHHHHh
Confidence            4679999999988888876544     22345889999999999999999985

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.61  E-value=0.11  Score=55.90  Aligned_cols=88  Identities=15%  Similarity=0.017  Sum_probs=54.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -.-++|+|.+|+|||||+..+.+... +.+-+.++++-+.+..+ +.++..++...-...       ..+..-.     .
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~-~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~  221 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNIS-KQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVV  221 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHH-hhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHH
Confidence            35799999999999999977777532 23557888888876543 345555554321110       1111111     1


Q ss_pred             HHHHHHHHHh---CCCeEEEEEcCC
Q 005860          264 SLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      .....+.+++   +++++|+++|++
T Consensus       222 ~~a~tiAEyfrd~~G~~VLl~~Dsl  246 (461)
T PRK12597        222 LTGLTIAEYLRDEEKEDVLLFIDNI  246 (461)
T ss_pred             HHHHHHHHHHHHhcCCceEEEeccc
Confidence            2233455555   489999999999

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.60  E-value=0.053  Score=55.79  Aligned_cols=114  Identities=12%  Similarity=0.050  Sum_probs=56.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      -..+.|+|..|+|||||++++....  ... ..++.+.-........  .....-...........-...+.+...++..
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~--~~~-~~iv~ied~~El~~~~--~~~~~l~~~~~~~~~~~~~~~~~l~~~Lr~~  218 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEI--PKD-ERIITIEDTREIFLPH--PNYVHLFYSKGGQGLAKVTPKDLLQSCLRMR  218 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccC--Ccc-ccEEEEcCccccCCCC--CCEEEEEecCCCCCcCccCHHHHHHHHhcCC
Confidence            3689999999999999999988752  111 1222221111111000  0000000000000011112345566677788


Q ss_pred             eEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHH
Q 005860          277 KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR  320 (673)
Q Consensus       277 r~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~  320 (673)
                      .=.||+|.+..  .+.++.+ .....+..|  ++.|+...++..
T Consensus       219 pd~ii~gE~r~--~e~~~~l-~a~~~g~~~--~i~T~Ha~~~~~  257 (308)
T TIGR02788       219 PDRIILGELRG--DEAFDFI-RAVNTGHPG--SITTLHAGSPEE  257 (308)
T ss_pred             CCeEEEeccCC--HHHHHHH-HHHhcCCCe--EEEEEeCCCHHH
Confidence            88899999954  3344432 223222222  577777665444

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR01069 mutS2 MutS2 family protein

Probab=94.60  E-value=0.033  Score=64.34  Aligned_cols=24  Identities=21%  Similarity=0.083  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++.|+|+.|.|||||.+.+...
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHHH
Confidence            478999999999999999888653

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=94.58  E-value=0.87  Score=40.89  Aligned_cols=111  Identities=10%  Similarity=0.156  Sum_probs=75.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhcc-cCCHHHHHHHHHHHHhhhhhhhhH
Q 005860            2 VDAIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQ-FKEETVRLWLDQLKDVSYYMGDVL   80 (673)
Q Consensus         2 a~a~v~~~~~~l~~~l~~~~~~e~~~~~~~~~~i~~L~~~L~~i~~~l~~a~~~~-~~~~~~~~wl~~lr~~ay~~ed~l   80 (673)
                      |+.+++++++.+.+.+...+.+..+.....+.-.++|...++.|.-++++.+... .-+..-+.-+.++.+..-++++++
T Consensus         3 ~eL~~gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~g~~LV   82 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEKGKELV   82 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHHHHHHH
Confidence            4555566666666666666666666667777888899999999999999887643 223334677888889999999999


Q ss_pred             HHHHHHHHHHHHhccCCCCcccccccccCCccccCccchhhhHHHHHHHHHHHHHHHHHH
Q 005860           81 DEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIA  140 (673)
Q Consensus        81 D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~l~~i~  140 (673)
                      ..|..-                            .++++....+.+++|+++.+.+....
T Consensus        83 ~k~sk~----------------------------~r~n~~kk~~y~~Ki~~le~~l~~f~  114 (147)
T PF05659_consen   83 EKCSKV----------------------------RRWNLYKKPRYARKIEELEESLRRFI  114 (147)
T ss_pred             HHhccc----------------------------cHHHHHhhHhHHHHHHHHHHHHHHHh
Confidence            988510                            01223334556777777777766554

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.53  E-value=0.021  Score=53.84  Aligned_cols=22  Identities=23%  Similarity=0.350  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ||.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998874

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=94.53  E-value=0.13  Score=54.59  Aligned_cols=85  Identities=19%  Similarity=0.183  Sum_probs=48.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+...    .+..+++.+.+.. ...++...+...=...       ..+..-.     .
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~  212 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYTE----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAA  212 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCC----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHH
Confidence            45799999999999999999988532    2344455555543 2334444333321100       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dsl  236 (411)
T TIGR03496       213 FYATAIAEYFRDQGKDVLLLMDSL  236 (411)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEeCh
Confidence            1122233443  589999999999

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK05922 type III secretion system ATPase; Validated

Probab=94.53  E-value=0.24  Score=52.77  Aligned_cols=85  Identities=16%  Similarity=0.128  Sum_probs=48.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCCC-------CCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGFV-------PTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~~-------~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||.+.+.+..    ..+...++.+++.. ...+.+.+.........       .+..-.     .
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~~----~~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~  232 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKGS----KSTINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAG  232 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccC----CCCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHH
Confidence            3568999999999999999998852    22444444444432 23344444443322211       111001     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       233 ~~a~tiAEyfrd~G~~VLl~~Dsl  256 (434)
T PRK05922        233 RAAMTIAEYFRDQGHRVLFIMDSL  256 (434)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccch
Confidence            1222344444  589999999999

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=94.53  E-value=0.037  Score=56.51  Aligned_cols=52  Identities=21%  Similarity=0.291  Sum_probs=42.7

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+++|.++.++++++.+...+.. ....-+|+.++|+.|.||||||..+.+-
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g-~~~~krIl~L~GPvg~GKSsl~~~Lk~~  111 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQG-LEERKRILLLLGPVGGGKSSLAELLKRG  111 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhc-cCccceEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999988654421 1355789999999999999999998884

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=94.52  E-value=0.066  Score=53.63  Aligned_cols=23  Identities=30%  Similarity=0.293  Sum_probs=18.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|.|.|.+|+||||+|+.+.+.
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            46899999999999999998884

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=94.51  E-value=0.021  Score=61.69  Aligned_cols=157  Identities=16%  Similarity=0.216  Sum_probs=87.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      +++||-+.-...|.+.+..+.-      ..-....|+-|+||||+|+.+.....-...       ....+++.-...+.|
T Consensus        16 ~evvGQe~v~~~L~nal~~~ri------~hAYlfsG~RGvGKTt~Ari~AkalNC~~~-------~~~ePC~~C~~Ck~I   82 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGRI------AHAYLFSGPRGVGKTTIARILAKALNCENG-------PTAEPCGKCISCKEI   82 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCcc------hhhhhhcCCCCcCchhHHHHHHHHhcCCCC-------CCCCcchhhhhhHhh
Confidence            5789999999999999876642      345677999999999999877663111100       111111111122222


Q ss_pred             HHH--hhC---CCCCcCcHHHHHHHHHHHh----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC-hhH
Q 005860          249 IEA--LEG---FVPTVGELNSLLESIRASL----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK-ETV  318 (673)
Q Consensus       249 ~~~--l~~---~~~~~~~~~~~~~~l~~~l----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~-~~v  318 (673)
                      -..  +..   ..-....+++.+..+.+..    ++|-=..|+|.|+--....|+.+...+......-+.|..|.+ ..+
T Consensus        83 ~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Ki  162 (515)
T COG2812          83 NEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKI  162 (515)
T ss_pred             hcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcC
Confidence            221  000   0000112223222222221    345558899999777777888888888765555555554444 433


Q ss_pred             HH-hccccceeecCCCCcccc
Q 005860          319 AR-MMESIHVISIKELSEQEC  338 (673)
Q Consensus       319 ~~-~~~~~~~~~l~~L~~~~~  338 (673)
                      .. ...-...|.++.++.++-
T Consensus       163 p~TIlSRcq~f~fkri~~~~I  183 (515)
T COG2812         163 PNTILSRCQRFDFKRLDLEEI  183 (515)
T ss_pred             chhhhhccccccccCCCHHHH
Confidence            32 334467788888887753

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.49  E-value=0.14  Score=50.61  Aligned_cols=21  Identities=29%  Similarity=0.422  Sum_probs=17.9

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +..|+|++|+|||+||..+.-
T Consensus         3 ~~ll~g~~G~GKS~lal~la~   23 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLAL   23 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHH
Confidence            567899999999999977654

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=94.49  E-value=0.028  Score=50.30  Aligned_cols=39  Identities=21%  Similarity=0.212  Sum_probs=26.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      ++|.|+|..|+|||||++.+.+.. .+..+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l-~~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINEL-KRRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHH-HHTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-hHcCCceEEEEEccC
Confidence            479999999999999999999962 224555555555443

>PRK08149 ATP synthase SpaL; Validated

Probab=94.47  E-value=0.14  Score=54.40  Aligned_cols=85  Identities=16%  Similarity=0.222  Sum_probs=49.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+...    -+.+++..+.... ++.++..+........       ..+....     .
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~----~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~  226 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSE----ADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAA  226 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCC----CCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHH
Confidence            45799999999999999999998532    2344444444332 4455555555532211       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  ++|++||++||+
T Consensus       227 ~~a~tiAE~fr~~G~~Vll~~Dsl  250 (428)
T PRK08149        227 LVATTVAEYFRDQGKRVVLFIDSM  250 (428)
T ss_pred             HHHHHHHHHHHHcCCCEEEEccch
Confidence            1222333443  589999999999

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=94.47  E-value=0.3  Score=56.64  Aligned_cols=24  Identities=33%  Similarity=0.505  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|+.|.|||||++.+...
T Consensus       507 Ge~vaIvG~SGsGKSTLl~lL~gl  530 (711)
T TIGR00958       507 GEVVALVGPSGSGKSTVAALLQNL  530 (711)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999874

>PRK06217 hypothetical protein; Validated

Probab=94.47  E-value=0.025  Score=53.42  Aligned_cols=23  Identities=35%  Similarity=0.367  Sum_probs=20.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcCc
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      .|.|.|.+|+||||+|+++.+..
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999998853

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=94.42  E-value=0.024  Score=52.68  Aligned_cols=87  Identities=26%  Similarity=0.372  Sum_probs=66.5

Q ss_pred             ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh--ccccccccccccceecCCCCcc
Q 005860          510 SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI--LKGIEKLIHLRYLRLVGLGTEE  587 (673)
Q Consensus       510 ~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l--p~~i~~L~~Lr~L~L~~~~i~~  587 (673)
                      .+..++.|.+|.+.+|.+    ..+-|..-.-+++|.+|.|.+       +.+.++  ...+..++.|+||.+-+|.++.
T Consensus        59 ~lp~l~rL~tLll~nNrI----t~I~p~L~~~~p~l~~L~Ltn-------Nsi~~l~dl~pLa~~p~L~~Ltll~Npv~~  127 (233)
T KOG1644|consen   59 NLPHLPRLHTLLLNNNRI----TRIDPDLDTFLPNLKTLILTN-------NSIQELGDLDPLASCPKLEYLTLLGNPVEH  127 (233)
T ss_pred             cCCCccccceEEecCCcc----eeeccchhhhccccceEEecC-------cchhhhhhcchhccCCccceeeecCCchhc
Confidence            455788999999998873    344444445667899999999       887776  3346667899999999998776


Q ss_pred             cch----hhhcCCCccEEEeccCC
Q 005860          588 LPE----TCCELLNLQVLEIEQCT  607 (673)
Q Consensus       588 LP~----~i~~L~~L~~L~l~~c~  607 (673)
                      .+.    -++++++|++||+.+-.
T Consensus       128 k~~YR~yvl~klp~l~~LDF~kVt  151 (233)
T KOG1644|consen  128 KKNYRLYVLYKLPSLRTLDFQKVT  151 (233)
T ss_pred             ccCceeEEEEecCcceEeehhhhh
Confidence            653    47889999999998743

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.39  E-value=0.026  Score=51.29  Aligned_cols=22  Identities=32%  Similarity=0.585  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|.|+|++|+||||+|+.+.+.
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            4789999999999999998885

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK14738 gmk guanylate kinase; Provisional

Probab=94.37  E-value=0.037  Score=53.28  Aligned_cols=26  Identities=19%  Similarity=0.321  Sum_probs=22.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...++|.|+|++|+|||||++.+.+.
T Consensus        11 ~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         11 AKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            45788999999999999999999764

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=94.37  E-value=0.25  Score=57.32  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..|+|+|..|+|||||++.+..-
T Consensus       491 G~~iaIvG~sGsGKSTLlklL~gl  514 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLGL  514 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999998774

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.33  E-value=0.062  Score=58.26  Aligned_cols=85  Identities=22%  Similarity=0.185  Sum_probs=48.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEE-EEEcCCcccHHHHHHHHHHHhhC----CCCCcC-----cHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRM-WVCVSDPFDELRIAKAIIEALEG----FVPTVG-----ELNSLL  266 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~-wv~vs~~~~~~~~~~~i~~~l~~----~~~~~~-----~~~~~~  266 (673)
                      -.-.+|+|.+|+|||||++.|.+... ..+-++.+ ++-|.+.....   .+|.+.+..    ...+..     ....+.
T Consensus       416 GQR~LIvgpp~aGKTtLL~~IAn~i~-~n~~~~~~ivvLIgERpeEV---tdm~rsVkgeVVasT~D~p~~~~~~~a~~a  491 (672)
T PRK12678        416 GQRGLIVSPPKAGKTTILQNIANAIT-TNNPECHLMVVLVDERPEEV---TDMQRSVKGEVIASTFDRPPSDHTTVAELA  491 (672)
T ss_pred             CCEeEEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEEEeCchhhH---HHHHHhccceEEEECCCCCHHHHHHHHHHH
Confidence            35689999999999999999998521 12334443 44455543222   223333311    111111     112233


Q ss_pred             HHHHHHh--CCCeEEEEEcCC
Q 005860          267 ESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       267 ~~l~~~l--~~kr~LlVLDdv  285 (673)
                      -.+.+++  .++.+||++|++
T Consensus       492 i~~Ae~fre~G~dVlillDSl  512 (672)
T PRK12678        492 IERAKRLVELGKDVVVLLDSI  512 (672)
T ss_pred             HHHHHHHHHcCCCEEEEEeCc
Confidence            3344444  689999999999

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.32  E-value=0.0086  Score=58.10  Aligned_cols=99  Identities=19%  Similarity=0.218  Sum_probs=71.0

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccc--hh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELP--ET  591 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP--~~  591 (673)
                      +.+.+-|++.++..    ..  -.+...|+.|.||.|+-       |.+..+- .+...+.|+.|.|+.|.|..|-  .-
T Consensus        18 l~~vkKLNcwg~~L----~D--Isic~kMp~lEVLsLSv-------NkIssL~-pl~rCtrLkElYLRkN~I~sldEL~Y   83 (388)
T KOG2123|consen   18 LENVKKLNCWGCGL----DD--ISICEKMPLLEVLSLSV-------NKISSLA-PLQRCTRLKELYLRKNCIESLDELEY   83 (388)
T ss_pred             HHHhhhhcccCCCc----cH--HHHHHhcccceeEEeec-------cccccch-hHHHHHHHHHHHHHhcccccHHHHHH
Confidence            45666677777653    11  13457899999999998       8877653 4677789999999999887775  34


Q ss_pred             hhcCCCccEEEeccCCCCcccccc-----ccccccCCeee
Q 005860          592 CCELLNLQVLEIEQCTSLKRLPLG-----IGKLVNLRHLT  626 (673)
Q Consensus       592 i~~L~~L~~L~l~~c~~l~~lP~~-----i~~L~~Lr~L~  626 (673)
                      +.+|++|++|+|..++...+-+..     +.-|+||+.||
T Consensus        84 LknlpsLr~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   84 LKNLPSLRTLWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             HhcCchhhhHhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            667888999999877655555443     45677777776

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.32  E-value=0.029  Score=52.53  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=21.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|.+.|++|+||||+|+.+.+.
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999999875

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK00300 gmk guanylate kinase; Provisional

Probab=94.31  E-value=0.031  Score=53.78  Aligned_cols=24  Identities=29%  Similarity=0.409  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+||||||+.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999885

>PRK06936 type III secretion system ATPase; Provisional

Probab=94.31  E-value=0.23  Score=52.90  Aligned_cols=85  Identities=18%  Similarity=0.173  Sum_probs=51.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcHH-----
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGELN-----  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~~-----  263 (673)
                      -..++|.|..|+|||||.+.+++...    -+.++++-+.+..+ +.++....+..-+..       ..+..-..     
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAG  237 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHH
Confidence            46899999999999999999999632    35678887877643 333333322221110       11111111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       238 ~~a~tiAEyfrd~G~~Vll~~Dsl  261 (439)
T PRK06936        238 FVATSIAEYFRDQGKRVLLLMDSV  261 (439)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccch
Confidence            1112233443  689999999999

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=94.30  E-value=0.22  Score=53.21  Aligned_cols=85  Identities=16%  Similarity=0.118  Sum_probs=48.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+..    ..+.+++..+.... +..++...+...-...       ..+..-.     .
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~~----~~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~  243 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRFT----EADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAA  243 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC----CCCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHH
Confidence            4579999999999999999998742    22344444444433 3344444443331111       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       244 ~~a~aiAEyfrd~G~~VLl~~Dsl  267 (451)
T PRK05688        244 MYCTRIAEYFRDKGKNVLLLMDSL  267 (451)
T ss_pred             HHHHHHHHHHHHCCCCEEEEecch
Confidence            1122334444  689999999999

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.29  E-value=0.071  Score=53.47  Aligned_cols=51  Identities=16%  Similarity=0.133  Sum_probs=37.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAII  249 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  249 (673)
                      +.-+++.|+|.+|+|||++|.++...  .......++||+..+.  +.++.+.+.
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~--~~~~ge~vlyvs~~e~--~~~l~~~~~   71 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYE--GAREGEPVLYVSTEES--PEELLENAR   71 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHH--HHhcCCcEEEEEecCC--HHHHHHHHH
Confidence            44689999999999999999555553  4455888999998774  444444433

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=94.29  E-value=0.027  Score=56.54  Aligned_cols=134  Identities=18%  Similarity=0.168  Sum_probs=85.8

Q ss_pred             cCceEEEEEEcCCCCcccc-----ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh--
Q 005860          491 QEKLRHSMLVLGYEASFPI-----SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN--  563 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-----~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~--  563 (673)
                      ..++|.+..+.+.....+.     .+...+.|..+.+..+.+.+.-...+...|..+++|++|||..       |.++  
T Consensus       156 ~~~Lrv~i~~rNrlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~D-------Ntft~e  228 (382)
T KOG1909|consen  156 KPKLRVFICGRNRLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRD-------NTFTLE  228 (382)
T ss_pred             CcceEEEEeeccccccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeeccc-------chhhhH
Confidence            4567777666665433222     2334567777777776653333345556677888999999988       6533  


Q ss_pred             ---hhccccccccccccceecCCCCcc-----cchhhh-cCCCccEEEeccCCCCc-----cccccccccccCCeeeccc
Q 005860          564 ---KILKGIEKLIHLRYLRLVGLGTEE-----LPETCC-ELLNLQVLEIEQCTSLK-----RLPLGIGKLVNLRHLTYDD  629 (673)
Q Consensus       564 ---~lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i~-~L~~L~~L~l~~c~~l~-----~lP~~i~~L~~Lr~L~l~~  629 (673)
                         .+...++.+++|+.|+++.|.++.     +-..+. ..++|++|.+.+|. +.     .+-..+...+.|+.|++++
T Consensus       229 gs~~LakaL~s~~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNe-It~da~~~la~~~~ek~dL~kLnLng  307 (382)
T KOG1909|consen  229 GSVALAKALSSWPHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNE-ITRDAALALAACMAEKPDLEKLNLNG  307 (382)
T ss_pred             HHHHHHHHhcccchheeecccccccccccHHHHHHHHhccCCCCceeccCcch-hHHHHHHHHHHHHhcchhhHHhcCCc
Confidence               345567778888888888887532     122222 35789999988875 42     2333456677888888888


Q ss_pred             ccc
Q 005860          630 SCL  632 (673)
Q Consensus       630 ~~l  632 (673)
                      |.+
T Consensus       308 N~l  310 (382)
T KOG1909|consen  308 NRL  310 (382)
T ss_pred             ccc
Confidence            876

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=94.28  E-value=0.029  Score=50.64  Aligned_cols=22  Identities=41%  Similarity=0.585  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|.|+|..|+||||+|+.+...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998874

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=94.27  E-value=0.034  Score=52.59  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=20.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            37899999999999999999775

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=94.26  E-value=0.04  Score=46.33  Aligned_cols=22  Identities=41%  Similarity=0.357  Sum_probs=20.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAY  218 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~  218 (673)
                      -..++|+|+.|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3689999999999999999976

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.26  E-value=0.11  Score=48.29  Aligned_cols=80  Identities=23%  Similarity=0.325  Sum_probs=43.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCC---cCcHHHHHHHHHHHhCC
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPT---VGELNSLLESIRASLVG  275 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~---~~~~~~~~~~l~~~l~~  275 (673)
                      ++.|.|.+|+||||+|..+.....     ...+++.-...++. +....|..........   .....++...+.....+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~-----~~~~~iat~~~~~~-e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~   76 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSG-----LQVLYIATAQPFDD-EMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAP   76 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcC-----CCcEeCcCCCCChH-HHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCC
Confidence            689999999999999988876411     12445554444333 4445554443332221   11112334444443333


Q ss_pred             CeEEEEEcCC
Q 005860          276 KKFLLILDDM  285 (673)
Q Consensus       276 kr~LlVLDdv  285 (673)
                      .. ++++|.+
T Consensus        77 ~~-~VlID~L   85 (170)
T PRK05800         77 GR-CVLVDCL   85 (170)
T ss_pred             CC-EEEehhH
Confidence            23 6888987

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=94.26  E-value=0.034  Score=53.36  Aligned_cols=24  Identities=38%  Similarity=0.448  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.++||+|..|+|||||++.+.--
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~Gl   56 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAGL   56 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhcc
Confidence            358999999999999999999874

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=94.25  E-value=0.29  Score=47.52  Aligned_cols=118  Identities=13%  Similarity=0.070  Sum_probs=58.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC---Cc----CcHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP---TV----GELNSLLESI  269 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---~~----~~~~~~~~~l  269 (673)
                      .+++.|.|+.|.||||+.+.+.-.. +..+-...+|..  . .. -..+.+|...++..+.   ..    .++.++...+
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~-~la~~G~~v~a~--~-~~-~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il  105 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALIT-IMAQIGSFVPAS--S-AT-LSIFDSVLTRMGASDSIQHGMSTFMVELSETSHIL  105 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHHhCCCEEEcC--c-eE-EeccceEEEEecCccccccccchHHHHHHHHHHHH
Confidence            4688999999999999998887731 111111112211  0 00 0011111111111111   11    1222333333


Q ss_pred             HHHhCCCeEEEEEcCCCCCCc----cc-hhhhhhhccCCCCCeEEEEEcCChhHHHhc
Q 005860          270 RASLVGKKFLLILDDMWTDDY----SK-WEPFHYCLKNGVRGSKILVTTRKETVARMM  322 (673)
Q Consensus       270 ~~~l~~kr~LlVLDdvw~~~~----~~-~~~l~~~l~~~~~gs~iivTtr~~~v~~~~  322 (673)
                      +.  .+++-|++||.......    .. -..+...+... .++.+|++|.+..++...
T Consensus       106 ~~--~~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~~~  160 (222)
T cd03287         106 SN--CTSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGEIL  160 (222)
T ss_pred             Hh--CCCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHHHH
Confidence            22  25789999999743211    11 11222333322 578999999998887654

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=94.23  E-value=0.02  Score=49.57  Aligned_cols=27  Identities=33%  Similarity=0.448  Sum_probs=18.6

Q ss_pred             EEEEccCCChHHHHHHHHhcCccccccCC
Q 005860          200 ITIVGMGGIGKTTLAQFAYNDSDVFEYFD  228 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~  228 (673)
                      |-|+|.+|+||||+|+.+...  +...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~--~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS--LGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH--TT--EE
T ss_pred             EeeECCCccHHHHHHHHHHHH--cCCcee
Confidence            679999999999999999985  555664

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=94.20  E-value=0.032  Score=49.85  Aligned_cols=22  Identities=32%  Similarity=0.610  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|+|+.|+|||||++.+.+.
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3789999999999999999885

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK04132 replication factor C small subunit; Provisional

Probab=94.19  E-value=0.27  Score=56.88  Aligned_cols=117  Identities=9%  Similarity=0.038  Sum_probs=70.6

Q ss_pred             cCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEc
Q 005860          205 MGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILD  283 (673)
Q Consensus       205 ~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLD  283 (673)
                      +.++||||+|.+++++. ..+.+ ..++-++.|+..... ..+++++.+....+.              -..+.-++|||
T Consensus       574 Ph~lGKTT~A~ala~~l-~g~~~~~~~lElNASd~rgid-~IR~iIk~~a~~~~~--------------~~~~~KVvIID  637 (846)
T PRK04132        574 PTVLHNTTAALALAREL-FGENWRHNFLELNASDERGIN-VIREKVKEFARTKPI--------------GGASFKIIFLD  637 (846)
T ss_pred             CCcccHHHHHHHHHHhh-hcccccCeEEEEeCCCcccHH-HHHHHHHHHHhcCCc--------------CCCCCEEEEEE
Confidence            67899999999999962 11222 235677777754544 333444433221110              01245799999


Q ss_pred             CCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHh-ccccceeecCCCCccc
Q 005860          284 DMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARM-MESIHVISIKELSEQE  337 (673)
Q Consensus       284 dvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~-~~~~~~~~l~~L~~~~  337 (673)
                      ++..-+....+.|...+......+++|++|.+. .+... ..-...+.+++++.++
T Consensus       638 EaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~  693 (846)
T PRK04132        638 EADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED  693 (846)
T ss_pred             CcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHH
Confidence            996666667777887777655667777766653 23222 2225677888877654

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.17  E-value=0.21  Score=54.87  Aligned_cols=98  Identities=15%  Similarity=0.151  Sum_probs=55.6

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCC-
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFV-  256 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~-  256 (673)
                      ++.+.++|..+-     ..-.++.|.|.+|+|||||+.++...  ....-..++|++.-+  ++.++...+ +.++-.. 
T Consensus       249 i~~lD~~lgGG~-----~~gs~~li~G~~G~GKt~l~~~f~~~--~~~~ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~  318 (484)
T TIGR02655       249 VVRLDEMCGGGF-----FKDSIILATGATGTGKTLLVSKFLEN--ACANKERAILFAYEE--SRAQLLRNA-YSWGIDFE  318 (484)
T ss_pred             hHhHHHHhcCCc-----cCCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEeeC--CHHHHHHHH-HHcCCChH
Confidence            455555554432     44689999999999999999666553  222335677877655  444555543 3333211 


Q ss_pred             --------------CCcCcHHHHHHHHHHHhCC-CeEEEEEcCC
Q 005860          257 --------------PTVGELNSLLESIRASLVG-KKFLLILDDM  285 (673)
Q Consensus       257 --------------~~~~~~~~~~~~l~~~l~~-kr~LlVLDdv  285 (673)
                                    +.....++....+.+.+.. +.-.||+|.+
T Consensus       319 ~~~~~g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi  362 (484)
T TIGR02655       319 EMEQQGLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSL  362 (484)
T ss_pred             HHhhCCcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCH
Confidence                          1112234445555555533 3446677766

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK13409 putative ATPase RIL; Provisional

Probab=94.17  E-value=0.28  Score=55.24  Aligned_cols=131  Identities=18%  Similarity=0.103  Sum_probs=67.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE-----EcCCc------ccHHHH-------------HHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV-----CVSDP------FDELRI-------------AKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv-----~vs~~------~~~~~~-------------~~~i~~~l  252 (673)
                      -.+++|+|..|+|||||++.+......   ..+.+++     .+.+.      .++.+.             ..++++.+
T Consensus       365 Geiv~l~G~NGsGKSTLlk~L~Gl~~p---~~G~I~~~~~i~y~~Q~~~~~~~~tv~e~l~~~~~~~~~~~~~~~~L~~l  441 (590)
T PRK13409        365 GEVIGIVGPNGIGKTTFAKLLAGVLKP---DEGEVDPELKISYKPQYIKPDYDGTVEDLLRSITDDLGSSYYKSEIIKPL  441 (590)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC---CceEEEEeeeEEEecccccCCCCCcHHHHHHHHhhhcChHHHHHHHHHHC
Confidence            358999999999999999999875321   1122211     11221      122222             12233333


Q ss_pred             hCCC---C---CcCcHHHHHHHHHHHhCCCeEEEEEcCCCC-CCccchhhhhhhccCC--CCCeEEEEEcCChhHHHhcc
Q 005860          253 EGFV---P---TVGELNSLLESIRASLVGKKFLLILDDMWT-DDYSKWEPFHYCLKNG--VRGSKILVTTRKETVARMME  323 (673)
Q Consensus       253 ~~~~---~---~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~~l~~~l~~~--~~gs~iivTtr~~~v~~~~~  323 (673)
                      +...   .   ....-+...-.+...+....-+++||.--+ -|...-..+...+...  ..|..||++|.+...+..+.
T Consensus       442 ~l~~~~~~~~~~LSGGe~QRvaiAraL~~~p~llLLDEPt~~LD~~~~~~l~~~l~~l~~~~g~tviivsHD~~~~~~~a  521 (590)
T PRK13409        442 QLERLLDKNVKDLSGGELQRVAIAACLSRDADLYLLDEPSAHLDVEQRLAVAKAIRRIAEEREATALVVDHDIYMIDYIS  521 (590)
T ss_pred             CCHHHHhCCcccCCHHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHhC
Confidence            3211   0   111112233345566677788999997622 1222223333333322  23667999999877665533


Q ss_pred             ccceeecC
Q 005860          324 SIHVISIK  331 (673)
Q Consensus       324 ~~~~~~l~  331 (673)
                       .+++.++
T Consensus       522 -Drvivl~  528 (590)
T PRK13409        522 -DRLMVFE  528 (590)
T ss_pred             -CEEEEEc
Confidence             3455444

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=94.17  E-value=0.29  Score=53.82  Aligned_cols=132  Identities=17%  Similarity=0.123  Sum_probs=73.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcc-----cc-ccCCeEEEEEcCC-----cccH------------HHHHHHHHHHhhC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSD-----VF-EYFDKRMWVCVSD-----PFDE------------LRIAKAIIEALEG  254 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~-----~~-~~F~~~~wv~vs~-----~~~~------------~~~~~~i~~~l~~  254 (673)
                      ..|+|+|+.|+|||||.+.+.....     +. ..--.+.|+.-..     .-++            ..-.+..+..++.
T Consensus       349 ~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~F  428 (530)
T COG0488         349 DRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFGF  428 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcCC
Confidence            4799999999999999999955311     11 0001122221111     0001            2333344444443


Q ss_pred             CCCC-------cCcHHHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccc
Q 005860          255 FVPT-------VGELNSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIH  326 (673)
Q Consensus       255 ~~~~-------~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~  326 (673)
                      ....       ...-+..+-.+...+-.+.-++|||.--++ |.+..+.+...+... +| .||++|.++.....+. ..
T Consensus       429 ~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f-~G-tvl~VSHDr~Fl~~va-~~  505 (530)
T COG0488         429 TGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDF-EG-TVLLVSHDRYFLDRVA-TR  505 (530)
T ss_pred             ChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhC-CC-eEEEEeCCHHHHHhhc-ce
Confidence            3221       111233444566667788899999976321 233455566666554 35 4999999998887755 44


Q ss_pred             eeecCC
Q 005860          327 VISIKE  332 (673)
Q Consensus       327 ~~~l~~  332 (673)
                      ++.+.+
T Consensus       506 i~~~~~  511 (530)
T COG0488         506 IWLVED  511 (530)
T ss_pred             EEEEcC
Confidence            555553

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=94.17  E-value=0.11  Score=48.13  Aligned_cols=80  Identities=16%  Similarity=0.208  Sum_probs=45.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCC--C
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG--K  276 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~--k  276 (673)
                      ++.|.|..|+|||++|.++...     ....++|+.-...++.+ ....|.+..... +......+....+.+.+..  +
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~e-m~~rI~~H~~~R-~~~w~t~E~~~~l~~~l~~~~~   73 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDDE-MAERIARHRKRR-PAHWRTIETPRDLVSALKELDP   73 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCHH-HHHHHHHHHHhC-CCCceEeecHHHHHHHHHhcCC
Confidence            3679999999999999877653     22467788777766553 444444432222 1111111222233333321  2


Q ss_pred             eEEEEEcCC
Q 005860          277 KFLLILDDM  285 (673)
Q Consensus       277 r~LlVLDdv  285 (673)
                      .-.|++|.+
T Consensus        74 ~~~VLIDcl   82 (169)
T cd00544          74 GDVVLIDCL   82 (169)
T ss_pred             CCEEEEEcH
Confidence            337999987

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.16  E-value=0.083  Score=55.55  Aligned_cols=82  Identities=21%  Similarity=0.189  Sum_probs=49.0

Q ss_pred             CcceechhhHHHHHHHhccC-------CcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC---CeEEEEEcCC-
Q 005860          169 SEIRGRDEEKSSLKSKLLCE-------SSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF---DKRMWVCVSD-  237 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~-------~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~-  237 (673)
                      ..++|.++.++.+...+...       ...........|.++|+.|+||||||+.+....  ...|   +...|...+. 
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l--~~~fi~vD~t~f~e~Gyv   92 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA--NAPFIKVEATKFTEVGYV   92 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHh--CChheeecchhhccCCcc
Confidence            46899999888888777431       000000123678999999999999999988852  2223   3332332221 


Q ss_pred             cccHHHHHHHHHHHh
Q 005860          238 PFDELRIAKAIIEAL  252 (673)
Q Consensus       238 ~~~~~~~~~~i~~~l  252 (673)
                      ..+...+.+++....
T Consensus        93 G~d~e~~ir~L~~~A  107 (443)
T PRK05201         93 GRDVESIIRDLVEIA  107 (443)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            124555555555544

>PRK13949 shikimate kinase; Provisional

Probab=94.14  E-value=0.033  Score=51.77  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=20.2

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|+.|+||||+++.+.+.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4899999999999999999885

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=94.14  E-value=0.18  Score=53.76  Aligned_cols=121  Identities=16%  Similarity=0.149  Sum_probs=62.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCC-------CCCcCc-----HH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGF-------VPTVGE-----LN  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~-----~~  263 (673)
                      -..++|+|..|+|||||++.+....+.   ...++ ..+.+. ..+.++..+.+..-+..       ..+...     ..
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~~~---~~gvI-~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~  231 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNAKA---DINVI-SLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAA  231 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCCC---CeEEE-EeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHH
Confidence            457899999999999999999886322   12233 233333 45556655555442211       111110     11


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCCCCCCccchhhhhhhccC-CCCCeEEEEEcCChhHHHhc
Q 005860          264 SLLESIRASL--VGKKFLLILDDMWTDDYSKWEPFHYCLKN-GVRGSKILVTTRKETVARMM  322 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdvw~~~~~~~~~l~~~l~~-~~~gs~iivTtr~~~v~~~~  322 (673)
                      .....+.+++  +++++||++||+-.- ......+...+.. ...|--..+.|....++...
T Consensus       232 ~~a~~iAEyfr~~G~~VLlilDslTr~-a~A~reisl~~~e~p~~G~~~~~~s~l~~L~ERa  292 (432)
T PRK06793        232 KLATSIAEYFRDQGNNVLLMMDSVTRF-ADARRSVDIAVKELPIGGKTLLMESYMKKLLERS  292 (432)
T ss_pred             HHHHHHHHHHHHcCCcEEEEecchHHH-HHHHHHHHHHhcCCCCCCeeeeeeccchhHHHHh
Confidence            1222333333  589999999999321 1122223222211 11255556655555555543

>PLN02318 phosphoribulokinase/uridine kinase

Probab=94.13  E-value=0.057  Score=59.01  Aligned_cols=26  Identities=27%  Similarity=0.456  Sum_probs=23.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+..+|+|.|..|+||||||+.+...
T Consensus        63 ~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         63 DGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             CCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            45789999999999999999999874

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=94.12  E-value=0.08  Score=49.02  Aligned_cols=45  Identities=27%  Similarity=0.391  Sum_probs=32.3

Q ss_pred             ceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          171 IRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       171 ~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|....+.++++.+..-..    .+.+ |.|+|..|+||+.+|+.+++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~----~~~p-VlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS----SDLP-VLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT----STS--EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhC----CCCC-EEEEcCCCCcHHHHHHHHHHh
Confidence            46778888888877754431    2233 569999999999999999995

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.11  E-value=0.18  Score=49.43  Aligned_cols=48  Identities=23%  Similarity=0.215  Sum_probs=31.4

Q ss_pred             CeEEEEEEccCCChHHHHHH-HHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQ-FAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~-~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .-.++.|.|..|+||||||. .++.-  .+.. ..++|++...  +..++.+.+
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~--~~~g-~~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGF--LQNG-YSVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH--HhCC-CcEEEEeCCC--CHHHHHHHH
Confidence            34699999999999999984 44442  1222 3567776433  455666665

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=94.10  E-value=0.2  Score=47.99  Aligned_cols=22  Identities=23%  Similarity=0.152  Sum_probs=20.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+++|+|..|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6899999999999999999883

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=94.10  E-value=0.12  Score=53.25  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.8

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.+.|++|+||||+++.+.+.
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~   22 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSAT   22 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999988864

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=94.09  E-value=0.33  Score=53.43  Aligned_cols=66  Identities=18%  Similarity=0.256  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccCCCCCeEEEEEcCChhHHHhccccceeecC
Q 005860          263 NSLLESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIHVISIK  331 (673)
Q Consensus       263 ~~~~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~~~~~~~l~  331 (673)
                      +..+-.|.+.|-.++=+++||.--+. |.....=+...+.. -+| .+||+|.++.....+.+ ++++++
T Consensus       158 ~r~Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~-~~g-tviiVSHDR~FLd~V~t-~I~~ld  224 (530)
T COG0488         158 WRRRVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKR-YPG-TVIVVSHDRYFLDNVAT-HILELD  224 (530)
T ss_pred             HHHHHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHh-CCC-cEEEEeCCHHHHHHHhh-heEEec
Confidence            34455677777888889999976221 11122223444443 345 79999999998887544 344444

>PTZ00494 tuzin-like protein; Provisional

Probab=94.09  E-value=0.3  Score=51.22  Aligned_cols=108  Identities=16%  Similarity=0.167  Sum_probs=73.7

Q ss_pred             ccccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHH
Q 005860          164 SLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       164 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      .+..+..+|.|+.+-..+...|..-..    .-++++.+.|.-|.||++|.+.....+.+     ..++|.|...   ++
T Consensus       366 a~a~~~~~V~R~~eE~~vRqvL~qld~----aHPRIvV~TG~~GcGKSslcRsAvrkE~~-----paV~VDVRg~---ED  433 (664)
T PTZ00494        366 AAAAEAFEVRREDEEALVRSVLTQMAP----SHPRIVALAGGSGGGRCVPCRRAVRVEGV-----ALVHVDVGGT---ED  433 (664)
T ss_pred             cccccccccchhhHHHHHHHHHhhccC----CCCcEEEEecCCCCCchHHHHHHHHHcCC-----CeEEEEecCC---cc
Confidence            344567899999998888888876653    45899999999999999999877765333     4677877654   44


Q ss_pred             HHHHHHHHhhCCCCC-cCcH----HHHHHHHHHHhCCCeEEEEEc
Q 005860          244 IAKAIIEALEGFVPT-VGEL----NSLLESIRASLVGKKFLLILD  283 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~-~~~~----~~~~~~l~~~l~~kr~LlVLD  283 (673)
                      -++.|++.++.+.-+ ..+.    .+.-..-+....++.-+||+-
T Consensus       434 tLrsVVKALgV~nve~CGDlLdFI~ea~~~A~~~~~g~~P~lVlk  478 (664)
T PTZ00494        434 TLRSVVRALGVSNVEVCGDLLGFVEEAMRGATVKASDGVPFLVMR  478 (664)
T ss_pred             hHHHHHHHhCCCChhhhccHHHHHHHHHHHHHHhcCCCCCEEEEE
Confidence            678899999876432 2222    222222333345666666654

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=94.07  E-value=0.16  Score=54.16  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|+|||||++.+...
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcc
Confidence            468999999999999999999885

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.05  E-value=0.24  Score=53.63  Aligned_cols=95  Identities=22%  Similarity=0.171  Sum_probs=54.4

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP  257 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~  257 (673)
                      ++++.+.|..+-     ..-.++.|.|.+|+|||||+.++...  ....-..++|++..+.  ...+.. -++.++....
T Consensus        66 i~~LD~~LgGGi-----~~Gs~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs~Ees--~~qi~~-ra~rlg~~~~  135 (446)
T PRK11823         66 IGELDRVLGGGL-----VPGSVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVSGEES--ASQIKL-RAERLGLPSD  135 (446)
T ss_pred             cHHHHHHhcCCc-----cCCEEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEcccc--HHHHHH-HHHHcCCChh
Confidence            345555554332     33569999999999999999777664  2222345788876543  333322 2444443211


Q ss_pred             -----CcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          258 -----TVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       258 -----~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                           ...+++.+...+.+   .+.-+||+|.+
T Consensus       136 ~l~~~~e~~l~~i~~~i~~---~~~~lVVIDSI  165 (446)
T PRK11823        136 NLYLLAETNLEAILATIEE---EKPDLVVIDSI  165 (446)
T ss_pred             cEEEeCCCCHHHHHHHHHh---hCCCEEEEech
Confidence                 12334444444432   35568999987

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=94.04  E-value=0.068  Score=48.67  Aligned_cols=36  Identities=25%  Similarity=0.408  Sum_probs=29.3

Q ss_pred             hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc
Q 005860          176 EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       176 ~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      +.+++|.+.|.         + +++.++|..|+|||||...+..+.
T Consensus        24 ~g~~~l~~~l~---------~-k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   24 EGIEELKELLK---------G-KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTHHHHHHHHT---------T-SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             cCHHHHHHHhc---------C-CEEEEECCCCCCHHHHHHHHHhhc
Confidence            45667777773         2 589999999999999999999863

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=94.04  E-value=0.063  Score=52.15  Aligned_cols=34  Identities=18%  Similarity=0.301  Sum_probs=26.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|..|+|||||++.+..-.   ....+.+++
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl~---~~~~G~i~~   62 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGIE---KPTRGKIRF   62 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCceEEEE
Confidence            3589999999999999999999842   233455544

>PRK09099 type III secretion system ATPase; Provisional

Probab=94.03  E-value=0.19  Score=53.68  Aligned_cols=85  Identities=16%  Similarity=0.219  Sum_probs=47.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|.|..|+|||||++.+......    +..+++-+.+. ..+.++...+...-...       ..+..-.     .
T Consensus       163 Gq~~~I~G~sG~GKTtLl~~ia~~~~~----d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~  238 (441)
T PRK09099        163 GQRMGIFAPAGVGKSTLMGMFARGTQC----DVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAA  238 (441)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHH
Confidence            468999999999999999999875322    23333444433 23444444443321110       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       239 ~~a~tiAEyfrd~G~~VLl~~Dsl  262 (441)
T PRK09099        239 YVATAIAEYFRDRGLRVLLMMDSL  262 (441)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccch
Confidence            1122334444  589999999999

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=94.02  E-value=0.04  Score=47.60  Aligned_cols=22  Identities=32%  Similarity=0.560  Sum_probs=19.8

Q ss_pred             EEEEccCCChHHHHHHHHhcCc
Q 005860          200 ITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      |.|+|..|+|||||.+.+.+..
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999988764

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.02  E-value=0.041  Score=49.95  Aligned_cols=20  Identities=40%  Similarity=0.718  Sum_probs=18.5

Q ss_pred             EEEEEccCCChHHHHHHHHh
Q 005860          199 IITIVGMGGIGKTTLAQFAY  218 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~  218 (673)
                      .|+|.|.+|+||||+++.+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999998887

>PRK13947 shikimate kinase; Provisional

Probab=94.01  E-value=0.035  Score=51.66  Aligned_cols=22  Identities=32%  Similarity=0.480  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|++|+||||+|+.+.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~   24 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATT   24 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            3889999999999999999884

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.99  E-value=0.33  Score=50.39  Aligned_cols=25  Identities=20%  Similarity=0.321  Sum_probs=22.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDS  221 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~  221 (673)
                      -.+++|+|..|.|||||++.++...
T Consensus       108 Ge~v~IvG~~GsGKSTLl~~L~g~~  132 (329)
T PRK14257        108 NKVTAFIGPSGCGKSTFLRNLNQLN  132 (329)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccc
Confidence            3589999999999999999999753

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=93.98  E-value=0.25  Score=56.07  Aligned_cols=24  Identities=38%  Similarity=0.443  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|.|||||++.+..-
T Consensus       361 G~~v~IvG~sGsGKSTLl~lL~gl  384 (588)
T PRK13657        361 GQTVAIVGPTGAGKSTLINLLQRV  384 (588)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998874

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.98  E-value=0.17  Score=53.82  Aligned_cols=25  Identities=32%  Similarity=0.355  Sum_probs=21.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.++|.+|+||||++..+...
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~  123 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYY  123 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3689999999999999999777653

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=93.96  E-value=0.067  Score=46.18  Aligned_cols=47  Identities=11%  Similarity=0.202  Sum_probs=32.8

Q ss_pred             cceechhhHHHHHHHh----ccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKL----LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L----~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|-+-..+.+++.+    ....    ..++-|++..|..|+|||.+++.+.+.
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~----p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPN----PRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCC----CCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            5667665555555444    3333    356899999999999999987666654

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PRK05973 replicative DNA helicase; Provisional

Probab=93.94  E-value=0.17  Score=49.48  Aligned_cols=48  Identities=13%  Similarity=0.080  Sum_probs=31.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      -.++.|.|.+|+||||+|.++.... .+ .=..++|++...  +..++...+
T Consensus        64 Gsl~LIaG~PG~GKT~lalqfa~~~-a~-~Ge~vlyfSlEe--s~~~i~~R~  111 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLELAVEA-MK-SGRTGVFFTLEY--TEQDVRDRL  111 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHH-Hh-cCCeEEEEEEeC--CHHHHHHHH
Confidence            4689999999999999997665431 22 234567776655  345555554

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=93.92  E-value=0.039  Score=53.47  Aligned_cols=26  Identities=42%  Similarity=0.514  Sum_probs=23.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|.++||+|+||||..|.++.+
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~h   42 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSH   42 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHH
Confidence            45678899999999999999999886

>COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=93.92  E-value=0.64  Score=42.25  Aligned_cols=84  Identities=18%  Similarity=0.177  Sum_probs=52.9

Q ss_pred             cHHHHHHHHHHHhhCCCC------CcCcHHHHHHHHHHHhCCCeEEEEEcCC----CCCCccchhhhhhhccCCCCCeEE
Q 005860          240 DELRIAKAIIEALEGFVP------TVGELNSLLESIRASLVGKKFLLILDDM----WTDDYSKWEPFHYCLKNGVRGSKI  309 (673)
Q Consensus       240 ~~~~~~~~i~~~l~~~~~------~~~~~~~~~~~l~~~l~~kr~LlVLDdv----w~~~~~~~~~l~~~l~~~~~gs~i  309 (673)
                      +.....+..+.+++....      +...-++-.-.+.+.+...+-+++-|.-    ....-.+..++...+. ...|+..
T Consensus       122 ~~~~~A~~lL~~vGLg~Rl~HyP~qLSGGEQQRVAiARAfa~~P~vLfADEPTGNLD~~Tg~~iaDLlF~ln-re~G~Tl  200 (228)
T COG4181         122 DSRAGAKALLEAVGLGKRLTHYPAQLSGGEQQRVALARAFAGRPDVLFADEPTGNLDRATGDKIADLLFALN-RERGTTL  200 (228)
T ss_pred             cHHHHHHHHHHHhCcccccccCccccCchHHHHHHHHHHhcCCCCEEeccCCCCCcchhHHHHHHHHHHHHh-hhcCceE
Confidence            455667777888765421      2223344456677888888888888854    1111223344443333 4578999


Q ss_pred             EEEcCChhHHHhccc
Q 005860          310 LVTTRKETVARMMES  324 (673)
Q Consensus       310 ivTtr~~~v~~~~~~  324 (673)
                      |+.|.+..++..|.-
T Consensus       201 VlVTHD~~LA~Rc~R  215 (228)
T COG4181         201 VLVTHDPQLAARCDR  215 (228)
T ss_pred             EEEeCCHHHHHhhhh
Confidence            999999999988654

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=93.90  E-value=0.061  Score=55.39  Aligned_cols=157  Identities=15%  Similarity=0.202  Sum_probs=81.5

Q ss_pred             cceechhhHHHHHHHhccCCcc--c--------ccCCeEEEEEEccCCChHHHHHHHHhcCcccc--ccC---CeEEEEE
Q 005860          170 EIRGRDEEKSSLKSKLLCESSE--E--------IINDIQIITIVGMGGIGKTTLAQFAYNDSDVF--EYF---DKRMWVC  234 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~--~--------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F---~~~~wv~  234 (673)
                      +..|-..+...|.+........  +        ..+.-.++.|+|.+|+||||+.+++.......  +.|   .+.+-+.
T Consensus       372 d~~~lp~e~~~IleSFGv~~r~ieryvlr~vNL~ikpGdvvaVvGqSGaGKttllRmi~G~~~~~~ee~y~p~sg~v~vp  451 (593)
T COG2401         372 DIKGLPNEFQDILESFGVRQRVIERYVLRNLNLEIKPGDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGKVEVP  451 (593)
T ss_pred             ecccCChHHHHHHHHhcchheeeeeeeeeceeeEecCCCeEEEEecCCCCcchHHHHHHHHhhcccccccCCCCCceecc
Confidence            4556666777776655322110  0        01223589999999999999998887642111  111   1111111


Q ss_pred             -------cC----CcccHHHHHHHHHHHh-------------hCCC--------CCcCcHHHHHHHHHHHhCCCeEEEEE
Q 005860          235 -------VS----DPFDELRIAKAIIEAL-------------EGFV--------PTVGELNSLLESIRASLVGKKFLLIL  282 (673)
Q Consensus       235 -------vs----~~~~~~~~~~~i~~~l-------------~~~~--------~~~~~~~~~~~~l~~~l~~kr~LlVL  282 (673)
                             +.    ..++...++.++.+..             +..+        .+..+-+.-...|.+.+.++.-+++.
T Consensus       452 ~nt~~a~iPge~Ep~f~~~tilehl~s~tGD~~~AveILnraGlsDAvlyRr~f~ELStGQKeR~KLAkllaerpn~~~i  531 (593)
T COG2401         452 KNTVSALIPGEYEPEFGEVTILEHLRSKTGDLNAAVEILNRAGLSDAVLYRRKFSELSTGQKERAKLAKLLAERPNVLLI  531 (593)
T ss_pred             ccchhhccCcccccccCchhHHHHHhhccCchhHHHHHHHhhccchhhhhhccHhhcCcchHHHHHHHHHHhcCCCcEEh
Confidence                   11    1122223333333322             2211        11122233455677888888889999


Q ss_pred             cCCCCCCccchh--hhhhhccC--CCCCeEEEEEcCChhHHHhccccce
Q 005860          283 DDMWTDDYSKWE--PFHYCLKN--GVRGSKILVTTRKETVARMMESIHV  327 (673)
Q Consensus       283 Ddvw~~~~~~~~--~l~~~l~~--~~~gs~iivTtr~~~v~~~~~~~~~  327 (673)
                      |..... .+...  .+...+..  ...|+.+++.|+.+++.+.+.++..
T Consensus       532 DEF~Ah-LD~~TA~rVArkiselaRe~giTlivvThrpEv~~AL~PD~l  579 (593)
T COG2401         532 DEFAAH-LDELTAVRVARKISELAREAGITLIVVTHRPEVGNALRPDTL  579 (593)
T ss_pred             hhhhhh-cCHHHHHHHHHHHHHHHHHhCCeEEEEecCHHHHhccCCcee
Confidence            987321 11111  12223332  2368888888888999887765443

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=93.90  E-value=0.072  Score=50.59  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|.|||||++.+...
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G~   41 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNGL   41 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999884

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>PRK14737 gmk guanylate kinase; Provisional

Probab=93.88  E-value=0.054  Score=51.14  Aligned_cols=25  Identities=24%  Similarity=0.385  Sum_probs=22.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +..+|.|+|++|+|||||++.+.+.
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3678999999999999999999875

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.88  E-value=0.17  Score=48.09  Aligned_cols=41  Identities=27%  Similarity=0.341  Sum_probs=26.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccC--------CeEEEEEcCCc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYF--------DKRMWVCVSDP  238 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--------~~~~wv~vs~~  238 (673)
                      .++.|+|.+|+||||++..+.-..-....|        ..++|+.....
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            478999999999999996666542221222        35788877665

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.88  E-value=0.32  Score=48.67  Aligned_cols=112  Identities=12%  Similarity=0.055  Sum_probs=55.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH--HHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE--LRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ..+++++|.+|+||||++..+...  ....=..+.+++.. .+..  ..-++...+.++.+.....+.+.+...+...-+
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~--l~~~~~~v~~i~~D-~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l~~  151 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQ--FHGKKKTVGFITTD-HSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKE  151 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEEecC-CCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHHHh
Confidence            468999999999999999877653  21111234555543 2222  222223333333221122334444444433222


Q ss_pred             -CCeEEEEEcCCCCC--CccchhhhhhhccCCCCCeEEEE
Q 005860          275 -GKKFLLILDDMWTD--DYSKWEPFHYCLKNGVRGSKILV  311 (673)
Q Consensus       275 -~kr~LlVLDdvw~~--~~~~~~~l~~~l~~~~~gs~iiv  311 (673)
                       .+.=++++|..-..  +....+.+...+....+.-.++|
T Consensus       152 ~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LV  191 (270)
T PRK06731        152 EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLT  191 (270)
T ss_pred             cCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEE
Confidence             24567888977432  22334444444433333334554

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=93.88  E-value=0.077  Score=51.77  Aligned_cols=39  Identities=28%  Similarity=0.397  Sum_probs=27.7

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...++++.+....     .+..+|||.|++|+||+||...+...
T Consensus        14 ~~~~ll~~l~~~~-----g~a~~iGiTG~PGaGKSTli~~l~~~   52 (266)
T PF03308_consen   14 EARELLKRLYPHT-----GRAHVIGITGPPGAGKSTLIDALIRE   52 (266)
T ss_dssp             HHHHHHHHHGGGT-----T-SEEEEEEE-TTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc-----CCceEEEeeCCCCCcHHHHHHHHHHH
Confidence            4456666665443     35689999999999999999777664

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=93.87  E-value=0.076  Score=51.51  Aligned_cols=35  Identities=23%  Similarity=0.295  Sum_probs=27.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .. .+++|+|..|+|||||++.+....   ....+.+++
T Consensus        22 ~~-e~~~i~G~nGsGKSTLl~~l~G~~---~~~~G~i~~   56 (214)
T cd03297          22 NE-EVTGIFGASGAGKSTLLRCIAGLE---KPDGGTIVL   56 (214)
T ss_pred             cc-eeEEEECCCCCCHHHHHHHHhCCC---CCCCceEEE
Confidence            45 799999999999999999998852   233455554

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=93.87  E-value=0.19  Score=48.69  Aligned_cols=22  Identities=32%  Similarity=0.288  Sum_probs=20.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +++.|+|+.|.||||+.+.+..
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999853

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=93.86  E-value=0.07  Score=51.90  Aligned_cols=34  Identities=26%  Similarity=0.266  Sum_probs=26.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|..|+|||||++.+..-.   ....+.+++
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl~---~~~~G~i~~   63 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGLD---RPTSGEVRV   63 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCCc---CCCceeEEE
Confidence            3589999999999999999999852   233445544

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=93.86  E-value=0.15  Score=54.50  Aligned_cols=88  Identities=13%  Similarity=0.055  Sum_probs=54.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -.-++|.|.+|+|||+|+..+.+... +.+-+.++|+-+.+..+ +.++...+...=...       ..+..-.     -
T Consensus       138 GQr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~  216 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVG  216 (449)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHH
Confidence            35789999999999999988766522 23347888988877654 345555554431110       1111111     1


Q ss_pred             HHHHHHHHHh---CCCeEEEEEcCC
Q 005860          264 SLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      .....+.+++   +++++|+++||+
T Consensus       217 ~~a~tiAEyfrd~~G~~VLl~~Dsl  241 (449)
T TIGR03305       217 HTALTMAEYFRDDEKQDVLLLIDNI  241 (449)
T ss_pred             HHHHHHHHHHHHhcCCceEEEecCh
Confidence            2233455555   469999999999

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=93.86  E-value=0.21  Score=47.03  Aligned_cols=25  Identities=28%  Similarity=0.395  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|.|.+|+||||+|+.+...
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~   41 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKK   41 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999998874

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=93.86  E-value=0.071  Score=51.71  Aligned_cols=34  Identities=24%  Similarity=0.344  Sum_probs=26.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|..|+|||||++.+..-.   ....+.+++
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~Gl~---~~~~G~i~~   61 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYGAL---TPSRGQVRI   61 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCCceEEE
Confidence            3589999999999999999998842   233455554

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=93.84  E-value=0.16  Score=54.12  Aligned_cols=55  Identities=25%  Similarity=0.237  Sum_probs=39.0

Q ss_pred             Ccceechh---hHHHHHHHhccCCcc-c-ccCCeEEEEEEccCCChHHHHHHHHhcCccc
Q 005860          169 SEIRGRDE---EKSSLKSKLLCESSE-E-IINDIQIITIVGMGGIGKTTLAQFAYNDSDV  223 (673)
Q Consensus       169 ~~~vGr~~---~~~~l~~~L~~~~~~-~-~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  223 (673)
                      .++-|-|+   |+++|+++|.++..- . +..=++=|.++|++|.|||-||++|.-...+
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V  363 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV  363 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCC
Confidence            46778775   567778888655320 0 1123467889999999999999999997544

>COG4240 Predicted kinase [General function prediction only]

Probab=93.82  E-value=0.21  Score=47.32  Aligned_cols=81  Identities=16%  Similarity=0.125  Sum_probs=52.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC-----CCCCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG-----FVPTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~-----~~~~~~~~~~~~~~l  269 (673)
                      ...-+++|.|+.|+||||++..+++...-+.. ..+...+..+-+-...-.-.++++...     .-+...+..-....+
T Consensus        48 grPli~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnVL  126 (300)
T COG4240          48 GRPLIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNVL  126 (300)
T ss_pred             CCceEEEeecCCCCchhhHHHHHHHHHHHhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHHH
Confidence            45789999999999999999999996332222 466677665544333334444554311     134456666667777


Q ss_pred             HHHhCCC
Q 005860          270 RASLVGK  276 (673)
Q Consensus       270 ~~~l~~k  276 (673)
                      ....+++
T Consensus       127 nai~~g~  133 (300)
T COG4240         127 NAIARGG  133 (300)
T ss_pred             HHHhcCC
Confidence            7777666

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=93.82  E-value=0.27  Score=52.40  Aligned_cols=85  Identities=18%  Similarity=0.175  Sum_probs=47.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc-cHHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF-DELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -..++|+|..|+|||||++.+.+....    +..+..-+.+.. ...++..+.+.+-+..       ..+....     .
T Consensus       137 Gqri~I~G~sG~GKTtLl~~i~~~~~~----~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~  212 (413)
T TIGR03497       137 GQRVGIFAGSGVGKSTLLGMIARNAKA----DINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAA  212 (413)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHH
Confidence            468999999999999999988885321    233333344433 3344444433321110       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .....+.+++  +++++|+++||+
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dsl  236 (413)
T TIGR03497       213 FTATAIAEYFRDQGKDVLLMMDSV  236 (413)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcCc
Confidence            1222334444  589999999999

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=93.80  E-value=0.22  Score=53.06  Aligned_cols=40  Identities=18%  Similarity=0.142  Sum_probs=28.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD  240 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  240 (673)
                      -..++|+|..|+|||||++.+.....    -+..+...+.+...
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~~~----~~v~vi~~iGergr  196 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKGCL----APIKVVALIGERGR  196 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhccC----CCEEEEEeeCccch
Confidence            45899999999999999999987522    24455555555443

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=93.80  E-value=0.076  Score=51.34  Aligned_cols=24  Identities=29%  Similarity=0.386  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|+|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999985

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=93.77  E-value=0.076  Score=51.74  Aligned_cols=34  Identities=26%  Similarity=0.221  Sum_probs=26.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|..|+|||||++.+....   ....+.+++
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~~---~~~~G~i~~   59 (220)
T cd03265          26 GEIFGLLGPNGAGKTTTIKMLTTLL---KPTSGRATV   59 (220)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC---CCCceEEEE
Confidence            3689999999999999999999842   334555555

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=93.75  E-value=0.043  Score=49.99  Aligned_cols=21  Identities=38%  Similarity=0.648  Sum_probs=19.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|++|+||||+|+.+...
T Consensus         2 i~l~G~~GsGKstla~~la~~   22 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKA   22 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            789999999999999999874

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=93.74  E-value=0.04  Score=53.35  Aligned_cols=82  Identities=22%  Similarity=0.286  Sum_probs=52.2

Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccC--CCCccccccccccccCCeeeccccccccccccCC---CCCCCC
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQC--TSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQ---RLTNLR  646 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c--~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~---~L~~L~  646 (673)
                      +..|.+|++.++.++.+- .+-.|++|++|.++.+  +-...++--..++++|++|++++|.++. ++.+.   .+.+|.
T Consensus        42 ~~~le~ls~~n~gltt~~-~~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~-lstl~pl~~l~nL~  119 (260)
T KOG2739|consen   42 FVELELLSVINVGLTTLT-NFPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKD-LSTLRPLKELENLK  119 (260)
T ss_pred             ccchhhhhhhccceeecc-cCCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCcccc-ccccchhhhhcchh
Confidence            344555555555433321 2336889999999987  3344566556677999999999998875 34444   455555


Q ss_pred             cCCeeEEcc
Q 005860          647 TLSEFVVVR  655 (673)
Q Consensus       647 ~L~~~~~~~  655 (673)
                      .|..|.++.
T Consensus       120 ~Ldl~n~~~  128 (260)
T KOG2739|consen  120 SLDLFNCSV  128 (260)
T ss_pred             hhhcccCCc
Confidence            555555543

>PRK14530 adenylate kinase; Provisional

Probab=93.74  E-value=0.042  Score=53.35  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|+|++|+||||+|+.+...
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999774

>TIGR00416 sms DNA repair protein RadA

Probab=93.73  E-value=0.33  Score=52.64  Aligned_cols=97  Identities=19%  Similarity=0.099  Sum_probs=53.9

Q ss_pred             hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCC
Q 005860          176 EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGF  255 (673)
Q Consensus       176 ~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~  255 (673)
                      .-+.++..+|..+-     ..-.++.|.|.+|+|||||+.++...  ....-..++|++..+.  ...+.. -++.++..
T Consensus        78 TGi~~LD~vLgGGi-----~~GsvilI~G~pGsGKTTL~lq~a~~--~a~~g~kvlYvs~EEs--~~qi~~-ra~rlg~~  147 (454)
T TIGR00416        78 SGFGELDRVLGGGI-----VPGSLILIGGDPGIGKSTLLLQVACQ--LAKNQMKVLYVSGEES--LQQIKM-RAIRLGLP  147 (454)
T ss_pred             cCcHHHHHHhcCCc-----cCCeEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEECcCC--HHHHHH-HHHHcCCC
Confidence            33456666554332     34579999999999999999777553  2222235788876543  333222 12233322


Q ss_pred             CC-----CcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          256 VP-----TVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       256 ~~-----~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                      .+     ...+++.+...+.+   .+.-++|+|.+
T Consensus       148 ~~~l~~~~e~~~~~I~~~i~~---~~~~~vVIDSI  179 (454)
T TIGR00416       148 EPNLYVLSETNWEQICANIEE---ENPQACVIDSI  179 (454)
T ss_pred             hHHeEEcCCCCHHHHHHHHHh---cCCcEEEEecc
Confidence            11     12344444444332   35568999987

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK13409 putative ATPase RIL; Provisional

Probab=93.73  E-value=0.32  Score=54.75  Aligned_cols=25  Identities=32%  Similarity=0.511  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-.+++|+|..|+|||||++.+...
T Consensus        98 ~Gev~gLvG~NGaGKSTLlkiL~G~  122 (590)
T PRK13409         98 EGKVTGILGPNGIGKTTAVKILSGE  122 (590)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999875

>PRK13975 thymidylate kinase; Provisional

Probab=93.72  E-value=0.048  Score=52.03  Aligned_cols=23  Identities=35%  Similarity=0.533  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999999985

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=93.70  E-value=0.2  Score=53.60  Aligned_cols=88  Identities=18%  Similarity=0.082  Sum_probs=52.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcH-----H
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGEL-----N  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----~  263 (673)
                      -.-++|.|..|+|||||+..+..... ..+=..++++-+.+... +.++..++...=...       ..+..-.     .
T Consensus       143 GQr~~If~~~G~GKt~L~~~~~~~~~-~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~  221 (461)
T TIGR01039       143 GGKIGLFGGAGVGKTVLIQELINNIA-KEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVA  221 (461)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHHHH-hcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            35789999999999999988776421 12224677887876543 455555554321110       1111111     1


Q ss_pred             HHHHHHHHHh---CCCeEEEEEcCC
Q 005860          264 SLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       264 ~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      .....+.+++   +++++|+++||+
T Consensus       222 ~~a~tiAEyfrd~~G~~VLll~Dsl  246 (461)
T TIGR01039       222 LTGLTMAEYFRDEQGQDVLLFIDNI  246 (461)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEecch
Confidence            1233455555   578999999999

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.69  E-value=0.038  Score=50.99  Aligned_cols=21  Identities=29%  Similarity=0.529  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|++|+||||+|+.+.+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999998885

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=93.68  E-value=0.047  Score=50.89  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|.|+|+.|+||||+|+.+.+.
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            46999999999999999999875

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.67  E-value=0.27  Score=56.19  Aligned_cols=84  Identities=18%  Similarity=0.119  Sum_probs=55.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l  269 (673)
                      +.-+++-|+|..|+||||||.++.-.  ....=..++|+.....+++.     .+++++....     .....+.....+
T Consensus        58 p~GsiteI~G~~GsGKTtLal~~~~~--a~~~G~~v~yId~E~t~~~~-----~A~~lGvDl~~llv~~~~~~E~~l~~i  130 (790)
T PRK09519         58 PRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAEHALDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIA  130 (790)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchhHH-----HHHHcCCChhHeEEecCCCHHHHHHHH
Confidence            34689999999999999999664442  22233567899887777643     5666655321     122334455555


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      ...++ ++--|||+|-+
T Consensus       131 ~~lv~~~~~~LVVIDSI  147 (790)
T PRK09519        131 DMLIRSGALDIVVIDSV  147 (790)
T ss_pred             HHHhhcCCCeEEEEcch
Confidence            55554 45668999987

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=93.66  E-value=0.48  Score=53.79  Aligned_cols=24  Identities=38%  Similarity=0.372  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|.|||||++.+...
T Consensus       376 G~~vaIvG~SGsGKSTL~~lL~g~  399 (588)
T PRK11174        376 GQRIALVGPSGAGKTSLLNALLGF  399 (588)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999998875

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=93.66  E-value=0.56  Score=52.44  Aligned_cols=24  Identities=29%  Similarity=0.405  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|.|||||++.+...
T Consensus       348 G~~~~ivG~sGsGKSTL~~ll~g~  371 (529)
T TIGR02857       348 GERVALVGPSGAGKSTLLNLLLGF  371 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999774

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=93.66  E-value=0.057  Score=48.55  Aligned_cols=24  Identities=33%  Similarity=0.686  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++.|+|.+|+||||+.+.+-..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~   27 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE   27 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH
Confidence            589999999999999999877764

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=93.66  E-value=0.042  Score=50.15  Aligned_cols=22  Identities=36%  Similarity=0.451  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |++|+|+.|+|||||+.++...
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~   22 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKA   22 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999988885

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=93.66  E-value=0.081  Score=54.76  Aligned_cols=44  Identities=27%  Similarity=0.336  Sum_probs=35.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhc
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+||.+..+..+.-.+..+.       ..-+.|.|..|+|||||++.+..
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~-------~g~vli~G~~G~gKttl~r~~~~   47 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPK-------IGGVMVMGDRGTGKSTAVRALAA   47 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCC-------CCeEEEEcCCCCCHHHHHHHHHH
Confidence            568999999988876666543       44577999999999999999975

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=93.66  E-value=0.14  Score=56.79  Aligned_cols=47  Identities=19%  Similarity=0.045  Sum_probs=35.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|....+.+++..+..-..     .-.-|.|+|..|+||+++|++++..
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~A~-----~~~pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKLAM-----LDAPLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             cceeECCHHHHHHHHHHHHHhC-----CCCCEEEECCCCccHHHHHHHHHHh
Confidence            4789998888887776643221     1123789999999999999998874

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.65  E-value=0.36  Score=49.70  Aligned_cols=25  Identities=32%  Similarity=0.436  Sum_probs=22.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+++|++|+||||++..+...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~  137 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK  137 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999999888764

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.64  E-value=0.15  Score=55.13  Aligned_cols=69  Identities=19%  Similarity=0.316  Sum_probs=43.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ..=|.+||++|.|||-||++|.|.  ..-.|     ++|-.+    ++    ++..-++     +.......+.+.-..-
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANE--ag~NF-----isVKGP----EL----lNkYVGE-----SErAVR~vFqRAR~sa  604 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANE--AGANF-----ISVKGP----EL----LNKYVGE-----SERAVRQVFQRARASA  604 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhh--ccCce-----EeecCH----HH----HHHHhhh-----HHHHHHHHHHHhhcCC
Confidence            456789999999999999999996  33344     555442    12    2221111     1123334444445678


Q ss_pred             eEEEEEcCC
Q 005860          277 KFLLILDDM  285 (673)
Q Consensus       277 r~LlVLDdv  285 (673)
                      +|.|.+|.+
T Consensus       605 PCVIFFDEi  613 (802)
T KOG0733|consen  605 PCVIFFDEI  613 (802)
T ss_pred             CeEEEecch
Confidence            999999998

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=93.64  E-value=0.49  Score=53.55  Aligned_cols=24  Identities=42%  Similarity=0.456  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|.|||||++.+...
T Consensus       361 G~~~~ivG~sGsGKSTL~~ll~g~  384 (585)
T TIGR01192       361 GQTVAIVGPTGAGKTTLINLLQRV  384 (585)
T ss_pred             CCEEEEECCCCCCHHHHHHHHccC
Confidence            468999999999999999998764

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=93.64  E-value=0.081  Score=51.16  Aligned_cols=24  Identities=33%  Similarity=0.427  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|+|||||++.+...
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999884

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=93.63  E-value=0.056  Score=52.15  Aligned_cols=26  Identities=23%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++++|+++|..|+|||||.+++.+.
T Consensus        20 ~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        20 HGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             cCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999999888774

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.62  E-value=0.084  Score=51.93  Aligned_cols=35  Identities=23%  Similarity=0.203  Sum_probs=27.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC  234 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  234 (673)
                      -.+++|+|+.|+|||||.+.++.-   -..-.+.+++.
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g~---l~p~~G~V~l~   62 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAGL---LKPKSGEVLLD   62 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc---CCCCCCEEEEC
Confidence            479999999999999999999993   33345566663

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=93.59  E-value=0.11  Score=58.39  Aligned_cols=75  Identities=12%  Similarity=0.092  Sum_probs=54.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      ++++|.++.++.|...+...         +.+.++|.+|+||||+|+.+.+.. ...+|+..+|..-+. .+...+++.+
T Consensus        31 ~~vigq~~a~~~L~~~~~~~---------~~~l~~G~~G~GKttla~~l~~~l-~~~~~~~~~~~~np~-~~~~~~~~~v   99 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR---------RHVMMIGSPGTGKSMLAKAMAELL-PKEELQDILVYPNPE-DPNNPKIRTV   99 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC---------CeEEEECCCCCcHHHHHHHHHHHc-ChHhHHHheEeeCCC-cchHHHHHHH
Confidence            47899998888887766432         358899999999999999988752 233567778876543 3566677777


Q ss_pred             HHHhhC
Q 005860          249 IEALEG  254 (673)
Q Consensus       249 ~~~l~~  254 (673)
                      ...++.
T Consensus       100 ~~~~G~  105 (637)
T PRK13765        100 PAGKGK  105 (637)
T ss_pred             HHhcCH
Confidence            665543

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=93.58  E-value=0.16  Score=54.15  Aligned_cols=24  Identities=21%  Similarity=0.231  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|+|||||++.+.+.
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCC
Confidence            467999999999999999999985

---

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	673
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-85
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	4e-77
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-47
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	4e-17
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	6e-14
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	6e-14
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-13
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-12
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	6e-11
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	5e-10
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-11
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	5e-09
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-04
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	2e-10
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	3e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-07
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-05
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-08
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	5e-08
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-04
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-07
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	7e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	5e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	4e-06
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	6e-06
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	1e-05
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	7e-04
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	1e-05
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	3e-05
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-04
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-05
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	3e-05
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	5e-04
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	4e-05
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	1e-04
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	5e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-04
3e6j_A	229	Variable lymphocyte receptor diversity region; var	7e-05
1o6v_A	466	Internalin A; bacterial infection, extracellular r	9e-05
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	1e-04
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	1e-04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	1e-04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	4e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	8e-04
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	2e-04
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	3e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-04
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	5e-04
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	5e-04
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	7e-04

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  279 bits (714), Expect = 2e-85
 Identities = 93/561 (16%), Positives = 167/561 (29%), Gaps = 114/561 (20%)

Query: 51  DAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDAL----VPQRKVCS 106
           DA+ R      ++      KD+      ++D   +    L I   + +      Q++   
Sbjct: 2   DAKARN---CLLQHREALEKDIK--TSYIMDHMISDGF-LTISEEEKVRNEPTQQQRAAM 55

Query: 107 FLPAASCFGFS--QTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIR---STENSERIQ 161
            +            +F    +    K +   L D        +        ++     + 
Sbjct: 56  LIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLC 115

Query: 162 STSLIDVSE-IRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND 220
              +         R +  ++++ KL      ++  +   +TI GM G GK+ LA  A  D
Sbjct: 116 EGGVPQRPVVFVTRKKLVNAIQQKLS-----KLKGEPGWVTIHGMAGCGKSVLAAEAVRD 170

Query: 221 SDVFEYF--DKRMWVCVSDPFDE--LRIAKAIIEALEGFVPTVGELNSLLESIRASLV-- 274
             + E        WV V        L   + +   L+        L   +E  +  L   
Sbjct: 171 HSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRIL 230

Query: 275 ----GKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMESIH--VI 328
                 + LLILDD+W       + F           +IL+TTR ++V   +      V 
Sbjct: 231 MLRKHPRSLLILDDVWDSWV--LKAFD-------SQCQILLTTRDKSVTDSVMGPKYVVP 281

Query: 329 SIKELSEQECW------------------------CKGLPLAAKTIGSLLRFKRTR-EEW 363
               L +++                          CKG PL    IG+LLR    R E +
Sbjct: 282 VESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYY 341

Query: 364 ESILDSELWQLEEFEK-----GLLAPLLLSYNDLPPMIKRCFQY-------YE-----LI 406
              L ++ ++            L   + +S   L   IK  +          +     L 
Sbjct: 342 LKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC 401

Query: 407 KLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQF 466
            LW  +               E+       +S       D  G   R  +HD+  DF   
Sbjct: 402 ILWDME-----------TEEVEDILQEFVNKSLLF---CDRNGKSFRYYLHDLQVDFLT- 446

Query: 467 LTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTL 526
             +  C  ++         +I  +Q   +   L    E       F A ++         
Sbjct: 447 --EKNCSQLQDLHK----KIITQFQRYHQPHTLSPDQEDCMYWYNFLAYHMA-------- 492

Query: 527 IQVSLTHVLQSLFDQLKCLRA 547
               +   L +L   L  ++A
Sbjct: 493 -SAKMHKELCALMFSLDWIKA 512

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  255 bits (653), Expect = 4e-77
 Identities = 74/559 (13%), Positives = 149/559 (26%), Gaps = 82/559 (14%)

Query: 48  VLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSF 107
            L  A  R   +   R  L  L+  + +  D  +  +      R+E +   +   +  + 
Sbjct: 9   ALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKM--STRLERIANFLRIYRRQAS 66

Query: 108 LPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSERIQSTSLID 167
                   F+   Q          I+  +++    + +             ++   ++  
Sbjct: 67  ELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPK 126

Query: 168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE-- 225
                 R+     +  KL          D   + + G  G GK+ +A  A + SD     
Sbjct: 127 QMTCYIREYHVDRVIKKLDEMCDL----DSFFLFLHGRAGSGKSVIASQALSKSDQLIGI 182

Query: 226 YFDKRMWVCVSDPFDE-----LRIAKAIIEALEGF-----VPTVGELNSLLESIRASLVG 275
            +D  +W+  S    +           ++++ +       V  V  +        A +  
Sbjct: 183 NYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDR 242

Query: 276 KKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVARMMES-IHVISIKELS 334
              L + DD+  ++  +W              + LVTTR   ++         I +  L 
Sbjct: 243 PNTLFVFDDVVQEETIRWAQ--------ELRLRCLVTTRDVEISNAASQTCEFIEVTSLE 294

Query: 335 EQECW--------------------------CKGLPLAAKTIGSLLRFKRTREEWE---- 364
             EC+                            G P            K   +  +    
Sbjct: 295 IDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNK 354

Query: 365 ---SILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQY-------YE-----LIKLW 409
                L           K L   L      L    +    +        +        + 
Sbjct: 355 LESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVI 414

Query: 410 MAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTK 469
                I     ++L+    +    L+ R             V+  K+  I+H F + +  
Sbjct: 415 PVD--ICSNEEEQLDDEVADRLKRLSKRGALLSG---KRMPVLTFKIDHIIHMFLKHVVD 469

Query: 470 NECIAIEVDDDEEPLSLI--NTYQEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTL 526
            + IA  +   E+ L  I  N      RH             S ++      ++      
Sbjct: 470 AQTIANGISILEQRLLEIGNNNVSVPERHIPSHFQKFRRSSASEMYPKTTEETVIRPEDF 529

Query: 527 IQVSLTHVLQSLFDQLKCL 545
            +    H  Q  +D LK  
Sbjct: 530 PKFMQLH--QKFYDSLKNF 546

>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 =  178 bits (451), Expect = 7e-47
 Identities = 99/640 (15%), Positives = 198/640 (30%), Gaps = 161/640 (25%)

Query: 31  IDNEVAKLKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLDEWNTARLKL 90
           +D E  + ++ +  I +V  DA    F +       D  KDV      +L   +   +  
Sbjct: 7   MDFETGEHQYQYKDILSVFEDA----FVDN-----FD-CKDVQDMPKSIL---SKEEIDH 53

Query: 91  RIEGVDALVPQRKVCSFL---PAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYN 147
            I   DA+    ++   L          F +   R +    +  I  +    +    MY 
Sbjct: 54  IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113

Query: 148 FNVIRSTENSERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGG 207
               R   +++        +VS    R +    L+  LL       +   + + I G+ G
Sbjct: 114 EQRDRLYNDNQVFAK---YNVS----RLQPYLKLRQALL------ELRPAKNVLIDGVLG 160

Query: 208 IGKTTLAQFAYNDSDVFEYFDKRM-WV---CVSDPFDEL--------RIAKAIIEALEGF 255
            GKT +A        V    D ++ W+     + P   L        +I        +  
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220

Query: 256 VPTVGELNSLLESIRASLVGKKF---LLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVT 312
                 ++S+   +R  L  K +   LL+L ++   +   W  F+          KIL+T
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ--NAKAWNAFNL-------SCKILLT 271

Query: 313 TRKETVARMMESIHV--------------------------ISIKELSEQECWCKGLPLA 346
           TR + V   + +                                ++L  +       P  
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV--LTTNPRR 329

Query: 347 AKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQYYE-- 404
              I   +R       W++       +L    +        S N L P   R  + ++  
Sbjct: 330 LSIIAESIRDGLAT--WDNWKHVNCDKLTTIIE-------SSLNVLEPAEYR--KMFDRL 378

Query: 405 -------------LIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFKDNEGVV 451
                        L  +W            ++ ++  +    L   S  ++  K++    
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKS------DVMVVVNK----LHKYSLVEKQPKES---- 424

Query: 452 VRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPL--SLINTYQ--EKLRHSMLVL----GY 503
               +  I         K +       ++E  L  S+++ Y   +      L+      Y
Sbjct: 425 -TISIPSI-----YLELKVKL------ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Query: 504 EASFPIS--IFKAKN------LRSLFINNTLIQVSLTHV------LQSLFDQLKCLRALR 549
             S  I   +   ++       R +F++   ++  + H         S+ + L+ L+  +
Sbjct: 473 FYSH-IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYK 531

Query: 550 --IATLMNTWD--VNSTNKILKGIE-KLIHLRYLRLVGLG 584
             I      ++  VN+    L  IE  LI  +Y  L+ + 
Sbjct: 532 PYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA 571

>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 = 59.5 bits (143), Expect = 3e-09
 Identities = 60/412 (14%), Positives = 122/412 (29%), Gaps = 132/412 (32%)

Query: 332 ELSEQECWCKG-LPLAAKTIGSLLRFKRTREEWESILDSELWQLEEFEKGLLAP------ 384
           E  E +   K  L +           K  ++  +SIL  E     E +  +++       
Sbjct: 10  ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKE-----EIDHIIMSKDAVSGT 64

Query: 385 -----LLLSYNDLPPMIKRCFQYYELIKLWMAQDY------IMPEGNKELEIIGEEYFDY 433
                 LLS  +            + ++  +  +Y      I  E  ++  ++   Y + 
Sbjct: 65  LRLFWTLLSKQEE--------MVQKFVEEVLRINYKFLMSPIKTE-QRQPSMMTRMYIEQ 115

Query: 434 L-AMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNE-------------CIAIEV-- 477
              + +  Q F K N   V R + +  +      L   +              +A++V  
Sbjct: 116 RDRLYNDNQVFAKYN---VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL 172

Query: 478 --------------------DDDEEPLSLINTYQEKLRHSMLVLG-YEASFPISIFKAKN 516
                               +  E  L ++     ++  +      + ++  + I   + 
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 517 -LRSLFIN----NTLI---QVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG 568
            LR L  +    N L+    V       + F+ L C    +I  L+ T     T+ +   
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNA-FN-LSC----KI--LLTTRFKQVTDFLSAA 284

Query: 569 IEK---LIHLR-----------YLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL 614
                 L H              L+ +    ++LP       N + L I           
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT-TNPRRLSI----------- 332

Query: 615 GIGKLV--------NLRHLTYD------DSCLEFI-PKGIQRLTNLRTLSEF 651
            I + +        N +H+  D      +S L  + P   +++     LS F
Sbjct: 333 -IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM--FDRLSVF 381

>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 = 46.8 bits (110), Expect = 2e-05
 Identities = 51/315 (16%), Positives = 98/315 (31%), Gaps = 117/315 (37%)

Query: 6   VSPLLEQLISISLEEAREQMKLVVGIDN----EVAKLKHNFLAIQAVLVDAEQRQ----- 56
            +P    +I+ S+ +           DN       KL     +   VL  AE R+     
Sbjct: 325 TNPRRLSIIAESIRDGLAT------WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378

Query: 57  --FKEET-------VRLWLD---------------------QLKDVSYYMGDVLDEWNTA 86
             F             +W D                     Q K+ +  +  +  E    
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE---- 434

Query: 87  RLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRRDIAVKIKAINGKLDDIAKQKDMY 146
            LK+++E   AL   R +         +   +TF   D+             I    D Y
Sbjct: 435 -LKVKLENEYAL--HRSI------VDHYNIPKTFDSDDL-------------IPPYLDQY 472

Query: 147 NFNVI----RSTENSERIQSTSLI--DVSEIRGRDEEKSSLK-SKLLCESSEEIINDIQI 199
            ++ I    ++ E+ ER+    ++  D   +  +      ++       +S  I+N +Q 
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK------IRHDSTAWNASGSILNTLQ- 525

Query: 200 ITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTV 259
                                  +  Y   + ++C +DP  E      ++ A+  F+P +
Sbjct: 526 ----------------------QLKFY---KPYICDNDPKYE-----RLVNAILDFLPKI 555

Query: 260 GELNSLLESIRASLV 274
            E  +L+ S    L+
Sbjct: 556 EE--NLICSKYTDLL 568

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 84.9 bits (210), Expect = 4e-17
 Identities = 69/337 (20%), Positives = 111/337 (32%), Gaps = 66/337 (19%)

Query: 173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQ-FAYNDSDVFEYF-DKR 230
            R +   +++ KL   + E        +TI GM G GK+ LA     + S +   F    
Sbjct: 128 TRKKLVHAIQQKLWKLNGEP-----GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGV 182

Query: 231 MWVCV--SDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVG------KKFLLIL 282
            WV +   D    L   + +   L+        L   +E  +  L         + LLIL
Sbjct: 183 HWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLIL 242

Query: 283 DDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR-KETVARMMESIHVISIKE-LSEQEC-- 338
           DD+W             LK      +IL+TTR K     +M   HV+ ++  L  ++   
Sbjct: 243 DDVWDPWV---------LKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLE 293

Query: 339 ----------------------WCKGLPLAAKTIGSLLRFKRTREE------WESILDSE 370
                                  CKG PL    IG+LLR    R                
Sbjct: 294 ILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRI 353

Query: 371 LWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQ----YYELIKLWMAQDYIMPEGNKELEII 426
                   + L   + +S   L   IK  +       + +K+      ++ +   E E+ 
Sbjct: 354 RKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETE-EV- 411

Query: 427 GEEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDF 463
            E+       +S     F +  G      +HD+  DF
Sbjct: 412 -EDILQEFVNKSL---LFCNRNGKSFCYYLHDLQVDF 444

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 72.7 bits (179), Expect = 6e-14
 Identities = 39/153 (25%), Positives = 56/153 (36%), Gaps = 19/153 (12%)

Query: 506 SFPISIFKAKNLRSLFI--NNTLIQV--SLTHV-LQSLFDQLKCLRALRIATLMNTWDVN 560
           + P SI     LR L I     L ++   L           L  L++LR+          
Sbjct: 141 ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL---------- 190

Query: 561 STNKIL---KGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIG 617
               I      I  L +L+ L++       L      L  L+ L++  CT+L+  P   G
Sbjct: 191 EWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFG 250

Query: 618 KLVNLRHLT-YDDSCLEFIPKGIQRLTNLRTLS 649
               L+ L   D S L  +P  I RLT L  L 
Sbjct: 251 GRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLD 283

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 72.3 bits (178), Expect = 6e-14
 Identities = 37/153 (24%), Positives = 56/153 (36%), Gaps = 23/153 (15%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
            FP   F+  +L+ + I+           L  L D ++    L   TL      N    +
Sbjct: 95  QFPDQAFRLSHLQHMTIDAAG--------LMELPDTMQQFAGLETLTLAR----NPLRAL 142

Query: 566 LKGIEKLIHLRYLRLVG----------LGTEELPETCCELLNLQVLEIEQCTSLKRLPLG 615
              I  L  LR L +            L + +       L+NLQ L + + T ++ LP  
Sbjct: 143 PASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL-EWTGIRSLPAS 201

Query: 616 IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL 648
           I  L NL+ L   +S L  +   I  L  L  L
Sbjct: 202 IANLQNLKSLKIRNSPLSALGPAIHHLPKLEEL 234

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 70.4 bits (173), Expect = 3e-13
 Identities = 33/145 (22%), Positives = 53/145 (36%), Gaps = 14/145 (9%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
                     NL+SL +  T I+      L +    L+ L++L+I         +  + +
Sbjct: 174 DASGEHQGLVNLQSLRLEWTGIRS-----LPASIANLQNLKSLKI-------RNSPLSAL 221

Query: 566 LKGIEKLIHLRYLRLVGL-GTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRH 624
              I  L  L  L L G       P        L+ L ++ C++L  LPL I +L  L  
Sbjct: 222 GPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEK 281

Query: 625 LTYDD-SCLEFIPKGIQRLTNLRTL 648
           L       L  +P  I +L     +
Sbjct: 282 LDLRGCVNLSRLPSLIAQLPANCII 306

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 67.7 bits (166), Expect = 2e-12
 Identities = 31/150 (20%), Positives = 53/150 (35%), Gaps = 21/150 (14%)

Query: 509 ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG 568
           +         +L + +      L       F +L  L+ + I       D     ++   
Sbjct: 75  LEDATQPGRVALELRSV----PLPQFPDQAF-RLSHLQHMTI-------DAAGLMELPDT 122

Query: 569 IEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGK---------L 619
           +++   L  L L       LP +   L  L+ L I  C  L  LP  +           L
Sbjct: 123 MQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGL 182

Query: 620 VNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
           VNL+ L  + + +  +P  I  L NL++L 
Sbjct: 183 VNLQSLRLEWTGIRSLPASIANLQNLKSLK 212

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 63.4 bits (155), Expect = 6e-11
 Identities = 31/133 (23%), Positives = 45/133 (33%), Gaps = 19/133 (14%)

Query: 535 LQSLFDQLKCLRAL------------RIATLMNTWDVNSTNKILKGIEKLI------HLR 576
           L+   D L   +              R A   N      T + LK    L+         
Sbjct: 25  LRPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPGRV 84

Query: 577 YLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP 636
            L L  +   + P+    L +LQ + I+    L  LP  + +   L  LT   + L  +P
Sbjct: 85  ALELRSVPLPQFPDQAFRLSHLQHMTIDAA-GLMELPDTMQQFAGLETLTLARNPLRALP 143

Query: 637 KGIQRLTNLRTLS 649
             I  L  LR LS
Sbjct: 144 ASIASLNRLRELS 156

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 60.3 bits (147), Expect = 5e-10
 Identities = 31/143 (21%), Positives = 49/143 (34%), Gaps = 18/143 (12%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
           S P SI   +NL+SL I N+     L+ +  ++   L  L  L +          +    
Sbjct: 197 SLPASIANLQNLKSLKIRNS----PLSALGPAI-HHLPKLEELDLR------GCTALRNY 245

Query: 566 LKGIEKLIHLRYLRLVG---LGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL 622
                    L+ L L     L    LP     L  L+ L++  C +L RLP  I +L   
Sbjct: 246 PPIFGGRAPLKRLILKDCSNL--LTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPAN 303

Query: 623 RHLTYDDSCLEFIPKGIQRLTNL 645
             +         + +   R    
Sbjct: 304 CIILVPPHLQAQLDQ--HRPVAR 324

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare} Length = 115

 Score = 57.9 bits (140), Expect = 2e-10
 Identities = 23/123 (18%), Positives = 55/123 (44%), Gaps = 12/123 (9%)

Query: 6   VSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFKE--ETVR 63
           +S L+ +L  +  EE     KL  G+   +  L     ++ A L+   +   ++     +
Sbjct: 3   ISNLIPKLGELLTEEF----KLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDK 58

Query: 64  LWLDQLKDVSYYMGDVLDEWNTARLKLRIEGVDALVPQRKVCSFLPAASCFGFSQTFQRR 123
           LW D+++++SY + DV+D++      ++++G+ +     K    +   +     +   + 
Sbjct: 59  LWADEVRELSYVIEDVVDKF-----LVQVDGIKSDDNNNKFKGLMKRTTEL-LKKVKHKH 112

Query: 124 DIA 126
            IA
Sbjct: 113 GIA 115

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 55.8 bits (135), Expect = 3e-08
 Identities = 25/156 (16%), Positives = 51/156 (32%), Gaps = 19/156 (12%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIAT-LMNTWDVNSTNK 564
               + FK  N+ S+ ++N      ++   + LF     L ++ +   ++     NS   
Sbjct: 424 PLDPTPFKGINVSSINLSNN----QISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLKD 479

Query: 565 ILKGIEKLIHLRYLRLVG--LGTEELPE--TCCELLNLQVLEIEQCTSLKRLPLGIGKLV 620
             +  +    L  + L    L   +L +      L  L  +++    S  + P       
Sbjct: 480 ENENFKNTYLLTSIDLRFNKL--TKLSDDFRATTLPYLVGIDLSYN-SFSKFPTQPLNSS 536

Query: 621 NLRHLTYDD-------SCLEFIPKGIQRLTNLRTLS 649
            L+     +         L   P+GI    +L  L 
Sbjct: 537 TLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQ 572

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 52.4 bits (126), Expect = 4e-07
 Identities = 19/176 (10%), Positives = 39/176 (22%), Gaps = 28/176 (15%)

Query: 494 LRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATL 553
           L      +      P  I       S             H  ++  D         +   
Sbjct: 112 LGSHGEKVNERLFGPKGI---SANMSDEQKQ----KMRMHYQKTFVDYDPREDFSDLIKD 164

Query: 554 MNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVL------------ 601
                      I K     +    +  +      + +    L  L+              
Sbjct: 165 CIN-SDPQQKSIKKSSRITLKDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNSPFVAENI 223

Query: 602 -------EIEQCTSLKRLPLGIGKLVNLRHLT-YDDSCLEFIPKGIQRLTNLRTLS 649
                    E     K   L    L +L  +  Y+   L  +P  ++ L  ++ ++
Sbjct: 224 CEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLIN 279

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 50.8 bits (122), Expect = 1e-06
 Identities = 21/144 (14%), Positives = 45/144 (31%), Gaps = 9/144 (6%)

Query: 509 ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG 568
           +S+     +  L +         +  +     QL  L  L + +  +   VN      KG
Sbjct: 75  VSLNSNGRVTGLSLEGF----GASGRVPDAIGQLTELEVLALGS--HGEKVNERLFGPKG 128

Query: 569 IEKLIHLRYLRLVGLGTEELPETC---CELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
           I   +     + + +  ++         +  +L    I      K +       +    +
Sbjct: 129 ISANMSDEQKQKMRMHYQKTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQI 188

Query: 626 TYDDSCLEFIPKGIQRLTNLRTLS 649
               + + F+ K + RLT LR   
Sbjct: 189 GQLSNNITFVSKAVMRLTKLRQFY 212

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 17/159 (10%), Positives = 47/159 (29%), Gaps = 30/159 (18%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHV-LQSLFDQLKCLRALRIATLMNTWDVNSTNK 564
                    + ++ ++I       +L    +++   ++K L  L              N+
Sbjct: 296 QALADAPVGEKIQIIYIGYN----NLKTFPVETSLQKMKKLGMLEC----------LYNQ 341

Query: 565 ILKGIEKLIHLRYLRLVGLGT---EELPETCCELL-NLQVLEIEQCTSLKRLP--LGIGK 618
           +   +        L  + L      E+P   C     ++ L       LK +P       
Sbjct: 342 LEGKLPAFGSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHN-KLKYIPNIFDAKS 400

Query: 619 LVNLRHL--------TYDDSCLEFIPKGIQRLTNLRTLS 649
           +  +  +        + D    + +     +  N+ +++
Sbjct: 401 VSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSIN 439

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 17/145 (11%), Positives = 43/145 (29%), Gaps = 17/145 (11%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNK 564
           S   S         +   +     ++T V +++  +L  LR   +         +    +
Sbjct: 174 SIKKSSRITLKDTQIGQLSN----NITFVSKAVM-RLTKLRQFYMGN-------SPFVAE 221

Query: 565 ILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRH 624
            +    +  +  Y +               L +L  +E+  C +L +LP  +  L  ++ 
Sbjct: 222 NICEAWENENSEYAQQYKT----EDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQL 277

Query: 625 LTYDDSCLEFIPKGIQRLTNLRTLS 649
           +    +      +       L    
Sbjct: 278 INVACNRGISGEQLKDDWQALADAP 302

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 15/155 (9%), Positives = 40/155 (25%), Gaps = 26/155 (16%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
               ++ +   LR  ++ N+               + +                      
Sbjct: 197 FVSKAVMRLTKLRQFYMGNS----PFVAENICEAWENENSEYA-----------QQYKTE 241

Query: 566 LKGIEKLIHLRYLRLVGLG-TEELPETCCELLNLQVL--------EIEQCTSLKRLPLGI 616
               + L  L  + +       +LP     L  +Q++          EQ     +     
Sbjct: 242 DLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADA 301

Query: 617 GKLVNLRHLTYDDSCLE--FIPKGIQRLTNLRTLS 649
                ++ +    + L+   +   +Q++  L  L 
Sbjct: 302 PVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLE 336

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 55.7 bits (134), Expect = 4e-08
 Identities = 21/161 (13%), Positives = 42/161 (26%), Gaps = 27/161 (16%)

Query: 504 EASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRAL-----RIATLMNTWD 558
             S  +  +K  N  ++ ++       +      LF     +  +      + ++     
Sbjct: 662 NISCSMDDYKGINASTVTLSYN----EIQKFPTELFATGSPISTIILSNNLMTSIPE--- 714

Query: 559 VNSTNKILKGIEKLIHLRYLRLVG--LGTEELPE--TCCELLNLQVLEIEQCTSLKRLPL 614
            NS        +    L  + L    L    L +      L  L  +++         P 
Sbjct: 715 -NSLKPKDGNYKNTYLLTTIDLRFNKL--TSLSDDFRATTLPYLSNMDVSYN-CFSSFPT 770

Query: 615 GIGKLVNLRHL-------TYDDSCLEFIPKGIQRLTNLRTL 648
                  L+            +  L   P GI    +L  L
Sbjct: 771 QPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQL 811

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 55.7 bits (134), Expect = 5e-08
 Identities = 24/180 (13%), Positives = 51/180 (28%), Gaps = 30/180 (16%)

Query: 482 EPLSLINTYQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQ 541
           +  S I+    ++ +    +        +I +   L+ ++  N+      T+   ++  +
Sbjct: 418 KKDSRISLKDTQIGNLTNRIT---FISKAIQRLTKLQIIYFANS----PFTYDNIAVDWE 470

Query: 542 LKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGL-GTEELPETCCELLNLQV 600
                                         L  L  + L       +LP+   +L  LQ 
Sbjct: 471 DANSDYA-----------KQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQS 519

Query: 601 LEI---------EQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPK--GIQRLTNLRTLS 649
           L I         +      RL         ++      + LE  P    +Q++  L  L 
Sbjct: 520 LNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLD 579

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 54.1 bits (130), Expect = 1e-07
 Identities = 20/152 (13%), Positives = 44/152 (28%), Gaps = 23/152 (15%)

Query: 508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK 567
           PI      +L+   I N      LT+ +  +   ++ L  L+I          + +    
Sbjct: 416 PIKKDSRISLKDTQIGN------LTNRITFISKAIQRLTKLQIIYF-------ANSPFTY 462

Query: 568 GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL-- 625
               +             E    +   L +L  +E+  C ++ +LP  +  L  L+ L  
Sbjct: 463 DNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLNI 522

Query: 626 --------TYDDSCLEFIPKGIQRLTNLRTLS 649
                       +    +         ++   
Sbjct: 523 ACNRGISAAQLKADWTRLADDEDTGPKIQIFY 554

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 44.5 bits (105), Expect = 1e-04
 Identities = 14/158 (8%), Positives = 42/158 (26%), Gaps = 28/158 (17%)

Query: 508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK 567
             +      + S+  +       +    +++   +   + +  +T+     ++  N+I K
Sbjct: 637 IFNAKSVYVMGSVDFSYN----KIGSEGRNISCSMDDYKGINASTV----TLSY-NEIQK 687

Query: 568 ----GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRL----------- 612
                      +  + L       +PE   +  +      +    L  +           
Sbjct: 688 FPTELFATGSPISTIILSNNLMTSIPENSLKPKDG---NYKNTYLLTTIDLRFNKLTSLS 744

Query: 613 -PLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
                  L  L ++    +C    P      + L+   
Sbjct: 745 DDFRATTLPYLSNMDVSYNCFSSFPTQPLNSSQLKAFG 782

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 21/166 (12%), Positives = 45/166 (27%), Gaps = 28/166 (16%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
             P +I +   L+ L         S T   +      + L         +   ++     
Sbjct: 338 RVPDAIGQLTELKVLSFGTH----SETVSGRLFG--DEELTPDMSEERKHRIRMHYKKMF 391

Query: 566 LKGIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCT-SLKRLPLGIGKLVNLR 623
           L   ++L     L+       E+ P      ++L+  +I   T  +  +   I +L  L+
Sbjct: 392 LDYDQRLNLSDLLQDAINRNPEMKPIKKDSRISLKDTQIGNLTNRITFISKAIQRLTKLQ 451

Query: 624 HL--------------------TYDDSCLEFIPKGIQRLTNLRTLS 649
            +                    +      E        L +L  + 
Sbjct: 452 IIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVE 497

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 51.5 bits (124), Expect = 3e-07
 Identities = 17/149 (11%), Positives = 43/149 (28%), Gaps = 23/149 (15%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
               S  +    +++++ N      +T +          ++ L +            N+I
Sbjct: 113 RVSCSRGQ--GKKNIYLANN----KITMLRDLDEGCRSRVQYLDL----------KLNEI 156

Query: 566 LK-----GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLV 620
                         L +L L      ++         L+ L++     L  +        
Sbjct: 157 DTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSN-KLAFMGPEFQSAA 214

Query: 621 NLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            +  ++  ++ L  I K ++   NL    
Sbjct: 215 GVTWISLRNNKLVLIEKALRFSQNLEHFD 243

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 49.6 bits (119), Expect = 2e-06
 Identities = 28/174 (16%), Positives = 49/174 (28%), Gaps = 42/174 (24%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSL------------FDQLKCLRALRIATL 553
             P      K+L     N   +   L  +L+ L                  L+ + +   
Sbjct: 105 ELPELPQSLKSLLVDNNNLKALS-DLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDV--- 160

Query: 554 MNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEI---------E 604
                    N + K  +    L ++       EELPE    L  L  +           +
Sbjct: 161 -------DNNSLKKLPDLPPSLEFIAAGNNQLEELPE-LQNLPFLTAIYADNNSLKKLPD 212

Query: 605 QCTSLKRLPLG---------IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
              SL+ +  G         +  L  L  +  D++ L+ +P     L  L    
Sbjct: 213 LPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRD 266

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 48.1 bits (115), Expect = 7e-06
 Identities = 25/160 (15%), Positives = 50/160 (31%), Gaps = 41/160 (25%)

Query: 510 SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI--LK 567
            +  +  L+ + ++N          L+ L D    L  +              N++  L 
Sbjct: 148 ELQNSSFLKIIDVDNNS--------LKKLPDLPPSLEFIAA----------GNNQLEELP 189

Query: 568 GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVL--------EIEQCTSLKRL------- 612
            ++ L  L  +       ++LP+    L ++           E++    L  +       
Sbjct: 190 ELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLL 249

Query: 613 ---PLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
              P       +L  L   D+ L  +P+  Q LT L    
Sbjct: 250 KTLPDLPP---SLEALNVRDNYLTDLPELPQSLTFLDVSE 286

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 45.0 bits (107), Expect = 5e-05
 Identities = 25/150 (16%), Positives = 42/150 (28%), Gaps = 29/150 (19%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
             P+     K+    +   +               + + +   R+   ++          
Sbjct: 25  EMPVEAENVKSKTEYYNAWS----EWERNAPPGNGEQREMAVSRLRDCLDR--------- 71

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
                       L L  LG   LPE      +L+ L    C SL  LP     L +L   
Sbjct: 72  --------QAHELELNNLGLSSLPE---LPPHLESLVA-SCNSLTELPELPQSLKSLLVD 119

Query: 626 TYDDSCLEFIPKGIQRLT----NLRTLSEF 651
             +   L  +P  ++ L      L  L E 
Sbjct: 120 NNNLKALSDLPPLLEYLGVSNNQLEKLPEL 149

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 17/149 (11%), Positives = 43/149 (28%), Gaps = 23/149 (15%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
               S  +    +++++ N      +T +          ++ L +            N+I
Sbjct: 113 RVSCSRGQ--GKKNIYLANN----KITMLRDLDEGCRSRVQYLDL----------KLNEI 156

Query: 566 LK-----GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLV 620
                         L +L L      ++         L+ L++     L  +        
Sbjct: 157 DTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSN-KLAFMGPEFQSAA 214

Query: 621 NLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            +  ++  ++ L  I K ++   NL    
Sbjct: 215 GVTWISLRNNKLVLIEKALRFSQNLEHFD 243

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 46.5 bits (111), Expect = 6e-06
 Identities = 25/154 (16%), Positives = 54/154 (35%), Gaps = 19/154 (12%)

Query: 499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD 558
            +LG  ++  I+  +  +L  + + N  +   LT       +    ++ L I        
Sbjct: 28  GLLGQSSTANITEAQMNSLTYITLANINVT-DLTG-----IEYAHNIKDLTI-------- 73

Query: 559 VNSTNKI--LKGIEKLIHLRYLRLVGLG-TEELPETCCELLNLQVLEIEQCTSLKRLPLG 615
             +         I  L +L  LR++G   T +       L +L +L+I        +   
Sbjct: 74  --NNIHATNYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTK 131

Query: 616 IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
           I  L  +  +    +        ++ L  L++L+
Sbjct: 132 INTLPKVNSIDLSYNGAITDIMPLKTLPELKSLN 165

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 24/145 (16%), Positives = 52/145 (35%), Gaps = 23/145 (15%)

Query: 516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI------ 569
            L  L I+ +     L          ++ +  L +        +     +L+        
Sbjct: 175 FLEELEIDAS----DLQSYEPKSLKSIQNVSHLIL-------HMKQHILLLEIFVDVTSS 223

Query: 570 EKLIHLRYLRLVGLGTEELPE----TCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
            + + LR   L      EL      +  +    + ++I    SL ++   + ++  L  L
Sbjct: 224 VECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKI-TDESLFQVMKLLNQISGLLEL 282

Query: 626 TYDDSCLEFIPKGI-QRLTNLRTLS 649
            +  + L+ +P GI  RLT+L+ + 
Sbjct: 283 EFSRNQLKSVPDGIFDRLTSLQKIW 307

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 41.3 bits (97), Expect = 7e-04
 Identities = 27/152 (17%), Positives = 51/152 (33%), Gaps = 19/152 (12%)

Query: 508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK 567
             S+F   +L  L I       + T + +  F  L  L  L I       D +       
Sbjct: 141 ETSLFS--HLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEI-------DASDLQSYEP 191

Query: 568 GI-EKLIHLRYLRLVGLGTEELPETCCELL-NLQVLEIE----QCTSLKRLPLGI----G 617
              + + ++ +L L       L E   ++  +++ LE+            L  G      
Sbjct: 192 KSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLI 251

Query: 618 KLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
           K    R++   D  L  + K + +++ L  L 
Sbjct: 252 KKFTFRNVKITDESLFQVMKLLNQISGLLELE 283

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 30/142 (21%), Positives = 50/142 (35%), Gaps = 23/142 (16%)

Query: 515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK--- 571
           ++L  L ++   I      +    F+ L  L  L +            N++   I     
Sbjct: 88  RHLEILQLSRNHI----RTIEIGAFNGLANLNTLEL----------FDNRL-TTIPNGAF 132

Query: 572 --LIHLRYLRLVGLGTEELPETC-CELLNLQVLEIEQCTSLKRLPLGI-GKLVNLRHLTY 627
             L  L+ L L     E +P      + +L+ L++ +   L  +  G    L NLR+L  
Sbjct: 133 VYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNL 192

Query: 628 DDSCLEFIPKGIQRLTNLRTLS 649
               L  IP  +  L  L  L 
Sbjct: 193 AMCNLREIP-NLTPLIKLDELD 213

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 46.1 bits (109), Expect = 3e-05
 Identities = 26/133 (19%), Positives = 46/133 (34%), Gaps = 17/133 (12%)

Query: 516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE--KLI 573
           N  SL  N+      ++      F          +          + N+ +  ++   + 
Sbjct: 9   NNFSLSQNSFYNT--ISGTYADYFSAWDKWEKQALPG-------ENRNEAVSLLKECLIN 59

Query: 574 HLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE 633
               L+L  L    LP+       + VLEI Q  +L  LP       +L +L   D+ L 
Sbjct: 60  QFSELQLNRLNLSSLPDNLPP--QITVLEITQN-ALISLPELPA---SLEYLDACDNRLS 113

Query: 634 FIPKGIQRLTNLR 646
            +P+    L +L 
Sbjct: 114 TLPELPASLKHLD 126

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 34/163 (20%), Positives = 54/163 (33%), Gaps = 31/163 (19%)

Query: 506 SFPISIFKAKNLRSLFI-NNTLIQV-----SLTHV------LQSLFDQLKCLRALRIATL 553
           S P ++     +  L I  N LI +     SL ++      L +L +    L+ L +   
Sbjct: 73  SLPDNLPP--QITVLEITQNALISLPELPASLEYLDACDNRLSTLPELPASLKHLDV--- 127

Query: 554 MNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLP 613
                    N++    E    L Y+         LPE      +L+VL +     L  LP
Sbjct: 128 -------DNNQLTMLPELPALLEYINADNNQLTMLPELPT---SLEVLSVRNN-QLTFLP 176

Query: 614 LGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRG 656
                  +L  L    + LE +P    R  +      F   R 
Sbjct: 177 ELPE---SLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRE 216

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 45.8 bits (109), Expect = 3e-05
 Identities = 21/149 (14%), Positives = 47/149 (31%), Gaps = 8/149 (5%)

Query: 506 SFPISIFKAKNLRSLFI-NNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVN-STN 563
              +S+    +L    +  N L  +++   ++ L      +  +R    +    +    N
Sbjct: 179 HVDLSLIP--SLFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHN 236

Query: 564 KI--LKGIEKLIHLRYLRLVGLGTEELPETCCE-LLNLQVLEIEQCTSLKRLPLGIGKLV 620
            +     +     L  + L     E++       +  L+ L I     L  L L    + 
Sbjct: 237 NLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYI-SNNRLVALNLYGQPIP 295

Query: 621 NLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            L+ L    + L  + +   +   L  L 
Sbjct: 296 TLKVLDLSHNHLLHVERNQPQFDRLENLY 324

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 26/140 (18%), Positives = 51/140 (36%), Gaps = 18/140 (12%)

Query: 516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI-EKLIH 574
            +R L I     Q  L + L +++  L+ ++ + +         +    +     + L  
Sbjct: 287 TIRRLHIP----QFYLFYDLSTVYSLLEKVKRITVEN-------SKVFLVPCSFSQHLKS 335

Query: 575 LRYLRLVG--LGTEELPETCC--ELLNLQVLEIE--QCTSLKRLPLGIGKLVNLRHLTYD 628
           L +L L    +  E L  + C     +LQ L +      S+++    +  L NL  L   
Sbjct: 336 LEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDIS 395

Query: 629 DSCLEFIPKGIQRLTNLRTL 648
            +    +P   Q    +R L
Sbjct: 396 RNTFHPMPDSCQWPEKMRFL 415

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 23/158 (14%), Positives = 51/158 (32%), Gaps = 19/158 (12%)

Query: 506 SFPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN- 563
                      ++R L + +T    +L     S     +    ++      +   + +  
Sbjct: 186 FLLEIFADILSSVRYLELRDT----NLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFN 241

Query: 564 ---KILKGIEKLIHLRYLRLVGLGTEELPE---------TCCELLNLQVLEIEQCTSLKR 611
              K+L+ I +L  + +      G  +               E + ++ L I Q      
Sbjct: 242 ELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYD 301

Query: 612 LPLGIGKLVNLRHLTYDDSCLEFIPKGI-QRLTNLRTL 648
           L      L  ++ +T ++S +  +P    Q L +L  L
Sbjct: 302 LSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFL 339

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 42.4 bits (100), Expect = 4e-04
 Identities = 22/146 (15%), Positives = 49/146 (33%), Gaps = 19/146 (13%)

Query: 506 SFPISIFK-AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRAL-----RIATLMNTWDV 559
             P S  +  K+L  L ++  L+         +       L+ L      + ++  T ++
Sbjct: 324 LVPCSFSQHLKSLEFLDLSENLMV-EEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEI 382

Query: 560 NSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKL 619
                       L +L  L +       +P++C     ++ L +     ++ +   I   
Sbjct: 383 LL---------TLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSST-GIRVVKTCI--P 430

Query: 620 VNLRHLTYDDSCLEFIPKGIQRLTNL 645
             L  L   ++ L+     + RL  L
Sbjct: 431 QTLEVLDVSNNNLDSFSLFLPRLQEL 456

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 30/154 (19%), Positives = 56/154 (36%), Gaps = 25/154 (16%)

Query: 506 SFPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK 564
           +     F +  +L  L +++      L+ +  S F  L  L+ L +            N 
Sbjct: 64  TIEGDAFYSLGSLEHLDLSDN----HLSSLSSSWFGPLSSLKYLNL----------MGNP 109

Query: 565 I-----LKGIEKLIHLRYLRLVG--LGTEELPETCCELLNLQVLEIEQCTSLKRLPLG-I 616
                       L +L+ LR+      +E        L +L  LEI+   SL+      +
Sbjct: 110 YQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKAL-SLRNYQSQSL 168

Query: 617 GKLVNLRHLTYDDSCLEFIPKGI-QRLTNLRTLS 649
             + ++ HLT   S   F+ +     L+++R L 
Sbjct: 169 KSIRDIHHLTLHLSESAFLLEIFADILSSVRYLE 202

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 28/144 (19%), Positives = 47/144 (32%), Gaps = 27/144 (18%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
           + P  +    ++ +L I +     +LT  L +L  +L+ L               S N++
Sbjct: 54  TLPDCLPA--HITTLVIPD----NNLTS-LPALPPELRTLEV-------------SGNQL 93

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
                    L  L +       LP        L  L I     L  LP+       L+ L
Sbjct: 94  TSLPVLPPGLLELSIFSNPLTHLPA---LPSGLCKLWIFGN-QLTSLPVLPP---GLQEL 146

Query: 626 TYDDSCLEFIPKGIQRLTNLRTLS 649
           +  D+ L  +P     L  L   +
Sbjct: 147 SVSDNQLASLPALPSELCKLWAYN 170

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 44.5 bits (105), Expect = 1e-04
 Identities = 28/144 (19%), Positives = 47/144 (32%), Gaps = 28/144 (19%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
           S P+       L+ L +++          L SL      L  L              N++
Sbjct: 175 SLPMLP---SGLQELSVSDNQ--------LASLPTLPSELYKLWA----------YNNRL 213

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
                    L+ L + G     LP    EL  L V        L  LP+       L  L
Sbjct: 214 TSLPALPSGLKELIVSGNRLTSLPVLPSELKELMVSG----NRLTSLPMLPS---GLLSL 266

Query: 626 TYDDSCLEFIPKGIQRLTNLRTLS 649
           +   + L  +P+ +  L++  T++
Sbjct: 267 SVYRNQLTRLPESLIHLSSETTVN 290

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 44.8 bits (107), Expect = 5e-05
 Identities = 25/156 (16%), Positives = 50/156 (32%), Gaps = 39/156 (25%)

Query: 515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI--LKGIEKL 572
                  +    +   +T       ++L+ +  L +          +  K+  ++GIE L
Sbjct: 22  AEGIRAVLQKASVTDVVT------QEELESITKLVV----------AGEKVASIQGIEYL 65

Query: 573 IHLRYLRLVGLGTEELPETCCELLNLQVL-----------EIEQCTSLKRLPL------- 614
            +L YL L G    ++      L+ L  L            ++  T+L+ L L       
Sbjct: 66  TNLEYLNLNGNQITDISPL-SNLVKLTNLYIGTNKITDISALQNLTNLRELYLNEDNISD 124

Query: 615 --GIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL 648
              +  L  +  L    +        +  +T L  L
Sbjct: 125 ISPLANLTKMYSLNLGANHNLSDLSPLSNMTGLNYL 160

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 25/155 (16%), Positives = 48/155 (30%), Gaps = 35/155 (22%)

Query: 515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIH 574
            NLR L++N   I    + +  S    L  + +L +         N     L  +  +  
Sbjct: 110 TNLRELYLNEDNI----SDI--SPLANLTKMYSLNLGA-------NHNLSDLSPLSNMTG 156

Query: 575 LRYLRLVGLGTEELPETCCELLNLQVLE-----------IEQCTSLKRLPLG-------- 615
           L YL +     +++      L +L  L            +   TSL              
Sbjct: 157 LNYLTVTESKVKDVTPI-ANLTDLYSLSLNYNQIEDISPLASLTSLHYFTAYVNQITDIT 215

Query: 616 -IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            +  +  L  L   ++ +  +   +  L+ L  L 
Sbjct: 216 PVANMTRLNSLKIGNNKITDLS-PLANLSQLTWLE 249

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus} Length = 229

 Score = 43.9 bits (104), Expect = 7e-05
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 571 KLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLGI-GKLVNLRHLTYD 628
            LI+L+ L L       LP      L  L VL++     L  LP  +  +LV+L+ L   
Sbjct: 62  SLINLKELYLGSNQLGALPVGVFDSLTQLTVLDL-GTNQLTVLPSAVFDRLVHLKELFMC 120

Query: 629 DSCLEFIPKGIQRLTNLRTLS 649
            + L  +P+GI+RLT+L  L+
Sbjct: 121 CNKLTELPRGIERLTHLTHLA 141

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 44.6 bits (106), Expect = 9e-05
 Identities = 28/144 (19%), Positives = 49/144 (34%), Gaps = 23/144 (15%)

Query: 508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-- 565
             ++    +L+ L   N +  +            L  L  L I          S+NK+  
Sbjct: 149 ISALSGLTSLQQLSFGNQVTDL-------KPLANLTTLERLDI----------SSNKVSD 191

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
           +  + KL +L  L        ++      L NL  L +     LK +   +  L NL  L
Sbjct: 192 ISVLAKLTNLESLIATNNQISDITP-LGILTNLDELSLNGN-QLKDIG-TLASLTNLTDL 248

Query: 626 TYDDSCLEFIPKGIQRLTNLRTLS 649
              ++ +  +   +  LT L  L 
Sbjct: 249 DLANNQISNLA-PLSGLTKLTELK 271

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 22/145 (15%), Positives = 46/145 (31%), Gaps = 24/145 (16%)

Query: 507 FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI- 565
           F  +           +  T +  +++         L  +  L+               I 
Sbjct: 18  FTDTALA--EKMKTVLGKTNVTDTVS------QTDLDQVTTLQA----------DRLGIK 59

Query: 566 -LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRH 624
            + G+E L +L  +        ++      L  L  + +     +  +   +  L NL  
Sbjct: 60  SIDGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNN-QIADIT-PLANLTNLTG 116

Query: 625 LTYDDSCLEFIPKGIQRLTNLRTLS 649
           LT  ++ +  I   ++ LTNL  L 
Sbjct: 117 LTLFNNQITDID-PLKNLTNLNRLE 140

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 597

 Score = 44.5 bits (105), Expect = 1e-04
 Identities = 21/149 (14%), Positives = 47/149 (31%), Gaps = 8/149 (5%)

Query: 506 SFPISIFKAKNLRSLFI-NNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVN-STN 563
              +S+    +L    +  N L  +++   ++ L      +  +R    +    +    N
Sbjct: 185 HVDLSLIP--SLFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHN 242

Query: 564 KI--LKGIEKLIHLRYLRLVGLGTEELPETCCE-LLNLQVLEIEQCTSLKRLPLGIGKLV 620
            +     +     L  + L     E++       +  L+ L I     L  L L    + 
Sbjct: 243 NLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISN-NRLVALNLYGQPIP 301

Query: 621 NLRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            L+ L    + L  + +   +   L  L 
Sbjct: 302 TLKVLDLSHNHLLHVERNQPQFDRLENLY 330

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 29/153 (18%), Positives = 46/153 (30%), Gaps = 23/153 (15%)

Query: 506 SFPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK 564
                 F+   NL+ L I+NT I     H+             L I            N 
Sbjct: 94  YINPEAFQNLPNLQYLLISNTGI----KHLPDVHKIHSLQKVLLDI----------QDNI 139

Query: 565 ILKGIEK------LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGI-G 617
            +  IE+            L L   G +E+  +      L  L +    +L+ LP  +  
Sbjct: 140 NIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFH 199

Query: 618 KLVNLRHLTYDDSCLEFIPKGI-QRLTNLRTLS 649
                  L    + +  +P    + L  LR  S
Sbjct: 200 GASGPVILDISRTRIHSLPSYGLENLKKLRARS 232

>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* Length = 567

 Score = 44.0 bits (103), Expect = 1e-04
 Identities = 35/268 (13%), Positives = 69/268 (25%), Gaps = 14/268 (5%)

Query: 386 LLSYNDLPPMIKRCFQYYELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAMRSFFQEFFK 445
           LL   +   ++       E   L  +  +  P              D   +   ++    
Sbjct: 235 LLGRAEPHDVLCCVHVSREEACL--SVCFSRPLTVGSRMGTLLLMVDEAPLSVEWRTPDG 292

Query: 446 DNEGVVVRCKMHDIVHDFAQFLTKNECIAIEVDDDEEPLSLINTYQEKLRHSMLVLGYEA 505
            N    V            Q       +     D ++   L+    E             
Sbjct: 293 RNRPSHVWLCDLPAASLNDQLPQHTFRVIWTGSDSQKECVLLKDRPECWCRDSATDEQLF 352

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
              +S+ K+  L+S   +   +Q         L   +  +RAL          +    + 
Sbjct: 353 RCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALD--------PLLYEKET 404

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL----GIGKLVN 621
           L+    L  +  +R   L            +        +   L    L     + +L+ 
Sbjct: 405 LQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLL 464

Query: 622 LRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
           + HL    + L  +P  +  L  L  L 
Sbjct: 465 VTHLDLSHNRLRALPPALAALRCLEVLQ 492

>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* Length = 567

 Score = 42.4 bits (99), Expect = 4e-04
 Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 561 STNKI--LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGK 618
           +   +  L  +E+L+ + +L L       LP     L  L+VL+     +L+ +  G+  
Sbjct: 449 AHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDN-ALENVD-GVAN 506

Query: 619 LVNLRHLTYDDSCLEFIP--KGIQRLTNLRTLS 649
           L  L+ L   ++ L+     + +     L  L+
Sbjct: 507 LPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLN 539

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 22/148 (14%), Positives = 48/148 (32%), Gaps = 11/148 (7%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
                 FK   L  L + N    +   +V+++    L  L   R+       + N     
Sbjct: 191 FIQPGAFKEIRLHKLTLRNNFDSL---NVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFD 247

Query: 566 LKGIEKLIHLRYLRL----VGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVN 621
              +E L +L         +    +++ +    L N+    +    +++R+         
Sbjct: 248 KSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSV-TIERVK-DFSYNFG 305

Query: 622 LRHLTYDDSCLEFIPKGIQRLTNLRTLS 649
            +HL   +      P     L +L+ L+
Sbjct: 306 WQHLELVNCKFGQFPTLK--LKSLKRLT 331

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 26/147 (17%), Positives = 41/147 (27%), Gaps = 15/147 (10%)

Query: 508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK 567
             S     +L  L ++   +  S              L+ L ++        N    +  
Sbjct: 340 AFSEVDLPSLEFLDLSRNGL--SFKGCCSQSDFGTTSLKYLDLSF-------NGVITMSS 390

Query: 568 GIEKLIHLRYLRLVG--LGTEELPETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRH 624
               L  L +L      L           L NL  L+I      +    G    L +L  
Sbjct: 391 NFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHT-HTRVAFNGIFNGLSSLEV 449

Query: 625 LTYDDSCLE--FIPKGIQRLTNLRTLS 649
           L    +  +  F+P     L NL  L 
Sbjct: 450 LKMAGNSFQENFLPDIFTELRNLTFLD 476

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A* Length = 285

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 32/153 (20%), Positives = 57/153 (37%), Gaps = 27/153 (17%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
           + P+ I      + +F++   I    +HV  + F   + L  L +           +N +
Sbjct: 25  AVPVGIPA--ASQRIFLHGNRI----SHVPAASFRACRNLTILWL----------HSNVL 68

Query: 566 LKGIEK-----LIHLRYLRLVG-LGTEELPETC-CELLNLQVLEIEQCTSLKRLPLGI-G 617
              I+      L  L  L L        +       L  L  L +++C  L+ L  G+  
Sbjct: 69  -ARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRC-GLQELGPGLFR 126

Query: 618 KLVNLRHLTYDDSCLEFIPKGI-QRLTNLRTLS 649
            L  L++L   D+ L+ +P    + L NL  L 
Sbjct: 127 GLAALQYLYLQDNALQALPDDTFRDLGNLTHLF 159

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus} Length = 562

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 24/144 (16%), Positives = 50/144 (34%), Gaps = 33/144 (22%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
           +F       KN+ SL   +  +    +H         + +  L +          S+N +
Sbjct: 391 NFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNL----------SSNML 440

Query: 566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHL 625
              +                  LP        ++VL++     +  +P  +  L  L+ L
Sbjct: 441 TGSV---------------FRCLPP------KVKVLDL-HNNRIMSIPKDVTHLQALQEL 478

Query: 626 TYDDSCLEFIPKGI-QRLTNLRTL 648
               + L+ +P G+  RLT+L+ +
Sbjct: 479 NVASNQLKSVPDGVFDRLTSLQYI 502

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 20/147 (13%), Positives = 43/147 (29%), Gaps = 10/147 (6%)

Query: 506 SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI 565
                 F+   L  L +         ++++++    L  L   R+       + N     
Sbjct: 195 FIQDQAFQGIKLHELTLRGNFN---SSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFE 251

Query: 566 LKGIEKLIHLRYLRLVGLG---TEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL 622
              +E L  +              +       L N+  + +    S+K L          
Sbjct: 252 PSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGV-SIKYLEDVPKHF-KW 309

Query: 623 RHLTYDDSCLEFIPKGIQRLTNLRTLS 649
           + L+     L+  P     L  L++L+
Sbjct: 310 QSLSIIRCQLKQFPT--LDLPFLKSLT 334

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A* Length = 276

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 33/154 (21%), Positives = 58/154 (37%), Gaps = 25/154 (16%)

Query: 506 SFPISIFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK 564
           S  +  F    +L+ L    T +  SL +        LK L+ L +          + N 
Sbjct: 90  SLALGAFSGLSSLQKLVAVETNLA-SLENFP---IGHLKTLKELNV----------AHNL 135

Query: 565 ILKGIE-----KLIHLRYLRLVGLGTEELPETCCE-LLNLQVLEIE---QCTSLKRLPLG 615
           I           L +L +L L     + +  T    L  + +L +        +  +  G
Sbjct: 136 IQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPG 195

Query: 616 IGKLVNLRHLTYDDSCLEFIPKGI-QRLTNLRTL 648
             K + L+ L  D + L+ +P GI  RLT+L+ +
Sbjct: 196 AFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKI 229

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 30/140 (21%), Positives = 50/140 (35%), Gaps = 20/140 (14%)

Query: 516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK----GIEK 571
           NL+SL + +  +     ++    F  L  L  L +              +       +  
Sbjct: 129 NLKSLEVGDNDL----VYISHRAFSGLNSLEQLTL----------EKCNLTSIPTEALSH 174

Query: 572 LIHLRYLRLVGLGTEELPETCCELL-NLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDS 630
           L  L  LRL  L    + +   + L  L+VLEI     L  +       +NL  L+    
Sbjct: 175 LHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHC 234

Query: 631 CLEFIPKG-IQRLTNLRTLS 649
            L  +P   ++ L  LR L+
Sbjct: 235 NLTAVPYLAVRHLVYLRFLN 254

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 35/140 (25%), Positives = 60/140 (42%), Gaps = 16/140 (11%)

Query: 513 KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI-EK 571
           +A  +++  ++ +     +  +L+S+F     L  L +A        N  NKI       
Sbjct: 273 EASGVKTCDLSKS----KIFALLKSVFSHFTDLEQLTLAQ-------NEINKIDDNAFWG 321

Query: 572 LIHLRYLRLVGLGTEELPETCCE-LLNLQVLEIEQCTSLKRLPLGI-GKLVNLRHLTYDD 629
           L HL  L L       +     E L  L+VL++     ++ L       L NL+ L  D 
Sbjct: 322 LTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYN-HIRALGDQSFLGLPNLKELALDT 380

Query: 630 SCLEFIPKGI-QRLTNLRTL 648
           + L+ +P GI  RLT+L+ +
Sbjct: 381 NQLKSVPDGIFDRLTSLQKI 400

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	673
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.97
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.65
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.53
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.46
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.43
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.4
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.38
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.38
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.36
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.34
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.33
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.31
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.31
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.3
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.29
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.29
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.28
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.27
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.27
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.27
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.26
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.26
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.26
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.26
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.26
2fna_A	357	Conserved hypothetical protein; structural genomic	99.25
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.25
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.25
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.25
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.24
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.24
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.24
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.24
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.23
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.23
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.22
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.22
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.2
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.2
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.2
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.2
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.2
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.19
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.19
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.18
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.18
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.17
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.17
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.17
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.16
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.16
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.16
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.14
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.14
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.14
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.14
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.13
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.13
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.12
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.12
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.12
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.12
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.12
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.11
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.11
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.1
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.1
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.1
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.1
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.09
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.09
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.09
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.09
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.09
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.09
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.08
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.08
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.08
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.08
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.08
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.08
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.07
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.07
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.07
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.06
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.06
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.06
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.06
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.05
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.05
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.04
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.04
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.04
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.03
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.02
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.02
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.02
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.02
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.01
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.0
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	98.99
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	98.99
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	98.98
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.97
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	98.97
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	98.97
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	98.96
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.96
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	98.96
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	98.96
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	98.96
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.95
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	98.95
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.95
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	98.94
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	98.93
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.93
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	98.92
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.92
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.92
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.91
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.89
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	98.88
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.88
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.87
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.86
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.85
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.85
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.83
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.81
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.81
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.79
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	98.75
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.74
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.69
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.65
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.51
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.48
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.44
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.44
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.43
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.43
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.39
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.35
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.33
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.3
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.29
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.27
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.21
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.2
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.17
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.13
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.04
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.99
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	97.96
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.89
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.89
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	97.88
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.85
3bos_A	242	Putative DNA replication factor; P-loop containing	97.83
3pvs_A	447	Replication-associated recombination protein A; ma	97.82
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.77
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.74
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.74
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	97.74
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.73
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.73
3co5_A	143	Putative two-component system transcriptional RES	97.72
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.7
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.69
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.61
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.59
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.59
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.55
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.54
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.53
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.52
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.52
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.5
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.46
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.43
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.37
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.32
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.23
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.22
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.22
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.17
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.14
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.1
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.09
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.08
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.08
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.02
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.98
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.96
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.94
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.93
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	96.93
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.93
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.93
2qgz_A	308	Helicase loader, putative primosome component; str	96.93
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.93
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.92
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.87
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	96.85
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	96.81
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.7
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.68
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.66
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.65
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	96.51
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.43
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.37
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.37
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.31
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.22
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.21
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.17
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.13
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.13
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.07
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.07
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	96.04
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.04
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.04
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.01
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.97
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.93
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.9
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.89
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.79
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	95.78
3io5_A	333	Recombination and repair protein; storage dimer, i	95.77
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.76
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.74
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.67
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.64
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.62
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.57
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.56
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	95.48
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.45
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.42
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.38
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.27
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.25
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.23
3ice_A	422	Transcription termination factor RHO; transcriptio	95.13
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.12
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.12
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.11
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.1
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.07
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.04
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.01
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.0
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.99
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.97
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	94.96
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	94.96
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.91
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	94.91
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.9
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.84
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.83
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.78
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.77
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.76
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	94.7
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.7
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.66
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.65
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.62
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.62
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.6
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.6
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.58
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.58
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.58
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.52
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.5
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.49
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.48
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.47
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.44
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.43
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.43
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.43
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.42
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.39
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.37
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.36
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.35
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	94.35
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	94.35
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.35
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.33
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.31
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.31
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	94.31
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.29
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.28
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.28
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.26
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.24
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.23
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.21
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.2
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.19
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.19
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.19
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.18
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.16
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.15
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.14
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.14
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.12
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.1
1via_A	175	Shikimate kinase; structural genomics, transferase	94.1
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.05
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.05
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.04
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.03
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.02
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.01
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.01
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.98
1g6h_A	257	High-affinity branched-chain amino acid transport	93.96
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.95
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	93.92
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.92
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.91
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.91
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	93.89
4a74_A	231	DNA repair and recombination protein RADA; hydrola	93.89
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.88
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.87
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.86
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.85
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	93.85
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.85
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.83
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.82
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.8
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	93.79
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.79
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.79
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.78
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.77
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.75
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.74
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.71
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.68
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.67
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.67
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	93.66
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.65
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.63
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	93.6
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.6
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.57
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	93.55
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.51
2vli_A	183	Antibiotic resistance protein; transferase, tunica	93.51
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.5
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	93.48
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	93.47
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.45
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	93.44
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.43
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.43
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.41
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.36
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	93.32
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.29
2xxa_A	433	Signal recognition particle protein; protein trans	93.27
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.26
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.25
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	93.22
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	93.19
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	93.19
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.19
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.17
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	93.12
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.08
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.07
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.05
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.03
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.02
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.0
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	92.96
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	92.96
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	92.95
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	92.93
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	92.9
2ghi_A	260	Transport protein; multidrug resistance protein, M	92.88
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	92.88
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	92.85
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	92.8
2og2_A	359	Putative signal recognition particle receptor; nuc	92.79
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	92.76
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	92.75
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.73
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	92.69
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	92.61
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.57
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	92.47
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	92.44
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	92.38
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	92.36
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.36
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	92.36
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.34
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.33
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	92.27
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.25
2wji_A	165	Ferrous iron transport protein B homolog; membrane	92.24
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.22
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	92.2
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.18
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.15
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.12
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	92.1
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	92.09
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	92.08
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	91.98
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	91.95
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	91.94
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	91.93
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.87
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.84
1tue_A	212	Replication protein E1; helicase, replication, E1E	91.81
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	91.78
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	91.78
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	91.75
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	91.74
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	91.73
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	91.7
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	91.69
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.68
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	91.68
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.68
3kta_A	182	Chromosome segregation protein SMC; structural mai	91.67
2ged_A	193	SR-beta, signal recognition particle receptor beta	91.64
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	91.62
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.61
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.58
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	91.57
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.56
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.56
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	91.55
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	91.53
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.52
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	91.48
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	91.43
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	91.42
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	91.35
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	91.29
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	91.24
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	91.13
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.11
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	91.08
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	91.08
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	91.07
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.05
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	90.95
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.94
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	90.93
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	90.89
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	90.82
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	90.81
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	90.81
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	90.74
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.72
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.68
3end_A	307	Light-independent protochlorophyllide reductase ir	90.66
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	90.64
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	90.61
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	90.61
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.51
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	90.5
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	90.48
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	90.48
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.47
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	90.4
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	90.35
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	90.33
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	90.32
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	90.32
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	90.3
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	90.24

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=3.2e-43  Score=390.70  Aligned_cols=282  Identities=20%  Similarity=0.240  Sum_probs=225.7

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhc--CccccccCCeEEEEEcCCcc--cHHHHHHH
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYN--DSDVFEYFDKRMWVCVSDPF--DELRIAKA  247 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~~~~~  247 (673)
                      |||+.++++|.++|....    ...+++|+|+||||+||||||+++|+  +.+++.+|++++||++++.+  ++..++..
T Consensus       131 ~GR~~~~~~l~~~L~~~~----~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~  206 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC----DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTD  206 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT----TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhccc----CCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHH
Confidence            599999999999997653    24589999999999999999999998  66899999999999999985  89999999


Q ss_pred             HHHHhhCCCC-------CcCcHHHHHHHHHHHhCCC-eEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHH
Q 005860          248 IIEALEGFVP-------TVGELNSLLESIRASLVGK-KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVA  319 (673)
Q Consensus       248 i~~~l~~~~~-------~~~~~~~~~~~l~~~l~~k-r~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~  319 (673)
                      |+.+++....       +..+.+.+...+++.|+++ ||||||||||+.+...|..        .+||+||||||++.++
T Consensus       207 il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~~--------~~gs~ilvTTR~~~v~  278 (549)
T 2a5y_B          207 ILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ--------ELRLRCLVTTRDVEIS  278 (549)
T ss_dssp             HHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHH--------HTTCEEEEEESBGGGG
T ss_pred             HHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhcccc--------cCCCEEEEEcCCHHHH
Confidence            9999986521       1234566789999999996 9999999999753222332        2799999999999999


Q ss_pred             Hhcc-ccceeecCCCCccccc--------------------------cCCchhhHHHHhhhhccCCCHHHHHHHHhhhcc
Q 005860          320 RMME-SIHVISIKELSEQECW--------------------------CKGLPLAAKTIGSLLRFKRTREEWESILDSELW  372 (673)
Q Consensus       320 ~~~~-~~~~~~l~~L~~~~~~--------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l~~~~~  372 (673)
                      ..++ ...+|+|++|+++++|                          |+|+||||+++|+.|+.+ . .+|...+....+
T Consensus       279 ~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~-~-w~~~~~l~~~l~  356 (549)
T 2a5y_B          279 NAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-T-FEKMAQLNNKLE  356 (549)
T ss_dssp             GGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-S-HHHHHHHHHHHH
T ss_pred             HHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccc-h-HHHHHHhHHHhh
Confidence            9876 4578999999999998                          999999999999999765 3 233344443333


Q ss_pred             cchhhhhccchhhhhcccCCChhhhhhhc-----------hHHH--------HHHHHHc--CCCCCCC-CCcHHHHHHHH
Q 005860          373 QLEEFEKGLLAPLLLSYNDLPPMIKRCFQ-----------YYEL--------IKLWMAQ--DYIMPEG-NKELEIIGEEY  430 (673)
Q Consensus       373 ~~~~~~~~i~~~l~~sy~~L~~~~k~cfl-----------~~~l--------~~~w~a~--g~i~~~~-~~~~e~~~~~~  430 (673)
                      ..  ...++.++|.+||++||+++|.||+           |..+        +..|+|+  ||+.... +.+.+++++ |
T Consensus       357 ~~--~~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~i~~w~a~~~G~i~~~~~~~~~~~~~~-~  433 (549)
T 2a5y_B          357 SR--GLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDICSNEEEQLDDEVAD-R  433 (549)
T ss_dssp             HH--CSSTTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEEHHHHHHHSCC-------CCCTHHHHH-H
T ss_pred             cc--cHHHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeeeeeeeeeeccceeccCCCCCCHHHHHH-H
Confidence            21  2457899999999999999999998           6211        7899999  9998765 667888888 9


Q ss_pred             HHHHHhcccccccccCCCCcEeEEEeChHHHHHHHHhcccceE
Q 005860          431 FDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNECI  473 (673)
Q Consensus       431 ~~~L~~~sli~~~~~~~~~~~~~~~mHdlv~~~a~~i~~~e~~  473 (673)
                      |++|+++||++....+   ...+|+|||++|++|++++.+++.
T Consensus       434 l~~L~~rsLl~~~~~~---~~~~~~mHdlv~~~a~~~~~~~~~  473 (549)
T 2a5y_B          434 LKRLSKRGALLSGKRM---PVLTFKIDHIIHMFLKHVVDAQTI  473 (549)
T ss_dssp             HHHTTTBSSCSEEECS---SSCEEECCHHHHHHHHTTSCTHHH
T ss_pred             HHHHHHcCCeeEecCC---CceEEEeChHHHHHHHHHHHHHHH
Confidence            9999999999986543   234899999999999999877653

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

Probab=100.00  E-value=1.2e-35  Score=333.63  Aligned_cols=256  Identities=19%  Similarity=0.170  Sum_probs=207.8

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCe-EEEEEcCCcccHHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDK-RMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~i  248 (673)
                      ..|||+.++++|.++|....      +.++|+|+||||+||||||+++|++.+++.+|+. ++|+++++.++...++..|
T Consensus       129 ~~VGRe~eLeeL~elL~~~d------~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~L  202 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR------PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML  202 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC------SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC------CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHH
Confidence            45999999999999997532      3789999999999999999999998778899986 9999999999998888888


Q ss_pred             HHHhhCCC------CC-----cCcHHHHHHHHHHHh---CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC
Q 005860          249 IEALEGFV------PT-----VGELNSLLESIRASL---VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       249 ~~~l~~~~------~~-----~~~~~~~~~~l~~~l---~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                      ++.++...      .+     ..+.+.+...+++.|   .+||+||||||||+  ..+|+.+    +   +||+||||||
T Consensus       203 l~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd--~eqLe~f----~---pGSRILVTTR  273 (1221)
T 1vt4_I          203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN--AKAWNAF----N---LSCKILLTTR  273 (1221)
T ss_dssp             HHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCC--HHHHHHH----H---SSCCEEEECS
T ss_pred             HHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcCh--HHHHHhh----C---CCeEEEEecc
Confidence            87654211      00     123455666777765   78999999999987  3566653    2   6899999999


Q ss_pred             ChhHHHhccccceeecC------CCCccccc------------------cCCchhhHHHHhhhhccCC-CHHHHHHHHhh
Q 005860          315 KETVARMMESIHVISIK------ELSEQECW------------------CKGLPLAAKTIGSLLRFKR-TREEWESILDS  369 (673)
Q Consensus       315 ~~~v~~~~~~~~~~~l~------~L~~~~~~------------------c~GlPLai~~~~~~L~~~~-~~~~w~~~l~~  369 (673)
                      ++.++..+.....|+++      +|+.+|+|                  |+|+||||+++|+.|+.+. +.++|+..   
T Consensus       274 d~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~eICgGLPLALkLaGs~Lr~k~~s~eeW~~~---  350 (1221)
T 1vt4_I          274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV---  350 (1221)
T ss_dssp             CSHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHHHHCCCCHHHHHHHHHHHHHSCSSHHHHHHC---
T ss_pred             ChHHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHHHHhCCCHHHHHHHHHHHhCCCCCHHHHhcC---
Confidence            99998765555567777      89999998                  9999999999999998774 67889763   


Q ss_pred             hcccchhhhhccchhhhhcccCCChhh-hhhhch------------HHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHh
Q 005860          370 ELWQLEEFEKGLLAPLLLSYNDLPPMI-KRCFQY------------YELIKLWMAQDYIMPEGNKELEIIGEEYFDYLAM  436 (673)
Q Consensus       370 ~~~~~~~~~~~i~~~l~~sy~~L~~~~-k~cfl~------------~~l~~~w~a~g~i~~~~~~~~e~~~~~~~~~L~~  436 (673)
                             ....+..+|.+||+.||++. |.||+|            ..++.+|.++|          ++.++.++++|++
T Consensus       351 -------~~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG----------eedAe~~L~eLvd  413 (1221)
T 1vt4_I          351 -------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI----------KSDVMVVVNKLHK  413 (1221)
T ss_dssp             -------SCHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC----------SHHHHHHHHHHHT
T ss_pred             -------ChhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC----------HHHHHHHHHHHHh
Confidence                   13568899999999999999 999999            46888998887          1347889999999


Q ss_pred             cccccccccCCCCcEeEEEeChHHHHHHH
Q 005860          437 RSFFQEFFKDNEGVVVRCKMHDIVHDFAQ  465 (673)
Q Consensus       437 ~sli~~~~~~~~~~~~~~~mHdlv~~~a~  465 (673)
                      +|||+...     ...+|+|||++++++.
T Consensus       414 RSLLq~d~-----~~~rYrMHDLllELr~  437 (1221)
T 1vt4_I          414 YSLVEKQP-----KESTISIPSIYLELKV  437 (1221)
T ss_dssp             SSSSSBCS-----SSSEEBCCCHHHHHHH
T ss_pred             hCCEEEeC-----CCCEEEehHHHHHHhc
Confidence            99998731     1237999999999653

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=5.7e-33  Score=339.99  Aligned_cols=278  Identities=23%  Similarity=0.273  Sum_probs=218.7

Q ss_pred             ccccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc-cccC-CeEEEEEcCCccc-
Q 005860          164 SLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV-FEYF-DKRMWVCVSDPFD-  240 (673)
Q Consensus       164 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F-~~~~wv~vs~~~~-  240 (673)
                      .+.+++.||||++++++|.++|....     ..+++|+|+||||+||||||+++|++.+. ..+| +.++||++++..+ 
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~-----~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~  193 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLN-----GEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKS  193 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTT-----TSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHH
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhcc-----CCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCch
Confidence            44456689999999999999997654     45899999999999999999999998543 4445 6788999998543 


Q ss_pred             -HHHHHHHHHHHhhCCC----CCcCcHHHHHHHHHHHhCCC--eEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEc
Q 005860          241 -ELRIAKAIIEALEGFV----PTVGELNSLLESIRASLVGK--KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT  313 (673)
Q Consensus       241 -~~~~~~~i~~~l~~~~----~~~~~~~~~~~~l~~~l~~k--r~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTt  313 (673)
                       ....+..++..+....    ....+.+++...++..+.++  ||||||||||+.  .+|..       .++||+|||||
T Consensus       194 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~--~~~~~-------~~~~~~ilvTt  264 (1249)
T 3sfz_A          194 GLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--WVLKA-------FDNQCQILLTT  264 (1249)
T ss_dssp             HHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH--HHHTT-------TCSSCEEEEEE
T ss_pred             HHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH--HHHHh-------hcCCCEEEEEc
Confidence             4455777888776543    23456788889999999887  999999999853  34444       36799999999


Q ss_pred             CChhHHHh-ccccceeecCC-CCccccc------------------------cCCchhhHHHHhhhhccCCCHHHHHHHH
Q 005860          314 RKETVARM-MESIHVISIKE-LSEQECW------------------------CKGLPLAAKTIGSLLRFKRTREEWESIL  367 (673)
Q Consensus       314 r~~~v~~~-~~~~~~~~l~~-L~~~~~~------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l  367 (673)
                      |++.++.. ++....+++.+ |+++|+|                        |+|+||||+++|++|+.+.  ..|...+
T Consensus       265 R~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~--~~~~~~l  342 (1249)
T 3sfz_A          265 RDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYL  342 (1249)
T ss_dssp             SSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS--SCHHHHH
T ss_pred             CCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh--hHHHHHH
Confidence            99999854 45678899996 9999987                        9999999999999998764  3566665


Q ss_pred             hhhcccc----h----hhhhccchhhhhcccCCChhhhhhhch------------HHHHHHHHHcCCCCCCCCCcHHHHH
Q 005860          368 DSELWQL----E----EFEKGLLAPLLLSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMPEGNKELEIIG  427 (673)
Q Consensus       368 ~~~~~~~----~----~~~~~i~~~l~~sy~~L~~~~k~cfl~------------~~l~~~w~a~g~i~~~~~~~~e~~~  427 (673)
                      +......    .    .....+..+|.+||+.||+++|.||+|            ..++..|.++           ++.+
T Consensus       343 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~-----------~~~~  411 (1249)
T 3sfz_A          343 RQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-----------TEEV  411 (1249)
T ss_dssp             HHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC-----------HHHH
T ss_pred             HHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC-----------HHHH
Confidence            5432211    1    112468899999999999999999999            5778888554           4667


Q ss_pred             HHHHHHHHhcccccccccCCCCcEeEEEeChHHHHHHHHhcccc
Q 005860          428 EEYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLTKNE  471 (673)
Q Consensus       428 ~~~~~~L~~~sli~~~~~~~~~~~~~~~mHdlv~~~a~~i~~~e  471 (673)
                      ++++++|+++||++...   ++...+|+||+++|++++..+.++
T Consensus       412 ~~~l~~L~~~sl~~~~~---~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          412 EDILQEFVNKSLLFCNR---NGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             HHHHHHHHHTTSCEEEE---SSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             HHHHHHHHhccceEEec---CCCceEEEecHHHHHHHHhhhhHH
Confidence            89999999999998643   334457999999999999987655

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.97  E-value=5.9e-30  Score=288.19  Aligned_cols=270  Identities=24%  Similarity=0.269  Sum_probs=200.7

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc-cccC-CeEEEEEcCCcccHHHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV-FEYF-DKRMWVCVSDPFDELRI  244 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F-~~~~wv~vs~~~~~~~~  244 (673)
                      .++.||||+.++++|.++|....     .+.++|+|+||||+||||||+.++++.++ ..+| +.++|++++.. +...+
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~-----~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~  195 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLK-----GEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGL  195 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTST-----TSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhccc-----CCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHH
Confidence            45679999999999999997543     35789999999999999999999998665 7889 58999999775 33334


Q ss_pred             HHHH---HHHhhCC----CCCcCcHHHHHHHHHHHhCC--CeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC
Q 005860          245 AKAI---IEALEGF----VPTVGELNSLLESIRASLVG--KKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       245 ~~~i---~~~l~~~----~~~~~~~~~~~~~l~~~l~~--kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~  315 (673)
                      +..+   +..++..    .....+.+.....++..+.+  +++||||||+|+.  ..+.       ..++|++||||||+
T Consensus       196 ~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~--~~l~-------~l~~~~~ilvTsR~  266 (591)
T 1z6t_A          196 LMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS--WVLK-------AFDSQCQILLTTRD  266 (591)
T ss_dssp             HHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH--HHHH-------TTCSSCEEEEEESC
T ss_pred             HHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH--HHHH-------HhcCCCeEEEECCC
Confidence            4443   4444421    22345667778888888866  7999999999853  2232       23578999999999


Q ss_pred             hhHHHhccccceeec---CCCCccccc------------------------cCCchhhHHHHhhhhccCCCHHHHHHHHh
Q 005860          316 ETVARMMESIHVISI---KELSEQECW------------------------CKGLPLAAKTIGSLLRFKRTREEWESILD  368 (673)
Q Consensus       316 ~~v~~~~~~~~~~~l---~~L~~~~~~------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l~  368 (673)
                      ..++..+. ...+++   ++|+.+|++                        |+|+|||+..+|+.++.+.  ..|...++
T Consensus       267 ~~~~~~~~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~--~~w~~~l~  343 (591)
T 1z6t_A          267 KSVTDSVM-GPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP--NRWEYYLK  343 (591)
T ss_dssp             GGGGTTCC-SCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST--TCHHHHHH
T ss_pred             cHHHHhcC-CCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc--hhHHHHHH
Confidence            98877643 234444   589998887                        9999999999999998764  36777665


Q ss_pred             hhcccc--------hhhhhccchhhhhcccCCChhhhhhhch------------HHHHHHHHHcCCCCCCCCCcHHHHHH
Q 005860          369 SELWQL--------EEFEKGLLAPLLLSYNDLPPMIKRCFQY------------YELIKLWMAQDYIMPEGNKELEIIGE  428 (673)
Q Consensus       369 ~~~~~~--------~~~~~~i~~~l~~sy~~L~~~~k~cfl~------------~~l~~~w~a~g~i~~~~~~~~e~~~~  428 (673)
                      ......        ......+..++..||+.||++.|.||++            ..+...|.++           .+.+.
T Consensus       344 ~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~-----------~~~~~  412 (591)
T 1z6t_A          344 QLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-----------TEEVE  412 (591)
T ss_dssp             HHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCC-----------HHHHH
T ss_pred             HHHHhHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccC-----------HHHHH
Confidence            432211        1122467889999999999999999998            3445556432           23467


Q ss_pred             HHHHHHHhcccccccccCCCCcEeEEEeChHHHHHHHHhc
Q 005860          429 EYFDYLAMRSFFQEFFKDNEGVVVRCKMHDIVHDFAQFLT  468 (673)
Q Consensus       429 ~~~~~L~~~sli~~~~~~~~~~~~~~~mHdlv~~~a~~i~  468 (673)
                      .++++|+++||++...   ++....|+||+++|++++...
T Consensus       413 ~~l~~L~~~~Ll~~~~---~~~~~~~~~H~lv~~~~~~~~  449 (591)
T 1z6t_A          413 DILQEFVNKSLLFCDR---NGKSFRYYLHDLQVDFLTEKN  449 (591)
T ss_dssp             HHHHHHHHTTSSEEEE---ETTEEEEECCHHHHHHHHHHT
T ss_pred             HHHHHHHhCcCeEEec---CCCccEEEEcHHHHHHHHhhh
Confidence            8999999999998543   233458999999999998773

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.65  E-value=1.9e-16  Score=135.12  Aligned_cols=80  Identities=24%  Similarity=0.475  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHhhhhhhhhHH
Q 005860            4 AIVSPLLEQLISISLEEAREQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQR--QFKEETVRLWLDQLKDVSYYMGDVLD   81 (673)
Q Consensus         4 a~v~~~~~~l~~~l~~~~~~e~~~~~~~~~~i~~L~~~L~~i~~~l~~a~~~--~~~~~~~~~wl~~lr~~ay~~ed~lD   81 (673)
                      |+|+++++||++.    +.+|+.++.||++++++|+++|.+|++||.+|+.+  +.+++.++.|+++||++|||+|||||
T Consensus         1 a~v~~ll~KL~~l----l~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD   76 (115)
T 3qfl_A            1 AAISNLIPKLGEL----LTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVD   76 (115)
T ss_dssp             CTTCSHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHH----HHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678888888887    57889999999999999999999999999999987  56899999999999999999999999


Q ss_pred             HHHHHH
Q 005860           82 EWNTAR   87 (673)
Q Consensus        82 ~~~~~~   87 (673)
                      +|.++.
T Consensus        77 ~f~~~~   82 (115)
T 3qfl_A           77 KFLVQV   82 (115)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            999764

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.53  E-value=4.1e-15  Score=153.88  Aligned_cols=169  Identities=21%  Similarity=0.218  Sum_probs=133.5

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~~i  569 (673)
                      ..+++.+.+..+....+|..+..+++|++|++.++..    . .+|..+.++++|++|++++       |. +..+|..+
T Consensus       103 l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~n~l----~-~lp~~l~~l~~L~~L~L~~-------n~~~~~~p~~~  170 (328)
T 4fcg_A          103 LSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPL----R-ALPASIASLNRLRELSIRA-------CPELTELPEPL  170 (328)
T ss_dssp             GTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEESCCC----C-CCCGGGGGCTTCCEEEEEE-------ETTCCCCCSCS
T ss_pred             CCCCCEEECCCCCccchhHHHhccCCCCEEECCCCcc----c-cCcHHHhcCcCCCEEECCC-------CCCccccChhH
Confidence            5678999999888887888888899999999998874    2 4566688999999999998       65 55677776


Q ss_pred             cc---------ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccc-ccccccC
Q 005860          570 EK---------LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCL-EFIPKGI  639 (673)
Q Consensus       570 ~~---------L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l-~~lP~~i  639 (673)
                      +.         +++|++|+|++|.+..+|..++++++|++|++++|. +..+|..++++++|++|++++|.+ ..+|..+
T Consensus       171 ~~~~~~~~~~~l~~L~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~N~-l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~  249 (328)
T 4fcg_A          171 ASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSP-LSALGPAIHHLPKLEELDLRGCTALRNYPPIF  249 (328)
T ss_dssp             EEEC-CCCEEESTTCCEEEEEEECCCCCCGGGGGCTTCCEEEEESSC-CCCCCGGGGGCTTCCEEECTTCTTCCBCCCCT
T ss_pred             hhccchhhhccCCCCCEEECcCCCcCcchHhhcCCCCCCEEEccCCC-CCcCchhhccCCCCCEEECcCCcchhhhHHHh
Confidence            65         999999999999999999999999999999999976 888999999999999999888654 4677788


Q ss_pred             CCCCCCCcCCeeEEcc--CCccCCCccccCCCCCC
Q 005860          640 QRLTNLRTLSEFVVVR--GGSKYGGKACNLEGLRY  672 (673)
Q Consensus       640 ~~L~~L~~L~~~~~~~--~~~~~~~~~~~l~~L~~  672 (673)
                      +.+++|+.|..-....  .-+..+..+.+|+.|.+
T Consensus       250 ~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L  284 (328)
T 4fcg_A          250 GGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDL  284 (328)
T ss_dssp             TCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEEC
T ss_pred             cCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeC
Confidence            8888888775433221  11122445666666654

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.46  E-value=3.9e-14  Score=146.55  Aligned_cols=149  Identities=26%  Similarity=0.303  Sum_probs=102.9

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHH---------hhhCCccceeeeccccccccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSL---------FDQLKCLRALRIATLMNTWDVNS  561 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~---------~~~l~~L~~L~L~~~~~~~~~~~  561 (673)
                      ..+++.+.+..+....+|..+..+++|++|.+.+|...    ..+|..         |.++++|++|++++       +.
T Consensus       126 l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L~L~~n~~~----~~~p~~~~~~~~~~~~~~l~~L~~L~L~~-------n~  194 (328)
T 4fcg_A          126 FAGLETLTLARNPLRALPASIASLNRLRELSIRACPEL----TELPEPLASTDASGEHQGLVNLQSLRLEW-------TG  194 (328)
T ss_dssp             GTTCSEEEEESCCCCCCCGGGGGCTTCCEEEEEEETTC----CCCCSCSEEEC-CCCEEESTTCCEEEEEE-------EC
T ss_pred             cCCCCEEECCCCccccCcHHHhcCcCCCEEECCCCCCc----cccChhHhhccchhhhccCCCCCEEECcC-------CC
Confidence            45678888887777777777777888888888775421    122222         23477777777777       77


Q ss_pred             hhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccc-cccccccCC
Q 005860          562 TNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSC-LEFIPKGIQ  640 (673)
Q Consensus       562 ~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~-l~~lP~~i~  640 (673)
                      +..+|..++.+++|++|+|++|.+..+|+.++.+++|++|++++|+....+|..++.+++|++|++++|. ...+|..++
T Consensus       195 l~~lp~~l~~l~~L~~L~L~~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~  274 (328)
T 4fcg_A          195 IRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIH  274 (328)
T ss_dssp             CCCCCGGGGGCTTCCEEEEESSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGG
T ss_pred             cCcchHhhcCCCCCCEEEccCCCCCcCchhhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhh
Confidence            6677777777777777777777777777777777777777777777667777777777777777766643 445666666


Q ss_pred             CCCCCCcCCe
Q 005860          641 RLTNLRTLSE  650 (673)
Q Consensus       641 ~L~~L~~L~~  650 (673)
                      ++++|+.|..
T Consensus       275 ~l~~L~~L~L  284 (328)
T 4fcg_A          275 RLTQLEKLDL  284 (328)
T ss_dssp             GCTTCCEEEC
T ss_pred             cCCCCCEEeC
Confidence            6666665543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.43  E-value=5.8e-13  Score=138.99  Aligned_cols=172  Identities=14%  Similarity=0.214  Sum_probs=114.7

Q ss_pred             ccCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc------
Q 005860          166 IDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF------  239 (673)
Q Consensus       166 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~------  239 (673)
                      ..+..|+||+.++++|.+++...         +++.|+|++|+|||||++++.+..      + .+|+.+....      
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~~---------~~v~i~G~~G~GKT~Ll~~~~~~~------~-~~~~~~~~~~~~~~~~   72 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLENY---------PLTLLLGIRRVGKSSLLRAFLNER------P-GILIDCRELYAERGHI   72 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHC---------SEEEEECCTTSSHHHHHHHHHHHS------S-EEEEEHHHHHHTTTCB
T ss_pred             CChHhcCChHHHHHHHHHHHhcC---------CeEEEECCCcCCHHHHHHHHHHHc------C-cEEEEeecccccccCC
Confidence            34567999999999999988531         589999999999999999998742      2 6788765432      


Q ss_pred             cHHHHHHHHHHHhhC----------------CCC--CcCcHHHHHHHHHHHhCC-CeEEEEEcCCCCCCc-------cch
Q 005860          240 DELRIAKAIIEALEG----------------FVP--TVGELNSLLESIRASLVG-KKFLLILDDMWTDDY-------SKW  293 (673)
Q Consensus       240 ~~~~~~~~i~~~l~~----------------~~~--~~~~~~~~~~~l~~~l~~-kr~LlVLDdvw~~~~-------~~~  293 (673)
                      +...++..+.+.+..                ...  ...+..++...+.+.... ++++|||||++.-+.       ..+
T Consensus        73 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~  152 (350)
T 2qen_A           73 TREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELL  152 (350)
T ss_dssp             CHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHH
Confidence            455666666665532                000  123455666666665543 389999999954321       112


Q ss_pred             hhhhhhccCCCCCeEEEEEcCChhHHHhc-----------cc-cceeecCCCCccccc----------------------
Q 005860          294 EPFHYCLKNGVRGSKILVTTRKETVARMM-----------ES-IHVISIKELSEQECW----------------------  339 (673)
Q Consensus       294 ~~l~~~l~~~~~gs~iivTtr~~~v~~~~-----------~~-~~~~~l~~L~~~~~~----------------------  339 (673)
                      ..+...... ..+.++|+|++...+...+           +. ...+++.+|+.+|+.                      
T Consensus       153 ~~L~~~~~~-~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i  231 (350)
T 2qen_A          153 ALFAYAYDS-LPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEA  231 (350)
T ss_dssp             HHHHHHHHH-CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHH
T ss_pred             HHHHHHHHh-cCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            223322222 2477899998876542211           11 247889999988764                      


Q ss_pred             ---cCCchhhHHHHhhhh
Q 005860          340 ---CKGLPLAAKTIGSLL  354 (673)
Q Consensus       340 ---c~GlPLai~~~~~~L  354 (673)
                         |+|+|+++..++..+
T Consensus       232 ~~~tgG~P~~l~~~~~~~  249 (350)
T 2qen_A          232 VELLDGIPGWLVVFGVEY  249 (350)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHH
Confidence               999999999988764

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.40  E-value=3.6e-13  Score=153.91  Aligned_cols=150  Identities=21%  Similarity=0.189  Sum_probs=86.0

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK  571 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~  571 (673)
                      ..++++.+..+.....+..+....+|+.+.+............++..|..+..|+.|+|++       +.+..+|..+..
T Consensus       173 ~~~~~l~L~~n~~~~~~~~~l~~l~Ls~~~i~~~~~~~n~~~~~~~~~~~l~~L~~L~Ls~-------n~l~~l~~~~~~  245 (727)
T 4b8c_D          173 PLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSN-------LQIFNISANIFK  245 (727)
T ss_dssp             -------------------------------------------------CCCCCCEEECTT-------SCCSCCCGGGGG
T ss_pred             CccceEEeeCCCCCcchhhHhhcCccCcccccCccccccceecChhhhccCCCCcEEECCC-------CCCCCCChhhcC
Confidence            3456666655544444444444444444444332211111224566778888888888888       888788888888


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      +.+|++|+|++|.+..+|.+|++|++|++|+|++|. +..+|..|++|++|++|++++|.+..+|.+|++|++|++|.
T Consensus       246 l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~-l~~lp~~~~~l~~L~~L~L~~N~l~~lp~~~~~l~~L~~L~  322 (727)
T 4b8c_D          246 YDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNR-LTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLG  322 (727)
T ss_dssp             CCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSC-CSSCCSSGGGGTTCSEEECCSSCCCCCCSSTTSCTTCCCEE
T ss_pred             CCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCc-CCccChhhcCCCCCCEEECCCCCCCccChhhhcCCCccEEe
Confidence            888888888888888888888888888888888876 77888888888888888888888888888888887777764

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.38  E-value=4.9e-13  Score=137.30  Aligned_cols=129  Identities=19%  Similarity=0.252  Sum_probs=58.7

Q ss_pred             ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhccccccccccccceecCCCCc
Q 005860          508 PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKGIEKLIHLRYLRLVGLGTE  586 (673)
Q Consensus       508 ~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~i~~L~~Lr~L~L~~~~i~  586 (673)
                      |..+..+++|++|.+.++..    ...+|..|.++++|++|++++       +.+. .+|..++.+++|++|+|++|.+.
T Consensus        94 p~~l~~l~~L~~L~Ls~n~l----~~~~p~~~~~l~~L~~L~Ls~-------N~l~~~~p~~~~~l~~L~~L~L~~N~l~  162 (313)
T 1ogq_A           94 PPAIAKLTQLHYLYITHTNV----SGAIPDFLSQIKTLVTLDFSY-------NALSGTLPPSISSLPNLVGITFDGNRIS  162 (313)
T ss_dssp             CGGGGGCTTCSEEEEEEECC----EEECCGGGGGCTTCCEEECCS-------SEEESCCCGGGGGCTTCCEEECCSSCCE
T ss_pred             ChhHhcCCCCCEEECcCCee----CCcCCHHHhCCCCCCEEeCCC-------CccCCcCChHHhcCCCCCeEECcCCccc
Confidence            33344444444444444431    112333344444555555544       4433 34444455555555555555443


Q ss_pred             -ccchhhhcCC-CccEEEeccCCCCccccccccccccCCeeecccccccc-ccccCCCCCCCCcC
Q 005860          587 -ELPETCCELL-NLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEF-IPKGIQRLTNLRTL  648 (673)
Q Consensus       587 -~LP~~i~~L~-~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~-lP~~i~~L~~L~~L  648 (673)
                       .+|..++.+. +|++|++++|..-..+|..++.+. |++|++++|.+.. .|..++.+++|+.|
T Consensus       163 ~~~p~~l~~l~~~L~~L~L~~N~l~~~~~~~~~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L  226 (313)
T 1ogq_A          163 GAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKI  226 (313)
T ss_dssp             EECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEE
T ss_pred             CcCCHHHhhhhhcCcEEECcCCeeeccCChHHhCCc-ccEEECcCCcccCcCCHHHhcCCCCCEE
Confidence             4454555544 455555554431124444444444 5555555554442 33344555555544

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.38  E-value=4.7e-12  Score=135.30  Aligned_cols=171  Identities=18%  Similarity=0.123  Sum_probs=108.0

Q ss_pred             CCcceechhhHHHHHHHh-ccCCcccccCCeEEEEE--EccCCChHHHHHHHHhcCcccc---ccCC-eEEEEEcCCccc
Q 005860          168 VSEIRGRDEEKSSLKSKL-LCESSEEIINDIQIITI--VGMGGIGKTTLAQFAYNDSDVF---EYFD-KRMWVCVSDPFD  240 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L-~~~~~~~~~~~~~vi~I--~G~gGiGKTtLa~~v~~~~~~~---~~F~-~~~wv~vs~~~~  240 (673)
                      +..++||+.+++++..+| ....... ......+.|  +|++|+||||||+.+++.....   ..|+ .++|+.+....+
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~~~~-~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLLSGA-GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPN   99 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSS-CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCS
T ss_pred             CCCCCChHHHHHHHHHHHhHHHhcCC-CCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCC
Confidence            468999999999999988 4211000 012345555  9999999999999999852211   0122 367888767778


Q ss_pred             HHHHHHHHHHHhhCCCCC-cCcHHHHHHHHHHHhC--CCeEEEEEcCCCCCC------ccchhhhhhhccCC---C--CC
Q 005860          241 ELRIAKAIIEALEGFVPT-VGELNSLLESIRASLV--GKKFLLILDDMWTDD------YSKWEPFHYCLKNG---V--RG  306 (673)
Q Consensus       241 ~~~~~~~i~~~l~~~~~~-~~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~------~~~~~~l~~~l~~~---~--~g  306 (673)
                      ...++..++.+++...+. ..+...+...+.+.+.  +++++|||||+|.-.      ...+..+...+...   +  ..
T Consensus       100 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~  179 (412)
T 1w5s_A          100 LYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNR  179 (412)
T ss_dssp             HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCB
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCce
Confidence            889999999999765332 2334555666666664  789999999996522      12233332333211   2  34


Q ss_pred             eEEEEEcCChhHHHhcc--------c-cceeecCCCCccccc
Q 005860          307 SKILVTTRKETVARMME--------S-IHVISIKELSEQECW  339 (673)
Q Consensus       307 s~iivTtr~~~v~~~~~--------~-~~~~~l~~L~~~~~~  339 (673)
                      ..||+||+...+...+.        . ...+++++++.++.+
T Consensus       180 v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~  221 (412)
T 1w5s_A          180 IGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELY  221 (412)
T ss_dssp             EEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHH
T ss_pred             EEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHH
Confidence            45888887655432211        1 223889999988765

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.36  E-value=7.9e-13  Score=132.74  Aligned_cols=146  Identities=27%  Similarity=0.436  Sum_probs=89.0

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      +..++++.+..+....+++ .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|.. 
T Consensus        36 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l----~~i~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~  104 (270)
T 2o6q_A           36 PADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKL----QTLPAGIFKELKNLETLWVTD-------NKLQALPIGV  104 (270)
T ss_dssp             CTTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCC----SCCCTTTTSSCTTCCEEECCS-------SCCCCCCTTT
T ss_pred             CCCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCcc----CeeChhhhcCCCCCCEEECCC-------CcCCcCCHhH
Confidence            3456777776666555543 455677777777766652    233344456667777777776       666655543 


Q ss_pred             cccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L  645 (673)
                      +..+.+|++|+|++|.+..+|. .+..+++|++|++++|. +..+|.. ++.+++|++|++++|.+..+|.. +.++++|
T Consensus       105 ~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  183 (270)
T 2o6q_A          105 FDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNE-LQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFDKLTEL  183 (270)
T ss_dssp             TTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTC
T ss_pred             cccccCCCEEECCCCccCeeCHHHhCcCcCCCEEECCCCc-CCccCHhHccCCcccceeEecCCcCcEeChhHhccCCCc
Confidence            4666667777777666666653 35666667777776654 6666644 56666666666666666666543 4555555


Q ss_pred             CcC
Q 005860          646 RTL  648 (673)
Q Consensus       646 ~~L  648 (673)
                      ++|
T Consensus       184 ~~L  186 (270)
T 2o6q_A          184 KTL  186 (270)
T ss_dssp             CEE
T ss_pred             CEE
Confidence            544

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.34  E-value=1.5e-12  Score=124.08  Aligned_cols=144  Identities=17%  Similarity=0.198  Sum_probs=121.0

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hcccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~~i  569 (673)
                      ..+++.+.+..+....++ .+..+++|++|.+.++..     ..+ ..+..++.|+.|++++       +.+.. .|..+
T Consensus        43 l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~~n~~-----~~~-~~l~~l~~L~~L~l~~-------n~l~~~~~~~l  108 (197)
T 4ezg_A           43 MNSLTYITLANINVTDLT-GIEYAHNIKDLTINNIHA-----TNY-NPISGLSNLERLRIMG-------KDVTSDKIPNL  108 (197)
T ss_dssp             HHTCCEEEEESSCCSCCT-TGGGCTTCSEEEEESCCC-----SCC-GGGTTCTTCCEEEEEC-------TTCBGGGSCCC
T ss_pred             cCCccEEeccCCCccChH-HHhcCCCCCEEEccCCCC-----Ccc-hhhhcCCCCCEEEeEC-------CccCcccChhh
Confidence            456889999988877666 678899999999998853     112 2577899999999999       88765 68889


Q ss_pred             ccccccccceecCCCCcc-cchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          570 EKLIHLRYLRLVGLGTEE-LPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~-LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      +.+++|++|+|++|.+.. .|..++.+++|++|++++|..+..+| .+..+++|++|++++|.+..+| .+..+++|+.|
T Consensus       109 ~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~i~~~~-~l~~l~~L~~L  186 (197)
T 4ezg_A          109 SGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDGVHDYR-GIEDFPKLNQL  186 (197)
T ss_dssp             TTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBCCCCCT-TGGGCSSCCEE
T ss_pred             cCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCCCcChH-HhccCCCCCEE
Confidence            999999999999999775 78889999999999999987688888 7999999999999999999887 67777776666


Q ss_pred             Ce
Q 005860          649 SE  650 (673)
Q Consensus       649 ~~  650 (673)
                      ..
T Consensus       187 ~l  188 (197)
T 4ezg_A          187 YA  188 (197)
T ss_dssp             EE
T ss_pred             Ee
Confidence            43

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.33  E-value=9.9e-13  Score=133.11  Aligned_cols=102  Identities=24%  Similarity=0.317  Sum_probs=46.6

Q ss_pred             hhhCCccceeeeccccccccccchhhh-ccccccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-  615 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-  615 (673)
                      |..+++|+.|++++       +.+..+ |..+..+++|++|+|++|.+..+|.. ++.+++|++|++++|. +..+|.. 
T Consensus       101 ~~~l~~L~~L~l~~-------n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~  172 (285)
T 1ozn_A          101 FHGLGRLHTLHLDR-------CGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNR-ISSVPERA  172 (285)
T ss_dssp             TTTCTTCCEEECTT-------SCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCEECTTT
T ss_pred             hcCCcCCCEEECCC-------CcCCEECHhHhhCCcCCCEEECCCCcccccCHhHhccCCCccEEECCCCc-ccccCHHH
Confidence            34444444444444       443333 23344445555555555554444432 4445555555555443 4444432 


Q ss_pred             ccccccCCeeeccccccccc-cccCCCCCCCCcC
Q 005860          616 IGKLVNLRHLTYDDSCLEFI-PKGIQRLTNLRTL  648 (673)
Q Consensus       616 i~~L~~Lr~L~l~~~~l~~l-P~~i~~L~~L~~L  648 (673)
                      +..+++|++|++++|.+..+ |..++++++|+.|
T Consensus       173 ~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L  206 (285)
T 1ozn_A          173 FRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTL  206 (285)
T ss_dssp             TTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEE
T ss_pred             hcCccccCEEECCCCcccccCHhHccCcccccEe
Confidence            44455555555555544443 3334444444433

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.31  E-value=1.9e-12  Score=131.34  Aligned_cols=145  Identities=23%  Similarity=0.240  Sum_probs=116.6

Q ss_pred             cCceEEEEEEcCCCCccc-cccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFP-ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~-~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      +..++.+.+..+....++ ..+..+++|++|.+.++...    . ++. ...+++|+.|++++       +.+..+|..+
T Consensus        30 ~~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~----~-~~~-~~~l~~L~~L~Ls~-------N~l~~l~~~~   96 (290)
T 1p9a_G           30 PKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELT----K-LQV-DGTLPVLGTLDLSH-------NQLQSLPLLG   96 (290)
T ss_dssp             CTTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCC----E-EEC-CSCCTTCCEEECCS-------SCCSSCCCCT
T ss_pred             CCCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCCccC----c-ccC-CCCCCcCCEEECCC-------CcCCcCchhh
Confidence            467888888887775553 45677899999999887641    1 111 26788999999999       8888999999


Q ss_pred             ccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeeccccccccccccC-CCCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKGI-QRLTNLR  646 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~i-~~L~~L~  646 (673)
                      ..+++|++|+|++|.+..+| ..+..+++|++|++++|. +..+|.. +..+++|++|++++|.++.+|.++ .++++|+
T Consensus        97 ~~l~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~  175 (290)
T 1p9a_G           97 QTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLD  175 (290)
T ss_dssp             TTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCC
T ss_pred             ccCCCCCEEECCCCcCcccCHHHHcCCCCCCEEECCCCC-CCccChhhcccccCCCEEECCCCcCCccCHHHhcCcCCCC
Confidence            99999999999999998887 568899999999999876 8888765 578999999999999999998764 5677766


Q ss_pred             cCC
Q 005860          647 TLS  649 (673)
Q Consensus       647 ~L~  649 (673)
                      .|.
T Consensus       176 ~L~  178 (290)
T 1p9a_G          176 TLL  178 (290)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            653

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.31  E-value=2.1e-12  Score=126.16  Aligned_cols=120  Identities=31%  Similarity=0.469  Sum_probs=61.9

Q ss_pred             cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-cccccccccceecCCCCcccchh-h
Q 005860          515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHLRYLRLVGLGTEELPET-C  592 (673)
Q Consensus       515 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~Lr~L~L~~~~i~~LP~~-i  592 (673)
                      ++|+.|.+.++..    ....+..|..+++|+.|+|++       +.+..+|.. +..+++|++|+|++|.+..+|.. +
T Consensus        40 ~~L~~L~Ls~n~i----~~~~~~~~~~l~~L~~L~L~~-------N~l~~i~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~  108 (229)
T 3e6j_A           40 TNAQILYLHDNQI----TKLEPGVFDSLINLKELYLGS-------NQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVF  108 (229)
T ss_dssp             TTCSEEECCSSCC----CCCCTTTTTTCTTCCEEECCS-------SCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTT
T ss_pred             CCCCEEEcCCCcc----CccCHHHhhCccCCcEEECCC-------CCCCCcChhhcccCCCcCEEECCCCcCCccChhHh
Confidence            4555555555442    222334445555555555555       555555433 35555555555555555555433 3


Q ss_pred             hcCCCccEEEeccCCCCccccccccccccCCeeecccccccccccc-CCCCCCCC
Q 005860          593 CELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLR  646 (673)
Q Consensus       593 ~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~  646 (673)
                      ..+++|++|+++++. +..+|..+.++++|++|++++|.+..+|.. +..+++|+
T Consensus       109 ~~l~~L~~L~Ls~N~-l~~lp~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~  162 (229)
T 3e6j_A          109 DRLVHLKELFMCCNK-LTELPRGIERLTHLTHLALDQNQLKSIPHGAFDRLSSLT  162 (229)
T ss_dssp             TTCTTCCEEECCSSC-CCSCCTTGGGCTTCSEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CcchhhCeEeccCCc-ccccCcccccCCCCCEEECCCCcCCccCHHHHhCCCCCC
Confidence            455555555555543 555555555555555555555555555532 33344333

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.30  E-value=2.4e-12  Score=127.64  Aligned_cols=147  Identities=23%  Similarity=0.297  Sum_probs=121.5

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~  568 (673)
                      +..++.+.+..+.....++ .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|. .
T Consensus        34 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  102 (251)
T 3m19_A           34 PADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQL----QTLSAGVFDDLTELGTLGLAN-------NQLASLPLGV  102 (251)
T ss_dssp             CTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCC----CCCCTTTTTTCTTCCEEECTT-------SCCCCCCTTT
T ss_pred             CCCCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcC----CccCHhHhccCCcCCEEECCC-------CcccccChhH
Confidence            4678889988887766544 467899999999998863    344566688999999999999       88888765 5


Q ss_pred             cccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccc-cCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPK-GIQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~~L  645 (673)
                      +..+.+|++|+|++|.+..+|.. +..+++|++|+|++|. +..+|. .++.+++|++|++++|.+..+|+ .+..+++|
T Consensus       103 ~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L  181 (251)
T 3m19_A          103 FDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQ-LQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKL  181 (251)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTC
T ss_pred             hcccCCCCEEEcCCCcCCCcChhHhccCCcccEEECcCCc-CCccCHHHcCcCcCCCEEECCCCcCCccCHHHHhCCCCC
Confidence            68999999999999999999876 5889999999999976 888887 58999999999999999998886 46667777


Q ss_pred             CcCC
Q 005860          646 RTLS  649 (673)
Q Consensus       646 ~~L~  649 (673)
                      +.|.
T Consensus       182 ~~L~  185 (251)
T 3m19_A          182 QTIT  185 (251)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            6653

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.29  E-value=1.6e-12  Score=131.58  Aligned_cols=143  Identities=24%  Similarity=0.317  Sum_probs=61.4

Q ss_pred             ceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhh-cccc
Q 005860          493 KLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKI-LKGI  569 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~l-p~~i  569 (673)
                      +++++.+..+.....++ .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +. +..+ |..+
T Consensus        33 ~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~~l~~~~~~~~  101 (285)
T 1ozn_A           33 ASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVL----ARIDAAAFTGLALLEQLDLSD-------NAQLRSVDPATF  101 (285)
T ss_dssp             TCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCC----CEECTTTTTTCTTCCEEECCS-------CTTCCCCCTTTT
T ss_pred             CceEEEeeCCcCCccCHHHcccCCCCCEEECCCCcc----ceeCHhhcCCccCCCEEeCCC-------CCCccccCHHHh
Confidence            44444444444333322 233444444444444431    122233344444455555444       43 3333 3344


Q ss_pred             ccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLR  646 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~  646 (673)
                      ..+++|++|+|++|.+..+ |..+.++++|++|++++|. +..+|.. ++++++|++|++++|.+..+|.. +..+++|+
T Consensus       102 ~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~  180 (285)
T 1ozn_A          102 HGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNA-LQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLD  180 (285)
T ss_dssp             TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCC
T ss_pred             cCCcCCCEEECCCCcCCEECHhHhhCCcCCCEEECCCCc-ccccCHhHhccCCCccEEECCCCcccccCHHHhcCccccC
Confidence            4444455555544444443 2334444455555554433 4444432 44444455555444444444432 33343333


Q ss_pred             c
Q 005860          647 T  647 (673)
Q Consensus       647 ~  647 (673)
                      .
T Consensus       181 ~  181 (285)
T 1ozn_A          181 R  181 (285)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.29  E-value=2.7e-12  Score=127.30  Aligned_cols=165  Identities=24%  Similarity=0.229  Sum_probs=125.2

Q ss_pred             eEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-ccccc
Q 005860          494 LRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKL  572 (673)
Q Consensus       494 ~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L  572 (673)
                      .+++.+.......+|..+.  ++++.|.+.++..    ....+..|.++++|++|++++       +.+..+++ .+..+
T Consensus        16 ~~~l~~~~~~l~~~p~~~~--~~l~~L~L~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~~~~l   82 (251)
T 3m19_A           16 KKEVDCQGKSLDSVPSGIP--ADTEKLDLQSTGL----ATLSDATFRGLTKLTWLNLDY-------NQLQTLSAGVFDDL   82 (251)
T ss_dssp             GTEEECTTCCCSSCCSCCC--TTCCEEECTTSCC----CCCCTTTTTTCTTCCEEECTT-------SCCCCCCTTTTTTC
T ss_pred             CeEEecCCCCccccCCCCC--CCCCEEEccCCCc----CccCHhHhcCcccCCEEECCC-------CcCCccCHhHhccC
Confidence            3445555555566665543  6899999998873    344556788999999999999       88877655 47999


Q ss_pred             cccccceecCCCCcccch-hhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCCCcCC
Q 005860          573 IHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLS  649 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~  649 (673)
                      ++|++|+|++|.+..+|. .+..+++|++|+|++|. +..+|.. ++.+++|++|++++|.+..+|.. ++.+++|++|.
T Consensus        83 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~  161 (251)
T 3m19_A           83 TELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQ-LKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLS  161 (251)
T ss_dssp             TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEE
T ss_pred             CcCCEEECCCCcccccChhHhcccCCCCEEEcCCCc-CCCcChhHhccCCcccEEECcCCcCCccCHHHcCcCcCCCEEE
Confidence            999999999999999884 56899999999999976 8888876 68999999999999999999874 77888877764


Q ss_pred             eeEE--ccCCccCCCccccCCCCCC
Q 005860          650 EFVV--VRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       650 ~~~~--~~~~~~~~~~~~~l~~L~~  672 (673)
                      .-.-  .......+..+.+|+.|.+
T Consensus       162 L~~N~l~~~~~~~~~~l~~L~~L~l  186 (251)
T 3m19_A          162 LSTNQLQSVPHGAFDRLGKLQTITL  186 (251)
T ss_dssp             CCSSCCSCCCTTTTTTCTTCCEEEC
T ss_pred             CCCCcCCccCHHHHhCCCCCCEEEe
Confidence            3221  2222223455666666654

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.28  E-value=3.1e-12  Score=131.01  Aligned_cols=140  Identities=19%  Similarity=0.238  Sum_probs=111.7

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+.....++ +..+++|++|.+.++...    . ++ .+..+++|+.|++++       +.+..++. +
T Consensus        61 ~l~~L~~L~L~~n~i~~~~~-~~~l~~L~~L~L~~n~l~----~-~~-~~~~l~~L~~L~l~~-------n~l~~~~~-l  125 (308)
T 1h6u_A           61 YLNNLIGLELKDNQITDLAP-LKNLTKITELELSGNPLK----N-VS-AIAGLQSIKTLDLTS-------TQITDVTP-L  125 (308)
T ss_dssp             GCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSCCCS----C-CG-GGTTCTTCCEEECTT-------SCCCCCGG-G
T ss_pred             ccCCCCEEEccCCcCCCChh-HccCCCCCEEEccCCcCC----C-ch-hhcCCCCCCEEECCC-------CCCCCchh-h
Confidence            35678888888887766665 778889999998887641    1 22 467888999999998       88777765 8


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      ..+++|++|+|++|.+..+|. ++.+++|++|++++|. +..+|. +.++++|++|++++|.+..+|. +..+++|+.|
T Consensus       126 ~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~-l~~~~~-l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L  200 (308)
T 1h6u_A          126 AGLSNLQVLYLDLNQITNISP-LAGLTNLQYLSIGNAQ-VSDLTP-LANLSKLTTLKADDNKISDISP-LASLPNLIEV  200 (308)
T ss_dssp             TTCTTCCEEECCSSCCCCCGG-GGGCTTCCEEECCSSC-CCCCGG-GTTCTTCCEEECCSSCCCCCGG-GGGCTTCCEE
T ss_pred             cCCCCCCEEECCCCccCcCcc-ccCCCCccEEEccCCc-CCCChh-hcCCCCCCEEECCCCccCcChh-hcCCCCCCEE
Confidence            888999999999999888887 8889999999999876 888876 8889999999999998888875 5556665555

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.27  E-value=2.2e-12  Score=119.35  Aligned_cols=129  Identities=19%  Similarity=0.180  Sum_probs=89.0

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcc-cchhh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEE-LPETC  592 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~-LP~~i  592 (673)
                      .++|+.|.+.++...   ...+|..+..+++|++|++++       +.+..+ ..++.+++|++|+|++|.+.. +|..+
T Consensus        23 ~~~L~~L~l~~n~l~---~~~i~~~~~~l~~L~~L~l~~-------n~l~~~-~~~~~l~~L~~L~Ls~N~l~~~~~~~~   91 (168)
T 2ell_A           23 PAAVRELVLDNCKSN---DGKIEGLTAEFVNLEFLSLIN-------VGLISV-SNLPKLPKLKKLELSENRIFGGLDMLA   91 (168)
T ss_dssp             TTSCSEEECCSCBCB---TTBCSSCCGGGGGCCEEEEES-------SCCCCC-SSCCCCSSCCEEEEESCCCCSCCCHHH
T ss_pred             cccCCEEECCCCCCC---hhhHHHHHHhCCCCCEEeCcC-------CCCCCh-hhhccCCCCCEEECcCCcCchHHHHHH
Confidence            356666666666531   013344456677777777777       766666 667777788888888777666 66666


Q ss_pred             hcCCCccEEEeccCCCCcccc--ccccccccCCeeeccccccccccc----cCCCCCCCCcCCeeEEc
Q 005860          593 CELLNLQVLEIEQCTSLKRLP--LGIGKLVNLRHLTYDDSCLEFIPK----GIQRLTNLRTLSEFVVV  654 (673)
Q Consensus       593 ~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~Lr~L~l~~~~l~~lP~----~i~~L~~L~~L~~~~~~  654 (673)
                      .++++|++|++++|. +..+|  ..++.+++|++|++++|.+..+|.    .+..+++|+.|......
T Consensus        92 ~~l~~L~~L~Ls~N~-l~~~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l~~n~  158 (168)
T 2ell_A           92 EKLPNLTHLNLSGNK-LKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDRE  158 (168)
T ss_dssp             HHCTTCCEEECBSSS-CCSSGGGGGGSSCSCCCEEECCSSGGGTSTTHHHHHHTTCSSCCEETTEETT
T ss_pred             hhCCCCCEEeccCCc-cCcchhHHHHhcCCCCCEEEeeCCcCcchHHHHHHHHHhCccCcEecCCCCC
Confidence            677888888887765 77766  567777788888877777777776    56777777777665543

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.27  E-value=3.6e-12  Score=137.52  Aligned_cols=145  Identities=21%  Similarity=0.215  Sum_probs=94.6

Q ss_pred             cCceEEEEEEcCCCCccc-cccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFP-ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~-~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~  568 (673)
                      +.+++.+.+..+.....+ ..+..+++|++|.+.++..    ....+..|.++++|+.|+|++       +.+..+|. .
T Consensus        63 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i----~~i~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  131 (440)
T 3zyj_A           63 STNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHI----RTIEIGAFNGLANLNTLELFD-------NRLTTIPNGA  131 (440)
T ss_dssp             CTTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSSCC----CEECGGGGTTCSSCCEEECCS-------SCCSSCCTTT
T ss_pred             CCCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCCcC----CccChhhccCCccCCEEECCC-------CcCCeeCHhH
Confidence            456777777777665544 4466778888888887753    234445677778888888887       77777665 4


Q ss_pred             cccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      +..+.+|++|+|++|.+..+|. .+.++++|++|++++|+.+..+|. .+.++++|++|++++|.+..+| .+..+++|+
T Consensus       132 ~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~  210 (440)
T 3zyj_A          132 FVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIP-NLTPLIKLD  210 (440)
T ss_dssp             SCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTSCCSSCC-CCTTCSSCC
T ss_pred             hhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCCcCcccc-ccCCCcccC
Confidence            7777778888887777777664 566666777777766655666554 3566666666666666555554 233344433


Q ss_pred             c
Q 005860          647 T  647 (673)
Q Consensus       647 ~  647 (673)
                      .
T Consensus       211 ~  211 (440)
T 3zyj_A          211 E  211 (440)
T ss_dssp             E
T ss_pred             E
Confidence            3

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.27  E-value=2.5e-12  Score=132.07  Aligned_cols=145  Identities=15%  Similarity=0.135  Sum_probs=73.2

Q ss_pred             CceEEEEEEcCCCC-ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhcccc
Q 005860          492 EKLRHSMLVLGYEA-SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKGI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~-~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~i  569 (673)
                      .+++++.+..+... ..|..+..+++|++|++.++..    ...+|..|..+++|++|++++       +.+. .+|..+
T Consensus       101 ~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~Ls~N~l----~~~~p~~~~~l~~L~~L~L~~-------N~l~~~~p~~l  169 (313)
T 1ogq_A          101 TQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNAL----SGTLPPSISSLPNLVGITFDG-------NRISGAIPDSY  169 (313)
T ss_dssp             TTCSEEEEEEECCEEECCGGGGGCTTCCEEECCSSEE----ESCCCGGGGGCTTCCEEECCS-------SCCEEECCGGG
T ss_pred             CCCCEEECcCCeeCCcCCHHHhCCCCCCEEeCCCCcc----CCcCChHHhcCCCCCeEECcC-------CcccCcCCHHH
Confidence            34555555554443 3344455555555555555442    112333444555555555555       4443 344444


Q ss_pred             cccc-ccccceecCCCCc-c-----------------------cchhhhcCCCccEEEeccCCCCccccccccccccCCe
Q 005860          570 EKLI-HLRYLRLVGLGTE-E-----------------------LPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRH  624 (673)
Q Consensus       570 ~~L~-~Lr~L~L~~~~i~-~-----------------------LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~  624 (673)
                      +.+. +|++|+|++|.+. .                       .|..+..+++|++|++++|. +...+..+..+++|++
T Consensus       170 ~~l~~~L~~L~L~~N~l~~~~~~~~~~l~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~l~~L~~  248 (313)
T 1ogq_A          170 GSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNS-LAFDLGKVGLSKNLNG  248 (313)
T ss_dssp             GCCCTTCCEEECCSSEEEEECCGGGGGCCCSEEECCSSEEEECCGGGCCTTSCCSEEECCSSE-ECCBGGGCCCCTTCCE
T ss_pred             hhhhhcCcEEECcCCeeeccCChHHhCCcccEEECcCCcccCcCCHHHhcCCCCCEEECCCCc-eeeecCcccccCCCCE
Confidence            4444 4455544444433 3                       34445555555555555544 4433334555666666


Q ss_pred             eeccccccc-cccccCCCCCCCCcC
Q 005860          625 LTYDDSCLE-FIPKGIQRLTNLRTL  648 (673)
Q Consensus       625 L~l~~~~l~-~lP~~i~~L~~L~~L  648 (673)
                      |++++|.+. .+|..++.+++|+.|
T Consensus       249 L~Ls~N~l~~~~p~~l~~l~~L~~L  273 (313)
T 1ogq_A          249 LDLRNNRIYGTLPQGLTQLKFLHSL  273 (313)
T ss_dssp             EECCSSCCEECCCGGGGGCTTCCEE
T ss_pred             EECcCCcccCcCChHHhcCcCCCEE
Confidence            666666655 455556555555554

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.26  E-value=5.9e-12  Score=126.33  Aligned_cols=147  Identities=29%  Similarity=0.418  Sum_probs=121.5

Q ss_pred             cCceEEEEEEcCCCCcccccc-ccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFPISI-FKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~  568 (673)
                      ..+++.+.+..+....++... ..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|+ .
T Consensus        60 l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~  128 (270)
T 2o6q_A           60 LTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKL----QALPIGVFDQLVNLAELRLDR-------NQLKSLPPRV  128 (270)
T ss_dssp             CTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCSSCC----CCCCTTTTTTCSSCCEEECCS-------SCCCCCCTTT
T ss_pred             CCCCCEEECCCCccCeeChhhhcCCCCCCEEECCCCcC----CcCCHhHcccccCCCEEECCC-------CccCeeCHHH
Confidence            467899999888777776654 5689999999998863    344456678899999999999       88887765 4


Q ss_pred             cccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccccccc-CCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L  645 (673)
                      +..+++|++|+|++|.+..+|.. +..+++|++|++++|. +..+|. .+.++++|++|++++|.+..+|.. +..+++|
T Consensus       129 ~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L  207 (270)
T 2o6q_A          129 FDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQ-LKRVPEGAFDKLTELKTLKLDNNQLKRVPEGAFDSLEKL  207 (270)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTC
T ss_pred             hCcCcCCCEEECCCCcCCccCHhHccCCcccceeEecCCc-CcEeChhHhccCCCcCEEECCCCcCCcCCHHHhccccCC
Confidence            78999999999999999999865 7899999999999976 888876 488999999999999999998875 6666666


Q ss_pred             CcCC
Q 005860          646 RTLS  649 (673)
Q Consensus       646 ~~L~  649 (673)
                      +.|.
T Consensus       208 ~~L~  211 (270)
T 2o6q_A          208 KMLQ  211 (270)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            6653

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.26  E-value=3.2e-12  Score=138.48  Aligned_cols=145  Identities=21%  Similarity=0.235  Sum_probs=97.7

Q ss_pred             cCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      +.+++.+.+..+..... +..+..+++|+.|.+.++..    ....+..|.++++|+.|+|++       +.+..+|+. 
T Consensus        74 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  142 (452)
T 3zyi_A           74 PSNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSI----RQIEVGAFNGLASLNTLELFD-------NWLTVIPSGA  142 (452)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEECCSSCC----CEECTTTTTTCTTCCEEECCS-------SCCSBCCTTT
T ss_pred             CCCccEEECcCCcCceECHHHcCCCCCCCEEECCCCcc----CCcChhhccCcccCCEEECCC-------CcCCccChhh
Confidence            45778888877776555 34566788888888887753    334455677788888888888       777776654 


Q ss_pred             cccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      +..+++|++|+|++|.+..+|. .+.++++|++|++++|+.+..+|. .+.++++|++|++++|.+..+| .+..+++|+
T Consensus       143 ~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~  221 (452)
T 3zyi_A          143 FEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDMP-NLTPLVGLE  221 (452)
T ss_dssp             SSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCCSSCC-CCTTCTTCC
T ss_pred             hcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCcccccc-ccccccccc
Confidence            6778888888888888777764 566677777777777666666664 3566666666666666665554 234444443


Q ss_pred             c
Q 005860          647 T  647 (673)
Q Consensus       647 ~  647 (673)
                      .
T Consensus       222 ~  222 (452)
T 3zyi_A          222 E  222 (452)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.26  E-value=8.2e-12  Score=125.41  Aligned_cols=147  Identities=27%  Similarity=0.411  Sum_probs=110.6

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      ...+++.+.+..+....+ +.+..+++|++|.+.++..    ....+..|..++.|+.|++++       +.+..+|+. 
T Consensus        61 ~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  128 (272)
T 3rfs_A           61 YLPNVRYLALGGNKLHDI-SALKELTNLTYLILTGNQL----QSLPNGVFDKLTNLKELVLVE-------NQLQSLPDGV  128 (272)
T ss_dssp             GCTTCCEEECTTSCCCCC-GGGTTCTTCCEEECTTSCC----CCCCTTTTTTCTTCCEEECTT-------SCCCCCCTTT
T ss_pred             cCCCCcEEECCCCCCCCc-hhhcCCCCCCEEECCCCcc----CccChhHhcCCcCCCEEECCC-------CcCCccCHHH
Confidence            356788888877766554 3566788888888888763    344555677888888888888       887777654 


Q ss_pred             cccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L  645 (673)
                      ++.+++|++|+|++|.+..+|.. ++.+++|++|++++|. +..+|.. ++.+++|++|++++|.+..+|+. ++.+++|
T Consensus       129 ~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L  207 (272)
T 3rfs_A          129 FDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQ-LQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSL  207 (272)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTC
T ss_pred             hccCCCCCEEECCCCccCccCHHHhccCccCCEEECCCCC-cCccCHHHhcCCccCCEEECCCCcCCccCHHHHhCCcCC
Confidence            68888889999988888888754 5788889999998876 7777654 57888889998888888887765 4666666


Q ss_pred             CcCC
Q 005860          646 RTLS  649 (673)
Q Consensus       646 ~~L~  649 (673)
                      +.|.
T Consensus       208 ~~L~  211 (272)
T 3rfs_A          208 QYIW  211 (272)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            6553

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.26  E-value=6e-12  Score=126.40  Aligned_cols=167  Identities=24%  Similarity=0.309  Sum_probs=115.6

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-c
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-I  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i  569 (673)
                      ..+++.+.+..+.....+ .+..+++|++|.+.++...    . + ..+..+++|++|++++       +.+..+|+. +
T Consensus        40 l~~L~~L~l~~~~i~~~~-~l~~l~~L~~L~l~~n~l~----~-~-~~l~~l~~L~~L~L~~-------n~l~~~~~~~~  105 (272)
T 3rfs_A           40 LNSIDQIIANNSDIKSVQ-GIQYLPNVRYLALGGNKLH----D-I-SALKELTNLTYLILTG-------NQLQSLPNGVF  105 (272)
T ss_dssp             HTTCCEEECTTSCCCCCT-TGGGCTTCCEEECTTSCCC----C-C-GGGTTCTTCCEEECTT-------SCCCCCCTTTT
T ss_pred             ccceeeeeeCCCCccccc-ccccCCCCcEEECCCCCCC----C-c-hhhcCCCCCCEEECCC-------CccCccChhHh
Confidence            345666766665554433 4667888888888887641    1 2 2467888888888888       887776654 5


Q ss_pred             ccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLR  646 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~  646 (673)
                      +.+++|++|+|++|.+..+|.. ++.+++|++|++++|. +..+|.. ++++++|++|++++|.+..+|.. ++.+++|+
T Consensus       106 ~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~  184 (272)
T 3rfs_A          106 DKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQ-LQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLK  184 (272)
T ss_dssp             TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             cCCcCCCEEECCCCcCCccCHHHhccCCCCCEEECCCCc-cCccCHHHhccCccCCEEECCCCCcCccCHHHhcCCccCC
Confidence            8888888888888888887754 6888888899888875 7777754 57888888888888888887765 46677777


Q ss_pred             cCCeeEE--ccCCccCCCccccCCCCCC
Q 005860          647 TLSEFVV--VRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       647 ~L~~~~~--~~~~~~~~~~~~~l~~L~~  672 (673)
                      .|.....  ....+..+..+.+|+.|.+
T Consensus       185 ~L~L~~N~l~~~~~~~~~~l~~L~~L~l  212 (272)
T 3rfs_A          185 DLRLYQNQLKSVPDGVFDRLTSLQYIWL  212 (272)
T ss_dssp             EEECCSSCCSCCCTTTTTTCTTCCEEEC
T ss_pred             EEECCCCcCCccCHHHHhCCcCCCEEEc
Confidence            6643321  1222223445566665544

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.26  E-value=2.8e-12  Score=118.74  Aligned_cols=135  Identities=22%  Similarity=0.130  Sum_probs=116.5

Q ss_pred             cCceEEEEEEcCCCC--ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hcc
Q 005860          491 QEKLRHSMLVLGYEA--SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILK  567 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~--~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~  567 (673)
                      +.+++++.+..+...  .+|..+..+++|+.|.+.++...    ..  ..+..+++|+.|++++       +.+.. +|.
T Consensus        23 ~~~L~~L~l~~n~l~~~~i~~~~~~l~~L~~L~l~~n~l~----~~--~~~~~l~~L~~L~Ls~-------N~l~~~~~~   89 (168)
T 2ell_A           23 PAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLI----SV--SNLPKLPKLKKLELSE-------NRIFGGLDM   89 (168)
T ss_dssp             TTSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESSCCC----CC--SSCCCCSSCCEEEEES-------CCCCSCCCH
T ss_pred             cccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCCCCC----Ch--hhhccCCCCCEEECcC-------CcCchHHHH
Confidence            467899999888776  67777788999999999998741    22  5678899999999999       88877 677


Q ss_pred             ccccccccccceecCCCCcccc--hhhhcCCCccEEEeccCCCCccccc----cccccccCCeeeccccccccccccC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELP--ETCCELLNLQVLEIEQCTSLKRLPL----GIGKLVNLRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP--~~i~~L~~L~~L~l~~c~~l~~lP~----~i~~L~~Lr~L~l~~~~l~~lP~~i  639 (673)
                      .+..+++|++|+|++|.+..+|  ..++.+++|++|++++|. +..+|.    .+..+++|++|+++.|.+..+|.+.
T Consensus        90 ~~~~l~~L~~L~Ls~N~l~~~~~~~~l~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~  166 (168)
T 2ell_A           90 LAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCE-VTNLNDYRESVFKLLPQLTYLDGYDREDQEAPDSD  166 (168)
T ss_dssp             HHHHCTTCCEEECBSSSCCSSGGGGGGSSCSCCCEEECCSSG-GGTSTTHHHHHHTTCSSCCEETTEETTSCBCCSSS
T ss_pred             HHhhCCCCCEEeccCCccCcchhHHHHhcCCCCCEEEeeCCc-CcchHHHHHHHHHhCccCcEecCCCCChhhccccc
Confidence            7778999999999999999987  789999999999999987 888887    7899999999999999998888653

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.25  E-value=2.5e-11  Score=126.79  Aligned_cols=180  Identities=13%  Similarity=0.151  Sum_probs=114.0

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-----ccH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-----FDE  241 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~  241 (673)
                      .+..|+||+.+++.|.+ +..          +++.|+|++|+|||||++.+.+..  ..   ..+|+.+...     .+.
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~----------~~v~i~G~~G~GKT~L~~~~~~~~--~~---~~~~~~~~~~~~~~~~~~   74 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA----------PITLVLGLRRTGKSSIIKIGINEL--NL---PYIYLDLRKFEERNYISY   74 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS----------SEEEEEESTTSSHHHHHHHHHHHH--TC---CEEEEEGGGGTTCSCCCH
T ss_pred             CHHHhcChHHHHHHHHH-hcC----------CcEEEECCCCCCHHHHHHHHHHhc--CC---CEEEEEchhhccccCCCH
Confidence            45679999999999998 732          489999999999999999998852  21   2578887642     244


Q ss_pred             HHHHHHHHHHhhC-------------C-------C---------CCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCc--
Q 005860          242 LRIAKAIIEALEG-------------F-------V---------PTVGELNSLLESIRASLVGKKFLLILDDMWTDDY--  290 (673)
Q Consensus       242 ~~~~~~i~~~l~~-------------~-------~---------~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~--  290 (673)
                      ..+...+.+.+..             .       .         .....+..+...+.+... ++++|||||++.-+.  
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~  153 (357)
T 2fna_A           75 KDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLR  153 (357)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCT
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccC
Confidence            4455554444311             0       0         012344555555554433 499999999954221  


Q ss_pred             -cchhhhhhhccCCCCCeEEEEEcCChhHHHhc-----------cc-cceeecCCCCccccc------------------
Q 005860          291 -SKWEPFHYCLKNGVRGSKILVTTRKETVARMM-----------ES-IHVISIKELSEQECW------------------  339 (673)
Q Consensus       291 -~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~-----------~~-~~~~~l~~L~~~~~~------------------  339 (673)
                       ..|..+...+.....+.++|+|++.......+           +. ...+++.+|+.+|+.                  
T Consensus       154 ~~~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~  233 (357)
T 2fna_A          154 GVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYE  233 (357)
T ss_dssp             TCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCHH
T ss_pred             chhHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcHH
Confidence             12322222222222467899999986542211           11 257889999988765                  


Q ss_pred             -----cCCchhhHHHHhhhhccCCCHHHH
Q 005860          340 -----CKGLPLAAKTIGSLLRFKRTREEW  363 (673)
Q Consensus       340 -----c~GlPLai~~~~~~L~~~~~~~~w  363 (673)
                           |+|+|+++..++..+....+...|
T Consensus       234 ~i~~~t~G~P~~l~~~~~~~~~~~~~~~~  262 (357)
T 2fna_A          234 VVYEKIGGIPGWLTYFGFIYLDNKNLDFA  262 (357)
T ss_dssp             HHHHHHCSCHHHHHHHHHHHHHHCCHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHccccchHHH
Confidence                 999999999998876433333334

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.25  E-value=3.9e-12  Score=130.18  Aligned_cols=143  Identities=17%  Similarity=0.228  Sum_probs=118.8

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....++ .+..+++|++|.+.++...    . ++. +..+++|+.|++++       +.+..++. +
T Consensus        83 ~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~L~l~~n~l~----~-~~~-l~~l~~L~~L~l~~-------n~l~~~~~-l  147 (308)
T 1h6u_A           83 NLTKITELELSGNPLKNVS-AIAGLQSIKTLDLTSTQIT----D-VTP-LAGLSNLQVLYLDL-------NQITNISP-L  147 (308)
T ss_dssp             TCCSCCEEECCSCCCSCCG-GGTTCTTCCEEECTTSCCC----C-CGG-GTTCTTCCEEECCS-------SCCCCCGG-G
T ss_pred             cCCCCCEEEccCCcCCCch-hhcCCCCCCEEECCCCCCC----C-chh-hcCCCCCCEEECCC-------CccCcCcc-c
Confidence            3567899999888776654 5778999999999988741    2 222 78899999999999       88887776 8


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      +.+++|++|+|++|.+..+|. +..+++|++|++++|. +..+|. +..+++|++|++++|.+..+|+ +..+++|+.|.
T Consensus       148 ~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~-l~~~~~-l~~l~~L~~L~L~~N~l~~~~~-l~~l~~L~~L~  223 (308)
T 1h6u_A          148 AGLTNLQYLSIGNAQVSDLTP-LANLSKLTTLKADDNK-ISDISP-LASLPNLIEVHLKNNQISDVSP-LANTSNLFIVT  223 (308)
T ss_dssp             GGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCCEEECTTSCCCBCGG-GTTCTTCCEEE
T ss_pred             cCCCCccEEEccCCcCCCChh-hcCCCCCCEEECCCCc-cCcChh-hcCCCCCCEEEccCCccCcccc-ccCCCCCCEEE
Confidence            899999999999999999888 8999999999999976 888885 8899999999999999998874 77788887775


Q ss_pred             ee
Q 005860          650 EF  651 (673)
Q Consensus       650 ~~  651 (673)
                      .-
T Consensus       224 l~  225 (308)
T 1h6u_A          224 LT  225 (308)
T ss_dssp             EE
T ss_pred             cc
Confidence            43

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.25  E-value=1.6e-12  Score=117.66  Aligned_cols=125  Identities=22%  Similarity=0.235  Sum_probs=101.1

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcc-cchhh
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEE-LPETC  592 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~-LP~~i  592 (673)
                      .++|+.|.+.++...   ...++..+..+++|+.|++++       +.+..+ ..++.+++|++|+|++|.+.. +|..+
T Consensus        16 ~~~l~~L~l~~n~l~---~~~~~~~~~~l~~L~~L~l~~-------n~l~~~-~~~~~l~~L~~L~Ls~n~i~~~~~~~~   84 (149)
T 2je0_A           16 PSDVKELVLDNSRSN---EGKLEGLTDEFEELEFLSTIN-------VGLTSI-ANLPKLNKLKKLELSDNRVSGGLEVLA   84 (149)
T ss_dssp             GGGCSEEECTTCBCB---TTBCCSCCTTCTTCCEEECTT-------SCCCCC-TTCCCCTTCCEEECCSSCCCSCTHHHH
T ss_pred             CccCeEEEccCCcCC---hhHHHHHHhhcCCCcEEECcC-------CCCCCc-hhhhcCCCCCEEECCCCcccchHHHHh
Confidence            467778887777631   023455667888999999999       887777 778899999999999999877 88888


Q ss_pred             hcCCCccEEEeccCCCCcccc--ccccccccCCeeeccccccccccc----cCCCCCCCCcCCe
Q 005860          593 CELLNLQVLEIEQCTSLKRLP--LGIGKLVNLRHLTYDDSCLEFIPK----GIQRLTNLRTLSE  650 (673)
Q Consensus       593 ~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~Lr~L~l~~~~l~~lP~----~i~~L~~L~~L~~  650 (673)
                      +.+++|++|++++|. +..+|  ..++.+++|++|++++|.+..+|.    .++.+++|+.|+.
T Consensus        85 ~~l~~L~~L~ls~N~-i~~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l  147 (149)
T 2je0_A           85 EKCPNLTHLNLSGNK-IKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDG  147 (149)
T ss_dssp             HHCTTCCEEECTTSC-CCSHHHHGGGGGCTTCCEEECTTCGGGGSTTHHHHHHHHCTTCCEETT
T ss_pred             hhCCCCCEEECCCCc-CCChHHHHHHhhCCCCCEEeCcCCcccchHHHHHHHHHHCCCcccccC
Confidence            889999999999876 88765  788999999999999999988876    5777888887764

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.25  E-value=1.5e-12  Score=147.13  Aligned_cols=108  Identities=15%  Similarity=0.200  Sum_probs=87.1

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhh------------------hccccc--cccccccceecCCC-Ccccchhhh
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNK------------------ILKGIE--KLIHLRYLRLVGLG-TEELPETCC  593 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~------------------lp~~i~--~L~~Lr~L~L~~~~-i~~LP~~i~  593 (673)
                      +|..+.++++|++|+|++       +.+..                  +|+.++  ++++|++|+|++|. ...+|..++
T Consensus       198 ip~~l~~l~~L~~L~Ls~-------n~l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~  270 (636)
T 4eco_A          198 VSKAVMRLTKLRQFYMGN-------SPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLK  270 (636)
T ss_dssp             ECGGGGGCTTCCEEEEES-------CCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSSCCTTTT
T ss_pred             CCHHHhcccCCCEEECcC-------CccccccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCccChHHHh
Confidence            556678888888888888       77766                  888888  88888888888888 667888888


Q ss_pred             cCCCccEEEeccCCCCc--ccccccccc------ccCCeeeccccccccccc--cCCCCCCCCcCC
Q 005860          594 ELLNLQVLEIEQCTSLK--RLPLGIGKL------VNLRHLTYDDSCLEFIPK--GIQRLTNLRTLS  649 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~--~lP~~i~~L------~~Lr~L~l~~~~l~~lP~--~i~~L~~L~~L~  649 (673)
                      +|++|++|++++|..+.  .+|..+++|      ++|++|++++|.+..+|.  .++++++|++|.
T Consensus       271 ~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~~ip~~~~l~~l~~L~~L~  336 (636)
T 4eco_A          271 ALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLE  336 (636)
T ss_dssp             TCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSCCSSCCCHHHHTTCTTCCEEE
T ss_pred             cCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCcCCccCchhhhccCCCCCEEe
Confidence            88888888888876354  588888776      888888888888888887  788888777764

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.24  E-value=3.7e-12  Score=130.31  Aligned_cols=148  Identities=17%  Similarity=0.114  Sum_probs=75.8

Q ss_pred             cCceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      +.+++++.+..+....++.. +..+++|++|.+.++....  ....+..+..+++|++|++++       +.+..+|..+
T Consensus        27 ~~~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~n~l~~--~~~~~~~~~~~~~L~~L~Ls~-------n~i~~l~~~~   97 (306)
T 2z66_A           27 PSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSF--KGCCSQSDFGTTSLKYLDLSF-------NGVITMSSNF   97 (306)
T ss_dssp             CTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCE--EEEEEHHHHSCSCCCEEECCS-------CSEEEEEEEE
T ss_pred             CCCCCEEECCCCccCccCHhHhhccccCCEEECCCCccCc--ccCcccccccccccCEEECCC-------CccccChhhc
Confidence            45677777777766666554 4567778888777765310  001122334566666666666       5555555555


Q ss_pred             ccccccccceecCCCCcccch--hhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccc--ccccCCCCCCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPE--TCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEF--IPKGIQRLTNL  645 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~--~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~--lP~~i~~L~~L  645 (673)
                      ..+++|++|++++|.+..+|.  .+..+++|++|++++|..-...|..+..+++|++|++++|.+..  +|..++.+++|
T Consensus        98 ~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L  177 (306)
T 2z66_A           98 LGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNL  177 (306)
T ss_dssp             ETCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTC
T ss_pred             CCCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCEEECCCCccccccchhHHhhCcCC
Confidence            555555555555555554442  44455555555555443111222334444444444444444432  33334433333


Q ss_pred             Cc
Q 005860          646 RT  647 (673)
Q Consensus       646 ~~  647 (673)
                      +.
T Consensus       178 ~~  179 (306)
T 2z66_A          178 TF  179 (306)
T ss_dssp             CE
T ss_pred             CE
Confidence            33

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.24  E-value=4.1e-12  Score=146.72  Aligned_cols=139  Identities=16%  Similarity=0.230  Sum_probs=73.3

Q ss_pred             CceEEEEEEcCCC-Cccccccccccccchhhhccch-hhhhhhhhHHHHhh-------hCCccceeeeccccccccccch
Q 005860          492 EKLRHSMLVLGYE-ASFPISIFKAKNLRSLFINNTL-IQVSLTHVLQSLFD-------QLKCLRALRIATLMNTWDVNST  562 (673)
Q Consensus       492 ~~~r~l~l~~~~~-~~~~~~~~~~~~Lr~L~l~~~~-~~~~~~~~~~~~~~-------~l~~L~~L~L~~~~~~~~~~~~  562 (673)
                      .+++.+.+..+.. ..+|..+.++++|++|.+.++. ...   ..+|..+.       .+++|+.|++++       +.+
T Consensus       491 ~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~L~Ls~N~~lsg---~~iP~~i~~L~~~~~~l~~L~~L~Ls~-------N~L  560 (876)
T 4ecn_A          491 KDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNRGISA---AQLKADWTRLADDEDTGPKIQIFYMGY-------NNL  560 (876)
T ss_dssp             TTCCEEEEESCTTCCSCCGGGGGCSSCCEEECTTCTTSCH---HHHHHHHHHHHHCTTTTTTCCEEECCS-------SCC
T ss_pred             CCCCEEECcCCCCCccChHHHhCCCCCCEEECcCCCCccc---ccchHHHHhhhhcccccCCccEEEeeC-------CcC
Confidence            4455555555432 3344445555555555555543 211   01222222       223556666655       555


Q ss_pred             hhhcc--ccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccccccccccc-CCeeeccccccccccccC
Q 005860          563 NKILK--GIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVN-LRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       563 ~~lp~--~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~-Lr~L~l~~~~l~~lP~~i  639 (673)
                      ..+|.  .++.+++|++|+|++|.+..+| .++++++|+.|+|++|. +..+|..++++++ |++|++++|.+..+|..+
T Consensus       561 ~~ip~~~~l~~L~~L~~L~Ls~N~l~~lp-~~~~L~~L~~L~Ls~N~-l~~lp~~l~~l~~~L~~L~Ls~N~L~~lp~~~  638 (876)
T 4ecn_A          561 EEFPASASLQKMVKLGLLDCVHNKVRHLE-AFGTNVKLTDLKLDYNQ-IEEIPEDFCAFTDQVEGLGFSHNKLKYIPNIF  638 (876)
T ss_dssp             CBCCCHHHHTTCTTCCEEECTTSCCCBCC-CCCTTSEESEEECCSSC-CSCCCTTSCEECTTCCEEECCSSCCCSCCSCC
T ss_pred             CccCChhhhhcCCCCCEEECCCCCcccch-hhcCCCcceEEECcCCc-cccchHHHhhccccCCEEECcCCCCCcCchhh
Confidence            55555  5666666666666666655555 55666666666666554 5556655666665 666666666665565544


Q ss_pred             CCC
Q 005860          640 QRL  642 (673)
Q Consensus       640 ~~L  642 (673)
                      +.+
T Consensus       639 ~~~  641 (876)
T 4ecn_A          639 NAK  641 (876)
T ss_dssp             CTT
T ss_pred             hcc
Confidence            443

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.24  E-value=3.5e-12  Score=119.06  Aligned_cols=130  Identities=20%  Similarity=0.133  Sum_probs=102.0

Q ss_pred             cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccch
Q 005860          511 IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE  590 (673)
Q Consensus       511 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~  590 (673)
                      +..+.+|+.|.+.++...    . ++.+....++|++|++++       +.+..+ +.++.+++|++|+|++|.+..+|+
T Consensus        15 ~~~~~~L~~L~l~~n~l~----~-i~~~~~~~~~L~~L~Ls~-------N~l~~~-~~l~~l~~L~~L~Ls~N~l~~~~~   81 (176)
T 1a9n_A           15 YTNAVRDRELDLRGYKIP----V-IENLGATLDQFDAIDFSD-------NEIRKL-DGFPLLRRLKTLLVNNNRICRIGE   81 (176)
T ss_dssp             EECTTSCEEEECTTSCCC----S-CCCGGGGTTCCSEEECCS-------SCCCEE-CCCCCCSSCCEEECCSSCCCEECS
T ss_pred             cCCcCCceEEEeeCCCCc----h-hHHhhhcCCCCCEEECCC-------CCCCcc-cccccCCCCCEEECCCCcccccCc
Confidence            446677888888877641    1 233333344899999998       887777 678888999999999999888886


Q ss_pred             hh-hcCCCccEEEeccCCCCccccc--cccccccCCeeecccccccccccc----CCCCCCCCcCCeeEEc
Q 005860          591 TC-CELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIPKG----IQRLTNLRTLSEFVVV  654 (673)
Q Consensus       591 ~i-~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP~~----i~~L~~L~~L~~~~~~  654 (673)
                      .+ +.+++|++|++++|. +..+|.  .++.+++|++|++++|.+..+|..    ++.+++|+.|+.-.+.
T Consensus        82 ~~~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~l~~N~i~~~~~~~~~~~~~l~~L~~Ld~~~n~  151 (176)
T 1a9n_A           82 GLDQALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCILRNPVTNKKHYRLYVIYKVPQVRVLDFQKVK  151 (176)
T ss_dssp             CHHHHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECCSSGGGGSTTHHHHHHHHCTTCSEETTEECC
T ss_pred             chhhcCCCCCEEECCCCc-CCcchhhHhhhcCCCCCEEEecCCCCCCcHhHHHHHHHHCCccceeCCCcCC
Confidence            65 889999999999876 888887  788899999999999988888875    7888888888776654

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.24  E-value=5.9e-12  Score=127.74  Aligned_cols=144  Identities=22%  Similarity=0.310  Sum_probs=118.7

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+.....++ +..+++|+.|.+.++...    . ++ .+..+++|+.|++++       +.+..+ +.+
T Consensus        66 ~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n~l~----~-~~-~l~~l~~L~~L~L~~-------n~i~~~-~~l  130 (291)
T 1h6t_A           66 YLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVK----D-LS-SLKDLKKLKSLSLEH-------NGISDI-NGL  130 (291)
T ss_dssp             GCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC----C-GG-GGTTCTTCCEEECTT-------SCCCCC-GGG
T ss_pred             cCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCCcCC----C-Ch-hhccCCCCCEEECCC-------CcCCCC-hhh
Confidence            35678999998887776665 778999999999988741    1 22 378899999999999       887776 468


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..+++|++|+|++|.+..+ +.++.+++|++|++++|. +..+|. +..+++|++|++++|.++.+|. +..+++|+.|.
T Consensus       131 ~~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~L~~N~-l~~~~~-l~~l~~L~~L~L~~N~i~~l~~-l~~l~~L~~L~  206 (291)
T 1h6t_A          131 VHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNHISDLRA-LAGLKNLDVLE  206 (291)
T ss_dssp             GGCTTCCEEECCSSCCCCC-GGGGGCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSCCCBCGG-GTTCTTCSEEE
T ss_pred             cCCCCCCEEEccCCcCCcc-hhhccCCCCCEEEccCCc-cccchh-hcCCCccCEEECCCCcCCCChh-hccCCCCCEEE
Confidence            8899999999999998888 578999999999999976 888876 8999999999999999998874 77888888776


Q ss_pred             eeE
Q 005860          650 EFV  652 (673)
Q Consensus       650 ~~~  652 (673)
                      ...
T Consensus       207 l~~  209 (291)
T 1h6t_A          207 LFS  209 (291)
T ss_dssp             EEE
T ss_pred             CcC
Confidence            544

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.23  E-value=3.9e-12  Score=146.89  Aligned_cols=107  Identities=20%  Similarity=0.265  Sum_probs=64.8

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhh------------------hccccc--cccccccceecCCC-Ccccchhhh
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNK------------------ILKGIE--KLIHLRYLRLVGLG-TEELPETCC  593 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~------------------lp~~i~--~L~~Lr~L~L~~~~-i~~LP~~i~  593 (673)
                      +|..|.++++|+.|+|++       +.+..                  +|+.++  .|++|++|+|++|. ...+|..++
T Consensus       440 IP~~l~~L~~L~~L~Ls~-------N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~iP~~l~  512 (876)
T 4ecn_A          440 ISKAIQRLTKLQIIYFAN-------SPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLY  512 (876)
T ss_dssp             ECGGGGGCTTCCEEEEES-------CCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCSCCGGGG
T ss_pred             hhHHHhcCCCCCEEECcC-------CcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCccChHHHh
Confidence            344566666666666666       55554                  666666  66666666666665 555666666


Q ss_pred             cCCCccEEEeccCCCCc--cccccccccc-------cCCeeeccccccccccc--cCCCCCCCCcC
Q 005860          594 ELLNLQVLEIEQCTSLK--RLPLGIGKLV-------NLRHLTYDDSCLEFIPK--GIQRLTNLRTL  648 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~--~lP~~i~~L~-------~Lr~L~l~~~~l~~lP~--~i~~L~~L~~L  648 (673)
                      +|++|++|+|++|..+.  .+|..++++.       +|++|++++|.+..+|.  .++++++|+.|
T Consensus       513 ~L~~L~~L~Ls~N~~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~~~~l~~L~~L~~L  578 (876)
T 4ecn_A          513 DLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLL  578 (876)
T ss_dssp             GCSSCCEEECTTCTTSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCCHHHHTTCTTCCEE
T ss_pred             CCCCCCEEECcCCCCcccccchHHHHhhhhcccccCCccEEEeeCCcCCccCChhhhhcCCCCCEE
Confidence            66666666666654243  3565555554       66666666666666665  55555555554

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.23  E-value=7.3e-12  Score=121.42  Aligned_cols=121  Identities=25%  Similarity=0.347  Sum_probs=61.8

Q ss_pred             cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceecCCCCcccchh-h
Q 005860          515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVGLGTEELPET-C  592 (673)
Q Consensus       515 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~-i  592 (673)
                      ++|+.|.+.++.+    ....+..|..+++|+.|+|++       +.+..+ |..+..+.+|++|+|++|.+..+|.. +
T Consensus        32 ~~l~~L~l~~n~i----~~i~~~~~~~l~~L~~L~Ls~-------N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f  100 (220)
T 2v9t_B           32 ETITEIRLEQNTI----KVIPPGAFSPYKKLRRIDLSN-------NQISELAPDAFQGLRSLNSLVLYGNKITELPKSLF  100 (220)
T ss_dssp             TTCCEEECCSSCC----CEECTTSSTTCTTCCEEECCS-------SCCCEECTTTTTTCSSCCEEECCSSCCCCCCTTTT
T ss_pred             cCCCEEECCCCcC----CCcCHhHhhCCCCCCEEECCC-------CcCCCcCHHHhhCCcCCCEEECCCCcCCccCHhHc
Confidence            3455555555442    122233445555555555555       554444 44555555555555555555555543 3


Q ss_pred             hcCCCccEEEeccCCCCccc-cccccccccCCeeecccccccccccc-CCCCCCCCc
Q 005860          593 CELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRT  647 (673)
Q Consensus       593 ~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~  647 (673)
                      ..+++|++|+|++|. +..+ |..+..+++|++|++++|.+..+|.. +..+++|++
T Consensus       101 ~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~  156 (220)
T 2v9t_B          101 EGLFSLQLLLLNANK-INCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQT  156 (220)
T ss_dssp             TTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCE
T ss_pred             cCCCCCCEEECCCCC-CCEeCHHHcCCCCCCCEEECCCCcCCEECHHHHhCCCCCCE
Confidence            455555555555544 4444 33455555555555555555555543 444444443

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.22  E-value=9.5e-12  Score=120.61  Aligned_cols=102  Identities=21%  Similarity=0.253  Sum_probs=53.9

Q ss_pred             hhhCCccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccc-ccc
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRL-PLG  615 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~l-P~~  615 (673)
                      |..+++|+.|++++       +.+..+++ .+..+.+|++|+|++|.+..+|. .+..+++|++|+|++|. +..+ |..
T Consensus        53 ~~~l~~L~~L~L~~-------N~i~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~  124 (220)
T 2v70_A           53 FKKLPQLRKINFSN-------NKITDIEEGAFEGASGVNEILLTSNRLENVQHKMFKGLESLKTLMLRSNR-ITCVGNDS  124 (220)
T ss_dssp             GGGCTTCCEEECCS-------SCCCEECTTTTTTCTTCCEEECCSSCCCCCCGGGGTTCSSCCEEECTTSC-CCCBCTTS
T ss_pred             hccCCCCCEEECCC-------CcCCEECHHHhCCCCCCCEEECCCCccCccCHhHhcCCcCCCEEECCCCc-CCeECHhH
Confidence            45555555555555       55554443 45555555555555555555543 25555555555555544 4444 344


Q ss_pred             ccccccCCeeeccccccccc-cccCCCCCCCCcC
Q 005860          616 IGKLVNLRHLTYDDSCLEFI-PKGIQRLTNLRTL  648 (673)
Q Consensus       616 i~~L~~Lr~L~l~~~~l~~l-P~~i~~L~~L~~L  648 (673)
                      +..+++|++|++++|.++.+ |..++.+++|++|
T Consensus       125 ~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L  158 (220)
T 2v70_A          125 FIGLSSVRLLSLYDNQITTVAPGAFDTLHSLSTL  158 (220)
T ss_dssp             STTCTTCSEEECTTSCCCCBCTTTTTTCTTCCEE
T ss_pred             cCCCccCCEEECCCCcCCEECHHHhcCCCCCCEE
Confidence            55555555555555555555 3334444444443

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.22  E-value=4.1e-12  Score=143.54  Aligned_cols=138  Identities=14%  Similarity=0.232  Sum_probs=78.8

Q ss_pred             CceEEEEEEcCCC-Cccccccccccccchhhhccch-hhhhhhh-hHHHHhhhC------Cccceeeeccccccccccch
Q 005860          492 EKLRHSMLVLGYE-ASFPISIFKAKNLRSLFINNTL-IQVSLTH-VLQSLFDQL------KCLRALRIATLMNTWDVNST  562 (673)
Q Consensus       492 ~~~r~l~l~~~~~-~~~~~~~~~~~~Lr~L~l~~~~-~~~~~~~-~~~~~~~~l------~~L~~L~L~~~~~~~~~~~~  562 (673)
                      .+++.+.+..+.. ..+|..+.++++|++|.+.++. .    .. .+|..+..+      ++|++|++++       +.+
T Consensus       249 ~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~~l----~~~~lp~~~~~L~~~~~l~~L~~L~L~~-------n~l  317 (636)
T 4eco_A          249 KDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGI----SGEQLKDDWQALADAPVGEKIQIIYIGY-------NNL  317 (636)
T ss_dssp             TTCCEEEEECCTTCSSCCTTTTTCSSCCEEECTTCTTS----CHHHHHHHHHHHHHSGGGGTCCEEECCS-------SCC
T ss_pred             CCCCEEEecCCcCCccChHHHhcCCCCCEEECcCCCCC----ccccchHHHHhhhccccCCCCCEEECCC-------CcC
Confidence            4455555555543 3344455556666666665553 2    11 233333333      5666666666       555


Q ss_pred             hhhcc--ccccccccccceecCCCCc-ccchhhhcCCCccEEEeccCCCCcccccccccccc-CCeeecccccccccccc
Q 005860          563 NKILK--GIEKLIHLRYLRLVGLGTE-ELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVN-LRHLTYDDSCLEFIPKG  638 (673)
Q Consensus       563 ~~lp~--~i~~L~~Lr~L~L~~~~i~-~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~-Lr~L~l~~~~l~~lP~~  638 (673)
                      ..+|.  .++.+++|++|+|++|.+. .+| .++.+++|++|++++|. +..+|..++++++ |++|++++|.+..+|..
T Consensus       318 ~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip-~~~~l~~L~~L~L~~N~-l~~lp~~l~~l~~~L~~L~Ls~N~l~~lp~~  395 (636)
T 4eco_A          318 KTFPVETSLQKMKKLGMLECLYNQLEGKLP-AFGSEIKLASLNLAYNQ-ITEIPANFCGFTEQVENLSFAHNKLKYIPNI  395 (636)
T ss_dssp             SSCCCHHHHTTCTTCCEEECCSCCCEEECC-CCEEEEEESEEECCSSE-EEECCTTSEEECTTCCEEECCSSCCSSCCSC
T ss_pred             CccCchhhhccCCCCCEEeCcCCcCccchh-hhCCCCCCCEEECCCCc-cccccHhhhhhcccCcEEEccCCcCcccchh
Confidence            56665  5666666666666666655 666 56666666666666654 5566666666666 66666666666666655


Q ss_pred             CCCC
Q 005860          639 IQRL  642 (673)
Q Consensus       639 i~~L  642 (673)
                      ++.+
T Consensus       396 ~~~~  399 (636)
T 4eco_A          396 FDAK  399 (636)
T ss_dssp             CCTT
T ss_pred             hhhc
Confidence            5443

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.20  E-value=4.3e-12  Score=132.69  Aligned_cols=147  Identities=22%  Similarity=0.314  Sum_probs=106.5

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      ..+++.+.+..+.....++ .+..+++|++|.+.++..    ....+..|.++++|++|++++       +.+..+|.. 
T Consensus        51 ~~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~~  119 (353)
T 2z80_A           51 TEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGI----NTIEEDSFSSLGSLEHLDLSY-------NYLSNLSSSW  119 (353)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCC----CEECTTTTTTCTTCCEEECCS-------SCCSSCCHHH
T ss_pred             cccCcEEECCCCcCcccCHHHhccCCCCCEEECCCCcc----CccCHhhcCCCCCCCEEECCC-------CcCCcCCHhH
Confidence            3567888887777666554 566788888888887753    234455677788888888888       777777665 


Q ss_pred             cccccccccceecCCCCcccch--hhhcCCCccEEEeccCCCCcccc-ccccccccCCeeeccccccccc-cccCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPE--TCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFI-PKGIQRLTN  644 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~--~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~l-P~~i~~L~~  644 (673)
                      ++.+++|++|+|++|.+..+|.  .+.++++|++|++++|..+..+| ..++++++|++|++++|.+..+ |..++++++
T Consensus       120 ~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~  199 (353)
T 2z80_A          120 FKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQN  199 (353)
T ss_dssp             HTTCTTCSEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSE
T ss_pred             hCCCccCCEEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHhcccc
Confidence            7778888888888888878876  67778888888888775566664 4677888888888877777665 555666666


Q ss_pred             CCcC
Q 005860          645 LRTL  648 (673)
Q Consensus       645 L~~L  648 (673)
                      |++|
T Consensus       200 L~~L  203 (353)
T 2z80_A          200 VSHL  203 (353)
T ss_dssp             EEEE
T ss_pred             CCee
Confidence            6554

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.20  E-value=1.2e-11  Score=125.28  Aligned_cols=145  Identities=23%  Similarity=0.226  Sum_probs=118.7

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-ccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~i  569 (673)
                      ..+++.+.+..+....++.. ..+++|++|.+.++..     ..+|..+..++.|+.|++++       +.+..+| ..+
T Consensus        54 l~~L~~L~L~~n~l~~~~~~-~~l~~L~~L~Ls~N~l-----~~l~~~~~~l~~L~~L~l~~-------N~l~~l~~~~~  120 (290)
T 1p9a_G           54 YTRLTQLNLDRAELTKLQVD-GTLPVLGTLDLSHNQL-----QSLPLLGQTLPALTVLDVSF-------NRLTSLPLGAL  120 (290)
T ss_dssp             CTTCCEEECTTSCCCEEECC-SCCTTCCEEECCSSCC-----SSCCCCTTTCTTCCEEECCS-------SCCCCCCSSTT
T ss_pred             CCCCCEEECCCCccCcccCC-CCCCcCCEEECCCCcC-----CcCchhhccCCCCCEEECCC-------CcCcccCHHHH
Confidence            45788888888777665543 6788999999998874     23455677889999999999       8888887 468


Q ss_pred             ccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccccccCCeeeccccccccccccCCCCCCCCc
Q 005860          570 EKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRT  647 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~  647 (673)
                      ..+++|++|+|++|.+..+|.. +..+++|+.|++++|. +..+|.. +.++++|++|++++|.+..+|.++..+.+|+.
T Consensus       121 ~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~L~~N~l~~ip~~~~~~~~L~~  199 (290)
T 1p9a_G          121 RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNN-LTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPF  199 (290)
T ss_dssp             TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSC-CSCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCCCSE
T ss_pred             cCCCCCCEEECCCCCCCccChhhcccccCCCEEECCCCc-CCccCHHHhcCcCCCCEEECCCCcCCccChhhcccccCCe
Confidence            8999999999999998888865 5789999999999876 8888875 47899999999999999999998888777776


Q ss_pred             CC
Q 005860          648 LS  649 (673)
Q Consensus       648 L~  649 (673)
                      |.
T Consensus       200 l~  201 (290)
T 1p9a_G          200 AF  201 (290)
T ss_dssp             EE
T ss_pred             EE
Confidence            53

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.20  E-value=1.1e-11  Score=133.70  Aligned_cols=168  Identities=21%  Similarity=0.278  Sum_probs=95.2

Q ss_pred             CceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhcc-c
Q 005860          492 EKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILK-G  568 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~-~  568 (673)
                      .+++.+.+..+....+++ .+..+++|++|.+.++..    ....+..|.++++|+.|++++       +. +..++. .
T Consensus       112 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~i----~~~~~~~~~~l~~L~~L~l~~-------~~~l~~i~~~~  180 (440)
T 3zyj_A          112 ANLNTLELFDNRLTTIPNGAFVYLSKLKELWLRNNPI----ESIPSYAFNRIPSLRRLDLGE-------LKRLSYISEGA  180 (440)
T ss_dssp             SSCCEEECCSSCCSSCCTTTSCSCSSCCEEECCSCCC----CEECTTTTTTCTTCCEEECCC-------CTTCCEECTTT
T ss_pred             ccCCEEECCCCcCCeeCHhHhhccccCceeeCCCCcc----cccCHHHhhhCcccCEeCCCC-------CCCcceeCcch
Confidence            455566665555544443 244556666666665542    223334455666666666665       33 344443 4


Q ss_pred             cccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccc-cccccccccCCeeeccccccccccc-cCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLEFIPK-GIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~~L~  646 (673)
                      +..+.+|++|+|++|.+..+|. +..+++|++|+|++|. +..+ |..+.++++|++|++++|.+..++. .+.++++|+
T Consensus       181 ~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  258 (440)
T 3zyj_A          181 FEGLSNLRYLNLAMCNLREIPN-LTPLIKLDELDLSGNH-LSAIRPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQSLV  258 (440)
T ss_dssp             TTTCSSCCEEECTTSCCSSCCC-CTTCSSCCEEECTTSC-CCEECTTTTTTCTTCCEEECTTCCCCEECTTSSTTCTTCC
T ss_pred             hhcccccCeecCCCCcCccccc-cCCCcccCEEECCCCc-cCccChhhhccCccCCEEECCCCceeEEChhhhcCCCCCC
Confidence            6667777777777777777764 6677777777777765 5555 5567777777777777777776643 355555555


Q ss_pred             cCCeeE--EccCCccCCCccccCCCCCC
Q 005860          647 TLSEFV--VVRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       647 ~L~~~~--~~~~~~~~~~~~~~l~~L~~  672 (673)
                      .|+.-.  +.......+..+.+|+.|.+
T Consensus       259 ~L~L~~N~l~~~~~~~~~~l~~L~~L~L  286 (440)
T 3zyj_A          259 EINLAHNNLTLLPHDLFTPLHHLERIHL  286 (440)
T ss_dssp             EEECTTSCCCCCCTTTTSSCTTCCEEEC
T ss_pred             EEECCCCCCCccChhHhccccCCCEEEc
Confidence            542211  11112223445556655544

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.20  E-value=9.4e-12  Score=125.23  Aligned_cols=144  Identities=19%  Similarity=0.215  Sum_probs=88.1

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-cc
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KG  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~  568 (673)
                      +..++++.+..+.....++ .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..++ ..
T Consensus        27 ~~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~   95 (276)
T 2z62_A           27 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEI----QTIEDGAYQSLSHLSTLILTG-------NPIQSLALGA   95 (276)
T ss_dssp             CTTCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------CCCCEECTTT
T ss_pred             CCCccEEECCCCcccccCHhHhccccCCcEEECCCCcC----CccCHHHccCCcCCCEEECCC-------CccCccChhh
Confidence            3456777776666555444 455677777777776652    233344566677777777777       6655544 45


Q ss_pred             cccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCcc--ccccccccccCCeeeccccccccccc-cCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKR--LPLGIGKLVNLRHLTYDDSCLEFIPK-GIQRLTN  644 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~--lP~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~~  644 (673)
                      +..+.+|++|++++|.+..+|. .++.+++|++|++++|. +..  +|..++++++|++|++++|.+..+|. .+..+++
T Consensus        96 ~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~l~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~  174 (276)
T 2z62_A           96 FSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNL-IQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ  174 (276)
T ss_dssp             TTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSC-CCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHHT
T ss_pred             hcCCccccEEECCCCCccccCchhcccCCCCCEEECcCCc-cceecCchhhccCCCCCEEECCCCCCCcCCHHHhhhhhh
Confidence            6666677777776666666654 56666677777776654 544  56666666677777666666665542 3444444


Q ss_pred             CC
Q 005860          645 LR  646 (673)
Q Consensus       645 L~  646 (673)
                      |+
T Consensus       175 L~  176 (276)
T 2z62_A          175 MP  176 (276)
T ss_dssp             CT
T ss_pred             cc
Confidence            44

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.20  E-value=9e-12  Score=138.89  Aligned_cols=142  Identities=22%  Similarity=0.296  Sum_probs=114.8

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....+++ +..+++|+.|.+.++...    . ++ .+..+++|+.|+|++       +.+..++ .+
T Consensus        63 ~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~----~-l~-~l~~l~~L~~L~Ls~-------N~l~~l~-~l  127 (605)
T 1m9s_A           63 YLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDENKIK----D-LS-SLKDLKKLKSLSLEH-------NGISDIN-GL  127 (605)
T ss_dssp             GCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSSCCC----C-CT-TSTTCTTCCEEECTT-------SCCCCCG-GG
T ss_pred             cCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCCCCC----C-Ch-hhccCCCCCEEEecC-------CCCCCCc-cc
Confidence            35678888888887766655 778899999999888641    1 22 467889999999999       8877764 58


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..|++|++|+|++|.+..+ +.++.|++|+.|+|++|. +..+|. +..|++|++|++++|.+..+| .+..|++|+.|.
T Consensus       128 ~~l~~L~~L~Ls~N~l~~l-~~l~~l~~L~~L~Ls~N~-l~~~~~-l~~l~~L~~L~Ls~N~i~~l~-~l~~l~~L~~L~  203 (605)
T 1m9s_A          128 VHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNHISDLR-ALAGLKNLDVLE  203 (605)
T ss_dssp             GGCTTCSEEECCSSCCCCC-GGGGSCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSCCCBCG-GGTTCTTCSEEE
T ss_pred             cCCCccCEEECCCCccCCc-hhhcccCCCCEEECcCCc-CCCchh-hccCCCCCEEECcCCCCCCCh-HHccCCCCCEEE
Confidence            8899999999999998888 568999999999999876 777765 889999999999999998885 577788887764


Q ss_pred             e
Q 005860          650 E  650 (673)
Q Consensus       650 ~  650 (673)
                      .
T Consensus       204 L  204 (605)
T 1m9s_A          204 L  204 (605)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.19  E-value=3.3e-11  Score=122.17  Aligned_cols=128  Identities=21%  Similarity=0.197  Sum_probs=72.4

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....++ .+..+++|++|.+.++...    . + ..+..+++|+.|++++       +.+..+ +.++
T Consensus        89 l~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~L~~n~i~----~-~-~~l~~l~~L~~L~l~~-------n~l~~~-~~l~  153 (291)
T 1h6t_A           89 LKNLGWLFLDENKVKDLS-SLKDLKKLKSLSLEHNGIS----D-I-NGLVHLPQLESLYLGN-------NKITDI-TVLS  153 (291)
T ss_dssp             CTTCCEEECCSSCCCCGG-GGTTCTTCCEEECTTSCCC----C-C-GGGGGCTTCCEEECCS-------SCCCCC-GGGG
T ss_pred             CCCCCEEECCCCcCCCCh-hhccCCCCCEEECCCCcCC----C-C-hhhcCCCCCCEEEccC-------CcCCcc-hhhc
Confidence            345566666555544433 2555666666666655431    1 1 2345566666666666       555554 4556


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccc
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      .+++|++|+|++|.+..+|+ +..+++|++|++++|. +..+| .+..+++|+.|++++|.+...|
T Consensus       154 ~l~~L~~L~L~~N~l~~~~~-l~~l~~L~~L~L~~N~-i~~l~-~l~~l~~L~~L~l~~n~i~~~~  216 (291)
T 1h6t_A          154 RLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLDVLELFSQECLNKP  216 (291)
T ss_dssp             GCTTCSEEECCSSCCCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCSEEEEEEEEEECCC
T ss_pred             cCCCCCEEEccCCccccchh-hcCCCccCEEECCCCc-CCCCh-hhccCCCCCEEECcCCcccCCc
Confidence            66666666666666666655 6666666666666654 55555 3566666666666666555443

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.19  E-value=9.6e-12  Score=127.18  Aligned_cols=131  Identities=24%  Similarity=0.278  Sum_probs=68.7

Q ss_pred             CceEEEEEEcCCCCcccc--ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh--hcc
Q 005860          492 EKLRHSMLVLGYEASFPI--SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK--ILK  567 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~--~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~--lp~  567 (673)
                      .+++++.+..+.....+.  .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..  +|.
T Consensus       101 ~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~  169 (306)
T 2z66_A          101 EQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHT----RVAFNGIFNGLSSLEVLKMAG-------NSFQENFLPD  169 (306)
T ss_dssp             TTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCC----EECSTTTTTTCTTCCEEECTT-------CEEGGGEECS
T ss_pred             CCCCEEECCCCcccccccchhhhhccCCCEEECCCCcC----CccchhhcccCcCCCEEECCC-------Cccccccchh
Confidence            344555544443333322  344455555555555432    122333445555666666655       55443  455


Q ss_pred             ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccc
Q 005860          568 GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~  634 (673)
                      .+..+++|++|+|++|.+..+ |..+..+++|++|++++|. +..+|. .+..+++|++|++++|.+..
T Consensus       170 ~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~  237 (306)
T 2z66_A          170 IFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNN-FFSLDTFPYKCLNSLQVLDYSLNHIMT  237 (306)
T ss_dssp             CCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSC-CSBCCSGGGTTCTTCCEEECTTSCCCB
T ss_pred             HHhhCcCCCEEECCCCCcCCcCHHHhcCCCCCCEEECCCCc-cCccChhhccCcccCCEeECCCCCCcc
Confidence            566666666666666665555 4455566666666666554 444443 45556666666666665554

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=99.18  E-value=1.1e-11  Score=139.44  Aligned_cols=146  Identities=18%  Similarity=0.174  Sum_probs=121.7

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cc
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~  567 (673)
                      .+..++++.+..+.....++ .+.++++|++|++.++..    ....+..|.++++|++|++++       +.+..+ |.
T Consensus        30 ~~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l----~~i~~~~~~~l~~L~~L~Ls~-------n~l~~~~p~   98 (606)
T 3vq2_A           30 IPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEI----ETIEDKAWHGLHHLSNLILTG-------NPIQSFSPG   98 (606)
T ss_dssp             SCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------CCCCCCCTT
T ss_pred             CCCCcCEEECCCCCcCEeChhhccCCccCcEEeCCCCcc----cccCHHHhhchhhcCEeECCC-------CcccccChh
Confidence            34678999998888766654 677899999999998863    345566788999999999999       888776 77


Q ss_pred             ccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCc--cccccccccccCCeeeccccccccccc-cCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLK--RLPLGIGKLVNLRHLTYDDSCLEFIPK-GIQRLT  643 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~--~lP~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~  643 (673)
                      .++.+.+|++|+|++|.+..+| ..++++++|++|++++|. +.  .+|..++++++|++|++++|.+..+|. .++.++
T Consensus        99 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~  177 (606)
T 3vq2_A           99 SFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNF-IHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLR  177 (606)
T ss_dssp             SSTTCTTCCEEECTTSCCCCSSSSCCTTCTTCCEEECCSSC-CCCCCCCGGGGTCTTCCEEECCSSCCCEECTTTTHHHH
T ss_pred             hcCCcccCCEEEccCCccccccccccCCCCCCCEEeCCCCc-ccceechHhHhhcCCCCEEEccCCcceecChhhhhhhh
Confidence            8999999999999999988887 789999999999999987 65  589999999999999999998887754 466666


Q ss_pred             CCCc
Q 005860          644 NLRT  647 (673)
Q Consensus       644 ~L~~  647 (673)
                      +|+.
T Consensus       178 ~L~~  181 (606)
T 3vq2_A          178 ENPQ  181 (606)
T ss_dssp             HCTT
T ss_pred             cccc
Confidence            6653

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.18  E-value=2.4e-11  Score=116.60  Aligned_cols=128  Identities=23%  Similarity=0.328  Sum_probs=69.5

Q ss_pred             CceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-c
Q 005860          492 EKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-I  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i  569 (673)
                      .+++.+.+..+.....++. +..+++|++|.+.++..    ....+..|..+++|++|++++       +.+..+|.. +
T Consensus        28 ~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~~~   96 (208)
T 2o6s_A           28 AQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKL----QSLPNGVFNKLTSLTYLNLST-------NQLQSLPNGVF   96 (208)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCC----CCCCTTTTTTCTTCCEEECCS-------SCCCCCCTTTT
T ss_pred             CCCcEEEcCCCccCcCChhhhcccccCcEEECCCCcc----CccChhhcCCCCCcCEEECCC-------CcCCccCHhHh
Confidence            3555666655555444332 33456666666655542    222333445556666666666       555555443 4


Q ss_pred             ccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccccccCCeeeccccc
Q 005860          570 EKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSC  631 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~  631 (673)
                      ..+.+|++|+|++|.+..+|.. +.++++|++|++++|. +..+|.. +.++++|++|++++|.
T Consensus        97 ~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~  159 (208)
T 2o6s_A           97 DKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQYIWLHDNP  159 (208)
T ss_dssp             TTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSCC
T ss_pred             cCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCCCc-cceeCHHHhccCCCccEEEecCCC
Confidence            5566666666666665555543 4556666666666544 5555543 4556666666665554

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.17  E-value=1.5e-11  Score=133.23  Aligned_cols=168  Identities=20%  Similarity=0.235  Sum_probs=100.7

Q ss_pred             CceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhcc-c
Q 005860          492 EKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILK-G  568 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~-~  568 (673)
                      .+++.+.+..+....+++. +..+++|++|.+.++..    ....+..|.++++|+.|++++       +. +..++. .
T Consensus       123 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l----~~~~~~~~~~l~~L~~L~l~~-------~~~l~~i~~~~  191 (452)
T 3zyi_A          123 ASLNTLELFDNWLTVIPSGAFEYLSKLRELWLRNNPI----ESIPSYAFNRVPSLMRLDLGE-------LKKLEYISEGA  191 (452)
T ss_dssp             TTCCEEECCSSCCSBCCTTTSSSCTTCCEEECCSCCC----CEECTTTTTTCTTCCEEECCC-------CTTCCEECTTT
T ss_pred             ccCCEEECCCCcCCccChhhhcccCCCCEEECCCCCc----ceeCHhHHhcCCcccEEeCCC-------CCCccccChhh
Confidence            4556666655555444433 44466666666666542    223334456666666666665       33 444443 4


Q ss_pred             cccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccc-cccccccccCCeeeccccccccccc-cCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLEFIPK-GIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~~L~  646 (673)
                      +..+.+|++|+|++|.+..+|. +..+++|++|+|++|. +..+ |..+.++++|+.|++++|.+..++. .+..+++|+
T Consensus       192 ~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  269 (452)
T 3zyi_A          192 FEGLFNLKYLNLGMCNIKDMPN-LTPLVGLEELEMSGNH-FPEIRPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLV  269 (452)
T ss_dssp             TTTCTTCCEEECTTSCCSSCCC-CTTCTTCCEEECTTSC-CSEECGGGGTTCTTCCEEECTTSCCCEECTTTTTTCTTCC
T ss_pred             ccCCCCCCEEECCCCccccccc-ccccccccEEECcCCc-CcccCcccccCccCCCEEEeCCCcCceECHHHhcCCCCCC
Confidence            6677777888887777777764 7777788888888766 5554 5667888888888888887776643 466666666


Q ss_pred             cCCeeEE--ccCCccCCCccccCCCCCC
Q 005860          647 TLSEFVV--VRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       647 ~L~~~~~--~~~~~~~~~~~~~l~~L~~  672 (673)
                      .|..-..  .......+..+.+|+.|.+
T Consensus       270 ~L~L~~N~l~~~~~~~~~~l~~L~~L~L  297 (452)
T 3zyi_A          270 ELNLAHNNLSSLPHDLFTPLRYLVELHL  297 (452)
T ss_dssp             EEECCSSCCSCCCTTSSTTCTTCCEEEC
T ss_pred             EEECCCCcCCccChHHhccccCCCEEEc
Confidence            5533211  1112223445566666554

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.17  E-value=8.9e-12  Score=122.53  Aligned_cols=144  Identities=13%  Similarity=0.117  Sum_probs=78.4

Q ss_pred             CceEEEEEEcCC-CCcccc-ccccccccchhhhcc-chhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc
Q 005860          492 EKLRHSMLVLGY-EASFPI-SIFKAKNLRSLFINN-TLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       492 ~~~r~l~l~~~~-~~~~~~-~~~~~~~Lr~L~l~~-~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      .+++.+.+..+. ...+++ .+..+++|++|.+.+ +..    ....+..|.++++|+.|++++       +.+..+|. 
T Consensus        55 ~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l----~~i~~~~f~~l~~L~~L~l~~-------n~l~~lp~-  122 (239)
T 2xwt_C           55 PNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNL----TYIDPDALKELPLLKFLGIFN-------TGLKMFPD-  122 (239)
T ss_dssp             TTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTC----CEECTTSEECCTTCCEEEEEE-------ECCCSCCC-
T ss_pred             CCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCe----eEcCHHHhCCCCCCCEEeCCC-------CCCccccc-
Confidence            445555555553 333333 344555566665554 331    122333455566666666666       55555554 


Q ss_pred             cccccccc---cceecCC-CCcccch-hhhcCCCcc-EEEeccCCCCccccccccccccCCeeeccccc-ccccccc-CC
Q 005860          569 IEKLIHLR---YLRLVGL-GTEELPE-TCCELLNLQ-VLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSC-LEFIPKG-IQ  640 (673)
Q Consensus       569 i~~L~~Lr---~L~L~~~-~i~~LP~-~i~~L~~L~-~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~-l~~lP~~-i~  640 (673)
                      +..+.+|+   +|++++| .+..+|. .+..+++|+ +|+++++. +..+|......++|++|++++|. ++.+|.. ++
T Consensus       123 ~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~-l~~i~~~~~~~~~L~~L~L~~n~~l~~i~~~~~~  201 (239)
T 2xwt_C          123 LTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNG-FTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFG  201 (239)
T ss_dssp             CTTCCBCCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCC-CCEECTTTTTTCEEEEEECTTCTTCCEECTTTTT
T ss_pred             cccccccccccEEECCCCcchhhcCcccccchhcceeEEEcCCCC-CcccCHhhcCCCCCCEEEcCCCCCcccCCHHHhh
Confidence            55555555   6666666 5666654 356666666 66666654 55666554444666666666663 6666543 44


Q ss_pred             CC-CCCCcC
Q 005860          641 RL-TNLRTL  648 (673)
Q Consensus       641 ~L-~~L~~L  648 (673)
                      .+ ++|+.|
T Consensus       202 ~l~~~L~~L  210 (239)
T 2xwt_C          202 GVYSGPSLL  210 (239)
T ss_dssp             TCSBCCSEE
T ss_pred             ccccCCcEE
Confidence            44 444444

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.17  E-value=1.7e-11  Score=123.42  Aligned_cols=146  Identities=18%  Similarity=0.205  Sum_probs=98.1

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~  568 (673)
                      ..+++.+.+..+.....++ .+..+++|++|.+.++..    ....+..|.++++|+.|++++       +.+..++. .
T Consensus        51 l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~  119 (276)
T 2z62_A           51 FPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPI----QSLALGAFSGLSSLQKLVAVE-------TNLASLENFP  119 (276)
T ss_dssp             CTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------SCCCCSTTCC
T ss_pred             ccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCcc----CccChhhhcCCccccEEECCC-------CCccccCchh
Confidence            3567777777776655543 456678888888887753    233445667788888888887       77666654 5


Q ss_pred             cccccccccceecCCCCcc--cchhhhcCCCccEEEeccCCCCcccc-ccccccccCC----eeeccccccccccccCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEE--LPETCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLR----HLTYDDSCLEFIPKGIQR  641 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~--LP~~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr----~L~l~~~~l~~lP~~i~~  641 (673)
                      ++.+++|++|+|++|.+..  +|..++++++|++|++++|. +..+| ..+..+.+|+    .|++++|.+..+|..+..
T Consensus       120 ~~~l~~L~~L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~l~l~L~ls~n~l~~~~~~~~~  198 (276)
T 2z62_A          120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK-IQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFK  198 (276)
T ss_dssp             CTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSC-CCEECGGGGHHHHTCTTCCEEEECCSSCCCEECTTSSC
T ss_pred             cccCCCCCEEECcCCccceecCchhhccCCCCCEEECCCCC-CCcCCHHHhhhhhhccccceeeecCCCcccccCccccC
Confidence            7778888888888887765  67778888888888888765 66554 3566666555    566666666666655444


Q ss_pred             CCCCCcC
Q 005860          642 LTNLRTL  648 (673)
Q Consensus       642 L~~L~~L  648 (673)
                      ..+|+.|
T Consensus       199 ~~~L~~L  205 (276)
T 2z62_A          199 EIRLKEL  205 (276)
T ss_dssp             SCCEEEE
T ss_pred             CCcccEE
Confidence            4444433

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.16  E-value=7.5e-12  Score=119.11  Aligned_cols=144  Identities=16%  Similarity=0.137  Sum_probs=109.8

Q ss_pred             ccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcc-cch
Q 005860          512 FKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEE-LPE  590 (673)
Q Consensus       512 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~-LP~  590 (673)
                      ..+++|++|.+.++...     .++ .+..+++|+.|++++       +.+..++ .+..+++|++|++++|.+.. .|.
T Consensus        41 ~~l~~L~~L~l~~n~i~-----~l~-~l~~l~~L~~L~l~~-------n~~~~~~-~l~~l~~L~~L~l~~n~l~~~~~~  106 (197)
T 4ezg_A           41 AQMNSLTYITLANINVT-----DLT-GIEYAHNIKDLTINN-------IHATNYN-PISGLSNLERLRIMGKDVTSDKIP  106 (197)
T ss_dssp             HHHHTCCEEEEESSCCS-----CCT-TGGGCTTCSEEEEES-------CCCSCCG-GGTTCTTCCEEEEECTTCBGGGSC
T ss_pred             hhcCCccEEeccCCCcc-----ChH-HHhcCCCCCEEEccC-------CCCCcch-hhhcCCCCCEEEeECCccCcccCh
Confidence            46789999999987641     223 477899999999999       7665554 78899999999999999775 788


Q ss_pred             hhhcCCCccEEEeccCCCCc-cccccccccccCCeeeccccc-cccccccCCCCCCCCcCCeeEEccCCccCCCccccCC
Q 005860          591 TCCELLNLQVLEIEQCTSLK-RLPLGIGKLVNLRHLTYDDSC-LEFIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLE  668 (673)
Q Consensus       591 ~i~~L~~L~~L~l~~c~~l~-~lP~~i~~L~~Lr~L~l~~~~-l~~lP~~i~~L~~L~~L~~~~~~~~~~~~~~~~~~l~  668 (673)
                      .++.+++|++|++++|. +. ..|..++++++|++|++++|. +..+| .++.+++|+.|..-...-.+-..+..+.+|+
T Consensus       107 ~l~~l~~L~~L~Ls~n~-i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~i~~~~~l~~l~~L~  184 (197)
T 4ezg_A          107 NLSGLTSLTLLDISHSA-HDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDGVHDYRGIEDFPKLN  184 (197)
T ss_dssp             CCTTCTTCCEEECCSSB-CBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBCCCCCTTGGGCSSCC
T ss_pred             hhcCCCCCCEEEecCCc-cCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCCCcChHHhccCCCCC
Confidence            99999999999999987 55 478889999999999999997 88887 5777777777644322211111234455555


Q ss_pred             CCC
Q 005860          669 GLR  671 (673)
Q Consensus       669 ~L~  671 (673)
                      .|.
T Consensus       185 ~L~  187 (197)
T 4ezg_A          185 QLY  187 (197)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            554

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.16  E-value=5e-11  Score=118.91  Aligned_cols=140  Identities=19%  Similarity=0.173  Sum_probs=103.6

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....++ .+..+++|++|.+.++..    ....+  +..++.|+.|++++       +.+..+|....
T Consensus        40 l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~L~~N~i----~~~~~--l~~l~~L~~L~L~~-------N~l~~l~~~~~  105 (263)
T 1xeu_A           40 LSGVQNFNGDNSNIQSLA-GMQFFTNLKELHLSHNQI----SDLSP--LKDLTKLEELSVNR-------NRLKNLNGIPS  105 (263)
T ss_dssp             HTTCSEEECTTSCCCCCT-TGGGCTTCCEEECCSSCC----CCCGG--GTTCSSCCEEECCS-------SCCSCCTTCCC
T ss_pred             cCcCcEEECcCCCcccch-HHhhCCCCCEEECCCCcc----CCChh--hccCCCCCEEECCC-------CccCCcCcccc
Confidence            346777777776665555 566788888888888763    22222  67888888888888       77777765444


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCe
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~  650 (673)
                        .+|++|+|++|.+..+| .++.+++|++|++++|. +..+| .++.+++|++|++++|.+..+ ..+..+++|+.|..
T Consensus       106 --~~L~~L~L~~N~l~~~~-~l~~l~~L~~L~Ls~N~-i~~~~-~l~~l~~L~~L~L~~N~i~~~-~~l~~l~~L~~L~l  179 (263)
T 1xeu_A          106 --ACLSRLFLDNNELRDTD-SLIHLKNLEILSIRNNK-LKSIV-MLGFLSKLEVLDLHGNEITNT-GGLTRLKKVNWIDL  179 (263)
T ss_dssp             --SSCCEEECCSSCCSBSG-GGTTCTTCCEEECTTSC-CCBCG-GGGGCTTCCEEECTTSCCCBC-TTSTTCCCCCEEEE
T ss_pred             --CcccEEEccCCccCCCh-hhcCcccccEEECCCCc-CCCCh-HHccCCCCCEEECCCCcCcch-HHhccCCCCCEEeC
Confidence              78888888888888876 48888888888888866 77777 688888888888888888777 45777777776643

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.16  E-value=3.1e-11  Score=117.78  Aligned_cols=133  Identities=22%  Similarity=0.284  Sum_probs=114.1

Q ss_pred             ccCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc
Q 005860          490 YQEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      .+.+++.+.+..+..... +..+..+++|+.|.+.++.+    ....+..|..+++|++|+|++       +.+..+|+.
T Consensus        38 ~~~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N~l----~~i~~~~~~~l~~L~~L~Ls~-------N~l~~l~~~  106 (229)
T 3e6j_A           38 IPTNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQL----GALPVGVFDSLTQLTVLDLGT-------NQLTVLPSA  106 (229)
T ss_dssp             CCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCC----CCCCTTTTTTCTTCCEEECCS-------SCCCCCCTT
T ss_pred             CCCCCCEEEcCCCccCccCHHHhhCccCCcEEECCCCCC----CCcChhhcccCCCcCEEECCC-------CcCCccChh
Confidence            357899999998887666 44567899999999999873    344456678999999999999       998888765


Q ss_pred             -cccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccc
Q 005860          569 -IEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       569 -i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~  634 (673)
                       +..+.+|++|+|++|.+..+|..+..+++|++|+|+++. +..+|. .+..+++|++|++++|.+..
T Consensus       107 ~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~~~c  173 (229)
T 3e6j_A          107 VFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQNQ-LKSIPHGAFDRLSSLTHAYLFGNPWDC  173 (229)
T ss_dssp             TTTTCTTCCEEECCSSCCCSCCTTGGGCTTCSEEECCSSC-CCCCCTTTTTTCTTCCEEECTTSCBCT
T ss_pred             HhCcchhhCeEeccCCcccccCcccccCCCCCEEECCCCc-CCccCHHHHhCCCCCCEEEeeCCCccC
Confidence             688999999999999999999999999999999999976 888885 58899999999999887653

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.14  E-value=3.2e-11  Score=125.63  Aligned_cols=141  Identities=18%  Similarity=0.222  Sum_probs=95.1

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+.....++ +..+++|++|.+.++...    . ++ .+..+++|+.|++++       +.+..++. +.
T Consensus        65 ~~~L~~L~l~~n~i~~~~~-~~~l~~L~~L~L~~n~i~----~-~~-~~~~l~~L~~L~l~~-------n~i~~~~~-~~  129 (347)
T 4fmz_A           65 LTNLEYLNLNGNQITDISP-LSNLVKLTNLYIGTNKIT----D-IS-ALQNLTNLRELYLNE-------DNISDISP-LA  129 (347)
T ss_dssp             CTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC----C-CG-GGTTCTTCSEEECTT-------SCCCCCGG-GT
T ss_pred             cCCccEEEccCCccccchh-hhcCCcCCEEEccCCccc----C-ch-HHcCCCcCCEEECcC-------CcccCchh-hc
Confidence            4567777777766655554 667777777777776531    1 12 366777778888777       77666665 77


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      .+++|++|++++|.....++.+..+++|++|++++|. +..+|. ++.+++|++|++++|.+..+|. +..+++|+.|.
T Consensus       130 ~l~~L~~L~l~~n~~~~~~~~~~~l~~L~~L~l~~~~-~~~~~~-~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~  205 (347)
T 4fmz_A          130 NLTKMYSLNLGANHNLSDLSPLSNMTGLNYLTVTESK-VKDVTP-IANLTDLYSLSLNYNQIEDISP-LASLTSLHYFT  205 (347)
T ss_dssp             TCTTCCEEECTTCTTCCCCGGGTTCTTCCEEECCSSC-CCCCGG-GGGCTTCSEEECTTSCCCCCGG-GGGCTTCCEEE
T ss_pred             cCCceeEEECCCCCCcccccchhhCCCCcEEEecCCC-cCCchh-hccCCCCCEEEccCCccccccc-ccCCCccceee
Confidence            7777888888777633333447777888888888766 666664 7778888888888877777765 55555555443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.14  E-value=1.6e-09  Score=114.45  Aligned_cols=168  Identities=15%  Similarity=0.098  Sum_probs=108.1

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc---c-CCeEEEEEcCCcccHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE---Y-FDKRMWVCVSDPFDELR  243 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~-F~~~~wv~vs~~~~~~~  243 (673)
                      ++.++||+.+++++..++...-.   ....+.+.|+|++|+||||||+.+++...-..   . -...+|+.+....+...
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~---~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   94 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALR---GEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYR   94 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTS---SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHc---CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHH
Confidence            47899999999999998854310   12356789999999999999999998521110   0 12467888888888889


Q ss_pred             HHHHHHHHhhCCCCC-cCcHHHHHHHHHHHh--CCCeEEEEEcCCCCCCcc--chhhhhhhccCC-----CCCeEEEEEc
Q 005860          244 IAKAIIEALEGFVPT-VGELNSLLESIRASL--VGKKFLLILDDMWTDDYS--KWEPFHYCLKNG-----VRGSKILVTT  313 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~-~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~~~~~--~~~~l~~~l~~~-----~~gs~iivTt  313 (673)
                      ++..++.+++...+. .....++...+.+.+  .+++.+||||++..-...  ..+.+...+...     ..+..+|.||
T Consensus        95 ~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t  174 (387)
T 2v1u_A           95 VASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGIT  174 (387)
T ss_dssp             HHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEEC
T ss_pred             HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEE
Confidence            999999999765332 223555566666666  456899999999542211  122233222211     3456778888


Q ss_pred             CChhH--------HHhccccceeecCCCCccccc
Q 005860          314 RKETV--------ARMMESIHVISIKELSEQECW  339 (673)
Q Consensus       314 r~~~v--------~~~~~~~~~~~l~~L~~~~~~  339 (673)
                      +....        ...++ ...+.+++++.++..
T Consensus       175 ~~~~~~~~l~~~l~~r~~-~~~i~l~~l~~~~~~  207 (387)
T 2v1u_A          175 NSLGFVENLEPRVKSSLG-EVELVFPPYTAPQLR  207 (387)
T ss_dssp             SCSTTSSSSCHHHHTTTT-SEECCBCCCCHHHHH
T ss_pred             CCCchHhhhCHHHHhcCC-CeEEeeCCCCHHHHH
Confidence            76522        11111 146888898877754

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.14  E-value=8.3e-11  Score=121.72  Aligned_cols=134  Identities=21%  Similarity=0.226  Sum_probs=102.3

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...++.+.+..+.....++ .+..+++|++|.+.++..    ....+..|.++++|+.|++++       +.+..+|..+
T Consensus        53 ~~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~l~~~~  121 (332)
T 2ft3_A           53 SPDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKI----SKIHEKAFSPLRKLQKLYISK-------NHLVEIPPNL  121 (332)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCC----CEECGGGSTTCTTCCEEECCS-------SCCCSCCSSC
T ss_pred             CCCCeEEECCCCcCCccCHhHhhCCCCCcEEECCCCcc----CccCHhHhhCcCCCCEEECCC-------CcCCccCccc
Confidence            4578889888887766644 577899999999998763    344566788999999999999       8888888877


Q ss_pred             ccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCc---cccccccccccCCeeeccccccccccccC
Q 005860          570 EKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLK---RLPLGIGKLVNLRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~---~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i  639 (673)
                      .  .+|++|++++|.+..+|. .+..+++|++|++++|. +.   ..|..+..+ +|++|++++|.+..+|..+
T Consensus       122 ~--~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~~~l-~L~~L~l~~n~l~~l~~~~  191 (332)
T 2ft3_A          122 P--SSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNP-LENSGFEPGAFDGL-KLNYLRISEAKLTGIPKDL  191 (332)
T ss_dssp             C--TTCCEEECCSSCCCCCCSGGGSSCSSCCEEECCSCC-CBGGGSCTTSSCSC-CCSCCBCCSSBCSSCCSSS
T ss_pred             c--ccCCEEECCCCccCccCHhHhCCCccCCEEECCCCc-cccCCCCcccccCC-ccCEEECcCCCCCccCccc
Confidence            6  789999999999888875 47889999999999876 54   345566666 6666666666655555443

>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=99.14  E-value=3.1e-11  Score=133.67  Aligned_cols=86  Identities=21%  Similarity=0.264  Sum_probs=41.1

Q ss_pred             cchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccc--cc
Q 005860          560 NSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFI--PK  637 (673)
Q Consensus       560 ~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~l--P~  637 (673)
                      +.+..+|. ++.+++|++|+|++|.+..+|..+++|++|++|+|++|. +..+| .+++|++|++|++++|.++.+  |.
T Consensus       451 n~l~~lp~-~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~-l~~lp-~l~~l~~L~~L~Ls~N~l~~~~~p~  527 (567)
T 1dce_A          451 KDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNA-LENVD-GVANLPRLQELLLCNNRLQQSAAIQ  527 (567)
T ss_dssp             SCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSC-CCCCG-GGTTCSSCCEEECCSSCCCSSSTTG
T ss_pred             CCCCCCcC-ccccccCcEeecCcccccccchhhhcCCCCCEEECCCCC-CCCCc-ccCCCCCCcEEECCCCCCCCCCCcH
Confidence            44444443 444455555555554444455445555555555554433 44444 444455555555444444444  44


Q ss_pred             cCCCCCCCCcC
Q 005860          638 GIQRLTNLRTL  648 (673)
Q Consensus       638 ~i~~L~~L~~L  648 (673)
                      .++.|++|++|
T Consensus       528 ~l~~l~~L~~L  538 (567)
T 1dce_A          528 PLVSCPRLVLL  538 (567)
T ss_dssp             GGGGCTTCCEE
T ss_pred             HHhcCCCCCEE
Confidence            44444444433

>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=99.13  E-value=1.2e-11  Score=136.95  Aligned_cols=147  Identities=20%  Similarity=0.238  Sum_probs=89.5

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhh---------hhhhhHHHHhhhCCccceee-eccccccccccch
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQV---------SLTHVLQSLFDQLKCLRALR-IATLMNTWDVNST  562 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~---------~~~~~~~~~~~~l~~L~~L~-L~~~~~~~~~~~~  562 (673)
                      .++++.+..+....+|..+..+++|+.|.+.++....         ......|..+..+++|+.|+ ++.       +.+
T Consensus       350 ~L~~L~Ls~n~L~~Lp~~i~~l~~L~~L~l~~n~~l~~l~~ll~~~~~~~~~~~~l~~l~~L~~L~~l~~-------n~~  422 (567)
T 1dce_A          350 QLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRA-------AYL  422 (567)
T ss_dssp             TSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGH-------HHH
T ss_pred             cceeccCChhhHHhhHHHHHHHHHHHHhccccchhhhhHHHHHHhcccccCCHHHHHHHHhcccCcchhh-------ccc
Confidence            4445555555555667777778888887775543100         01233455566666666666 333       222


Q ss_pred             hhhcc------ccccc--cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccc
Q 005860          563 NKILK------GIEKL--IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       563 ~~lp~------~i~~L--~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~  634 (673)
                      ..++.      .+..+  ..|++|+|++|.+..+|. ++.|++|++|+|++|. +..+|..+++|++|++|++++|.++.
T Consensus       423 ~~L~~l~l~~n~i~~l~~~~L~~L~Ls~n~l~~lp~-~~~l~~L~~L~Ls~N~-l~~lp~~~~~l~~L~~L~Ls~N~l~~  500 (567)
T 1dce_A          423 DDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNR-LRALPPALAALRCLEVLQASDNALEN  500 (567)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSEEECTTSCCSSCCC-GGGGTTCCEEECCSSC-CCCCCGGGGGCTTCCEEECCSSCCCC
T ss_pred             chhhhhhhhcccccccCccCceEEEecCCCCCCCcC-ccccccCcEeecCccc-ccccchhhhcCCCCCEEECCCCCCCC
Confidence            22211      11111  246777777777777776 7777777777777765 66777777777777777777777777


Q ss_pred             ccccCCCCCCCCcCC
Q 005860          635 IPKGIQRLTNLRTLS  649 (673)
Q Consensus       635 lP~~i~~L~~L~~L~  649 (673)
                      +| ++++|++|++|.
T Consensus       501 lp-~l~~l~~L~~L~  514 (567)
T 1dce_A          501 VD-GVANLPRLQELL  514 (567)
T ss_dssp             CG-GGTTCSSCCEEE
T ss_pred             Cc-ccCCCCCCcEEE
Confidence            76 666666666653

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.13  E-value=2e-11  Score=139.49  Aligned_cols=111  Identities=23%  Similarity=0.269  Sum_probs=65.7

Q ss_pred             ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccc
Q 005860          510 SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELP  589 (673)
Q Consensus       510 ~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP  589 (673)
                      .+..+++|+.|.+.++.+    . .++..+..+++|+.|+|++       |.+..+|..++.|.+|++|+|++|.+..+|
T Consensus       219 ~~~~l~~L~~L~Ls~n~l----~-~l~~~~~~l~~L~~L~Ls~-------N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp  286 (727)
T 4b8c_D          219 SKYDDQLWHALDLSNLQI----F-NISANIFKYDFLTRLYLNG-------NSLTELPAEIKNLSNLRVLDLSHNRLTSLP  286 (727)
T ss_dssp             ---CCCCCCEEECTTSCC----S-CCCGGGGGCCSCSCCBCTT-------SCCSCCCGGGGGGTTCCEEECTTSCCSSCC
T ss_pred             hhccCCCCcEEECCCCCC----C-CCChhhcCCCCCCEEEeeC-------CcCcccChhhhCCCCCCEEeCcCCcCCccC
Confidence            344556666666666542    1 1222233566666666666       666566666666666666666666666666


Q ss_pred             hhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc
Q 005860          590 ETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       590 ~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      .+|++|++|++|+|++|. +..+|.+|++|++|++|++++|.+.
T Consensus       287 ~~~~~l~~L~~L~L~~N~-l~~lp~~~~~l~~L~~L~L~~N~l~  329 (727)
T 4b8c_D          287 AELGSCFQLKYFYFFDNM-VTTLPWEFGNLCNLQFLGVEGNPLE  329 (727)
T ss_dssp             SSGGGGTTCSEEECCSSC-CCCCCSSTTSCTTCCCEECTTSCCC
T ss_pred             hhhcCCCCCCEEECCCCC-CCccChhhhcCCCccEEeCCCCccC
Confidence            666666666666666654 6666666666666666666666555

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.12  E-value=4.1e-11  Score=116.11  Aligned_cols=131  Identities=15%  Similarity=0.144  Sum_probs=110.4

Q ss_pred             cCceEEEEEEcCCCCcccc--ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-
Q 005860          491 QEKLRHSMLVLGYEASFPI--SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-  567 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~--~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-  567 (673)
                      +..++.+.+..+.....++  .+..+++|++|.+.++..    ....+..|.++++|+.|+|++       +.+..+|+ 
T Consensus        31 ~~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N~i----~~i~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~   99 (220)
T 2v70_A           31 PQYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKI----TDIEEGAFEGASGVNEILLTS-------NRLENVQHK   99 (220)
T ss_dssp             CTTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSSCC----CEECTTTTTTCTTCCEEECCS-------SCCCCCCGG
T ss_pred             CCCCCEEEcCCCcCCccCchhhhccCCCCCEEECCCCcC----CEECHHHhCCCCCCCEEECCC-------CccCccCHh
Confidence            4567888888888766633  367899999999999873    344556788999999999999       99888766 


Q ss_pred             ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccc-cccccccccCCeeeccccccc
Q 005860          568 GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      .+..+.+|++|+|++|.+..+ |..+..+++|++|+|++|. +..+ |..+..+++|++|++++|.+.
T Consensus       100 ~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~  166 (220)
T 2v70_A          100 MFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQ-ITTVAPGAFDTLHSLSTLNLLANPFN  166 (220)
T ss_dssp             GGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSC-CCCBCTTTTTTCTTCCEEECCSCCEE
T ss_pred             HhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCc-CCEECHHHhcCCCCCCEEEecCcCCc
Confidence            488999999999999998888 6789999999999999976 7777 778999999999999988764

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.12  E-value=5.8e-11  Score=122.79  Aligned_cols=133  Identities=18%  Similarity=0.166  Sum_probs=90.6

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      +..++.+.+..+.....++ .+..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|..+
T Consensus        51 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~l~~~~  119 (330)
T 1xku_A           51 PPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKI----SKISPGAFAPLVKLERLYLSK-------NQLKELPEKM  119 (330)
T ss_dssp             CTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCC----CCBCTTTTTTCTTCCEEECCS-------SCCSBCCSSC
T ss_pred             CCCCeEEECCCCcCCEeChhhhccCCCCCEEECCCCcC----CeeCHHHhcCCCCCCEEECCC-------CcCCccChhh
Confidence            4577888888877766654 567788999999888763    334466778888899999988       7777777666


Q ss_pred             ccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCc---cccccccccccCCeeeccccccccccc
Q 005860          570 EKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLK---RLPLGIGKLVNLRHLTYDDSCLEFIPK  637 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~---~lP~~i~~L~~Lr~L~l~~~~l~~lP~  637 (673)
                      .  .+|++|++++|.+..+|. .+.++++|++|++++|. +.   ..|..+.++++|++|++++|.+..+|.
T Consensus       120 ~--~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~~~l~~L~~L~l~~n~l~~l~~  188 (330)
T 1xku_A          120 P--KTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNP-LKSSGIENGAFQGMKKLSYIRIADTNITTIPQ  188 (330)
T ss_dssp             C--TTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSC-CCGGGBCTTGGGGCTTCCEEECCSSCCCSCCS
T ss_pred             c--ccccEEECCCCcccccCHhHhcCCccccEEECCCCc-CCccCcChhhccCCCCcCEEECCCCccccCCc
Confidence            5  567777777777666653 46666777777776654 32   344556666666666665555555543

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.12  E-value=9.5e-10  Score=116.15  Aligned_cols=169  Identities=14%  Similarity=0.121  Sum_probs=110.0

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc----cc--CCeEEEEEcCCcc-c
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF----EY--FDKRMWVCVSDPF-D  240 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~--F~~~~wv~vs~~~-~  240 (673)
                      ++.++||+.+++++..++.....   ....+.+.|+|++|+||||||+.+++...-.    ..  ....+|++++... +
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~---~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   95 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVK---NEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGT   95 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHT---TCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSC
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc---CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCC
Confidence            36899999999999988754210   1234689999999999999999999852111    01  3356788877666 7


Q ss_pred             HHHHHHHHHHHhhCCCCC--cCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhh-hhhccCCCCCeEEEEEcCChh
Q 005860          241 ELRIAKAIIEALEGFVPT--VGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPF-HYCLKNGVRGSKILVTTRKET  317 (673)
Q Consensus       241 ~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l-~~~l~~~~~gs~iivTtr~~~  317 (673)
                      ...++..++.++......  ..........+.+.+..++.+|||||++.-....+..+ ...+.....+..||+||+...
T Consensus        96 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~  175 (384)
T 2qby_B           96 PQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDIN  175 (384)
T ss_dssp             HHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTT
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCc
Confidence            888999999988543221  22345667777888887777999999954222111222 222322226788999998653


Q ss_pred             HHH----hc--cccceeecCCCCccccc
Q 005860          318 VAR----MM--ESIHVISIKELSEQECW  339 (673)
Q Consensus       318 v~~----~~--~~~~~~~l~~L~~~~~~  339 (673)
                      ...    ..  .....+++++++.++..
T Consensus       176 ~~~~l~~~l~sr~~~~i~l~~l~~~~~~  203 (384)
T 2qby_B          176 VRDYMEPRVLSSLGPSVIFKPYDAEQLK  203 (384)
T ss_dssp             TTTTSCHHHHHTCCCEEEECCCCHHHHH
T ss_pred             hHhhhCHHHHhcCCCeEEECCCCHHHHH
Confidence            211    11  11237889999887754

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.12  E-value=4.6e-11  Score=138.14  Aligned_cols=81  Identities=19%  Similarity=0.248  Sum_probs=59.3

Q ss_pred             ccccccccccceecCCCCc-ccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc-cccccCCCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTE-ELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE-FIPKGIQRLTNL  645 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~-~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~-~lP~~i~~L~~L  645 (673)
                      .++.+..|++|+|++|.+. .+|..+++|++|++|+|++|.--..+|..+++|++|+.|++++|.++ .+|..+++|++|
T Consensus       627 ~~~~l~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~Ls~N~l~g~ip~~l~~L~~L~~LdLs~N~l~g~ip~~l~~l~~L  706 (768)
T 3rgz_A          627 TFDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTML  706 (768)
T ss_dssp             SCSSSBCCCEEECCSSCCBSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEECCCGGGGGCCCC
T ss_pred             hhhccccccEEECcCCcccccCCHHHhccccCCEEeCcCCccCCCCChHHhCCCCCCEEECCCCcccCcCChHHhCCCCC
Confidence            3445567777778777744 67778888888888888877633477888888888888888887777 567777777766


Q ss_pred             CcC
Q 005860          646 RTL  648 (673)
Q Consensus       646 ~~L  648 (673)
                      ++|
T Consensus       707 ~~L  709 (768)
T 3rgz_A          707 TEI  709 (768)
T ss_dssp             SEE
T ss_pred             CEE
Confidence            665

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.12  E-value=2.4e-11  Score=124.51  Aligned_cols=115  Identities=17%  Similarity=0.198  Sum_probs=56.0

Q ss_pred             cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh---hcc--ccccccccccceecCCCCcc
Q 005860          513 KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK---ILK--GIEKLIHLRYLRLVGLGTEE  587 (673)
Q Consensus       513 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~---lp~--~i~~L~~Lr~L~L~~~~i~~  587 (673)
                      .+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..   ++.  .++.+++|++|+|++|.++.
T Consensus       143 ~~~~L~~L~Ls~n~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~  211 (310)
T 4glp_A          143 LKPGLKVLSIAQAHS----PAFSCEQVRAFPALTSLDLSD-------NPGLGERGLMAALCPHKFPAIQNLALRNTGMET  211 (310)
T ss_dssp             BCSCCCEEEEECCSS----CCCCTTSCCCCTTCCEEECCS-------CTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCC
T ss_pred             hccCCCEEEeeCCCc----chhhHHHhccCCCCCEEECCC-------CCCccchhhhHHHhhhcCCCCCEEECCCCCCCc
Confidence            345555555555442    222333444555555555555       44221   222  12455555555555555554


Q ss_pred             cchh----hhcCCCccEEEeccCCCCccc-ccccccc---ccCCeeeccccccccccccC
Q 005860          588 LPET----CCELLNLQVLEIEQCTSLKRL-PLGIGKL---VNLRHLTYDDSCLEFIPKGI  639 (673)
Q Consensus       588 LP~~----i~~L~~L~~L~l~~c~~l~~l-P~~i~~L---~~Lr~L~l~~~~l~~lP~~i  639 (673)
                      +|..    ++.+++|++|++++|. +..+ |..++.+   ++|++|++++|.++.+|..+
T Consensus       212 l~~~~~~l~~~l~~L~~L~Ls~N~-l~~~~p~~~~~~~~~~~L~~L~Ls~N~l~~lp~~~  270 (310)
T 4glp_A          212 PTGVCAALAAAGVQPHSLDLSHNS-LRATVNPSAPRCMWSSALNSLNLSFAGLEQVPKGL  270 (310)
T ss_dssp             HHHHHHHHHHHTCCCSSEECTTSC-CCCCCCSCCSSCCCCTTCCCEECCSSCCCSCCSCC
T ss_pred             hHHHHHHHHhcCCCCCEEECCCCC-CCccchhhHHhccCcCcCCEEECCCCCCCchhhhh
Confidence            4432    3445555555555544 4433 5444444   35555555555555555544

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.11  E-value=5.4e-11  Score=115.28  Aligned_cols=131  Identities=20%  Similarity=0.248  Sum_probs=112.1

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      +..++.+.+..+....+++ .+..+++|+.|.+.++..    ....+..|.++++|++|+|++       +.+..+|+. 
T Consensus        31 ~~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N~i----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~l~~~~   99 (220)
T 2v9t_B           31 PETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQI----SELAPDAFQGLRSLNSLVLYG-------NKITELPKSL   99 (220)
T ss_dssp             CTTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSSCC----CEECTTTTTTCSSCCEEECCS-------SCCCCCCTTT
T ss_pred             CcCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCCcC----CCcCHHHhhCCcCCCEEECCC-------CcCCccCHhH
Confidence            4678999999888776665 567799999999999873    345567789999999999999       999998876 


Q ss_pred             cccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccc
Q 005860          569 IEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~  633 (673)
                      +..+.+|++|+|++|.+..+ |..+..+++|++|+|++|. +..+|. .+..+++|++|++++|.+.
T Consensus       100 f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~~  165 (220)
T 2v9t_B          100 FEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNK-LQTIAKGTFSPLRAIQTMHLAQNPFI  165 (220)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             ccCCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCCCc-CCEECHHHHhCCCCCCEEEeCCCCcC
Confidence            58899999999999998888 4679999999999999976 888876 4889999999999888754

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.11  E-value=3.3e-11  Score=118.47  Aligned_cols=149  Identities=15%  Similarity=0.231  Sum_probs=102.4

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-c
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-K  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~  567 (673)
                      .+..++.+.+..+....+++ .+..+++|++|.+.++..   +....+..|.++++|+.|++++.      +.+..+| .
T Consensus        29 ~~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~---l~~i~~~~f~~l~~L~~L~l~~~------n~l~~i~~~   99 (239)
T 2xwt_C           29 LPPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVT---LQQLESHSFYNLSKVTHIEIRNT------RNLTYIDPD   99 (239)
T ss_dssp             CCTTCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSS---CCEECTTTEESCTTCCEEEEEEE------TTCCEECTT
T ss_pred             CCCcccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCC---cceeCHhHcCCCcCCcEEECCCC------CCeeEcCHH
Confidence            34567788887777766655 455678888888877641   11233445677788888888741      3455655 3


Q ss_pred             ccccccccccceecCCCCcccchhhhcCCCcc---EEEeccCCCCcccccc-ccccccCC-eeeccccccccccccCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELPETCCELLNLQ---VLEIEQCTSLKRLPLG-IGKLVNLR-HLTYDDSCLEFIPKGIQRL  642 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~---~L~l~~c~~l~~lP~~-i~~L~~Lr-~L~l~~~~l~~lP~~i~~L  642 (673)
                      .+..+++|++|++++|.+..+|. ++.+++|+   +|++++|+.+..+|.. +..+++|+ +|++++|.+..+|......
T Consensus       100 ~f~~l~~L~~L~l~~n~l~~lp~-~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l~~i~~~~~~~  178 (239)
T 2xwt_C          100 ALKELPLLKFLGIFNTGLKMFPD-LTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFTSVQGYAFNG  178 (239)
T ss_dssp             SEECCTTCCEEEEEEECCCSCCC-CTTCCBCCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCCCEECTTTTTT
T ss_pred             HhCCCCCCCEEeCCCCCCccccc-cccccccccccEEECCCCcchhhcCcccccchhcceeEEEcCCCCCcccCHhhcCC
Confidence            56778888888888888777876 77777777   8888887347777754 77788888 8888888887777665444


Q ss_pred             CCCCcC
Q 005860          643 TNLRTL  648 (673)
Q Consensus       643 ~~L~~L  648 (673)
                      ++|+.|
T Consensus       179 ~~L~~L  184 (239)
T 2xwt_C          179 TKLDAV  184 (239)
T ss_dssp             CEEEEE
T ss_pred             CCCCEE
Confidence            555544

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.10  E-value=3.2e-11  Score=135.33  Aligned_cols=80  Identities=18%  Similarity=0.123  Sum_probs=49.1

Q ss_pred             ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      .++.+++|++|+|++|.+..+ |..++.+++|++|+|++|. +..+|..++.+++|++|++++|.+..+|..++.+++|+
T Consensus       249 ~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~l~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~l~~L~  327 (597)
T 3oja_B          249 WLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNR-LVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQFDRLE  327 (597)
T ss_dssp             GGGGCTTCSEEECCSSCCCEEESGGGTTCSSCCEEECTTSC-CCEEECSSSCCTTCCEEECCSSCCCCCGGGHHHHTTCS
T ss_pred             hhccCCCCCEEECCCCccCCCCHHHhcCccCCCEEECCCCC-CCCCCcccccCCCCcEEECCCCCCCccCcccccCCCCC
Confidence            355556666666666665444 4566666666666666654 66666666666666666666666666666555555555


Q ss_pred             cC
Q 005860          647 TL  648 (673)
Q Consensus       647 ~L  648 (673)
                      .|
T Consensus       328 ~L  329 (597)
T 3oja_B          328 NL  329 (597)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.10  E-value=2.6e-11  Score=132.17  Aligned_cols=146  Identities=23%  Similarity=0.234  Sum_probs=96.1

Q ss_pred             cCceEEEEEEcCCCCccc-cccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASFP-ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~-~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      +..++.+.+..+.....+ ..+..+++|++|.+.++..    ....+..|.++++|+.|+|++       +.+..+|.. 
T Consensus        31 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~i----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~   99 (477)
T 2id5_A           31 PTETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIV----SAVEPGAFNNLFNLRTLGLRS-------NRLKLIPLGV   99 (477)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEECTTSCC----CEECTTTTTTCTTCCEEECCS-------SCCCSCCTTS
T ss_pred             CCCCcEEECCCCccceECHhHccCCCCCCEEECCCCcc----CEeChhhhhCCccCCEEECCC-------CcCCccCccc
Confidence            456777777777665553 3566778888888877652    233455677777788888877       777666654 


Q ss_pred             cccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccc-cccccccccCCeeecccccccccccc-CCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L  645 (673)
                      +..+.+|++|+|++|.+..+ |..+.++++|++|++++|. +..+ |..++++++|++|++++|.+..+|.. ++++++|
T Consensus       100 ~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L  178 (477)
T 2id5_A          100 FTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDND-LVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGL  178 (477)
T ss_dssp             STTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECCTT-CCEECTTSSTTCTTCCEEEEESCCCSSCCHHHHTTCTTC
T ss_pred             ccCCCCCCEEECCCCccccCChhHccccccCCEEECCCCc-cceeChhhccCCCCCCEEECCCCcCcccChhHhcccCCC
Confidence            56777777777777776555 4566777777777777755 4444 34566777777777776666666543 4555555


Q ss_pred             CcC
Q 005860          646 RTL  648 (673)
Q Consensus       646 ~~L  648 (673)
                      +.|
T Consensus       179 ~~L  181 (477)
T 2id5_A          179 IVL  181 (477)
T ss_dssp             CEE
T ss_pred             cEE
Confidence            544

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=99.10  E-value=5.1e-11  Score=134.07  Aligned_cols=138  Identities=21%  Similarity=0.248  Sum_probs=115.2

Q ss_pred             EEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cccccccccccc
Q 005860          499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRY  577 (673)
Q Consensus       499 l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~  577 (673)
                      ........+|..+.  ++|++|++.++..    ....+..|.++++|++|++++       +.+..+ |..++.+++|++
T Consensus        18 c~~~~l~~ip~~~~--~~l~~L~Ls~n~l----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~i~~~~~~~l~~L~~   84 (606)
T 3vq2_A           18 CMDQKLSKVPDDIP--SSTKNIDLSFNPL----KILKSYSFSNFSELQWLDLSR-------CEIETIEDKAWHGLHHLSN   84 (606)
T ss_dssp             CTTSCCSSCCTTSC--TTCCEEECTTSCC----CEECTTTTTTCTTCCEEECTT-------CCCCEECTTTTTTCTTCCE
T ss_pred             ccCCCcccCCCCCC--CCcCEEECCCCCc----CEeChhhccCCccCcEEeCCC-------CcccccCHHHhhchhhcCE
Confidence            33334455665443  7899999999873    345556789999999999999       888877 557899999999


Q ss_pred             ceecCCCCccc-chhhhcCCCccEEEeccCCCCcccc-ccccccccCCeeeccccccc--cccccCCCCCCCCcCCe
Q 005860          578 LRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLE--FIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       578 L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~--~lP~~i~~L~~L~~L~~  650 (673)
                      |+|++|.+..+ |..+++|++|++|++++|. +..+| ..++++++|++|++++|.+.  .+|..++++++|+.|..
T Consensus        85 L~Ls~n~l~~~~p~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~L  160 (606)
T 3vq2_A           85 LILTGNPIQSFSPGSFSGLTSLENLVAVETK-LASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDL  160 (606)
T ss_dssp             EECTTCCCCCCCTTSSTTCTTCCEEECTTSC-CCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEEC
T ss_pred             eECCCCcccccChhhcCCcccCCEEEccCCc-cccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEc
Confidence            99999998888 7899999999999999987 77777 67999999999999999987  47888999999998743

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.10  E-value=2.6e-11  Score=109.62  Aligned_cols=124  Identities=20%  Similarity=0.161  Sum_probs=106.1

Q ss_pred             cCceEEEEEEcCCCC--ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hcc
Q 005860          491 QEKLRHSMLVLGYEA--SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILK  567 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~--~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~  567 (673)
                      ..+++++.+..+...  .++..+..+++|+.|.+.++...    ..  ..+..+++|++|++++       +.+.. +|.
T Consensus        16 ~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~----~~--~~~~~l~~L~~L~Ls~-------n~i~~~~~~   82 (149)
T 2je0_A           16 PSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLT----SI--ANLPKLNKLKKLELSD-------NRVSGGLEV   82 (149)
T ss_dssp             GGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCC----CC--TTCCCCTTCCEEECCS-------SCCCSCTHH
T ss_pred             CccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCC----Cc--hhhhcCCCCCEEECCC-------CcccchHHH
Confidence            457888988888776  66777788999999999998741    22  5678899999999999       88877 788


Q ss_pred             ccccccccccceecCCCCcccc--hhhhcCCCccEEEeccCCCCccccc----cccccccCCeeecc
Q 005860          568 GIEKLIHLRYLRLVGLGTEELP--ETCCELLNLQVLEIEQCTSLKRLPL----GIGKLVNLRHLTYD  628 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP--~~i~~L~~L~~L~l~~c~~l~~lP~----~i~~L~~Lr~L~l~  628 (673)
                      .++.+++|++|++++|.+..+|  ..++.+++|++|++++|. +..+|.    .++.+++|++|+++
T Consensus        83 ~~~~l~~L~~L~ls~N~i~~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           83 LAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCE-VTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             HHHHCTTCCEEECTTSCCCSHHHHGGGGGCTTCCEEECTTCG-GGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             HhhhCCCCCEEECCCCcCCChHHHHHHhhCCCCCEEeCcCCc-ccchHHHHHHHHHHCCCcccccCC
Confidence            8888999999999999999876  889999999999999986 888886    68999999999865

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.09  E-value=1.8e-10  Score=128.32  Aligned_cols=130  Identities=21%  Similarity=0.183  Sum_probs=102.9

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....++ .+..+++|+.|.+.++.+.    . + ..+..+++|+.|+|++       |.+..+ +.+
T Consensus        85 ~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~Ls~N~l~----~-l-~~l~~l~~L~~L~Ls~-------N~l~~l-~~l  149 (605)
T 1m9s_A           85 NLKNLGWLFLDENKIKDLS-SLKDLKKLKSLSLEHNGIS----D-I-NGLVHLPQLESLYLGN-------NKITDI-TVL  149 (605)
T ss_dssp             GCTTCCEEECCSSCCCCCT-TSTTCTTCCEEECTTSCCC----C-C-GGGGGCTTCSEEECCS-------SCCCCC-GGG
T ss_pred             cCCCCCEEECcCCCCCCCh-hhccCCCCCEEEecCCCCC----C-C-ccccCCCccCEEECCC-------CccCCc-hhh
Confidence            4567888888887766544 5778888999988887642    1 2 2367888899999988       877776 578


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccc
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPK  637 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~  637 (673)
                      +.|++|++|+|++|.+..+|+ +..|++|+.|+|++|. +..+| .+..|++|+.|++++|.+...|.
T Consensus       150 ~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~-i~~l~-~l~~l~~L~~L~L~~N~l~~~p~  214 (605)
T 1m9s_A          150 SRLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLDVLELFSQECLNKPI  214 (605)
T ss_dssp             GSCTTCSEEECCSSCCCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCSEEECCSEEEECCCC
T ss_pred             cccCCCCEEECcCCcCCCchh-hccCCCCCEEECcCCC-CCCCh-HHccCCCCCEEEccCCcCcCCcc
Confidence            888899999999998888877 8889999999999876 87776 68888999999988888776653

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.09  E-value=6.7e-11  Score=125.36  Aligned_cols=143  Identities=14%  Similarity=0.153  Sum_probs=112.1

Q ss_pred             cCceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~  568 (673)
                      ..+++.+.+..+....+|+. +..+++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|+ .
T Consensus        44 l~~l~~l~l~~~~l~~l~~~~~~~l~~L~~L~L~~n~i----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  112 (390)
T 3o6n_A           44 LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQI----EEIDTYAFAYAHTIQKLYMGF-------NAIRYLPPHV  112 (390)
T ss_dssp             GCCCSEEEEESCEESEECTHHHHHCCCCSEEECTTSCC----CEECTTTTTTCTTCCEEECCS-------SCCCCCCTTT
T ss_pred             cCCceEEEecCCchhhCChhHhcccccCcEEECCCCcc----cccChhhccCCCCcCEEECCC-------CCCCcCCHHH
Confidence            46788888888877777765 45688999999988763    334455678899999999999       88777654 5


Q ss_pred             cccccccccceecCCCCcccchhh-hcCCCccEEEeccCCCCcccc-ccccccccCCeeeccccccccccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPETC-CELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~i-~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      ++.+++|++|+|++|.+..+|..+ +++++|++|++++|. +..+| ..++++++|++|++++|.+..+|  ++.+++|+
T Consensus       113 ~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~--~~~l~~L~  189 (390)
T 3o6n_A          113 FQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNN-LERIEDDTFQATTSLQNLQLSSNRLTHVD--LSLIPSLF  189 (390)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTSSCTTCCEEECCSSCCSBCC--GGGCTTCS
T ss_pred             hcCCCCCCEEECCCCccCcCCHHHhcCCCCCcEEECCCCc-cCccChhhccCCCCCCEEECCCCcCCccc--cccccccc
Confidence            789999999999999999998774 889999999999876 66665 45889999999999988887764  34455554


Q ss_pred             c
Q 005860          647 T  647 (673)
Q Consensus       647 ~  647 (673)
                      .
T Consensus       190 ~  190 (390)
T 3o6n_A          190 H  190 (390)
T ss_dssp             E
T ss_pred             e
Confidence            4

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.09  E-value=3e-11  Score=123.92  Aligned_cols=62  Identities=23%  Similarity=0.276  Sum_probs=26.8

Q ss_pred             ccccccceecCCCCcccc--hhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccc
Q 005860          572 LIHLRYLRLVGLGTEELP--ETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP--~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +++|++|+|++|.+...+  ..+..+++|++|++++|. +..+|..+.  ++|++|++++|.++.+|
T Consensus       227 l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~Ls~N~-l~~ip~~~~--~~L~~L~Ls~N~l~~~p  290 (312)
T 1wwl_A          227 RVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTG-LKQVPKGLP--AKLSVLDLSYNRLDRNP  290 (312)
T ss_dssp             TCCCSEEECTTSCCCSSCCCSCCCCCTTCCEEECTTSC-CSSCCSSCC--SEEEEEECCSSCCCSCC
T ss_pred             CCCCCEEECCCCcCCcccchhhhhhcCCCCEEECCCCc-cChhhhhcc--CCceEEECCCCCCCCCh
Confidence            344444444444443332  223334444444444433 444444433  44444444444444443

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.09  E-value=1e-10  Score=121.86  Aligned_cols=142  Identities=18%  Similarity=0.267  Sum_probs=101.4

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....++ .+..+++|++|.+.++..    .. .+. +..++.|+.|++++       +.....++.+
T Consensus        86 ~l~~L~~L~L~~n~i~~~~-~~~~l~~L~~L~l~~n~i----~~-~~~-~~~l~~L~~L~l~~-------n~~~~~~~~~  151 (347)
T 4fmz_A           86 NLVKLTNLYIGTNKITDIS-ALQNLTNLRELYLNEDNI----SD-ISP-LANLTKMYSLNLGA-------NHNLSDLSPL  151 (347)
T ss_dssp             TCTTCCEEECCSSCCCCCG-GGTTCTTCSEEECTTSCC----CC-CGG-GTTCTTCCEEECTT-------CTTCCCCGGG
T ss_pred             cCCcCCEEEccCCcccCch-HHcCCCcCCEEECcCCcc----cC-chh-hccCCceeEEECCC-------CCCcccccch
Confidence            3467788888777665543 466788888888887763    11 222 67788888888888       6533344457


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..+++|++|++++|.+..+|. +..+++|++|++++|. +..+|. +..+++|++|++++|.+..++. ++.+++|++|.
T Consensus       152 ~~l~~L~~L~l~~~~~~~~~~-~~~l~~L~~L~l~~n~-l~~~~~-~~~l~~L~~L~l~~n~l~~~~~-~~~~~~L~~L~  227 (347)
T 4fmz_A          152 SNMTGLNYLTVTESKVKDVTP-IANLTDLYSLSLNYNQ-IEDISP-LASLTSLHYFTAYVNQITDITP-VANMTRLNSLK  227 (347)
T ss_dssp             TTCTTCCEEECCSSCCCCCGG-GGGCTTCSEEECTTSC-CCCCGG-GGGCTTCCEEECCSSCCCCCGG-GGGCTTCCEEE
T ss_pred             hhCCCCcEEEecCCCcCCchh-hccCCCCCEEEccCCc-cccccc-ccCCCccceeecccCCCCCCch-hhcCCcCCEEE
Confidence            888888888888888777776 7788888888888876 777775 7788888888888887777665 55666666554

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.09  E-value=9.3e-11  Score=120.08  Aligned_cols=146  Identities=14%  Similarity=0.132  Sum_probs=114.9

Q ss_pred             cCceEEEEEEcCCCCccc-cccccccccchhhhccchhhhhhhhhH-HHHhhhCCccceeeeccccccccccchhhhccc
Q 005860          491 QEKLRHSMLVLGYEASFP-ISIFKAKNLRSLFINNTLIQVSLTHVL-QSLFDQLKCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~-~~~~~~~~Lr~L~l~~~~~~~~~~~~~-~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      ..+++.+.+..+.....+ ..+..+++|++|++++|..... .... +..+..+++|++|++++       +.+..++..
T Consensus       144 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~-~~~~~~~~~~~l~~L~~L~Ls~-------N~l~~l~~~  215 (310)
T 4glp_A          144 KPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGE-RGLMAALCPHKFPAIQNLALRN-------TGMETPTGV  215 (310)
T ss_dssp             CSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHH-HHHHTTSCTTSSCCCCSCBCCS-------SCCCCHHHH
T ss_pred             ccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccc-hhhhHHHhhhcCCCCCEEECCC-------CCCCchHHH
Confidence            567899999988876655 4567899999999999863111 1111 22346889999999999       887665542


Q ss_pred             ----cccccccccceecCCCCccc-chhhhcC---CCccEEEeccCCCCccccccccccccCCeeeccccccccccccCC
Q 005860          569 ----IEKLIHLRYLRLVGLGTEEL-PETCCEL---LNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQ  640 (673)
Q Consensus       569 ----i~~L~~Lr~L~L~~~~i~~L-P~~i~~L---~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~  640 (673)
                          ++.+++|++|+|++|.+..+ |+.++.+   ++|++|++++|. +..+|..+.  ++|++|++++|.++.+|. +.
T Consensus       216 ~~~l~~~l~~L~~L~Ls~N~l~~~~p~~~~~~~~~~~L~~L~Ls~N~-l~~lp~~~~--~~L~~L~Ls~N~l~~~~~-~~  291 (310)
T 4glp_A          216 CAALAAAGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAG-LEQVPKGLP--AKLRVLDLSSNRLNRAPQ-PD  291 (310)
T ss_dssp             HHHHHHHTCCCSSEECTTSCCCCCCCSCCSSCCCCTTCCCEECCSSC-CCSCCSCCC--SCCSCEECCSCCCCSCCC-TT
T ss_pred             HHHHHhcCCCCCEEECCCCCCCccchhhHHhccCcCcCCEEECCCCC-CCchhhhhc--CCCCEEECCCCcCCCCch-hh
Confidence                57889999999999998887 8888887   699999999976 889998875  799999999999998875 56


Q ss_pred             CCCCCCcC
Q 005860          641 RLTNLRTL  648 (673)
Q Consensus       641 ~L~~L~~L  648 (673)
                      .+++|+.|
T Consensus       292 ~l~~L~~L  299 (310)
T 4glp_A          292 ELPEVDNL  299 (310)
T ss_dssp             SCCCCSCE
T ss_pred             hCCCccEE
Confidence            66666655

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.09  E-value=3.8e-11  Score=119.80  Aligned_cols=121  Identities=20%  Similarity=0.192  Sum_probs=101.1

Q ss_pred             ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccc
Q 005860          510 SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELP  589 (673)
Q Consensus       510 ~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP  589 (673)
                      .+..+++|++|.+.++...     .++ .+..+++|+.|++++       +.+..+|+ +..+++|++|+|++|.+..+|
T Consensus        36 ~~~~l~~L~~L~l~~n~i~-----~l~-~l~~l~~L~~L~L~~-------N~i~~~~~-l~~l~~L~~L~L~~N~l~~l~  101 (263)
T 1xeu_A           36 SQKELSGVQNFNGDNSNIQ-----SLA-GMQFFTNLKELHLSH-------NQISDLSP-LKDLTKLEELSVNRNRLKNLN  101 (263)
T ss_dssp             CHHHHTTCSEEECTTSCCC-----CCT-TGGGCTTCCEEECCS-------SCCCCCGG-GTTCSSCCEEECCSSCCSCCT
T ss_pred             chhhcCcCcEEECcCCCcc-----cch-HHhhCCCCCEEECCC-------CccCCChh-hccCCCCCEEECCCCccCCcC
Confidence            4567889999999988641     123 467899999999999       99888887 999999999999999999998


Q ss_pred             hhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          590 ETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       590 ~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ....  .+|++|++++|. +..+| .++++++|++|++++|.++.+| .++.+++|+.|.
T Consensus       102 ~~~~--~~L~~L~L~~N~-l~~~~-~l~~l~~L~~L~Ls~N~i~~~~-~l~~l~~L~~L~  156 (263)
T 1xeu_A          102 GIPS--ACLSRLFLDNNE-LRDTD-SLIHLKNLEILSIRNNKLKSIV-MLGFLSKLEVLD  156 (263)
T ss_dssp             TCCC--SSCCEEECCSSC-CSBSG-GGTTCTTCCEEECTTSCCCBCG-GGGGCTTCCEEE
T ss_pred             cccc--CcccEEEccCCc-cCCCh-hhcCcccccEEECCCCcCCCCh-HHccCCCCCEEE
Confidence            6444  999999999986 88887 6999999999999999999986 577777766653

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.08  E-value=3.2e-11  Score=133.96  Aligned_cols=147  Identities=18%  Similarity=0.278  Sum_probs=113.9

Q ss_pred             cCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      ...++++.+..+..... +..+..+++|++|.+.++..    ....+..|.++++|++|++++       +.+..+|+. 
T Consensus        25 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~~   93 (549)
T 2z81_A           25 TAAMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRI----NTIEGDAFYSLGSLEHLDLSD-------NHLSSLSSSW   93 (549)
T ss_dssp             CTTCCEEECCSSCCCEECSSTTSSCTTCCEEECTTSCC----CEECTTTTTTCTTCCEEECTT-------SCCCSCCHHH
T ss_pred             CCCccEEECcCCccCccChhhhhcCCcccEEECCCCCc----CccChhhccccccCCEEECCC-------CccCccCHHH
Confidence            35788888888877555 34577889999999988763    344556678889999999998       887777665 


Q ss_pred             cccccccccceecCCCCcc--cchhhhcCCCccEEEeccCCCCcccc-ccccccccCCeeecccccccc-ccccCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEE--LPETCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEF-IPKGIQRLTN  644 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~--LP~~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~-lP~~i~~L~~  644 (673)
                      ++.+++|++|+|++|.+..  .|..++++++|++|++++|..+..+| ..++++++|++|++++|.+.. .|..++++++
T Consensus        94 ~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~  173 (549)
T 2z81_A           94 FGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRD  173 (549)
T ss_dssp             HTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSE
T ss_pred             hccCCCCcEEECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhhcccc
Confidence            8889999999999998774  46788889999999999877677777 478888999999988888775 5666766665


Q ss_pred             CCcC
Q 005860          645 LRTL  648 (673)
Q Consensus       645 L~~L  648 (673)
                      |+.|
T Consensus       174 L~~L  177 (549)
T 2z81_A          174 IHHL  177 (549)
T ss_dssp             EEEE
T ss_pred             CceE
Confidence            5544

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.08  E-value=7.8e-11  Score=113.03  Aligned_cols=124  Identities=27%  Similarity=0.428  Sum_probs=103.4

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-cccccccccceecCCCCcccchh-
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHLRYLRLVGLGTEELPET-  591 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~Lr~L~L~~~~i~~LP~~-  591 (673)
                      .++|++|.+.++..    ....+..|..+++|+.|++++       +.+..+|.. +..+.+|++|+|++|.+..+|.. 
T Consensus        27 ~~~l~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~   95 (208)
T 2o6s_A           27 PAQTTYLDLETNSL----KSLPNGVFDELTSLTQLYLGG-------NKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGV   95 (208)
T ss_dssp             CTTCSEEECCSSCC----CCCCTTTTTTCTTCSEEECCS-------SCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTT
T ss_pred             CCCCcEEEcCCCcc----CcCChhhhcccccCcEEECCC-------CccCccChhhcCCCCCcCEEECCCCcCCccCHhH
Confidence            46899999998863    344555678999999999999       888888765 58899999999999999998865 


Q ss_pred             hhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCCCcCC
Q 005860          592 CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLS  649 (673)
Q Consensus       592 i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~  649 (673)
                      +..+++|++|+++++. +..+|.. ++++++|++|++++|.+..+|.. ++.+++|+.|.
T Consensus        96 ~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~  154 (208)
T 2o6s_A           96 FDKLTQLKELALNTNQ-LQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIW  154 (208)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEE
T ss_pred             hcCccCCCEEEcCCCc-CcccCHhHhccCCcCCEEECCCCccceeCHHHhccCCCccEEE
Confidence            6899999999999976 8888865 78999999999999999988876 56677666653

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.08  E-value=1.5e-10  Score=119.74  Aligned_cols=145  Identities=16%  Similarity=0.196  Sum_probs=70.5

Q ss_pred             CceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          492 EKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      .+++.+.+..+.....++ .+..+++|++|.+.++...  .....+..|.++++|+.|++++       +.+..+|..+.
T Consensus       121 ~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~--~~~~~~~~~~~l~~L~~L~l~~-------n~l~~l~~~~~  191 (330)
T 1xku_A          121 KTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLK--SSGIENGAFQGMKKLSYIRIAD-------TNITTIPQGLP  191 (330)
T ss_dssp             TTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCC--GGGBCTTGGGGCTTCCEEECCS-------SCCCSCCSSCC
T ss_pred             ccccEEECCCCcccccCHhHhcCCccccEEECCCCcCC--ccCcChhhccCCCCcCEEECCC-------CccccCCcccc
Confidence            356666666555544433 2445666666666665421  0112334455666666666665       54444444333


Q ss_pred             cccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          571 KLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                        .+|++|+|++|.+..+ |..+..+++|++|++++|. +..+|. .++.+++|++|++++|.+..+|.++..+++|++|
T Consensus       192 --~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~L~~L  268 (330)
T 1xku_A          192 --PSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVV  268 (330)
T ss_dssp             --TTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSC-CCEECTTTGGGSTTCCEEECCSSCCSSCCTTTTTCSSCCEE
T ss_pred             --ccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCc-CceeChhhccCCCCCCEEECCCCcCccCChhhccCCCcCEE
Confidence              4455555555544443 3444445555555555443 333332 3444455555555555444454444444444433

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.08  E-value=6.2e-11  Score=135.31  Aligned_cols=148  Identities=16%  Similarity=0.184  Sum_probs=121.1

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-  567 (673)
                      .+.+++++.+..+.....++ .+..+++|++|++.++.    +....+..|.++++|++|++++       +.+..+|+ 
T Consensus        23 ~~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~----l~~~~~~~~~~l~~L~~L~L~~-------n~l~~l~~~   91 (680)
T 1ziw_A           23 LPTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNT----ISKLEPELCQKLPMLKVLNLQH-------NELSQLSDK   91 (680)
T ss_dssp             SCTTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSSC----CCCCCTTHHHHCTTCCEEECCS-------SCCCCCCTT
T ss_pred             cCCCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCCc----cCccCHHHHhcccCcCEEECCC-------CccCccChh
Confidence            34689999999888766665 47789999999999876    3345567789999999999999       88888887 


Q ss_pred             ccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCcc-ccccccccccCCeeecccccccccccc-C--CCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKR-LPLGIGKLVNLRHLTYDDSCLEFIPKG-I--QRL  642 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~-lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i--~~L  642 (673)
                      .++.+.+|++|+|++|.+..+| ..++++++|++|++++|. +.. .|..++++++|++|++++|.+..+|.. +  ..+
T Consensus        92 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~  170 (680)
T 1ziw_A           92 TFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNG-LSSTKLGTQVQLENLQELLLSNNKIQALKSEELDIFAN  170 (680)
T ss_dssp             TTTTCTTCSEEECCSSCCCCCCSCTTTTCTTCCEEECCSSC-CSCCCCCSSSCCTTCCEEECCSSCCCCBCHHHHGGGTT
T ss_pred             hhccCCCCCEEECCCCccCccChhHccccCCCCEEECCCCc-ccccCchhhcccccCCEEEccCCcccccCHHHhhcccc
Confidence            5999999999999999988887 679999999999999987 544 456789999999999999988877653 2  234


Q ss_pred             CCCCcCC
Q 005860          643 TNLRTLS  649 (673)
Q Consensus       643 ~~L~~L~  649 (673)
                      ++|+.|.
T Consensus       171 ~~L~~L~  177 (680)
T 1ziw_A          171 SSLKKLE  177 (680)
T ss_dssp             CEESEEE
T ss_pred             ccccEEE
Confidence            5566553

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.08  E-value=4.6e-11  Score=134.98  Aligned_cols=146  Identities=18%  Similarity=0.214  Sum_probs=112.9

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-  567 (673)
                      .+..++++.+..+....+++ .+..+++|++|+++++.+    ....+..|.++++|++|+|++       +.+..+|+ 
T Consensus        50 lp~~~~~LdLs~N~i~~l~~~~f~~l~~L~~L~Ls~N~i----~~i~~~~f~~L~~L~~L~Ls~-------N~l~~l~~~  118 (635)
T 4g8a_A           50 LPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEI----QTIEDGAYQSLSHLSTLILTG-------NPIQSLALG  118 (635)
T ss_dssp             SCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------CCCCEECGG
T ss_pred             CCcCCCEEEeeCCCCCCCCHHHHhCCCCCCEEECCCCcC----CCcChhHhcCCCCCCEEEccC-------CcCCCCCHH
Confidence            35678888888888776654 567788999999988763    344556788889999999998       88888775 


Q ss_pred             ccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCc--cccccccccccCCeeeccccccccccc-cCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLK--RLPLGIGKLVNLRHLTYDDSCLEFIPK-GIQRLT  643 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~--~lP~~i~~L~~Lr~L~l~~~~l~~lP~-~i~~L~  643 (673)
                      .+..|.+|++|+|++|.+..+|+ .+++|++|++|++++|. +.  .+|..+++|++|++|++++|.++.++. .+..++
T Consensus       119 ~f~~L~~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~-l~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~l~~L~  197 (635)
T 4g8a_A          119 AFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNL-IQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLH  197 (635)
T ss_dssp             GGTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSC-CCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHH
T ss_pred             HhcCCCCCCEEECCCCcCCCCChhhhhcCcccCeeccccCc-cccCCCchhhccchhhhhhcccCccccccccccccchh
Confidence            47888999999999998888875 58889999999998876 54  357788889999999988888877653 355555


Q ss_pred             CCCc
Q 005860          644 NLRT  647 (673)
Q Consensus       644 ~L~~  647 (673)
                      +++.
T Consensus       198 ~l~~  201 (635)
T 4g8a_A          198 QMPL  201 (635)
T ss_dssp             TCTT
T ss_pred             hhhh
Confidence            4443

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.08  E-value=6.7e-11  Score=125.38  Aligned_cols=127  Identities=20%  Similarity=0.246  Sum_probs=107.8

Q ss_pred             ccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcccc-
Q 005860          512 FKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEELP-  589 (673)
Q Consensus       512 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP-  589 (673)
                      ..+++++.|.+.++.    +...++..|..+++|++|++++       +.+..+++ .+..+++|++|+|++|.+..+| 
T Consensus        42 ~~l~~l~~l~l~~~~----l~~l~~~~~~~l~~L~~L~L~~-------n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~  110 (390)
T 3o6n_A           42 ITLNNQKIVTFKNST----MRKLPAALLDSFRQVELLNLND-------LQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPP  110 (390)
T ss_dssp             GGGCCCSEEEEESCE----ESEECTHHHHHCCCCSEEECTT-------SCCCEECTTTTTTCTTCCEEECCSSCCCCCCT
T ss_pred             cccCCceEEEecCCc----hhhCChhHhcccccCcEEECCC-------CcccccChhhccCCCCcCEEECCCCCCCcCCH
Confidence            357899999998876    3345566788999999999999       88887765 8999999999999999988886 


Q ss_pred             hhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCCCcCCe
Q 005860          590 ETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLSE  650 (673)
Q Consensus       590 ~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~~  650 (673)
                      ..++++++|++|++++|. +..+|.. ++++++|++|++++|.+..+|+. ++.+++|++|..
T Consensus       111 ~~~~~l~~L~~L~L~~n~-l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l  172 (390)
T 3o6n_A          111 HVFQNVPLLTVLVLERND-LSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQL  172 (390)
T ss_dssp             TTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEEC
T ss_pred             HHhcCCCCCCEEECCCCc-cCcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEEC
Confidence            458999999999999976 9999987 48999999999999999888654 778888877743

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.08  E-value=1.2e-10  Score=119.50  Aligned_cols=169  Identities=17%  Similarity=0.113  Sum_probs=124.0

Q ss_pred             ccCceEEEEEEcCCCCccccccccc-----cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKA-----KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK  564 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~-----~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~  564 (673)
                      ...+++++.+..+.....|..+..+     ++|++|.+.++..    ....+..|..+++|+.|++++       +.+..
T Consensus       119 ~l~~L~~L~Ls~N~l~~~~~~~~~l~~~~~~~L~~L~L~~N~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~  187 (312)
T 1wwl_A          119 TGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHS----LNFSCEQVRVFPALSTLDLSD-------NPELG  187 (312)
T ss_dssp             CSCCCSEEEEESCBCSSSSSHHHHHHTTCCTTCCEEEEESCSC----CCCCTTTCCCCSSCCEEECCS-------CTTCH
T ss_pred             cCCCccEEEccCCCCcchhHHHHHHHHhhcCCCcEEEeeCCCC----ccchHHHhccCCCCCEEECCC-------CCcCc
Confidence            4568999999998887666656555     8999999999873    344556788999999999999       87432


Q ss_pred             ---hcccc--ccccccccceecCCCCcccc---h-hhhcCCCccEEEeccCCCCcccc--ccccccccCCeeeccccccc
Q 005860          565 ---ILKGI--EKLIHLRYLRLVGLGTEELP---E-TCCELLNLQVLEIEQCTSLKRLP--LGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       565 ---lp~~i--~~L~~Lr~L~L~~~~i~~LP---~-~i~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~Lr~L~l~~~~l~  633 (673)
                         +|..+  +.+++|++|+|++|.+..+|   . .+..+++|++|++++|. +...+  ..+..+++|++|++++|.++
T Consensus       188 ~~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~~l~~L~~L~Ls~N~l~  266 (312)
T 1wwl_A          188 ERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNS-LRDAAGAPSCDWPSQLNSLNLSFTGLK  266 (312)
T ss_dssp             HHHHHHHSCTTSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTSC-CCSSCCCSCCCCCTTCCEEECTTSCCS
T ss_pred             chHHHHHHHhccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCCc-CCcccchhhhhhcCCCCEEECCCCccC
Confidence               45555  88999999999999988554   2 33578999999999977 76654  45677899999999999999


Q ss_pred             cccccCCCCCCCCcCCeeEEccCCccCCCccccCCCCCC
Q 005860          634 FIPKGIQRLTNLRTLSEFVVVRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       634 ~lP~~i~~L~~L~~L~~~~~~~~~~~~~~~~~~l~~L~~  672 (673)
                      .+|..+.  ++|+.|..-.-.-.....+..+.+|+.|.+
T Consensus       267 ~ip~~~~--~~L~~L~Ls~N~l~~~p~~~~l~~L~~L~L  303 (312)
T 1wwl_A          267 QVPKGLP--AKLSVLDLSYNRLDRNPSPDELPQVGNLSL  303 (312)
T ss_dssp             SCCSSCC--SEEEEEECCSSCCCSCCCTTTSCEEEEEEC
T ss_pred             hhhhhcc--CCceEEECCCCCCCCChhHhhCCCCCEEec
Confidence            9998876  566655322111111011445566665544

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.07  E-value=3.4e-11  Score=123.79  Aligned_cols=147  Identities=11%  Similarity=0.034  Sum_probs=98.9

Q ss_pred             CceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHH-HhhhCCccceeeeccccccccccchhhhcccc
Q 005860          492 EKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQS-LFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~-~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      .+++.+.+..+.....++ .+..+++|++|++.++..    ....+. ++..++.|++|++++       +.+..+|...
T Consensus       120 ~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l----~~~~~~~~~~~l~~L~~L~L~~-------N~l~~~~~~~  188 (317)
T 3o53_A          120 QGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEI----DTVNFAELAASSDTLEHLNLQY-------NFIYDVKGQV  188 (317)
T ss_dssp             SSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSCC----CEEEGGGGGGGTTTCCEEECTT-------SCCCEEECCC
T ss_pred             CCCCEEECCCCCCCCccchhhhccCCCCEEECCCCCC----CcccHHHHhhccCcCCEEECCC-------CcCccccccc
Confidence            456777777666655433 455677777777777653    122222 234667778888777       7766665433


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc--cccccCCCCCCCCc
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE--FIPKGIQRLTNLRT  647 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~--~lP~~i~~L~~L~~  647 (673)
                       .+++|++|+|++|.+..+|+.+..+++|++|++++|. +..+|..+..+++|++|++++|.+.  .+|..++.+++|+.
T Consensus       189 -~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~l~~L~~L~l~~N~~~~~~~~~~~~~~~~L~~  266 (317)
T 3o53_A          189 -VFAKLKTLDLSSNKLAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQT  266 (317)
T ss_dssp             -CCTTCCEEECCSSCCCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTCCEEECTTCCCBHHHHHHHHHTCHHHHH
T ss_pred             -ccccCCEEECCCCcCCcchhhhcccCcccEEECcCCc-ccchhhHhhcCCCCCEEEccCCCccCcCHHHHHhccccceE
Confidence             4777888888887777777777777888888887765 7777777777778888887777766  55566666666666


Q ss_pred             CCee
Q 005860          648 LSEF  651 (673)
Q Consensus       648 L~~~  651 (673)
                      |...
T Consensus       267 l~l~  270 (317)
T 3o53_A          267 VAKQ  270 (317)
T ss_dssp             HHHH
T ss_pred             EECC
Confidence            5443

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.07  E-value=1e-10  Score=120.27  Aligned_cols=143  Identities=12%  Similarity=0.102  Sum_probs=115.5

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-ccc-
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KGI-  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~i-  569 (673)
                      .+++.+.+..+.....+..  .+++|++|.+.++..    ....+..|..++.|+.|++++       +.+..++ ..+ 
T Consensus        99 ~~L~~L~l~~n~l~~~~~~--~~~~L~~L~l~~N~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~~~~  165 (317)
T 3o53_A           99 PSIETLHAANNNISRVSCS--RGQGKKNIYLANNKI----TMLRDLDEGCRSRVQYLDLKL-------NEIDTVNFAELA  165 (317)
T ss_dssp             TTCCEEECCSSCCSEEEEC--CCSSCEEEECCSSCC----CSGGGBCTGGGSSEEEEECTT-------SCCCEEEGGGGG
T ss_pred             CCcCEEECCCCccCCcCcc--ccCCCCEEECCCCCC----CCccchhhhccCCCCEEECCC-------CCCCcccHHHHh
Confidence            5677777777766555433  367899999998873    334455678899999999999       8877653 444 


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..+++|++|+|++|.+..+|.. ..+++|++|++++|. +..+|..+..+++|++|++++|.+..+|..++.+++|+.|.
T Consensus       166 ~~l~~L~~L~L~~N~l~~~~~~-~~l~~L~~L~Ls~N~-l~~l~~~~~~l~~L~~L~L~~N~l~~l~~~~~~l~~L~~L~  243 (317)
T 3o53_A          166 ASSDTLEHLNLQYNFIYDVKGQ-VVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNKLVLIEKALRFSQNLEHFD  243 (317)
T ss_dssp             GGTTTCCEEECTTSCCCEEECC-CCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSCCCEECTTCCCCTTCCEEE
T ss_pred             hccCcCCEEECCCCcCcccccc-cccccCCEEECCCCc-CCcchhhhcccCcccEEECcCCcccchhhHhhcCCCCCEEE
Confidence            4789999999999999999764 459999999999976 99999999999999999999999999998888777777664

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.07  E-value=8.5e-11  Score=132.75  Aligned_cols=131  Identities=24%  Similarity=0.278  Sum_probs=110.6

Q ss_pred             CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-ccccccccccceecCC
Q 005860          505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGL  583 (673)
Q Consensus       505 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~  583 (673)
                      ..+|..+  .++++.|+++++.    +....+..|.++++|++|+|++       +.+..+|+ .+..|++|++|+|++|
T Consensus        44 ~~vP~~l--p~~~~~LdLs~N~----i~~l~~~~f~~l~~L~~L~Ls~-------N~i~~i~~~~f~~L~~L~~L~Ls~N  110 (635)
T 4g8a_A           44 YKIPDNL--PFSTKNLDLSFNP----LRHLGSYSFFSFPELQVLDLSR-------CEIQTIEDGAYQSLSHLSTLILTGN  110 (635)
T ss_dssp             SSCCSSS--CTTCCEEECTTSC----CCEECTTTTTTCTTCCEEECTT-------CCCCEECTTTTTTCTTCCEEECTTC
T ss_pred             CccCCCC--CcCCCEEEeeCCC----CCCCCHHHHhCCCCCCEEECCC-------CcCCCcChhHhcCCCCCCEEEccCC
Confidence            4556544  3579999999987    3445567789999999999999       99988866 5899999999999999


Q ss_pred             CCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccc--ccccCCCCCCCCcCC
Q 005860          584 GTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEF--IPKGIQRLTNLRTLS  649 (673)
Q Consensus       584 ~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~--lP~~i~~L~~L~~L~  649 (673)
                      .++.+|+ .+.+|++|++|++++|. +..+|. .|++|++|++|++++|.+..  +|..++.+++|++|.
T Consensus       111 ~l~~l~~~~f~~L~~L~~L~Ls~N~-l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~  179 (635)
T 4g8a_A          111 PIQSLALGAFSGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLD  179 (635)
T ss_dssp             CCCEECGGGGTTCTTCCEEECTTSC-CCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEE
T ss_pred             cCCCCCHHHhcCCCCCCEEECCCCc-CCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhc
Confidence            9999985 57999999999999986 888886 58999999999999998875  466788888888774

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.06  E-value=5.2e-11  Score=124.40  Aligned_cols=139  Identities=24%  Similarity=0.195  Sum_probs=112.2

Q ss_pred             EcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-cccccccccccc
Q 005860          500 VLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KGIEKLIHLRYL  578 (673)
Q Consensus       500 ~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~i~~L~~Lr~L  578 (673)
                      ..+....+|..+.  ++|++|.+.++..    ....+..|.++++|+.|++++       +.+..++ ..++.+++|++|
T Consensus        39 ~~~~l~~iP~~~~--~~L~~L~l~~n~i----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~~~~l~~L~~L  105 (353)
T 2z80_A           39 SSGSLNSIPSGLT--EAVKSLDLSNNRI----TYISNSDLQRCVNLQALVLTS-------NGINTIEEDSFSSLGSLEHL  105 (353)
T ss_dssp             CSTTCSSCCTTCC--TTCCEEECTTSCC----CEECTTTTTTCTTCCEEECTT-------SCCCEECTTTTTTCTTCCEE
T ss_pred             CCCCccccccccc--ccCcEEECCCCcC----cccCHHHhccCCCCCEEECCC-------CccCccCHhhcCCCCCCCEE
Confidence            3344455665443  5899999998863    334445688999999999999       8887764 569999999999


Q ss_pred             eecCCCCcccchh-hhcCCCccEEEeccCCCCccccc--cccccccCCeeecccc-cccccc-ccCCCCCCCCcCCeeE
Q 005860          579 RLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDS-CLEFIP-KGIQRLTNLRTLSEFV  652 (673)
Q Consensus       579 ~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~-~l~~lP-~~i~~L~~L~~L~~~~  652 (673)
                      +|++|.+..+|.. ++++++|++|++++|. +..+|.  .++++++|++|++++| .+..+| ..++++++|+.|..-.
T Consensus       106 ~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~  183 (353)
T 2z80_A          106 DLSYNYLSNLSSSWFKPLSSLTFLNLLGNP-YKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDA  183 (353)
T ss_dssp             ECCSSCCSSCCHHHHTTCTTCSEEECTTCC-CSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEE
T ss_pred             ECCCCcCCcCCHhHhCCCccCCEEECCCCC-CcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCC
Confidence            9999999999976 8999999999999976 889997  6899999999999887 477765 4588888888775543

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=99.06  E-value=2.1e-12  Score=123.04  Aligned_cols=135  Identities=21%  Similarity=0.179  Sum_probs=109.5

Q ss_pred             CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCC
Q 005860          505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG  584 (673)
Q Consensus       505 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~  584 (673)
                      ..++..+..+++|++|.+.++..    .. ++ .+..+++|+.|++++       +.+..+|..+..+++|++|+|++|.
T Consensus        38 ~~l~~~~~~l~~L~~L~ls~n~l----~~-l~-~~~~l~~L~~L~l~~-------n~l~~l~~~~~~~~~L~~L~L~~N~  104 (198)
T 1ds9_A           38 EKMDATLSTLKACKHLALSTNNI----EK-IS-SLSGMENLRILSLGR-------NLIKKIENLDAVADTLEELWISYNQ  104 (198)
T ss_dssp             CCCHHHHHHTTTCSEEECSEEEE----SC-CC-CHHHHTTCCEEEEEE-------EEECSCSSHHHHHHHCSEEEEEEEE
T ss_pred             hhhhHHHhcCCCCCEEECCCCCC----cc-cc-ccccCCCCCEEECCC-------CCcccccchhhcCCcCCEEECcCCc
Confidence            34455677889999999998864    12 34 677889999999999       8888888888888999999999999


Q ss_pred             CcccchhhhcCCCccEEEeccCCCCccccc--cccccccCCeeecccccccccccc-----------CCCCCCCCcCCee
Q 005860          585 TEELPETCCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIPKG-----------IQRLTNLRTLSEF  651 (673)
Q Consensus       585 i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP~~-----------i~~L~~L~~L~~~  651 (673)
                      +..+| .++.+++|++|++++|. +..+|.  .+..+++|++|++++|.+...++.           +..+++|+.|++.
T Consensus       105 l~~l~-~~~~l~~L~~L~l~~N~-i~~~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~~~~~~~~l~~L~~Ld~~  182 (198)
T 1ds9_A          105 IASLS-GIEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGM  182 (198)
T ss_dssp             CCCHH-HHHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEECSCHHHHHHHTTTTHHHHHHHHHHHCSSCSEECCG
T ss_pred             CCcCC-ccccCCCCCEEECCCCc-CCchhHHHHHhcCCCCCEEEecCCccccccccccchHHHHHHHHHhCCCcEEECCc
Confidence            98888 68999999999999876 887775  688999999999999888665433           6788888888755


Q ss_pred             EEc
Q 005860          652 VVV  654 (673)
Q Consensus       652 ~~~  654 (673)
                      .+.
T Consensus       183 ~i~  185 (198)
T 1ds9_A          183 PVD  185 (198)
T ss_dssp             GGT
T ss_pred             ccC
Confidence            444

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.06  E-value=1.9e-11  Score=126.67  Aligned_cols=147  Identities=16%  Similarity=0.143  Sum_probs=81.8

Q ss_pred             CceEEEEEEcCCCCc--cccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecccccccccc-chh--hhc
Q 005860          492 EKLRHSMLVLGYEAS--FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVN-STN--KIL  566 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~--~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~-~~~--~lp  566 (673)
                      .+++++.+..+....  ++..+..+++|++|.+.++..    ....+..+..+++|+.|++++       + .+.  .++
T Consensus        93 ~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~~~l----~~~~~~~l~~~~~L~~L~L~~-------~~~l~~~~l~  161 (336)
T 2ast_B           93 FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRL----SDPIVNTLAKNSNLVRLNLSG-------CSGFSEFALQ  161 (336)
T ss_dssp             BCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBC----CHHHHHHHTTCTTCSEEECTT-------CBSCCHHHHH
T ss_pred             CCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcCccc----CHHHHHHHhcCCCCCEEECCC-------CCCCCHHHHH
Confidence            456666665554321  333445566677776666542    223444555566666666666       5 333  245


Q ss_pred             cccccccccccceecCC-CCcc--cchhhhcCC-CccEEEeccCC-CC--ccccccccccccCCeeeccccc-cc-cccc
Q 005860          567 KGIEKLIHLRYLRLVGL-GTEE--LPETCCELL-NLQVLEIEQCT-SL--KRLPLGIGKLVNLRHLTYDDSC-LE-FIPK  637 (673)
Q Consensus       567 ~~i~~L~~Lr~L~L~~~-~i~~--LP~~i~~L~-~L~~L~l~~c~-~l--~~lP~~i~~L~~Lr~L~l~~~~-l~-~lP~  637 (673)
                      ..+..+++|++|+|++| .+..  +|..+..++ +|++|++++|. .+  ..+|..+.++++|++|++++|. ++ ..|.
T Consensus       162 ~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~  241 (336)
T 2ast_B          162 TLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQ  241 (336)
T ss_dssp             HHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGG
T ss_pred             HHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHH
Confidence            55666666666666666 4543  555566666 66666666653 13  3455555666666666666655 32 3344


Q ss_pred             cCCCCCCCCcCC
Q 005860          638 GIQRLTNLRTLS  649 (673)
Q Consensus       638 ~i~~L~~L~~L~  649 (673)
                      .++++++|+.|.
T Consensus       242 ~l~~l~~L~~L~  253 (336)
T 2ast_B          242 EFFQLNYLQHLS  253 (336)
T ss_dssp             GGGGCTTCCEEE
T ss_pred             HHhCCCCCCEee
Confidence            455555555543

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.06  E-value=1e-10  Score=127.49  Aligned_cols=146  Identities=10%  Similarity=0.038  Sum_probs=88.5

Q ss_pred             CceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHh-hhCCccceeeeccccccccccchhhhcccc
Q 005860          492 EKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLF-DQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~-~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      .+++.+.+..+..... +..+..+++|++|++++|.+    ....+..+ ..+++|+.|+|++       |.+..+|.. 
T Consensus       120 ~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l----~~~~~~~l~~~l~~L~~L~Ls~-------N~l~~~~~~-  187 (487)
T 3oja_A          120 QGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEI----DTVNFAELAASSDTLEHLNLQY-------NFIYDVKGQ-  187 (487)
T ss_dssp             SSCEEEECCSSCCCSGGGBCGGGGSSEEEEECTTSCC----CEEEGGGGGGGTTTCCEEECTT-------SCCCEEECC-
T ss_pred             CCCCEEECCCCCCCCCCchhhcCCCCCCEEECCCCCC----CCcChHHHhhhCCcccEEecCC-------Ccccccccc-
Confidence            4566666666655443 33455566677776666653    12222222 3566677777776       666555443 


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc--cccccCCCCCCCCc
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE--FIPKGIQRLTNLRT  647 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~--~lP~~i~~L~~L~~  647 (673)
                      ..+++|++|+|++|.+..+|+.++.+++|++|++++|. +..+|..++.+++|++|++++|.+.  .+|..++.++.|+.
T Consensus       188 ~~l~~L~~L~Ls~N~l~~~~~~~~~l~~L~~L~Ls~N~-l~~lp~~l~~l~~L~~L~l~~N~l~c~~~~~~~~~l~~L~~  266 (487)
T 3oja_A          188 VVFAKLKTLDLSSNKLAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQT  266 (487)
T ss_dssp             CCCTTCCEEECCSSCCCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTCCEEECTTCCBCHHHHHHHHTTCHHHHH
T ss_pred             ccCCCCCEEECCCCCCCCCCHhHcCCCCccEEEecCCc-CcccchhhccCCCCCEEEcCCCCCcCcchHHHHHhCCCCcE
Confidence            34666777777777766676667677777777777654 6666766666777777776666665  55555666666555


Q ss_pred             CCe
Q 005860          648 LSE  650 (673)
Q Consensus       648 L~~  650 (673)
                      |..
T Consensus       267 l~~  269 (487)
T 3oja_A          267 VAK  269 (487)
T ss_dssp             HHH
T ss_pred             Eec
Confidence            543

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.06  E-value=1.1e-10  Score=122.25  Aligned_cols=143  Identities=20%  Similarity=0.221  Sum_probs=111.8

Q ss_pred             ccCceEEEEEEcCCCCcccccc-c-cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc
Q 005860          490 YQEKLRHSMLVLGYEASFPISI-F-KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~-~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~  567 (673)
                      .+..++.+.+..+....+++.. . .+++|++|.+.++.+    ....+..|.++++|+.|+|++       +.+..+|+
T Consensus        37 ~~~~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i----~~i~~~~~~~l~~L~~L~Ls~-------N~l~~~~~  105 (361)
T 2xot_A           37 LPSYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHL----NFISSEAFVPVPNLRYLDLSS-------NHLHTLDE  105 (361)
T ss_dssp             CCTTCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCC----CEECTTTTTTCTTCCEEECCS-------SCCCEECT
T ss_pred             CCCCCCEEECCCCCCCccChhhhhhcccccCEEECCCCcC----CccChhhccCCCCCCEEECCC-------CcCCcCCH
Confidence            3456788888888776665543 3 788999999988763    344456688899999999999       88888765


Q ss_pred             -ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccccc----cccccCCeeecccccccccccc-CC
Q 005860          568 -GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPLGI----GKLVNLRHLTYDDSCLEFIPKG-IQ  640 (673)
Q Consensus       568 -~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~~i----~~L~~Lr~L~l~~~~l~~lP~~-i~  640 (673)
                       .+..+.+|++|+|++|.+..+ |..+..|++|++|+|++|. +..+|..+    .++++|++|++++|.+..+|.. +.
T Consensus       106 ~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~  184 (361)
T 2xot_A          106 FLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQ-ISRFPVELIKDGNKLPKLMLLDLSSNKLKKLPLTDLQ  184 (361)
T ss_dssp             TTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC-CCSCCGGGTC----CTTCCEEECCSSCCCCCCHHHHH
T ss_pred             HHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCc-CCeeCHHHhcCcccCCcCCEEECCCCCCCccCHHHhh
Confidence             578899999999999998877 5688899999999999876 88898765    6789999999999998888743 44


Q ss_pred             CCCC
Q 005860          641 RLTN  644 (673)
Q Consensus       641 ~L~~  644 (673)
                      .+++
T Consensus       185 ~l~~  188 (361)
T 2xot_A          185 KLPA  188 (361)
T ss_dssp             HSCH
T ss_pred             hccH
Confidence            4444

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.06  E-value=1.1e-10  Score=135.03  Aligned_cols=146  Identities=21%  Similarity=0.228  Sum_probs=86.9

Q ss_pred             CceEEEEEEcCCCC-ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhcccc
Q 005860          492 EKLRHSMLVLGYEA-SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKGI  569 (673)
Q Consensus       492 ~~~r~l~l~~~~~~-~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~i  569 (673)
                      ..++.+.+..+... ..|..+..+++|++|.+.++..    ....|..|..+++|+.|++++       +.+. .+|..+
T Consensus       394 ~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~N~l----~~~~p~~l~~l~~L~~L~L~~-------n~l~~~~p~~~  462 (768)
T 3rgz_A          394 NTLQELYLQNNGFTGKIPPTLSNCSELVSLHLSFNYL----SGTIPSSLGSLSKLRDLKLWL-------NMLEGEIPQEL  462 (768)
T ss_dssp             CCCCEEECCSSEEEEECCGGGGGCTTCCEEECCSSEE----ESCCCGGGGGCTTCCEEECCS-------SCCCSCCCGGG
T ss_pred             CCccEEECCCCccccccCHHHhcCCCCCEEECcCCcc----cCcccHHHhcCCCCCEEECCC-------CcccCcCCHHH
Confidence            34666666555443 3455566667777777766652    223445556666666666666       5544 455666


Q ss_pred             ccccccccceecCCCCc-ccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccc-cccccCCCCCCCCc
Q 005860          570 EKLIHLRYLRLVGLGTE-ELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLE-FIPKGIQRLTNLRT  647 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~-~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~-~lP~~i~~L~~L~~  647 (673)
                      +.+++|++|+|++|.+. .+|..++++++|++|++++|.....+|..++++++|++|++++|.+. .+|..++++++|+.
T Consensus       463 ~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~  542 (768)
T 3rgz_A          463 MYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIW  542 (768)
T ss_dssp             GGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCE
T ss_pred             cCCCCceEEEecCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCE
Confidence            66666666666666644 55666666666666666665533356666666666666666666655 45555666665555


Q ss_pred             C
Q 005860          648 L  648 (673)
Q Consensus       648 L  648 (673)
                      |
T Consensus       543 L  543 (768)
T 3rgz_A          543 L  543 (768)
T ss_dssp             E
T ss_pred             E
Confidence            4

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.05  E-value=6.6e-11  Score=132.05  Aligned_cols=144  Identities=19%  Similarity=0.224  Sum_probs=111.8

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-c
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-K  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~  567 (673)
                      .+..++++.+..+.....++ .+..+++|++|++.++..    ....+..|.++++|++|++++       +.+..+| .
T Consensus        26 l~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i----~~i~~~~~~~l~~L~~L~L~~-------n~l~~~~~~   94 (570)
T 2z63_A           26 LPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEI----QTIEDGAYQSLSHLSTLILTG-------NPIQSLALG   94 (570)
T ss_dssp             SCSSCCEEECCSCCCCEECTTTTTTCSSCCEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------CCCCEECTT
T ss_pred             ccccccEEEccCCccCccChhHhhCCCCceEEECCCCcC----CccCcccccCchhCCEEeCcC-------CcCCccCHh
Confidence            34578888888877755543 567789999999988763    344556678889999999998       8877765 5


Q ss_pred             ccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCcc--ccccccccccCCeeecccccccccc-ccCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKR--LPLGIGKLVNLRHLTYDDSCLEFIP-KGIQRLT  643 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~--lP~~i~~L~~Lr~L~l~~~~l~~lP-~~i~~L~  643 (673)
                      .++.+.+|++|++++|.+..+|. .++++++|++|++++|. +..  +|..++++++|++|++++|.+..+| ..++.++
T Consensus        95 ~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~lp~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~  173 (570)
T 2z63_A           95 AFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNL-IQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLH  173 (570)
T ss_dssp             TTTTCTTCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSSC-CCCCCCCGGGGGCTTCCEEECTTSCCCEECGGGGHHHH
T ss_pred             hhcCccccccccccccccccCCCccccccccccEEecCCCc-cceecChhhhcccCCCCEEeCcCCccceecHHHccchh
Confidence            78888999999999988888875 68889999999998876 554  6888889999999998888877665 3455555


Q ss_pred             CC
Q 005860          644 NL  645 (673)
Q Consensus       644 ~L  645 (673)
                      +|
T Consensus       174 ~L  175 (570)
T 2z63_A          174 QM  175 (570)
T ss_dssp             TC
T ss_pred             cc
Confidence            55

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.05  E-value=1.7e-11  Score=127.16  Aligned_cols=171  Identities=15%  Similarity=0.131  Sum_probs=124.8

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILKGIE  570 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~~i~  570 (673)
                      ..++.+.+..+.....++.+..+++|++|.+.++..   ....++..+..+++|+.|++++       +.+. ..|..++
T Consensus        70 ~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~~l---~~~~~~~~~~~~~~L~~L~L~~-------~~l~~~~~~~l~  139 (336)
T 2ast_B           70 QGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVI---EVSTLHGILSQCSKLQNLSLEG-------LRLSDPIVNTLA  139 (336)
T ss_dssp             TTCSEEECTTCEECSCCCSCCCCBCCCEEECTTCEE---CHHHHHHHHTTBCCCSEEECTT-------CBCCHHHHHHHT
T ss_pred             ccceEEEcCCccccccchhhccCCCCCEEEccCCCc---CHHHHHHHHhhCCCCCEEeCcC-------cccCHHHHHHHh
Confidence            345666665555444455567889999999998863   1123677789999999999999       8755 5778889


Q ss_pred             cccccccceecCC-CCc--ccchhhhcCCCccEEEeccCCCCcc--ccccccccc-cCCeeecccccc----ccccccCC
Q 005860          571 KLIHLRYLRLVGL-GTE--ELPETCCELLNLQVLEIEQCTSLKR--LPLGIGKLV-NLRHLTYDDSCL----EFIPKGIQ  640 (673)
Q Consensus       571 ~L~~Lr~L~L~~~-~i~--~LP~~i~~L~~L~~L~l~~c~~l~~--lP~~i~~L~-~Lr~L~l~~~~l----~~lP~~i~  640 (673)
                      .+++|++|+|++| .+.  .+|..+.++++|++|++++|..+..  +|..+.+++ +|++|++++|.+    ..+|..++
T Consensus       140 ~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~  219 (336)
T 2ast_B          140 KNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVR  219 (336)
T ss_dssp             TCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHH
T ss_pred             cCCCCCEEECCCCCCCCHHHHHHHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHh
Confidence            9999999999999 476  4888899999999999999944765  788899999 999999998843    45666666


Q ss_pred             CCCCCCcCCeeEEcc---CCccCCCccccCCCCCC
Q 005860          641 RLTNLRTLSEFVVVR---GGSKYGGKACNLEGLRY  672 (673)
Q Consensus       641 ~L~~L~~L~~~~~~~---~~~~~~~~~~~l~~L~~  672 (673)
                      ++++|+.|..-....   .....+..+.+|+.|.+
T Consensus       220 ~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L~~L~l  254 (336)
T 2ast_B          220 RCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSL  254 (336)
T ss_dssp             HCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEEC
T ss_pred             hCCCCCEEeCCCCCcCCHHHHHHHhCCCCCCEeeC
Confidence            777777765433321   11122344455555543

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.04  E-value=1.1e-10  Score=130.96  Aligned_cols=143  Identities=14%  Similarity=0.158  Sum_probs=106.7

Q ss_pred             cCceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-
Q 005860          491 QEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-  568 (673)
                      ..+++.+.+..+....+|+. +..+++|++|.+.++..    ....+..|..+++|+.|+|++       +.+..+|+. 
T Consensus        50 l~~l~~l~l~~~~l~~lp~~~~~~l~~L~~L~L~~n~l----~~~~~~~~~~l~~L~~L~L~~-------n~l~~~~~~~  118 (597)
T 3oja_B           50 LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQI----EEIDTYAFAYAHTIQKLYMGF-------NAIRYLPPHV  118 (597)
T ss_dssp             GCCCSEEEESSCEESEECTHHHHHCCCCSEEECTTSCC----CEECTTTTTTCTTCCEEECCS-------SCCCCCCTTT
T ss_pred             CCCceEEEeeCCCCCCcCHHHHccCCCCcEEECCCCCC----CCCChHHhcCCCCCCEEECCC-------CcCCCCCHHH
Confidence            35667777777766666655 34588888888888763    344555678888899999988       887776654 


Q ss_pred             cccccccccceecCCCCcccchhh-hcCCCccEEEeccCCCCcccc-ccccccccCCeeeccccccccccccCCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELPETC-CELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLR  646 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP~~i-~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~  646 (673)
                      ++.+++|++|+|++|.+..+|+.+ +++++|++|+|++|. +..+| ..++++++|++|++++|.+..+|  ++.+++|+
T Consensus       119 ~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~--~~~l~~L~  195 (597)
T 3oja_B          119 FQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNN-LERIEDDTFQATTSLQNLQLSSNRLTHVD--LSLIPSLF  195 (597)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTTTCTTCCEEECTTSCCSBCC--GGGCTTCS
T ss_pred             HcCCCCCCEEEeeCCCCCCCCHHHhccCCCCCEEEeeCCc-CCCCChhhhhcCCcCcEEECcCCCCCCcC--hhhhhhhh
Confidence            688889999999988888888764 788899999998876 65554 46888889999998888887765  33445544


Q ss_pred             c
Q 005860          647 T  647 (673)
Q Consensus       647 ~  647 (673)
                      .
T Consensus       196 ~  196 (597)
T 3oja_B          196 H  196 (597)
T ss_dssp             E
T ss_pred             h
Confidence            4

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.04  E-value=4e-10  Score=124.20  Aligned_cols=148  Identities=20%  Similarity=0.211  Sum_probs=119.9

Q ss_pred             ccCceEEEEEEcCCCCc-cccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hcc
Q 005860          490 YQEKLRHSMLVLGYEAS-FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~-~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~  567 (673)
                      ...+++.+.+..+.... .+..+..+++|++|.+.++...  ....++..+..+++|+.|++++       +.+.. +|.
T Consensus       322 ~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~--~l~~~~~~~~~l~~L~~L~Ls~-------N~l~~~l~~  392 (520)
T 2z7x_B          322 KISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLK--ELSKIAEMTTQMKSLQQLDISQ-------NSVSYDEKK  392 (520)
T ss_dssp             SCCCCCEEECCSSCCCTTTTTTCCCCSSCCEEECCSSCCC--BHHHHHHHHTTCTTCCEEECCS-------SCCBCCGGG
T ss_pred             hCCcccEEEeECCccChhhhhhhccCCCCCEEEccCCccC--ccccchHHHhhCCCCCEEECCC-------CcCCccccc
Confidence            45678888888887654 5667788999999999988741  1123556788999999999999       88877 777


Q ss_pred             c-cccccccccceecCCCC-cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccccc-CCCCCC
Q 005860          568 G-IEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTN  644 (673)
Q Consensus       568 ~-i~~L~~Lr~L~L~~~~i-~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~  644 (673)
                      . +..+++|++|+|++|.+ ..+|..+.  ++|++|++++|. +..+|..+..+++|++|++++|.++.+|.. +..+++
T Consensus       393 ~~~~~l~~L~~L~Ls~N~l~~~~~~~l~--~~L~~L~Ls~N~-l~~ip~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~  469 (520)
T 2z7x_B          393 GDCSWTKSLLSLNMSSNILTDTIFRCLP--PRIKVLDLHSNK-IKSIPKQVVKLEALQELNVASNQLKSVPDGIFDRLTS  469 (520)
T ss_dssp             CSCCCCTTCCEEECCSSCCCGGGGGSCC--TTCCEEECCSSC-CCCCCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTT
T ss_pred             chhccCccCCEEECcCCCCCcchhhhhc--ccCCEEECCCCc-ccccchhhhcCCCCCEEECCCCcCCccCHHHhccCCc
Confidence            5 78889999999999996 55666554  799999999986 889999999999999999999999999987 667776


Q ss_pred             CCcCC
Q 005860          645 LRTLS  649 (673)
Q Consensus       645 L~~L~  649 (673)
                      |++|.
T Consensus       470 L~~L~  474 (520)
T 2z7x_B          470 LQKIW  474 (520)
T ss_dssp             CCEEE
T ss_pred             ccEEE
Confidence            66653

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.04  E-value=6.3e-11  Score=129.22  Aligned_cols=143  Identities=12%  Similarity=0.095  Sum_probs=119.6

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILKGIE  570 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~~i~  570 (673)
                      .+++.+.+..+.....+..  .+++|++|.+.++..    ....+..|..+++|+.|++++       +.+.. .|..+.
T Consensus        99 ~~L~~L~L~~N~l~~~~~~--~l~~L~~L~L~~N~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~~l~  165 (487)
T 3oja_A           99 PSIETLHAANNNISRVSCS--RGQGKKNIYLANNKI----TMLRDLDEGCRSRVQYLDLKL-------NEIDTVNFAELA  165 (487)
T ss_dssp             TTCCEEECCSSCCCCEEEC--CCSSCEEEECCSSCC----CSGGGBCGGGGSSEEEEECTT-------SCCCEEEGGGGG
T ss_pred             CCcCEEECcCCcCCCCCcc--ccCCCCEEECCCCCC----CCCCchhhcCCCCCCEEECCC-------CCCCCcChHHHh
Confidence            5688888888777655543  468899999999873    344566778899999999999       88776 456665


Q ss_pred             -cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          571 -KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       571 -~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                       .+++|++|+|++|.+..+|. ...+++|++|+|++|. +..+|..++.+++|++|++++|.+..+|..++.+++|+.|.
T Consensus       166 ~~l~~L~~L~Ls~N~l~~~~~-~~~l~~L~~L~Ls~N~-l~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~l~~l~~L~~L~  243 (487)
T 3oja_A          166 ASSDTLEHLNLQYNFIYDVKG-QVVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNKLVLIEKALRFSQNLEHFD  243 (487)
T ss_dssp             GGTTTCCEEECTTSCCCEEEC-CCCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSCCCEECTTCCCCTTCCEEE
T ss_pred             hhCCcccEEecCCCccccccc-cccCCCCCEEECCCCC-CCCCCHhHcCCCCccEEEecCCcCcccchhhccCCCCCEEE
Confidence             79999999999999999876 4469999999999976 99999999999999999999999999999888887777664

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.04  E-value=1.4e-10  Score=125.91  Aligned_cols=34  Identities=12%  Similarity=0.125  Sum_probs=15.8

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccch
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTL  526 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~  526 (673)
                      .+++.+.+..+.....++ +..+++|++|.+.++.
T Consensus        68 ~~L~~L~Ls~n~l~~~~~-~~~l~~L~~L~l~~n~  101 (466)
T 1o6v_A           68 NNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQ  101 (466)
T ss_dssp             TTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSC
T ss_pred             cCCCEEECCCCccCCchh-hhccccCCEEECCCCc
Confidence            344555554444433333 4444555555554443

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.04  E-value=8.3e-11  Score=109.63  Aligned_cols=129  Identities=20%  Similarity=0.150  Sum_probs=108.6

Q ss_pred             cCceEEEEEEcCCCCcccccccccc-ccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAK-NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~-~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ..+++.+.+..+....++ .+..+. +|++|++.++...    . + ..|..+++|+.|++++       +.+..+|+.+
T Consensus        18 ~~~L~~L~l~~n~l~~i~-~~~~~~~~L~~L~Ls~N~l~----~-~-~~l~~l~~L~~L~Ls~-------N~l~~~~~~~   83 (176)
T 1a9n_A           18 AVRDRELDLRGYKIPVIE-NLGATLDQFDAIDFSDNEIR----K-L-DGFPLLRRLKTLLVNN-------NRICRIGEGL   83 (176)
T ss_dssp             TTSCEEEECTTSCCCSCC-CGGGGTTCCSEEECCSSCCC----E-E-CCCCCCSSCCEEECCS-------SCCCEECSCH
T ss_pred             cCCceEEEeeCCCCchhH-HhhhcCCCCCEEECCCCCCC----c-c-cccccCCCCCEEECCC-------CcccccCcch
Confidence            457888988888776664 344544 9999999998742    2 2 4578899999999999       9999988776


Q ss_pred             -ccccccccceecCCCCcccch--hhhcCCCccEEEeccCCCCcccccc----ccccccCCeeecccccccc
Q 005860          570 -EKLIHLRYLRLVGLGTEELPE--TCCELLNLQVLEIEQCTSLKRLPLG----IGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       570 -~~L~~Lr~L~L~~~~i~~LP~--~i~~L~~L~~L~l~~c~~l~~lP~~----i~~L~~Lr~L~l~~~~l~~  634 (673)
                       +.+++|++|+|++|.+..+|.  .++.+++|++|++++|+ +..+|..    ++.+++|++|+++.+....
T Consensus        84 ~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~l~~N~-i~~~~~~~~~~~~~l~~L~~Ld~~~n~~~~  154 (176)
T 1a9n_A           84 DQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNP-VTNKKHYRLYVIYKVPQVRVLDFQKVKLKE  154 (176)
T ss_dssp             HHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSG-GGGSTTHHHHHHHHCTTCSEETTEECCHHH
T ss_pred             hhcCCCCCEEECCCCcCCcchhhHhhhcCCCCCEEEecCCC-CCCcHhHHHHHHHHCCccceeCCCcCCHHH
Confidence             899999999999999999997  89999999999999987 8899985    8999999999988876543

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.03  E-value=2.4e-10  Score=126.92  Aligned_cols=87  Identities=22%  Similarity=0.291  Sum_probs=44.6

Q ss_pred             HhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccccccc
Q 005860          538 LFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIG  617 (673)
Q Consensus       538 ~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~  617 (673)
                      .+..+++|+.|++++       +.+..+|..++.+.+|++|+|++|.+..+|..+.  ++|++|++++|. +..+|   +
T Consensus       382 ~~~~l~~L~~L~Ls~-------N~l~~lp~~~~~~~~L~~L~Ls~N~l~~l~~~~~--~~L~~L~Ls~N~-l~~~~---~  448 (549)
T 2z81_A          382 ILLTLKNLTSLDISR-------NTFHPMPDSCQWPEKMRFLNLSSTGIRVVKTCIP--QTLEVLDVSNNN-LDSFS---L  448 (549)
T ss_dssp             HGGGCTTCCEEECTT-------CCCCCCCSCCCCCTTCCEEECTTSCCSCCCTTSC--TTCSEEECCSSC-CSCCC---C
T ss_pred             hhhcCCCCCEEECCC-------CCCccCChhhcccccccEEECCCCCcccccchhc--CCceEEECCCCC-hhhhc---c
Confidence            355566666666666       5555666666666666666666666655554332  223333333222 22221   2


Q ss_pred             ccccCCeeeccccccccccc
Q 005860          618 KLVNLRHLTYDDSCLEFIPK  637 (673)
Q Consensus       618 ~L~~Lr~L~l~~~~l~~lP~  637 (673)
                      .+++|++|++++|.++.+|.
T Consensus       449 ~l~~L~~L~Ls~N~l~~ip~  468 (549)
T 2z81_A          449 FLPRLQELYISRNKLKTLPD  468 (549)
T ss_dssp             CCTTCCEEECCSSCCSSCCC
T ss_pred             cCChhcEEECCCCccCcCCC
Confidence            44555555555555555553

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.02  E-value=1.6e-10  Score=119.55  Aligned_cols=88  Identities=18%  Similarity=0.218  Sum_probs=71.5

Q ss_pred             Cccceeeeccccccccccchhhhc-cccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccccccccc
Q 005860          543 KCLRALRIATLMNTWDVNSTNKIL-KGIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLGIGKLV  620 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  620 (673)
                      +.|+.|++++       +.+..++ ..+..+++|++|+|++|.+..+|. .++.+++|++|++++|. +..+|..++.++
T Consensus       193 ~~L~~L~l~~-------n~i~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~lp~~l~~l~  264 (332)
T 2ft3_A          193 ETLNELHLDH-------NKIQAIELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNK-LSRVPAGLPDLK  264 (332)
T ss_dssp             SSCSCCBCCS-------SCCCCCCTTSSTTCTTCSCCBCCSSCCCCCCTTGGGGCTTCCEEECCSSC-CCBCCTTGGGCT
T ss_pred             CCCCEEECCC-------CcCCccCHHHhcCCCCCCEEECCCCcCCcCChhHhhCCCCCCEEECCCCc-CeecChhhhcCc
Confidence            4667777777       6666654 578888899999999988887764 78889999999999876 888998899999


Q ss_pred             cCCeeecccccccccccc
Q 005860          621 NLRHLTYDDSCLEFIPKG  638 (673)
Q Consensus       621 ~Lr~L~l~~~~l~~lP~~  638 (673)
                      +|++|++++|.++.+|..
T Consensus       265 ~L~~L~l~~N~l~~~~~~  282 (332)
T 2ft3_A          265 LLQVVYLHTNNITKVGVN  282 (332)
T ss_dssp             TCCEEECCSSCCCBCCTT
T ss_pred             cCCEEECCCCCCCccChh
Confidence            999999988888888754

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.02  E-value=1.6e-10  Score=127.49  Aligned_cols=125  Identities=18%  Similarity=0.148  Sum_probs=59.2

Q ss_pred             CceEEEEEEcCCCCccc-cccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          492 EKLRHSMLVLGYEASFP-ISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~-~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      .+++++.+..+.....+ ..+..+++|++|++.++..    ....|..|.++++|++|++++       +.+..+|..  
T Consensus        21 ~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~lp~~--   87 (520)
T 2z7x_B           21 QKTTILNISQNYISELWTSDILSLSKLRILIISHNRI----QYLDISVFKFNQELEYLDLSH-------NKLVKISCH--   87 (520)
T ss_dssp             TTCSEEECCSSCCCCCCHHHHTTCTTCCEEECCSSCC----CEEEGGGGTTCTTCCEEECCS-------SCCCEEECC--
T ss_pred             ccccEEECCCCcccccChhhccccccccEEecCCCcc----CCcChHHhhcccCCCEEecCC-------CceeecCcc--
Confidence            34555555544443333 2344455555555555431    222334445555555555555       554444444  


Q ss_pred             cccccccceecCCCCcc--cchhhhcCCCccEEEeccCCCCccccccccccccC--Ceeecccccc
Q 005860          571 KLIHLRYLRLVGLGTEE--LPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL--RHLTYDDSCL  632 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~--LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L--r~L~l~~~~l  632 (673)
                      .+.+|++|+|++|.+..  +|..++++++|++|++++|. +..  ..++.+++|  ++|++++|.+
T Consensus        88 ~l~~L~~L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n~-l~~--~~~~~l~~L~L~~L~l~~n~l  150 (520)
T 2z7x_B           88 PTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTTH-LEK--SSVLPIAHLNISKVLLVLGET  150 (520)
T ss_dssp             CCCCCSEEECCSSCCSSCCCCGGGGGCTTCCEEEEEESS-CCG--GGGGGGTTSCEEEEEEEECTT
T ss_pred             ccCCccEEeccCCccccccchhhhccCCcceEEEecCcc-cch--hhccccccceeeEEEeecccc
Confidence            45555555555555443  34455555555555555543 332  234444444  5555544443

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=99.02  E-value=2.8e-10  Score=127.99  Aligned_cols=131  Identities=18%  Similarity=0.134  Sum_probs=68.0

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-hhcc-c
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-KILK-G  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-~lp~-~  568 (673)
                      ..+++.+.+..+....+|..+..+++|++|.+.++..    ....+..+..+++|+.|++++       +.+. .+|. .
T Consensus       277 l~~L~~L~l~~n~l~~lp~~l~~l~~L~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~~~~~~~~~~  345 (606)
T 3t6q_A          277 FSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKF----ENLCQISASNFPSLTHLSIKG-------NTKRLELGTGC  345 (606)
T ss_dssp             CTTCSEEECTTSCCSCCCSSCCSCTTCCEEECTTCCC----SBGGGGCGGGCTTCSEEECCS-------CSSCCBCCSST
T ss_pred             ccCCCEEeccCCccCCCChhhcccccCCEEECccCCc----CcCchhhhhccCcCCEEECCC-------CCcccccchhh
Confidence            3466777777666666666666677777777776652    223344455566666666665       4432 2332 2


Q ss_pred             cccccccccceecCCCCccc---chhhhcCCCccEEEeccCCCCcc-ccccccccccCCeeeccccccc
Q 005860          569 IEKLIHLRYLRLVGLGTEEL---PETCCELLNLQVLEIEQCTSLKR-LPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~L---P~~i~~L~~L~~L~l~~c~~l~~-lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      ++.+++|++|++++|.+..+   |..++.+++|++|++++|. +.. .|..++++++|++|++++|.+.
T Consensus       346 ~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~  413 (606)
T 3t6q_A          346 LENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNE-PLSLKTEAFKECPQLELLDLAFTRLK  413 (606)
T ss_dssp             TTTCTTCCEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCS-CEEECTTTTTTCTTCSEEECTTCCEE
T ss_pred             hhccCcCCEEECCCCccccccCcchhcccCCCCCEEECCCCc-CCcCCHHHhcCCccCCeEECCCCcCC
Confidence            44455555555555544433   3344455555555555443 222 2334444444444444444443

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.02  E-value=1.3e-10  Score=121.62  Aligned_cols=139  Identities=19%  Similarity=0.198  Sum_probs=109.0

Q ss_pred             EEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhh-hCCccceeeeccccccccccchhhhcc-cccccc
Q 005860          496 HSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFD-QLKCLRALRIATLMNTWDVNSTNKILK-GIEKLI  573 (673)
Q Consensus       496 ~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~-~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~  573 (673)
                      .+.+..+....+|..+  ...++.|+++++.+    ....+..|. ++++|+.|+|++       +.+..+++ .+..+.
T Consensus        22 ~l~c~~~~l~~iP~~~--~~~l~~L~Ls~N~l----~~l~~~~~~~~l~~L~~L~L~~-------N~i~~i~~~~~~~l~   88 (361)
T 2xot_A           22 ILSCSKQQLPNVPQSL--PSYTALLDLSHNNL----SRLRAEWTPTRLTNLHSLLLSH-------NHLNFISSEAFVPVP   88 (361)
T ss_dssp             EEECCSSCCSSCCSSC--CTTCSEEECCSSCC----CEECTTSSSSCCTTCCEEECCS-------SCCCEECTTTTTTCT
T ss_pred             EEEeCCCCcCccCccC--CCCCCEEECCCCCC----CccChhhhhhcccccCEEECCC-------CcCCccChhhccCCC
Confidence            3444444455566544  34688999998863    344455566 899999999999       99888765 699999


Q ss_pred             ccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccc-cccccccccCCeeeccccccccccccC----CCCCCCCc
Q 005860          574 HLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLEFIPKGI----QRLTNLRT  647 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~~lP~~i----~~L~~L~~  647 (673)
                      +|++|+|++|.+..+|. .+..|++|++|+|++|. +..+ |..+.++++|++|++++|.+..+|..+    +.+++|+.
T Consensus        89 ~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-i~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~~l~~L~~  167 (361)
T 2xot_A           89 NLRYLDLSSNHLHTLDEFLFSDLQALEVLLLYNNH-IVVVDRNAFEDMAQLQKLYLSQNQISRFPVELIKDGNKLPKLML  167 (361)
T ss_dssp             TCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSCCCSCCGGGTC----CTTCCE
T ss_pred             CCCEEECCCCcCCcCCHHHhCCCcCCCEEECCCCc-ccEECHHHhCCcccCCEEECCCCcCCeeCHHHhcCcccCCcCCE
Confidence            99999999999999875 58899999999999977 7776 568999999999999999999999774    34555554


Q ss_pred             C
Q 005860          648 L  648 (673)
Q Consensus       648 L  648 (673)
                      |
T Consensus       168 L  168 (361)
T 2xot_A          168 L  168 (361)
T ss_dssp             E
T ss_pred             E
Confidence            4

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.01  E-value=3.9e-10  Score=122.47  Aligned_cols=140  Identities=21%  Similarity=0.243  Sum_probs=95.0

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+..... +.+..+++|+.|.+.++..    ....+  +..++.|+.|++++       +.+..+|+ +.
T Consensus       220 l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~l~~n~l----~~~~~--~~~l~~L~~L~l~~-------n~l~~~~~-~~  284 (466)
T 1o6v_A          220 LTNLDELSLNGNQLKDI-GTLASLTNLTDLDLANNQI----SNLAP--LSGLTKLTELKLGA-------NQISNISP-LA  284 (466)
T ss_dssp             CTTCCEEECCSSCCCCC-GGGGGCTTCSEEECCSSCC----CCCGG--GTTCTTCSEEECCS-------SCCCCCGG-GT
T ss_pred             cCCCCEEECCCCCcccc-hhhhcCCCCCEEECCCCcc----ccchh--hhcCCCCCEEECCC-------CccCcccc-cc
Confidence            45566666666655443 2455667777777776653    11111  56777777777777       77666665 77


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      .+++|++|+|++|.+..+|. ++.+++|++|++++|. +..+|. ++.+++|+.|++++|.+..+| .++++++|+.|.
T Consensus       285 ~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~  359 (466)
T 1o6v_A          285 GLTALTNLELNENQLEDISP-ISNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFYNNKVSDVS-SLANLTNINWLS  359 (466)
T ss_dssp             TCTTCSEEECCSSCCSCCGG-GGGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECCSSCCCCCG-GGTTCTTCCEEE
T ss_pred             CCCccCeEEcCCCcccCchh-hcCCCCCCEEECcCCc-CCCchh-hccCccCCEeECCCCccCCch-hhccCCCCCEEe
Confidence            77888888888887777766 7778888888888775 666554 677888888888888777764 466666665553

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.00  E-value=1.8e-10  Score=124.42  Aligned_cols=135  Identities=19%  Similarity=0.154  Sum_probs=105.2

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+.....| .+..+++|++|.+.++...    . ++  +..++.|++|++++       +.+..+|  ++
T Consensus        41 l~~L~~L~Ls~n~l~~~~-~l~~l~~L~~L~Ls~n~l~----~-~~--~~~l~~L~~L~Ls~-------N~l~~~~--~~  103 (457)
T 3bz5_A           41 LATLTSLDCHNSSITDMT-GIEKLTGLTKLICTSNNIT----T-LD--LSQNTNLTYLACDS-------NKLTNLD--VT  103 (457)
T ss_dssp             HTTCCEEECCSSCCCCCT-TGGGCTTCSEEECCSSCCS----C-CC--CTTCTTCSEEECCS-------SCCSCCC--CT
T ss_pred             cCCCCEEEccCCCcccCh-hhcccCCCCEEEccCCcCC----e-Ec--cccCCCCCEEECcC-------CCCceee--cC
Confidence            467888888887776664 6778889999999888641    1 22  67888999999998       8877775  88


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccc-ccccccccCCCCCCCCcCC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDS-CLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~-~l~~lP~~i~~L~~L~~L~  649 (673)
                      .+++|++|+|++|.+..+|  ++.+++|++|++++|. +..+|  ++++++|++|+++.| .+..+  .++.+++|+.|.
T Consensus       104 ~l~~L~~L~L~~N~l~~l~--~~~l~~L~~L~l~~N~-l~~l~--l~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~  176 (457)
T 3bz5_A          104 PLTKLTYLNCDTNKLTKLD--VSQNPLLTYLNCARNT-LTEID--VSHNTQLTELDCHLNKKITKL--DVTPQTQLTTLD  176 (457)
T ss_dssp             TCTTCCEEECCSSCCSCCC--CTTCTTCCEEECTTSC-CSCCC--CTTCTTCCEEECTTCSCCCCC--CCTTCTTCCEEE
T ss_pred             CCCcCCEEECCCCcCCeec--CCCCCcCCEEECCCCc-cceec--cccCCcCCEEECCCCCccccc--ccccCCcCCEEE
Confidence            8999999999999988886  8889999999999876 77775  788899999998877 44444  356666666653

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=98.99  E-value=3.3e-10  Score=132.38  Aligned_cols=148  Identities=18%  Similarity=0.256  Sum_probs=117.6

Q ss_pred             ccCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cc
Q 005860          490 YQEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~  567 (673)
                      .+.+++++.+..+..... +..+..+++|++|++.++..   .....+..|.++++|++|+|++       +.+..+ |.
T Consensus        22 lp~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~---~~~i~~~~f~~L~~L~~L~Ls~-------N~l~~~~p~   91 (844)
T 3j0a_A           22 VLNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYT---PLTIDKEAFRNLPNLRILDLGS-------SKIYFLHPD   91 (844)
T ss_dssp             SCTTCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCC---CCEECTTTTSSCTTCCEEECTT-------CCCCEECTT
T ss_pred             CCCCcCEEECCCCcCCccChhHCcccccCeEEeCCCCCC---ccccCHHHhcCCCCCCEEECCC-------CcCcccCHh
Confidence            567899999999887655 45678899999999998842   2233366789999999999999       887776 78


Q ss_pred             ccccccccccceecCCCCcc-cchh--hhcCCCccEEEeccCCCCcccc--ccccccccCCeeeccccccccc-cccCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEE-LPET--CCELLNLQVLEIEQCTSLKRLP--LGIGKLVNLRHLTYDDSCLEFI-PKGIQR  641 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~-LP~~--i~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~Lr~L~l~~~~l~~l-P~~i~~  641 (673)
                      .++.+.+|++|+|++|.+.. +|..  +++|++|++|+|++|. +..++  ..+++|++|++|++++|.+..+ |..++.
T Consensus        92 ~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~-l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~~l~~  170 (844)
T 3j0a_A           92 AFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQ-IRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEP  170 (844)
T ss_dssp             SSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCC-CCCCCCCGGGGTCSSCCEEEEESSCCCCCCSGGGHH
T ss_pred             HccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCc-ccccccchhHhhCCCCCEEECCCCcCCeeCHHHccc
Confidence            89999999999999999765 5665  8999999999999977 66553  5789999999999999887654 344555


Q ss_pred             C--CCCCcC
Q 005860          642 L--TNLRTL  648 (673)
Q Consensus       642 L--~~L~~L  648 (673)
                      +  ++|+.|
T Consensus       171 l~~~~L~~L  179 (844)
T 3j0a_A          171 LQGKTLSFF  179 (844)
T ss_dssp             HHHCSSCCC
T ss_pred             ccCCccceE
Confidence            5  555554

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=98.99  E-value=4.4e-10  Score=122.48  Aligned_cols=168  Identities=18%  Similarity=0.172  Sum_probs=88.9

Q ss_pred             ceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhhccccc
Q 005860          493 KLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKILKGIE  570 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~~i~  570 (673)
                      +++.+.+..+....++. .+..+++|+.|.+.++..    ....+..|..+++|+.|++++       +. +..+|..+.
T Consensus       153 ~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n~i----~~~~~~~~~~l~~L~~L~l~~-------~~~~~~~~~~~~  221 (477)
T 2id5_A          153 SLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNI----NAIRDYSFKRLYRLKVLEISH-------WPYLDTMTPNCL  221 (477)
T ss_dssp             TCCEEEEESCCCSSCCHHHHTTCTTCCEEEEESCCC----CEECTTCSCSCTTCCEEEEEC-------CTTCCEECTTTT
T ss_pred             CCCEEECCCCcCcccChhHhcccCCCcEEeCCCCcC----cEeChhhcccCcccceeeCCC-------CccccccCcccc
Confidence            34444444443333322 133344444444444331    112222344455555555554       33 334455555


Q ss_pred             cccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccc-cccCCCCCCCCc
Q 005860          571 KLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFI-PKGIQRLTNLRT  647 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~l-P~~i~~L~~L~~  647 (673)
                      ...+|++|+|++|.+..+| ..+..+++|++|+|++|. +..+|. .+.++++|+.|++++|.+..+ |..+..+++|+.
T Consensus       222 ~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  300 (477)
T 2id5_A          222 YGLNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSYNP-ISTIEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRV  300 (477)
T ss_dssp             TTCCCSEEEEESSCCCSCCHHHHTTCTTCCEEECCSSC-CCEECTTSCTTCTTCCEEECCSSCCSEECTTTBTTCTTCCE
T ss_pred             cCccccEEECcCCcccccCHHHhcCccccCeeECCCCc-CCccChhhccccccCCEEECCCCccceECHHHhcCcccCCE
Confidence            5556777777777777776 356777777777777765 655553 467777777777777777765 344666666665


Q ss_pred             CCeeE--EccCCccCCCccccCCCCCC
Q 005860          648 LSEFV--VVRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       648 L~~~~--~~~~~~~~~~~~~~l~~L~~  672 (673)
                      |..-.  +.......+..+.+|+.|.+
T Consensus       301 L~L~~N~l~~~~~~~~~~l~~L~~L~l  327 (477)
T 2id5_A          301 LNVSGNQLTTLEESVFHSVGNLETLIL  327 (477)
T ss_dssp             EECCSSCCSCCCGGGBSCGGGCCEEEC
T ss_pred             EECCCCcCceeCHhHcCCCcccCEEEc
Confidence            53221  11112223445566666654

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=98.98  E-value=4.4e-10  Score=121.59  Aligned_cols=98  Identities=15%  Similarity=0.180  Sum_probs=58.7

Q ss_pred             ccceeeeccccccccccchhh-hccccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccc-cccccccc
Q 005860          544 CLRALRIATLMNTWDVNSTNK-ILKGIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRL-PLGIGKLV  620 (673)
Q Consensus       544 ~L~~L~L~~~~~~~~~~~~~~-lp~~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~  620 (673)
                      .|+.|++++       +.+.. .|..++.+++|++|+|++|.+..+ |..++.+++|++|++++|. +..+ |..+++++
T Consensus       276 ~L~~L~l~~-------n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~  347 (455)
T 3v47_A          276 GVKTCDLSK-------SKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNF-LGSIDSRMFENLD  347 (455)
T ss_dssp             CCCEEECCS-------SCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSC-CCEECGGGGTTCT
T ss_pred             CceEEEecC-------ccccccchhhcccCCCCCEEECCCCcccccChhHhcCcccCCEEECCCCc-cCCcChhHhcCcc
Confidence            455555555       44433 344566666777777777766555 3466666777777777655 5544 44566667


Q ss_pred             cCCeeeccccccccc-cccCCCCCCCCcCC
Q 005860          621 NLRHLTYDDSCLEFI-PKGIQRLTNLRTLS  649 (673)
Q Consensus       621 ~Lr~L~l~~~~l~~l-P~~i~~L~~L~~L~  649 (673)
                      +|++|++++|.+..+ |..++.+++|++|.
T Consensus       348 ~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~  377 (455)
T 3v47_A          348 KLEVLDLSYNHIRALGDQSFLGLPNLKELA  377 (455)
T ss_dssp             TCCEEECCSSCCCEECTTTTTTCTTCCEEE
T ss_pred             cCCEEECCCCcccccChhhccccccccEEE
Confidence            777777666666655 44455665555553

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.97  E-value=1.9e-11  Score=116.48  Aligned_cols=127  Identities=22%  Similarity=0.211  Sum_probs=101.1

Q ss_pred             ccccchhhhccchhhhh--hhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchh
Q 005860          514 AKNLRSLFINNTLIQVS--LTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPET  591 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~--~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~  591 (673)
                      ...+..+.+..+.....  ....++..+..+++|+.|++++       +.+..+| .+..+++|++|+|++|.+..+|..
T Consensus        17 ~~~l~~l~l~~~~l~~~~~~l~~l~~~~~~l~~L~~L~ls~-------n~l~~l~-~~~~l~~L~~L~l~~n~l~~l~~~   88 (198)
T 1ds9_A           17 RKSVVATEAEKVELHGMIPPIEKMDATLSTLKACKHLALST-------NNIEKIS-SLSGMENLRILSLGRNLIKKIENL   88 (198)
T ss_dssp             TTCCCCTTCSEEECCBCCTTCCCCHHHHHHTTTCSEEECSE-------EEESCCC-CHHHHTTCCEEEEEEEEECSCSSH
T ss_pred             cccccCcchheeEeccccCcHhhhhHHHhcCCCCCEEECCC-------CCCcccc-ccccCCCCCEEECCCCCcccccch
Confidence            34455555544432111  1122345788999999999999       8888888 899999999999999999999999


Q ss_pred             hhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccc--cCCCCCCCCcCCe
Q 005860          592 CCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPK--GIQRLTNLRTLSE  650 (673)
Q Consensus       592 i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~--~i~~L~~L~~L~~  650 (673)
                      ++.+++|++|++++|. +..+| .++++++|++|++++|.+..+|.  .++.+++|++|..
T Consensus        89 ~~~~~~L~~L~L~~N~-l~~l~-~~~~l~~L~~L~l~~N~i~~~~~~~~l~~l~~L~~L~l  147 (198)
T 1ds9_A           89 DAVADTLEELWISYNQ-IASLS-GIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLL  147 (198)
T ss_dssp             HHHHHHCSEEEEEEEE-CCCHH-HHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEEE
T ss_pred             hhcCCcCCEEECcCCc-CCcCC-ccccCCCCCEEECCCCcCCchhHHHHHhcCCCCCEEEe
Confidence            9999999999999986 88888 79999999999999999998774  5677777666543

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=98.97  E-value=9e-10  Score=104.18  Aligned_cols=120  Identities=18%  Similarity=0.254  Sum_probs=86.0

Q ss_pred             EEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-cccccccccc
Q 005860          499 LVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRY  577 (673)
Q Consensus       499 l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~  577 (673)
                      +..+....+|..+  .++|++|.+.++.+     ..+|..|..+++|+.|+|++       +.+..+++ .+..|.+|++
T Consensus        17 ~~~~~l~~ip~~~--~~~l~~L~L~~n~i-----~~ip~~~~~l~~L~~L~Ls~-------N~i~~i~~~~f~~l~~L~~   82 (193)
T 2wfh_A           17 CSNKGLKVLPKGI--PRDVTELYLDGNQF-----TLVPKELSNYKHLTLIDLSN-------NRISTLSNQSFSNMTQLLT   82 (193)
T ss_dssp             CTTSCCSSCCSCC--CTTCCEEECCSSCC-----CSCCGGGGGCTTCCEEECCS-------SCCCCCCTTTTTTCTTCCE
T ss_pred             cCCCCCCcCCCCC--CCCCCEEECCCCcC-----chhHHHhhcccCCCEEECCC-------CcCCEeCHhHccCCCCCCE
Confidence            3333444555443  25788888887764     13345677888888888888       77777654 5788888888


Q ss_pred             ceecCCCCcccch-hhhcCCCccEEEeccCCCCcccccc-ccccccCCeeeccccccc
Q 005860          578 LRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       578 L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~  633 (673)
                      |+|++|.+..+|+ .+..|++|++|+|+++. +..+|.. +..+++|++|++++|.+.
T Consensus        83 L~Ls~N~l~~i~~~~f~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~~  139 (193)
T 2wfh_A           83 LILSYNRLRCIPPRTFDGLKSLRLLSLHGND-ISVVPEGAFNDLSALSHLAIGANPLY  139 (193)
T ss_dssp             EECCSSCCCBCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             EECCCCccCEeCHHHhCCCCCCCEEECCCCC-CCeeChhhhhcCccccEEEeCCCCee
Confidence            8888888877764 57888888888888865 7777764 677888888888776653

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=98.97  E-value=4.7e-10  Score=124.89  Aligned_cols=133  Identities=16%  Similarity=0.180  Sum_probs=95.1

Q ss_pred             EEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cccccccc
Q 005860          495 RHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLI  573 (673)
Q Consensus       495 r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~  573 (673)
                      +++.+..+....+|..+.  ++|++|++.++..    ....+..|.++++|++|++++       +.+..+ |..++.++
T Consensus        34 ~~l~ls~~~L~~ip~~~~--~~L~~L~Ls~N~i----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~~~~~l~  100 (562)
T 3a79_B           34 SMVDYSNRNLTHVPKDLP--PRTKALSLSQNSI----SELRMPDISFLSELRVLRLSH-------NRIRSLDFHVFLFNQ  100 (562)
T ss_dssp             CEEECTTSCCCSCCTTSC--TTCCEEECCSSCC----CCCCGGGTTTCTTCCEEECCS-------CCCCEECTTTTTTCT
T ss_pred             cEEEcCCCCCccCCCCCC--CCcCEEECCCCCc----cccChhhhccCCCccEEECCC-------CCCCcCCHHHhCCCC
Confidence            556666665555665443  6788888887763    344455677888888888888       777666 55678888


Q ss_pred             ccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccc--ccccccccCCeeeccccccccccccCCCCCCC
Q 005860          574 HLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLP--LGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNL  645 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L  645 (673)
                      +|++|+|++|.+..+|..  .+++|++|++++|. +..+|  ..++++++|++|++++|.+..  ..++.+++|
T Consensus       101 ~L~~L~Ls~N~l~~lp~~--~l~~L~~L~Ls~N~-l~~l~~p~~~~~l~~L~~L~L~~n~l~~--~~~~~l~~L  169 (562)
T 3a79_B          101 DLEYLDVSHNRLQNISCC--PMASLRHLDLSFND-FDVLPVCKEFGNLTKLTFLGLSAAKFRQ--LDLLPVAHL  169 (562)
T ss_dssp             TCCEEECTTSCCCEECSC--CCTTCSEEECCSSC-CSBCCCCGGGGGCTTCCEEEEECSBCCT--TTTGGGTTS
T ss_pred             CCCEEECCCCcCCccCcc--ccccCCEEECCCCC-ccccCchHhhcccCcccEEecCCCcccc--Cchhhhhhc
Confidence            888888888888888876  78888888888866 66654  678888888888888777664  245555555

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=98.96  E-value=5.4e-10  Score=120.75  Aligned_cols=134  Identities=16%  Similarity=0.155  Sum_probs=90.5

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....++  +..+++|++|.+.++...    . ++  +..++.|++|++++       +.+..+|  ++
T Consensus        63 l~~L~~L~Ls~n~l~~~~--~~~l~~L~~L~Ls~N~l~----~-~~--~~~l~~L~~L~L~~-------N~l~~l~--~~  124 (457)
T 3bz5_A           63 LTGLTKLICTSNNITTLD--LSQNTNLTYLACDSNKLT----N-LD--VTPLTKLTYLNCDT-------NKLTKLD--VS  124 (457)
T ss_dssp             CTTCSEEECCSSCCSCCC--CTTCTTCSEEECCSSCCS----C-CC--CTTCTTCCEEECCS-------SCCSCCC--CT
T ss_pred             cCCCCEEEccCCcCCeEc--cccCCCCCEEECcCCCCc----e-ee--cCCCCcCCEEECCC-------CcCCeec--CC
Confidence            456777777777665553  667788888888777641    1 12  56777888888887       7766664  77


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      .+++|++|++++|.+..+|  ++.+++|++|++++|..+..+  .++.+++|++|++++|.++.+|  ++.+++|+.|
T Consensus       125 ~l~~L~~L~l~~N~l~~l~--l~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~ls~n~l~~l~--l~~l~~L~~L  196 (457)
T 3bz5_A          125 QNPLLTYLNCARNTLTEID--VSHNTQLTELDCHLNKKITKL--DVTPQTQLTTLDCSFNKITELD--VSQNKLLNRL  196 (457)
T ss_dssp             TCTTCCEEECTTSCCSCCC--CTTCTTCCEEECTTCSCCCCC--CCTTCTTCCEEECCSSCCCCCC--CTTCTTCCEE
T ss_pred             CCCcCCEEECCCCccceec--cccCCcCCEEECCCCCccccc--ccccCCcCCEEECCCCccceec--cccCCCCCEE
Confidence            7778888888877777765  667777777777776555555  3566677777777666666665  4444444443

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.96  E-value=3.9e-10  Score=106.64  Aligned_cols=124  Identities=19%  Similarity=0.208  Sum_probs=92.4

Q ss_pred             EEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHH-HHhhhCCccceeeeccccccccccchhhh-cccccccc
Q 005860          496 HSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQ-SLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLI  573 (673)
Q Consensus       496 ~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~-~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~  573 (673)
                      .+.+..+....+|..+.  .+|++|.+.++.+    ....+ ..|..+++|+.|+|++       +.+..+ |..+..+.
T Consensus        12 ~l~~s~~~l~~ip~~~~--~~l~~L~l~~n~i----~~~~~~~~~~~l~~L~~L~Ls~-------N~l~~~~~~~~~~l~   78 (192)
T 1w8a_A           12 TVDCTGRGLKEIPRDIP--LHTTELLLNDNEL----GRISSDGLFGRLPHLVKLELKR-------NQLTGIEPNAFEGAS   78 (192)
T ss_dssp             EEECTTSCCSSCCSCCC--TTCSEEECCSCCC----CSBCCSCSGGGCTTCCEEECCS-------SCCCCBCTTTTTTCT
T ss_pred             EEEcCCCCcCcCccCCC--CCCCEEECCCCcC----CccCCccccccCCCCCEEECCC-------CCCCCcCHhHcCCcc
Confidence            45555555556665443  3788888888763    22222 2477888899999988       887776 66788889


Q ss_pred             ccccceecCCCCcccchh-hhcCCCccEEEeccCCCCccc-cccccccccCCeeeccccccc
Q 005860          574 HLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRL-PLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       574 ~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      +|++|+|++|.+..+|.. +..+++|++|+|+++. +..+ |..++.+++|++|++++|.+.
T Consensus        79 ~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~  139 (192)
T 1w8a_A           79 HIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQ-ISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             TCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSC-CCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCc-CCeeCHHHhhcCCCCCEEEeCCCCcc
Confidence            999999999888887654 7888999999998876 6554 677888889999998888765

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=98.96  E-value=2.4e-10  Score=128.53  Aligned_cols=146  Identities=11%  Similarity=0.118  Sum_probs=117.7

Q ss_pred             ccCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cc
Q 005860          490 YQEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~  567 (673)
                      .+..++++.+..+..... +..+..+++|++|++.++..    ....|..|.++++|++|++++       +.+..+ |.
T Consensus        31 l~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~i----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~   99 (606)
T 3t6q_A           31 LPNSTECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQI----YWIHEDTFQSQHRLDTLVLTA-------NPLIFMAET   99 (606)
T ss_dssp             SCTTCCEEECTTCCCSEECTTTSTTCTTCSEEECTTCCC----CEECTTTTTTCTTCCEEECTT-------CCCSEECTT
T ss_pred             CCCcCcEEEccCCccCcCChhHhccCccceEEECCCCcc----ceeChhhccCccccCeeeCCC-------CcccccChh
Confidence            456789999998887666 44677899999999998863    345567788999999999999       887665 66


Q ss_pred             ccccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCcccc-ccccccccCCeeecccccccccc-ccCCCCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFIP-KGIQRLTN  644 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~lP-~~i~~L~~  644 (673)
                      .++.+++|++|+|++|.+..+ |..++++++|++|++++|. +..++ ..+..+++|++|++++|.+..++ ..++.+++
T Consensus       100 ~~~~l~~L~~L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~  178 (606)
T 3t6q_A          100 ALSGPKALKHLFFIQTGISSIDFIPLHNQKTLESLYLGSNH-ISSIKLPKGFPTEKLKVLDFQNNAIHYLSKEDMSSLQQ  178 (606)
T ss_dssp             TTSSCTTCCEEECTTSCCSCGGGSCCTTCTTCCEEECCSSC-CCCCCCCTTCCCTTCCEEECCSSCCCEECHHHHHTTTT
T ss_pred             hhcccccccEeeccccCcccCCcchhccCCcccEEECCCCc-ccccCcccccCCcccCEEEcccCcccccChhhhhhhcc
Confidence            899999999999999998887 6788999999999999976 77653 34445899999999999888774 44777777


Q ss_pred             CCc
Q 005860          645 LRT  647 (673)
Q Consensus       645 L~~  647 (673)
                      |+.
T Consensus       179 L~~  181 (606)
T 3t6q_A          179 ATN  181 (606)
T ss_dssp             CCS
T ss_pred             cce
Confidence            773

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=98.96  E-value=2.3e-10  Score=133.68  Aligned_cols=136  Identities=19%  Similarity=0.219  Sum_probs=110.4

Q ss_pred             cCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhhh-ccccccccccccc
Q 005860          501 LGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNKI-LKGIEKLIHLRYL  578 (673)
Q Consensus       501 ~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~l-p~~i~~L~~Lr~L  578 (673)
                      .+....+|.   -.++|++|+++++..    ....+..|.++++|++|+|++       +. +..+ |..++++++|++|
T Consensus        13 ~~~L~~vP~---lp~~l~~LdLs~N~i----~~i~~~~~~~l~~L~~LdLs~-------n~~~~~i~~~~f~~L~~L~~L   78 (844)
T 3j0a_A           13 FCNLTQVPQ---VLNTTERLLLSFNYI----RTVTASSFPFLEQLQLLELGS-------QYTPLTIDKEAFRNLPNLRIL   78 (844)
T ss_dssp             CCCSSCCCS---SCTTCCEEEEESCCC----CEECSSSCSSCCSCSEEEECT-------TCCCCEECTTTTSSCTTCCEE
T ss_pred             CCCCCCCCC---CCCCcCEEECCCCcC----CccChhHCcccccCeEEeCCC-------CCCccccCHHHhcCCCCCCEE
Confidence            334455554   457899999998873    344566789999999999999       74 5556 7789999999999


Q ss_pred             eecCCCCccc-chhhhcCCCccEEEeccCCCCcccccc--ccccccCCeeecccccccccc--ccCCCCCCCCcCCe
Q 005860          579 RLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPLG--IGKLVNLRHLTYDDSCLEFIP--KGIQRLTNLRTLSE  650 (673)
Q Consensus       579 ~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~~--i~~L~~Lr~L~l~~~~l~~lP--~~i~~L~~L~~L~~  650 (673)
                      +|++|.+..+ |..+++|++|++|+|++|.....+|..  +++|++|++|++++|.+..++  ..++++++|++|..
T Consensus        79 ~Ls~N~l~~~~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~L  155 (844)
T 3j0a_A           79 DLGSSKIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDF  155 (844)
T ss_dssp             ECTTCCCCEECTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEE
T ss_pred             ECCCCcCcccCHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEEC
Confidence            9999998877 889999999999999998733346665  899999999999999988764  45888888888754

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=98.96  E-value=6.3e-10  Score=105.26  Aligned_cols=98  Identities=20%  Similarity=0.324  Sum_probs=78.3

Q ss_pred             CccceeeeccccccccccchhhhccccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccccc
Q 005860          543 KCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLV  620 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~  620 (673)
                      +.|+.|++++       +.+..+|..+..+.+|++|+|++|.+..+| ..+..|++|++|+|+++. +..+|. .++.++
T Consensus        31 ~~l~~L~L~~-------n~i~~ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~-l~~i~~~~f~~l~  102 (193)
T 2wfh_A           31 RDVTELYLDG-------NQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNR-LRCIPPRTFDGLK  102 (193)
T ss_dssp             TTCCEEECCS-------SCCCSCCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTTTCT
T ss_pred             CCCCEEECCC-------CcCchhHHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCc-cCEeCHHHhCCCC
Confidence            4788888888       888888888888888888888888888876 458888888888888866 777764 588888


Q ss_pred             cCCeeecccccccccccc-CCCCCCCCcC
Q 005860          621 NLRHLTYDDSCLEFIPKG-IQRLTNLRTL  648 (673)
Q Consensus       621 ~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L  648 (673)
                      +|++|++++|.+..+|.+ +..+++|+.|
T Consensus       103 ~L~~L~L~~N~l~~~~~~~~~~l~~L~~L  131 (193)
T 2wfh_A          103 SLRLLSLHGNDISVVPEGAFNDLSALSHL  131 (193)
T ss_dssp             TCCEEECCSSCCCBCCTTTTTTCTTCCEE
T ss_pred             CCCEEECCCCCCCeeChhhhhcCccccEE
Confidence            888888888888888865 5666666655

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.95  E-value=4e-10  Score=106.57  Aligned_cols=75  Identities=20%  Similarity=0.233  Sum_probs=34.2

Q ss_pred             cchhhhccc--cccccccccceecCCCCccc-chhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccc
Q 005860          560 NSTNKILKG--IEKLIHLRYLRLVGLGTEEL-PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFI  635 (673)
Q Consensus       560 ~~~~~lp~~--i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~l  635 (673)
                      +.+..+++.  ++.+++|++|+|++|.+..+ |..+..+++|++|+|+++. +..+|. .++.+++|++|++++|.++.+
T Consensus        39 n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~  117 (192)
T 1w8a_A           39 NELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENK-IKEISNKMFLGLHQLKTLNLYDNQISCV  117 (192)
T ss_dssp             CCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCC-CCEECSSSSTTCTTCCEEECCSSCCCEE
T ss_pred             CcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCCCc-CCccCHHHhcCCCCCCEEECCCCcCCee
Confidence            444444332  44444555555554444444 3444444555555554433 443332 244444555555444444433

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=98.95  E-value=7.7e-10  Score=119.66  Aligned_cols=142  Identities=15%  Similarity=0.169  Sum_probs=114.4

Q ss_pred             ccCceEEEEEEcCCCCcc-ccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cc
Q 005860          490 YQEKLRHSMLVLGYEASF-PISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~  567 (673)
                      .+.+++++.+..+..... +..+..+++|++|.+.++..   .....+..|.++++|++|++++       +.+..+ |.
T Consensus        28 l~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~~---~~~i~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~   97 (455)
T 3v47_A           28 LPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTP---GLVIRNNTFRGLSSLIILKLDY-------NQFLQLETG   97 (455)
T ss_dssp             CCTTCCEEECCSSCCCEECTTTTSSCTTCCEEECCCCST---TCEECTTTTTTCTTCCEEECTT-------CTTCEECTT
T ss_pred             CCCccCEEEecCCccCcCChhHhccCccccEEECcCCcc---cceECcccccccccCCEEeCCC-------CccCccChh
Confidence            457899999998887665 55678899999999998863   1123356688999999999999       887765 77


Q ss_pred             ccccccccccceecCCCCcc-cchh--hhcCCCccEEEeccCCCCccc-ccc-ccccccCCeeecccccccccc-ccCCC
Q 005860          568 GIEKLIHLRYLRLVGLGTEE-LPET--CCELLNLQVLEIEQCTSLKRL-PLG-IGKLVNLRHLTYDDSCLEFIP-KGIQR  641 (673)
Q Consensus       568 ~i~~L~~Lr~L~L~~~~i~~-LP~~--i~~L~~L~~L~l~~c~~l~~l-P~~-i~~L~~Lr~L~l~~~~l~~lP-~~i~~  641 (673)
                      .++.+++|++|+|++|.+.. .|..  ++++++|++|++++|. +..+ |.. ++++++|++|++++|.+..++ ..++.
T Consensus        98 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~  176 (455)
T 3v47_A           98 AFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNN-IKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLN  176 (455)
T ss_dssp             TTTTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSB-CCSCCCCGGGGGCTTCCEEECTTCCBSCCCTTTSGG
T ss_pred             hccCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCc-cCccCcccccCCCCcccEEeCCCCcccccChhhhhc
Confidence            89999999999999999775 4555  8999999999999987 6666 655 899999999999999887664 33444


Q ss_pred             C
Q 005860          642 L  642 (673)
Q Consensus       642 L  642 (673)
                      +
T Consensus       177 l  177 (455)
T 3v47_A          177 F  177 (455)
T ss_dssp             G
T ss_pred             c
Confidence            4

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.95  E-value=5.4e-09  Score=110.46  Aligned_cols=169  Identities=14%  Similarity=0.085  Sum_probs=113.6

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~  246 (673)
                      ++.++||+.+++++..++....... ....+.+.|+|++|+||||||+.+++.  ..... ...+|+.++...+...+..
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~-~~~~~~~li~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~i~~~~~~~~~~~~~   92 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNP-GHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAIIG   92 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHST-TSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCC-CCCCCeEEEECCCCCCHHHHHHHHHHH--HhhhcCeeEEEEeCccCCCHHHHHH
Confidence            3689999999999999886521000 122348999999999999999999985  22221 2467888888778889999


Q ss_pred             HHHHHhhCCCCC-cCcHHHHHHHHHHHhC--CCeEEEEEcCCCCCCccchhhhhhhccCCC----CCeEEEEEcCChhHH
Q 005860          247 AIIEALEGFVPT-VGELNSLLESIRASLV--GKKFLLILDDMWTDDYSKWEPFHYCLKNGV----RGSKILVTTRKETVA  319 (673)
Q Consensus       247 ~i~~~l~~~~~~-~~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~----~gs~iivTtr~~~v~  319 (673)
                      .++..++...+. ......+...+...+.  +++.+||||++..-+......+...+....    .+..||+||++....
T Consensus        93 ~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~  172 (389)
T 1fnn_A           93 EIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVL  172 (389)
T ss_dssp             HHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHH
T ss_pred             HHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHH
Confidence            999988764332 2244555556655553  678999999996554444555554443311    467788888876543


Q ss_pred             Hhccc-------cceeecCCCCccccc
Q 005860          320 RMMES-------IHVISIKELSEQECW  339 (673)
Q Consensus       320 ~~~~~-------~~~~~l~~L~~~~~~  339 (673)
                      ..+..       ...+.+++++.++..
T Consensus       173 ~~l~~~~~~r~~~~~i~~~pl~~~~~~  199 (389)
T 1fnn_A          173 NNLDPSTRGIMGKYVIRFSPYTKDQIF  199 (389)
T ss_dssp             HTSCHHHHHHHTTCEEECCCCBHHHHH
T ss_pred             HHhCHHhhhcCCCceEEeCCCCHHHHH
Confidence            33221       236889999887654

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=98.94  E-value=6.1e-10  Score=124.19  Aligned_cols=126  Identities=21%  Similarity=0.209  Sum_probs=80.4

Q ss_pred             hhhCCccceeeeccccccccccchhhhc--cccccccccccceecCCCCcc-cchhhhcCCCccEEEeccCCCCc--ccc
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKIL--KGIEKLIHLRYLRLVGLGTEE-LPETCCELLNLQVLEIEQCTSLK--RLP  613 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp--~~i~~L~~Lr~L~L~~~~i~~-LP~~i~~L~~L~~L~l~~c~~l~--~lP  613 (673)
                      +..+++|+.|++++       +.+...+  ..+..+++|++|++++|.+.. .|..++.+++|++|++++|. +.  .+|
T Consensus       392 ~~~l~~L~~L~l~~-------n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~p  463 (570)
T 2z63_A          392 FLGLEQLEHLDFQH-------SNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNS-FQENFLP  463 (570)
T ss_dssp             EETCTTCCEEECTT-------SEEESCTTSCTTTTCTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCE-EGGGEEC
T ss_pred             ccccCCCCEEEccC-------CccccccchhhhhcCCCCCEEeCcCCcccccchhhhhcCCcCcEEECcCCc-Cccccch
Confidence            44555666666665       5554433  256677777777777777544 45667778888888888776 43  577


Q ss_pred             ccccccccCCeeeccccccccc-cccCCCCCCCCcCCeeEE--ccCCccCCCccccCCCCCC
Q 005860          614 LGIGKLVNLRHLTYDDSCLEFI-PKGIQRLTNLRTLSEFVV--VRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       614 ~~i~~L~~Lr~L~l~~~~l~~l-P~~i~~L~~L~~L~~~~~--~~~~~~~~~~~~~l~~L~~  672 (673)
                      ..++.+++|+.|++++|.+..+ |..++++++|+.|..-..  ....+..+..+.+|+.|.+
T Consensus       464 ~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l  525 (570)
T 2z63_A          464 DIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASNQLKSVPDGIFDRLTSLQKIWL  525 (570)
T ss_dssp             SCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEEC
T ss_pred             hhhhcccCCCEEECCCCccccCChhhhhcccCCCEEeCCCCcCCCCCHHHhhcccCCcEEEe
Confidence            7788888888888888877776 556777777776643221  2222223455666666554

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=98.93  E-value=1.5e-09  Score=120.92  Aligned_cols=148  Identities=16%  Similarity=0.171  Sum_probs=116.7

Q ss_pred             ccCceEEEEEEcCCCCc-cccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hcc
Q 005860          490 YQEKLRHSMLVLGYEAS-FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~-~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~  567 (673)
                      ...+++++.+..+.... .+..+..+++|+.|.+.++...  .....+..|..+++|+.|++++       +.+.. +|.
T Consensus       351 ~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~--~~~~~~~~~~~l~~L~~L~l~~-------N~l~~~~~~  421 (562)
T 3a79_B          351 SPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLK--NFFKVALMTKNMSSLETLDVSL-------NSLNSHAYD  421 (562)
T ss_dssp             SCCCCCEEECCSSCCCTTTTTTCCSCSSCCEEECCSSCCC--BTTHHHHTTTTCTTCCEEECTT-------SCCBSCCSS
T ss_pred             CCCCceEEECCCCccccchhhhhcccCCCCEEECCCCCcC--CcccchhhhcCCCCCCEEECCC-------CcCCCccCh
Confidence            35678888888877654 4566778899999999988641  1113456678899999999999       88776 776


Q ss_pred             c-cccccccccceecCCCC-cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccccc-CCCCCC
Q 005860          568 G-IEKLIHLRYLRLVGLGT-EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTN  644 (673)
Q Consensus       568 ~-i~~L~~Lr~L~L~~~~i-~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~  644 (673)
                      . +..+.+|++|+|++|.+ ...|..+.  ++|++|++++|. +..+|..+..+++|++|++++|.++.+|.. ++.+++
T Consensus       422 ~~~~~l~~L~~L~l~~n~l~~~~~~~l~--~~L~~L~L~~N~-l~~ip~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~  498 (562)
T 3a79_B          422 RTCAWAESILVLNLSSNMLTGSVFRCLP--PKVKVLDLHNNR-IMSIPKDVTHLQALQELNVASNQLKSVPDGVFDRLTS  498 (562)
T ss_dssp             CCCCCCTTCCEEECCSSCCCGGGGSSCC--TTCSEEECCSSC-CCCCCTTTTSSCCCSEEECCSSCCCCCCTTSTTTCTT
T ss_pred             hhhcCcccCCEEECCCCCCCcchhhhhc--CcCCEEECCCCc-CcccChhhcCCCCCCEEECCCCCCCCCCHHHHhcCCC
Confidence            4 77889999999999986 44555443  689999999975 899999888999999999999999999987 777777


Q ss_pred             CCcCC
Q 005860          645 LRTLS  649 (673)
Q Consensus       645 L~~L~  649 (673)
                      |+.|.
T Consensus       499 L~~L~  503 (562)
T 3a79_B          499 LQYIW  503 (562)
T ss_dssp             CCCEE
T ss_pred             CCEEE
Confidence            77653

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.93  E-value=1.1e-09  Score=115.65  Aligned_cols=167  Identities=16%  Similarity=0.183  Sum_probs=106.8

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC---CeEEEEEcCCcccHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF---DKRMWVCVSDPFDELRI  244 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~~~~~~~  244 (673)
                      ++.++||+.+++.+.+++.....   ......+.|+|++|+||||||+.+++.  ....+   ...+|+.+....+...+
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~---~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~~   93 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYR---EEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYRV   93 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGG---TCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc---CCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHHH
Confidence            46899999999999998864210   123568999999999999999999985  33332   24677877666677778


Q ss_pred             HHHHHHHhhCCCCC-cCcHHHHHHHHHHHhC--CCeEEEEEcCCCCCC----ccchhhhhhhccC-CCCCeEEEEEcCCh
Q 005860          245 AKAIIEALEGFVPT-VGELNSLLESIRASLV--GKKFLLILDDMWTDD----YSKWEPFHYCLKN-GVRGSKILVTTRKE  316 (673)
Q Consensus       245 ~~~i~~~l~~~~~~-~~~~~~~~~~l~~~l~--~kr~LlVLDdvw~~~----~~~~~~l~~~l~~-~~~gs~iivTtr~~  316 (673)
                      +..++..++..... ..+..+....+.+.+.  +++.+||||+++.-.    ...+..+...+.. ...+..+|+||+..
T Consensus        94 ~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~  173 (386)
T 2qby_A           94 LADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDV  173 (386)
T ss_dssp             HHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCG
T ss_pred             HHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCC
Confidence            88888777554322 2234555556665554  458999999995421    1223333333322 23455678888765


Q ss_pred             hHHHhccc-------cceeecCCCCccccc
Q 005860          317 TVARMMES-------IHVISIKELSEQECW  339 (673)
Q Consensus       317 ~v~~~~~~-------~~~~~l~~L~~~~~~  339 (673)
                      .....+..       ...+++++++.++..
T Consensus       174 ~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~  203 (386)
T 2qby_A          174 KFVDLLDPRVKSSLSEEEIIFPPYNAEELE  203 (386)
T ss_dssp             GGGGGCTTHHHHTTTTEEEEECCCCHHHHH
T ss_pred             ChHhhhCHHHhccCCCeeEEeCCCCHHHHH
Confidence            43222211       147889999887754

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=98.92  E-value=8.3e-10  Score=125.92  Aligned_cols=133  Identities=20%  Similarity=0.201  Sum_probs=109.6

Q ss_pred             CCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceec
Q 005860          503 YEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLV  581 (673)
Q Consensus       503 ~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~  581 (673)
                      ....+|..+.  +++++|.+.++..    ....+..|.++++|++|++++       +.+..+ |..++.+++|++|+|+
T Consensus        15 ~L~~ip~~~~--~~l~~L~Ls~n~l----~~~~~~~~~~l~~L~~L~Ls~-------n~l~~~~~~~~~~l~~L~~L~L~   81 (680)
T 1ziw_A           15 KLTQVPDDLP--TNITVLNLTHNQL----RRLPAANFTRYSQLTSLDVGF-------NTISKLEPELCQKLPMLKVLNLQ   81 (680)
T ss_dssp             CCSSCCSCSC--TTCSEEECCSSCC----CCCCGGGGGGGTTCSEEECCS-------SCCCCCCTTHHHHCTTCCEEECC
T ss_pred             CccccccccC--CCCcEEECCCCCC----CCcCHHHHhCCCcCcEEECCC-------CccCccCHHHHhcccCcCEEECC
Confidence            3445555443  7899999998863    344556789999999999999       887765 5678999999999999


Q ss_pred             CCCCcccch-hhhcCCCccEEEeccCCCCcccc-ccccccccCCeeecccccccccc-ccCCCCCCCCcCC
Q 005860          582 GLGTEELPE-TCCELLNLQVLEIEQCTSLKRLP-LGIGKLVNLRHLTYDDSCLEFIP-KGIQRLTNLRTLS  649 (673)
Q Consensus       582 ~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L~~Lr~L~l~~~~l~~lP-~~i~~L~~L~~L~  649 (673)
                      +|.+..+|+ .++++++|++|++++|. +..+| ..++++++|++|++++|.+..+| ..++++++|++|.
T Consensus        82 ~n~l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~  151 (680)
T 1ziw_A           82 HNELSQLSDKTFAFCTNLTELHLMSNS-IQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELL  151 (680)
T ss_dssp             SSCCCCCCTTTTTTCTTCSEEECCSSC-CCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEE
T ss_pred             CCccCccChhhhccCCCCCEEECCCCc-cCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEE
Confidence            999999997 69999999999999987 77777 57999999999999999888765 4477788887764

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=98.92  E-value=1.3e-09  Score=121.54  Aligned_cols=130  Identities=23%  Similarity=0.220  Sum_probs=92.4

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....+|.   .+++|++|++++|.+    . .+|.   .+++|+.|++++       |.+..+|.   
T Consensus        60 ~~~L~~L~L~~N~l~~lp~---~l~~L~~L~Ls~N~l----~-~lp~---~l~~L~~L~Ls~-------N~l~~l~~---  118 (622)
T 3g06_A           60 PAHITTLVIPDNNLTSLPA---LPPELRTLEVSGNQL----T-SLPV---LPPGLLELSIFS-------NPLTHLPA---  118 (622)
T ss_dssp             CTTCSEEEECSCCCSCCCC---CCTTCCEEEECSCCC----S-CCCC---CCTTCCEEEECS-------CCCCCCCC---
T ss_pred             CCCCcEEEecCCCCCCCCC---cCCCCCEEEcCCCcC----C-cCCC---CCCCCCEEECcC-------CcCCCCCC---
Confidence            3678888888887776665   568899999888864    1 1222   678899999988       88887777   


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccccccccc-----------------ccCCeeeccccccc
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKL-----------------VNLRHLTYDDSCLE  633 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L-----------------~~Lr~L~l~~~~l~  633 (673)
                      .+.+|++|+|++|.+..+|..   +++|++|++++|. +..+|..+.+|                 ++|++|++++|.++
T Consensus       119 ~l~~L~~L~L~~N~l~~lp~~---l~~L~~L~Ls~N~-l~~l~~~~~~L~~L~L~~N~l~~l~~~~~~L~~L~Ls~N~l~  194 (622)
T 3g06_A          119 LPSGLCKLWIFGNQLTSLPVL---PPGLQELSVSDNQ-LASLPALPSELCKLWAYNNQLTSLPMLPSGLQELSVSDNQLA  194 (622)
T ss_dssp             CCTTCCEEECCSSCCSCCCCC---CTTCCEEECCSSC-CSCCCCCCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCS
T ss_pred             CCCCcCEEECCCCCCCcCCCC---CCCCCEEECcCCc-CCCcCCccCCCCEEECCCCCCCCCcccCCCCcEEECCCCCCC
Confidence            567788888888888888874   4788888888875 76666543322                 56666777777776


Q ss_pred             cccccCCCCCCC
Q 005860          634 FIPKGIQRLTNL  645 (673)
Q Consensus       634 ~lP~~i~~L~~L  645 (673)
                      .+|..+.+|+.|
T Consensus       195 ~l~~~~~~L~~L  206 (622)
T 3g06_A          195 SLPTLPSELYKL  206 (622)
T ss_dssp             CCCCCCTTCCEE
T ss_pred             CCCCccchhhEE
Confidence            666554444333

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.92  E-value=9.6e-10  Score=102.43  Aligned_cols=125  Identities=22%  Similarity=0.294  Sum_probs=91.6

Q ss_pred             EEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-cccccccc
Q 005860          498 MLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHLR  576 (673)
Q Consensus       498 ~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~Lr  576 (673)
                      .+..+....+|..+  .++|++|.+.++..    ....+..|..+++|++|++++       +.+..+|+. +..+.+|+
T Consensus        13 ~~~~~~l~~~p~~~--~~~l~~L~l~~n~l----~~~~~~~~~~l~~L~~L~l~~-------n~l~~~~~~~~~~l~~L~   79 (177)
T 2o6r_A           13 RCNSKGLTSVPTGI--PSSATRLELESNKL----QSLPHGVFDKLTQLTKLSLSQ-------NQIQSLPDGVFDKLTKLT   79 (177)
T ss_dssp             ECCSSCCSSCCTTC--CTTCSEEECCSSCC----CCCCTTTTTTCTTCSEEECCS-------SCCCCCCTTTTTTCTTCC
T ss_pred             EecCCCCccCCCCC--CCCCcEEEeCCCcc----cEeCHHHhcCcccccEEECCC-------CcceEeChhHccCCCccC
Confidence            33333334444333  36788888887763    234455677888899999988       888777665 58888999


Q ss_pred             cceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccc
Q 005860          577 YLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       577 ~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +|+|++|.+..+|.. +..+++|++|+++++. +..+|.. +..+++|++|++++|.+...+
T Consensus        80 ~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~~~~~~  140 (177)
T 2o6r_A           80 ILYLHENKLQSLPNGVFDKLTQLKELALDTNQ-LKSVPDGIFDRLTSLQKIWLHTNPWDCSC  140 (177)
T ss_dssp             EEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCBCCCH
T ss_pred             EEECCCCCccccCHHHhhCCcccCEEECcCCc-ceEeCHHHhcCCcccCEEEecCCCeeccC
Confidence            999999888888765 5788899999998875 8888876 477889999998888765433

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.91  E-value=3.8e-09  Score=103.52  Aligned_cols=158  Identities=11%  Similarity=0.104  Sum_probs=89.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++||+..++.+..++....      ....+.|+|++|+||||||+.+++.......+..   .......+.    ..+
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~------~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~---~~~~~~~~~----~~~   89 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR------IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA---TPCGVCDNC----REI   89 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC------CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS---SCCSCSHHH----HHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCC------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC---CCCcccHHH----HHH
Confidence            469999999999999986543      1347899999999999999999874221111100   000000000    000


Q ss_pred             HHHhh-----CCCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhH-
Q 005860          249 IEALE-----GFVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETV-  318 (673)
Q Consensus       249 ~~~l~-----~~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v-  318 (673)
                      .....     .........+.....+...    ..+++.+||+||++.-+...++.+...+.....+..+|+||+.... 
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~  169 (250)
T 1njg_A           90 EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  169 (250)
T ss_dssp             HTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGS
T ss_pred             hccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhC
Confidence            00000     0000001111111111111    2356899999999665555677777777666667889998876431 


Q ss_pred             HH-hccccceeecCCCCccccc
Q 005860          319 AR-MMESIHVISIKELSEQECW  339 (673)
Q Consensus       319 ~~-~~~~~~~~~l~~L~~~~~~  339 (673)
                      .. .......+++++++.++..
T Consensus       170 ~~~l~~r~~~i~l~~l~~~e~~  191 (250)
T 1njg_A          170 PVTILSRCLQFHLKALDVEQIR  191 (250)
T ss_dssp             CHHHHTTSEEEECCCCCHHHHH
T ss_pred             CHHHHHHhhhccCCCCCHHHHH
Confidence            11 1122467889999987754

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.89  E-value=2.2e-09  Score=99.64  Aligned_cols=111  Identities=18%  Similarity=0.218  Sum_probs=89.2

Q ss_pred             chhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceecCCCCcccchh-hhcC
Q 005860          518 RSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVGLGTEELPET-CCEL  595 (673)
Q Consensus       518 r~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L  595 (673)
                      +++++.++..     ..+|..+  .+.|+.|+|++       +.+..+ |..+..+++|++|+|++|.+..+|.. +.+|
T Consensus        15 ~~l~~~~n~l-----~~iP~~~--~~~L~~L~Ls~-------N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l   80 (174)
T 2r9u_A           15 TLVNCQNIRL-----ASVPAGI--PTDKQRLWLNN-------NQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKL   80 (174)
T ss_dssp             SEEECCSSCC-----SSCCSCC--CTTCSEEECCS-------SCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTC
T ss_pred             cEEEeCCCCC-----CccCCCc--CCCCcEEEeCC-------CCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCc
Confidence            5667776653     1223222  37899999999       998887 55789999999999999999999976 4899


Q ss_pred             CCccEEEeccCCCCcccccc-ccccccCCeeeccccccccccccCCCCC
Q 005860          596 LNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKGIQRLT  643 (673)
Q Consensus       596 ~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~i~~L~  643 (673)
                      ++|++|+|+++. +..+|.. ++.+++|++|++++|.+...|..+..|.
T Consensus        81 ~~L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~L~~N~~~c~~~~~~~l~  128 (174)
T 2r9u_A           81 TQLTQLDLNDNH-LKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLR  128 (174)
T ss_dssp             TTCCEEECCSSC-CCCCCTTTTTTCTTCSEEECCSSCBCTTBGGGHHHH
T ss_pred             chhhEEECCCCc-cceeCHHHhccccCCCEEEeCCCCcccccccHHHHH
Confidence            999999999976 8899876 8999999999999999887776555444

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=98.88  E-value=8.1e-10  Score=121.78  Aligned_cols=130  Identities=18%  Similarity=0.176  Sum_probs=68.1

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....+|. +..  +|++|.+.+|.+.    . +|.   .+++|+.|++++       |.+..+|.   
T Consensus        99 l~~L~~L~Ls~N~l~~ip~-l~~--~L~~L~Ls~N~l~----~-lp~---~l~~L~~L~Ls~-------N~l~~lp~---  157 (571)
T 3cvr_A           99 PASLEYLDACDNRLSTLPE-LPA--SLKHLDVDNNQLT----M-LPE---LPALLEYINADN-------NQLTMLPE---  157 (571)
T ss_dssp             CTTCCEEECCSSCCSCCCC-CCT--TCCEEECCSSCCS----C-CCC---CCTTCCEEECCS-------SCCSCCCC---
T ss_pred             cCCCCEEEccCCCCCCcch-hhc--CCCEEECCCCcCC----C-CCC---cCccccEEeCCC-------CccCcCCC---
Confidence            3455566665555544444 322  5666666555421    1 222   345566666666       55555554   


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccC-------CeeeccccccccccccCCCCC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL-------RHLTYDDSCLEFIPKGIQRLT  643 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L-------r~L~l~~~~l~~lP~~i~~L~  643 (673)
                      .+++|++|+|++|.+..+|. ++  ++|++|+|++|. +..+|. +..  +|       +.|++++|.++.+|.++.+++
T Consensus       158 ~l~~L~~L~Ls~N~L~~lp~-l~--~~L~~L~Ls~N~-L~~lp~-~~~--~L~~~~~~L~~L~Ls~N~l~~lp~~l~~l~  230 (571)
T 3cvr_A          158 LPTSLEVLSVRNNQLTFLPE-LP--ESLEALDVSTNL-LESLPA-VPV--RNHHSEETEIFFRCRENRITHIPENILSLD  230 (571)
T ss_dssp             CCTTCCEEECCSSCCSCCCC-CC--TTCCEEECCSSC-CSSCCC-CC----------CCEEEECCSSCCCCCCGGGGGSC
T ss_pred             cCCCcCEEECCCCCCCCcch-hh--CCCCEEECcCCC-CCchhh-HHH--hhhcccccceEEecCCCcceecCHHHhcCC
Confidence            34556666666666555555 44  566666666543 555555 433  44       666666666666665555555


Q ss_pred             CCCcC
Q 005860          644 NLRTL  648 (673)
Q Consensus       644 ~L~~L  648 (673)
                      +|+.|
T Consensus       231 ~L~~L  235 (571)
T 3cvr_A          231 PTCTI  235 (571)
T ss_dssp             TTEEE
T ss_pred             CCCEE
Confidence            54443

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=98.88  E-value=9.5e-10  Score=114.61  Aligned_cols=161  Identities=17%  Similarity=0.151  Sum_probs=109.0

Q ss_pred             cCceEEEEEEcCCCCccccc-cccccccchhhhccchhhh----------------------hhhhhHHHHhhhCCccce
Q 005860          491 QEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQV----------------------SLTHVLQSLFDQLKCLRA  547 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~----------------------~~~~~~~~~~~~l~~L~~  547 (673)
                      +.+++.+.+..+....+++. +..+++|++|+++++....                      .+....+..|..+++|+.
T Consensus        29 ~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~L~~  108 (350)
T 4ay9_X           29 PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQY  108 (350)
T ss_dssp             CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCCE
T ss_pred             CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhcccccc
Confidence            34566677776666655543 4556777777666554210                      012233556778888999


Q ss_pred             eeecccc--ccc----------------cccchhhhcc-ccccc-cccccceecCCCCcccchhhhcCCCccEEEeccCC
Q 005860          548 LRIATLM--NTW----------------DVNSTNKILK-GIEKL-IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCT  607 (673)
Q Consensus       548 L~L~~~~--~~~----------------~~~~~~~lp~-~i~~L-~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~  607 (673)
                      |++++-.  ...                +.+.+..+|. .+..+ ..|++|+|++|.++.+|..+....+|+.|++++++
T Consensus       109 L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~i~~i~~~~f~~~~L~~l~l~~~n  188 (350)
T 4ay9_X          109 LLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNN  188 (350)
T ss_dssp             EEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEECTTSSTTEEEEEEECTTCT
T ss_pred             ccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhccccccccCCChhhccccchhHHhhccCC
Confidence            9887710  000                0011222222 22333 35888999999999999988888899999999888


Q ss_pred             CCcccccc-ccccccCCeeecccccccccccc-CCCCCCCCcCCee
Q 005860          608 SLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLSEF  651 (673)
Q Consensus       608 ~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~~~  651 (673)
                      .+..+|.+ +..+++|++|++++|.++.+|.+ +.+|++|+.+...
T Consensus       189 ~l~~i~~~~f~~l~~L~~LdLs~N~l~~lp~~~~~~L~~L~~l~~~  234 (350)
T 4ay9_X          189 NLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTY  234 (350)
T ss_dssp             TCCCCCTTTTTTEECCSEEECTTSCCCCCCSSSCTTCCEEECTTCT
T ss_pred             cccCCCHHHhccCcccchhhcCCCCcCccChhhhccchHhhhccCC
Confidence            89999975 69999999999999999999875 6667777666543

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.87  E-value=2.9e-09  Score=98.47  Aligned_cols=107  Identities=18%  Similarity=0.191  Sum_probs=81.3

Q ss_pred             ccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceecCCCCcccchh-hh
Q 005860          516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVGLGTEELPET-CC  593 (673)
Q Consensus       516 ~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~-i~  593 (673)
                      ..+++++.++..    .. +|..+  .+.|+.|+|++       +.+..+ |..+..+.+|++|+|++|.+..+|+. +.
T Consensus        10 ~~~~l~~s~n~l----~~-ip~~~--~~~l~~L~L~~-------N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~   75 (170)
T 3g39_A           10 SGTTVDCSGKSL----AS-VPTGI--PTTTQVLYLYD-------NQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFD   75 (170)
T ss_dssp             ETTEEECTTSCC----SS-CCSCC--CTTCSEEECCS-------SCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTT
T ss_pred             CCCEEEeCCCCc----Cc-cCccC--CCCCcEEEcCC-------CcCCccChhhhcCcccCCEEECCCCCcCccChhhcc
Confidence            356677777653    12 22222  37788999999       888877 55688899999999999998888875 47


Q ss_pred             cCCCccEEEeccCCCCcccccc-ccccccCCeeeccccccccccc
Q 005860          594 ELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPK  637 (673)
Q Consensus       594 ~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~  637 (673)
                      .+++|++|+|+++. +..+|.. +.++++|++|++++|.+...++
T Consensus        76 ~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~~c~c~  119 (170)
T 3g39_A           76 KLTQLTQLSLNDNQ-LKSIPRGAFDNLKSLTHIWLLNNPWDCACS  119 (170)
T ss_dssp             TCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCBCTTBG
T ss_pred             CCCCCCEEECCCCc-cCEeCHHHhcCCCCCCEEEeCCCCCCCCch
Confidence            89999999999865 8888864 7889999999998887765443

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.86  E-value=1.5e-08  Score=97.81  Aligned_cols=148  Identities=16%  Similarity=0.090  Sum_probs=91.1

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|++..++.+..++....       ...+.|+|++|+|||+||+.+++... ...+ ...+.+..+.......+...
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKT~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~   88 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERKN-------IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVVRHK   88 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC-------CCCEEEECSTTSSHHHHHHHHHHHHH-GGGGGGGEEEEETTCTTCHHHHHHH
T ss_pred             HHHcCcHHHHHHHHHHHhCCC-------CCeEEEECCCCCCHHHHHHHHHHHHh-ccccccceEEeccccccChHHHHHH
Confidence            468999999999999986543       22389999999999999999987421 1122 22344444443333322221


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhH-HH-hcccc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETV-AR-MMESI  325 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v-~~-~~~~~  325 (673)
                      +. .+....              ....+++.+||+||+..-.....+.+...+.....+.++|+||+.... .. .....
T Consensus        89 ~~-~~~~~~--------------~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~  153 (226)
T 2chg_A           89 IK-EFARTA--------------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRC  153 (226)
T ss_dssp             HH-HHHTSC--------------CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             HH-HHhccc--------------CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhC
Confidence            11 111100              011357899999999655445556666666655667889998876431 11 11223


Q ss_pred             ceeecCCCCccccc
Q 005860          326 HVISIKELSEQECW  339 (673)
Q Consensus       326 ~~~~l~~L~~~~~~  339 (673)
                      ..+++.+++.++..
T Consensus       154 ~~i~~~~~~~~~~~  167 (226)
T 2chg_A          154 AVFRFKPVPKEAMK  167 (226)
T ss_dssp             EEEECCCCCHHHHH
T ss_pred             ceeecCCCCHHHHH
Confidence            47888999887753

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=98.85  E-value=1.1e-09  Score=118.34  Aligned_cols=36  Identities=8%  Similarity=0.025  Sum_probs=11.1

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchh
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLI  527 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~  527 (673)
                      ..++.+.+..+....+|..+.++++|++|.+.++.+
T Consensus        11 ~~L~~L~l~~n~l~~iP~~i~~L~~L~~L~l~~n~~   46 (454)
T 1jl5_A           11 TFLQEPLRHSSNLTEMPVEAENVKSKTEYYNAWSEW   46 (454)
T ss_dssp             -----------------------CCHHHHHHHHHHH
T ss_pred             ccchhhhcccCchhhCChhHhcccchhhhhccCCcc
Confidence            457777787777777888899999999999988764

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=98.85  E-value=3.7e-09  Score=117.98  Aligned_cols=122  Identities=25%  Similarity=0.177  Sum_probs=86.9

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....+|.   .+++|++|.+.+|..    .. ++.   .+++|+.|++++       |.+..+|..+
T Consensus        79 ~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N~l----~~-l~~---~l~~L~~L~L~~-------N~l~~lp~~l  140 (622)
T 3g06_A           79 LPPELRTLEVSGNQLTSLPV---LPPGLLELSIFSNPL----TH-LPA---LPSGLCKLWIFG-------NQLTSLPVLP  140 (622)
T ss_dssp             CCTTCCEEEECSCCCSCCCC---CCTTCCEEEECSCCC----CC-CCC---CCTTCCEEECCS-------SCCSCCCCCC
T ss_pred             cCCCCCEEEcCCCcCCcCCC---CCCCCCEEECcCCcC----CC-CCC---CCCCcCEEECCC-------CCCCcCCCCC
Confidence            46789999999988777765   678999999998864    11 222   567889999988       8888887753


Q ss_pred             ccccccccceecCCCCcccchhhhcC-----------------CCccEEEeccCCCCccccccccccccCCeeecccccc
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCEL-----------------LNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCL  632 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L-----------------~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l  632 (673)
                         ++|++|+|++|.+..+|..+.+|                 ++|++|++++|. +..+|..+   ++|+.|++++|.+
T Consensus       141 ---~~L~~L~Ls~N~l~~l~~~~~~L~~L~L~~N~l~~l~~~~~~L~~L~Ls~N~-l~~l~~~~---~~L~~L~L~~N~l  213 (622)
T 3g06_A          141 ---PGLQELSVSDNQLASLPALPSELCKLWAYNNQLTSLPMLPSGLQELSVSDNQ-LASLPTLP---SELYKLWAYNNRL  213 (622)
T ss_dssp             ---TTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSC-CSCCCCCC---TTCCEEECCSSCC
T ss_pred             ---CCCCEEECcCCcCCCcCCccCCCCEEECCCCCCCCCcccCCCCcEEECCCCC-CCCCCCcc---chhhEEECcCCcc
Confidence               77888888888877766544333                 788999999876 87777543   3444455444444


Q ss_pred             cccc
Q 005860          633 EFIP  636 (673)
Q Consensus       633 ~~lP  636 (673)
                      ..+|
T Consensus       214 ~~l~  217 (622)
T 3g06_A          214 TSLP  217 (622)
T ss_dssp             SSCC
T ss_pred             cccC
Confidence            4444

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=98.83  E-value=9.9e-10  Score=116.11  Aligned_cols=127  Identities=18%  Similarity=0.253  Sum_probs=81.7

Q ss_pred             cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh------hhccccccccccccceecCCCC---
Q 005860          515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN------KILKGIEKLIHLRYLRLVGLGT---  585 (673)
Q Consensus       515 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~------~lp~~i~~L~~Lr~L~L~~~~i---  585 (673)
                      ++|++|.+.+|.........+...+..+++|+.|++++       |.+.      -.|..+..+++|++|+|++|.+   
T Consensus       159 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~-------n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~  231 (386)
T 2ca6_A          159 PPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQ-------NGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHL  231 (386)
T ss_dssp             CCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCS-------SCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHH
T ss_pred             CCCcEEECCCCCCCcHHHHHHHHHHHhCCCcCEEECcC-------CCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcH
Confidence            66777777766542111122234556677777777777       6544      2333677777788888877776   


Q ss_pred             --cccchhhhcCCCccEEEeccCCCCcc-----ccccc--cccccCCeeecccccccc-----ccccC-CCCCCCCcCC
Q 005860          586 --EELPETCCELLNLQVLEIEQCTSLKR-----LPLGI--GKLVNLRHLTYDDSCLEF-----IPKGI-QRLTNLRTLS  649 (673)
Q Consensus       586 --~~LP~~i~~L~~L~~L~l~~c~~l~~-----lP~~i--~~L~~Lr~L~l~~~~l~~-----lP~~i-~~L~~L~~L~  649 (673)
                        ..+|..+..+++|++|+|++|. +..     +|..+  +++++|++|++++|.+..     +|..+ .++++|++|.
T Consensus       232 g~~~l~~~l~~~~~L~~L~L~~n~-i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~~g~~~l~~~l~~~l~~L~~L~  309 (386)
T 2ca6_A          232 GSSALAIALKSWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLE  309 (386)
T ss_dssp             HHHHHHHHGGGCTTCCEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEE
T ss_pred             HHHHHHHHHccCCCcCEEECCCCC-CchhhHHHHHHHHhhccCCCeEEEECcCCcCCHHHHHHHHHHHHhcCCCceEEE
Confidence              5677777777788888887766 543     45555  447778888877777776     77665 4456666553

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.81  E-value=7e-09  Score=96.51  Aligned_cols=100  Identities=30%  Similarity=0.482  Sum_probs=85.5

Q ss_pred             CCccceeeeccccccccccchhhhccc-cccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCcccccc-ccc
Q 005860          542 LKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLG-IGK  618 (673)
Q Consensus       542 l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~  618 (673)
                      .+.|+.|++++       +.+..+|.. ++.+.+|++|+|++|.+..+|.. ++.+++|++|+++++. +..+|.. +++
T Consensus        27 ~~~l~~L~l~~-------n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~   98 (177)
T 2o6r_A           27 PSSATRLELES-------NKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENK-LQSLPNGVFDK   98 (177)
T ss_dssp             CTTCSEEECCS-------SCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTT
T ss_pred             CCCCcEEEeCC-------CcccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCCCC-ccccCHHHhhC
Confidence            36899999999       888887765 68999999999999999999865 6899999999999976 8888865 689


Q ss_pred             cccCCeeeccccccccccccC-CCCCCCCcCC
Q 005860          619 LVNLRHLTYDDSCLEFIPKGI-QRLTNLRTLS  649 (673)
Q Consensus       619 L~~Lr~L~l~~~~l~~lP~~i-~~L~~L~~L~  649 (673)
                      +++|++|++++|.+..+|..+ ..+++|+.|.
T Consensus        99 l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~  130 (177)
T 2o6r_A           99 LTQLKELALDTNQLKSVPDGIFDRLTSLQKIW  130 (177)
T ss_dssp             CTTCCEEECCSSCCSCCCTTTTTTCTTCCEEE
T ss_pred             CcccCEEECcCCcceEeCHHHhcCCcccCEEE
Confidence            999999999999999998764 6666666653

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=98.81  E-value=1.1e-09  Score=115.81  Aligned_cols=137  Identities=17%  Similarity=0.147  Sum_probs=94.0

Q ss_pred             CceEEEEEEcCCCC--ccc---cccccccccchhhhccchhhh-hhhhhHHHHhhhCCccceeeeccccccccccch---
Q 005860          492 EKLRHSMLVLGYEA--SFP---ISIFKAKNLRSLFINNTLIQV-SLTHVLQSLFDQLKCLRALRIATLMNTWDVNST---  562 (673)
Q Consensus       492 ~~~r~l~l~~~~~~--~~~---~~~~~~~~Lr~L~l~~~~~~~-~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~---  562 (673)
                      .+++++.+..+...  ..+   ..+..+++|++|.+.+|.... ......+..+..+++|+.|+|++       |.+   
T Consensus       159 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~-------n~l~~~  231 (386)
T 2ca6_A          159 PPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQD-------NTFTHL  231 (386)
T ss_dssp             CCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCS-------SCCHHH
T ss_pred             CCCcEEECCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcC-------CCCCcH
Confidence            57778877776653  222   234467788888888776421 11223343667788888888888       766   


Q ss_pred             --hhhccccccccccccceecCCCCcc-----cchhh--hcCCCccEEEeccCCCCcc-----ccccc-cccccCCeeec
Q 005860          563 --NKILKGIEKLIHLRYLRLVGLGTEE-----LPETC--CELLNLQVLEIEQCTSLKR-----LPLGI-GKLVNLRHLTY  627 (673)
Q Consensus       563 --~~lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i--~~L~~L~~L~l~~c~~l~~-----lP~~i-~~L~~Lr~L~l  627 (673)
                        ..+|..+..+++|++|+|++|.+..     +|..+  +++++|++|+|++|. +..     +|..+ .++++|++|++
T Consensus       232 g~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~-i~~~g~~~l~~~l~~~l~~L~~L~l  310 (386)
T 2ca6_A          232 GSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLEL  310 (386)
T ss_dssp             HHHHHHHHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEEC
T ss_pred             HHHHHHHHHccCCCcCEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCc-CCHHHHHHHHHHHHhcCCCceEEEc
Confidence              5577778888888888888887654     46666  347888888888876 655     77777 66788888888


Q ss_pred             ccccccccc
Q 005860          628 DDSCLEFIP  636 (673)
Q Consensus       628 ~~~~l~~lP  636 (673)
                      ++|.+...+
T Consensus       311 ~~N~l~~~~  319 (386)
T 2ca6_A          311 NGNRFSEED  319 (386)
T ss_dssp             TTSBSCTTS
T ss_pred             cCCcCCcch
Confidence            887766443

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.79  E-value=4.3e-09  Score=97.63  Aligned_cols=110  Identities=25%  Similarity=0.214  Sum_probs=80.9

Q ss_pred             EEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-ccccccc
Q 005860          497 SMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHL  575 (673)
Q Consensus       497 l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~L  575 (673)
                      +.+..+....+|..+.  ++|+.|.+.++.+    ....+..|.++++|+.|+|++       +.+..+|.. +..+.+|
T Consensus        17 l~~~~n~l~~iP~~~~--~~L~~L~Ls~N~l----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~i~~~~~~~l~~L   83 (174)
T 2r9u_A           17 VNCQNIRLASVPAGIP--TDKQRLWLNNNQI----TKLEPGVFDHLVNLQQLYFNS-------NKLTAIPTGVFDKLTQL   83 (174)
T ss_dssp             EECCSSCCSSCCSCCC--TTCSEEECCSSCC----CCCCTTTTTTCTTCCEEECCS-------SCCCCCCTTTTTTCTTC
T ss_pred             EEeCCCCCCccCCCcC--CCCcEEEeCCCCc----cccCHHHhcCCcCCCEEECCC-------CCCCccChhHhCCcchh
Confidence            4444444455565443  7788888888763    344566778888888888888       888888776 4788888


Q ss_pred             ccceecCCCCcccchh-hhcCCCccEEEeccCCCCccccccccccc
Q 005860          576 RYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPLGIGKLV  620 (673)
Q Consensus       576 r~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  620 (673)
                      ++|+|++|.+..+|+. +..+++|++|+|++++ +...|..+..|.
T Consensus        84 ~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~-~~c~~~~~~~l~  128 (174)
T 2r9u_A           84 TQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNP-WDCECRDIMYLR  128 (174)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCSEEECCSSC-BCTTBGGGHHHH
T ss_pred             hEEECCCCccceeCHHHhccccCCCEEEeCCCC-cccccccHHHHH
Confidence            8899888888888875 8888888888888866 776666555444

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=98.75  E-value=6.1e-09  Score=114.78  Aligned_cols=122  Identities=20%  Similarity=0.219  Sum_probs=101.2

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....+|   ..+++|++|++.+|.+    .. +|. +.+  +|+.|++++       |.+..+|.   
T Consensus        79 ~~~L~~L~Ls~N~l~~ip---~~l~~L~~L~Ls~N~l----~~-ip~-l~~--~L~~L~Ls~-------N~l~~lp~---  137 (571)
T 3cvr_A           79 PPQITVLEITQNALISLP---ELPASLEYLDACDNRL----ST-LPE-LPA--SLKHLDVDN-------NQLTMLPE---  137 (571)
T ss_dssp             CTTCSEEECCSSCCSCCC---CCCTTCCEEECCSSCC----SC-CCC-CCT--TCCEEECCS-------SCCSCCCC---
T ss_pred             cCCCCEEECcCCCCcccc---cccCCCCEEEccCCCC----CC-cch-hhc--CCCEEECCC-------CcCCCCCC---
Confidence            467899999988887766   3578999999998874    22 333 333  899999999       88888887   


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCC
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQR  641 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~  641 (673)
                      .+++|++|+|++|.++.+|.   .+++|++|+|++|. +..+|. ++  ++|++|++++|.++.+|. +..
T Consensus       138 ~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N~-L~~lp~-l~--~~L~~L~Ls~N~L~~lp~-~~~  200 (571)
T 3cvr_A          138 LPALLEYINADNNQLTMLPE---LPTSLEVLSVRNNQ-LTFLPE-LP--ESLEALDVSTNLLESLPA-VPV  200 (571)
T ss_dssp             CCTTCCEEECCSSCCSCCCC---CCTTCCEEECCSSC-CSCCCC-CC--TTCCEEECCSSCCSSCCC-CC-
T ss_pred             cCccccEEeCCCCccCcCCC---cCCCcCEEECCCCC-CCCcch-hh--CCCCEEECcCCCCCchhh-HHH
Confidence            68899999999999999997   67899999999976 888998 66  899999999999999998 654

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=98.74  E-value=5.9e-09  Score=112.43  Aligned_cols=133  Identities=21%  Similarity=0.228  Sum_probs=84.2

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK  571 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~  571 (673)
                      .+++.+.+..+....++..   .++|++|.+.++..    .. +| .|.++++|++|++++       +.+..+|..+  
T Consensus       111 ~~L~~L~l~~n~l~~l~~~---~~~L~~L~L~~n~l----~~-lp-~~~~l~~L~~L~l~~-------N~l~~lp~~~--  172 (454)
T 1jl5_A          111 QSLKSLLVDNNNLKALSDL---PPLLEYLGVSNNQL----EK-LP-ELQNSSFLKIIDVDN-------NSLKKLPDLP--  172 (454)
T ss_dssp             TTCCEEECCSSCCSCCCSC---CTTCCEEECCSSCC----SS-CC-CCTTCTTCCEEECCS-------SCCSCCCCCC--
T ss_pred             CCCcEEECCCCccCcccCC---CCCCCEEECcCCCC----CC-Cc-ccCCCCCCCEEECCC-------CcCcccCCCc--
Confidence            4556666655544333221   14667777766653    11 23 366777777777777       6666666543  


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                       .+|++|++++|.+..+| +++++++|++|++++|. +..+|...   .+|++|++++|.+..+| .++.+++|++|.
T Consensus       173 -~~L~~L~L~~n~l~~l~-~~~~l~~L~~L~l~~N~-l~~l~~~~---~~L~~L~l~~n~l~~lp-~~~~l~~L~~L~  243 (454)
T 1jl5_A          173 -PSLEFIAAGNNQLEELP-ELQNLPFLTAIYADNNS-LKKLPDLP---LSLESIVAGNNILEELP-ELQNLPFLTTIY  243 (454)
T ss_dssp             -TTCCEEECCSSCCSSCC-CCTTCTTCCEEECCSSC-CSSCCCCC---TTCCEEECCSSCCSSCC-CCTTCTTCCEEE
T ss_pred             -ccccEEECcCCcCCcCc-cccCCCCCCEEECCCCc-CCcCCCCc---CcccEEECcCCcCCccc-ccCCCCCCCEEE
Confidence             36777777777777776 47777777777777765 66666433   46777777777777777 366666666654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.69  E-value=4e-08  Score=100.88  Aligned_cols=148  Identities=18%  Similarity=0.189  Sum_probs=91.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|++..++.+..++....       .+.+.|+|++|+||||+|+.+++... ...+ ...+++..++...... .++
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~~-i~~   91 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGN-------MPHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGIDV-VRN   91 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC-------CCCEEEECSTTSSHHHHHHHHHHHHH-GGGHHHHEEEECTTSCCSHHH-HHT
T ss_pred             HHHHCCHHHHHHHHHHHHcCC-------CCeEEEECcCCCCHHHHHHHHHHHhc-CCcccCCEEEecCccccChHH-HHH
Confidence            579999999999999986543       22389999999999999999988521 1112 1244454444323221 122


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHh-CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHH-hccc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASL-VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VAR-MMES  324 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l-~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~-~~~~  324 (673)
                      +++.+....              ..+ .+++.+||+||++.-....++.+...+.....++.+|+||.... +.. ....
T Consensus        92 ~~~~~~~~~--------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr  157 (323)
T 1sxj_B           92 QIKHFAQKK--------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQ  157 (323)
T ss_dssp             HHHHHHHBC--------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTT
T ss_pred             HHHHHHhcc--------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhh
Confidence            222221000              011 45688999999966555556667766666566788888887643 111 1122


Q ss_pred             cceeecCCCCccccc
Q 005860          325 IHVISIKELSEQECW  339 (673)
Q Consensus       325 ~~~~~l~~L~~~~~~  339 (673)
                      ...+++.+++.++..
T Consensus       158 ~~~i~~~~~~~~~~~  172 (323)
T 1sxj_B          158 CAILRYSKLSDEDVL  172 (323)
T ss_dssp             SEEEECCCCCHHHHH
T ss_pred             ceEEeecCCCHHHHH
Confidence            457889999887754

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.65  E-value=3.4e-08  Score=91.15  Aligned_cols=98  Identities=22%  Similarity=0.262  Sum_probs=60.9

Q ss_pred             EEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc-ccccccc
Q 005860          497 SMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG-IEKLIHL  575 (673)
Q Consensus       497 l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~-i~~L~~L  575 (673)
                      +.+..+....+|..+  .++|++|++.++.+    ....+..|.++++|++|+|++       +.+..+|+. +..+.+|
T Consensus        14 l~~s~n~l~~ip~~~--~~~l~~L~L~~N~i----~~~~~~~~~~l~~L~~L~Ls~-------N~l~~l~~~~f~~l~~L   80 (170)
T 3g39_A           14 VDCSGKSLASVPTGI--PTTTQVLYLYDNQI----TKLEPGVFDRLTQLTRLDLDN-------NQLTVLPAGVFDKLTQL   80 (170)
T ss_dssp             EECTTSCCSSCCSCC--CTTCSEEECCSSCC----CCCCTTTTTTCTTCSEEECCS-------SCCCCCCTTTTTTCTTC
T ss_pred             EEeCCCCcCccCccC--CCCCcEEEcCCCcC----CccChhhhcCcccCCEEECCC-------CCcCccChhhccCCCCC
Confidence            333333444444433  25677777776652    333455566777777777777       766666654 3667777


Q ss_pred             ccceecCCCCcccchh-hhcCCCccEEEeccCC
Q 005860          576 RYLRLVGLGTEELPET-CCELLNLQVLEIEQCT  607 (673)
Q Consensus       576 r~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~  607 (673)
                      ++|+|++|.+..+|+. +..+++|++|+|++++
T Consensus        81 ~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  113 (170)
T 3g39_A           81 TQLSLNDNQLKSIPRGAFDNLKSLTHIWLLNNP  113 (170)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CEEECCCCccCEeCHHHhcCCCCCCEEEeCCCC
Confidence            7777777777777653 6677777777777654

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.51  E-value=1e-07  Score=97.90  Aligned_cols=50  Identities=26%  Similarity=0.401  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|++..++.+..++......  ......|.|+|++|+||||||+.+++.
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~--~~~~~~vll~G~~GtGKT~la~~i~~~   61 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKAR--KEPLEHLLLFGPPGLGKTTLAHVIAHE   61 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHH--CSCCCCCEEECCTTCCCHHHHHHHHHH
T ss_pred             HHhhCHHHHHHHHHHHHHHHHcc--CCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999988887532100  012356889999999999999999884

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.48  E-value=1.6e-07  Score=97.53  Aligned_cols=87  Identities=18%  Similarity=0.175  Sum_probs=52.3

Q ss_pred             hhhCCccceeeec-cccccccccchhhhc-cccccccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCcccccc
Q 005860          539 FDQLKCLRALRIA-TLMNTWDVNSTNKIL-KGIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPLG  615 (673)
Q Consensus       539 ~~~l~~L~~L~L~-~~~~~~~~~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~  615 (673)
                      +..+.+|+.|+|+ .       +.+..+| ..++.|.+|++|+|++|.+..+|+ .|.+|++|++|+|+++. +..+|..
T Consensus        27 l~~~~~L~~L~l~~~-------n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~   98 (347)
T 2ifg_A           27 LPGAENLTELYIENQ-------QHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNA-LESLSWK   98 (347)
T ss_dssp             SCSCSCCSEEECCSC-------SSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSC-CSCCCST
T ss_pred             CCCCCCeeEEEccCC-------CCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCc-cceeCHH
Confidence            5566666666665 3       4455554 346666666666666666666553 45666666666666644 6666654


Q ss_pred             ccccccCCeeeccccccc
Q 005860          616 IGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       616 i~~L~~Lr~L~l~~~~l~  633 (673)
                      +....+|+.|++.+|.+.
T Consensus        99 ~~~~~~L~~l~l~~N~~~  116 (347)
T 2ifg_A           99 TVQGLSLQELVLSGNPLH  116 (347)
T ss_dssp             TTCSCCCCEEECCSSCCC
T ss_pred             HcccCCceEEEeeCCCcc
Confidence            433333666666665544

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.44  E-value=1.8e-07  Score=97.72  Aligned_cols=132  Identities=13%  Similarity=0.039  Sum_probs=72.2

Q ss_pred             CceEEEEEEcCCCCccccc-----ccc-ccccchhhhccchhhhhhhhhHHHHhhhCC-ccceeeeccccccccccchhh
Q 005860          492 EKLRHSMLVLGYEASFPIS-----IFK-AKNLRSLFINNTLIQVSLTHVLQSLFDQLK-CLRALRIATLMNTWDVNSTNK  564 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~-----~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~-~L~~L~L~~~~~~~~~~~~~~  564 (673)
                      .+++.+.+..+.....+..     +.. .++|++|++.+|.........++..+..++ .|+.|++++       |.+..
T Consensus       109 ~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~-------n~l~~  181 (362)
T 3goz_A          109 FTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQILAAIPANVNSLNLRG-------NNLAS  181 (362)
T ss_dssp             TTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTT-------SCGGG
T ss_pred             CCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHHHhcCCccccEeeecC-------CCCch
Confidence            4566666666554333221     112 246677776666543222233444445554 677777776       65543


Q ss_pred             h-cc----ccccc-cccccceecCCCCcc-----cchhhhcC-CCccEEEeccCCCCcccc-----ccccccccCCeeec
Q 005860          565 I-LK----GIEKL-IHLRYLRLVGLGTEE-----LPETCCEL-LNLQVLEIEQCTSLKRLP-----LGIGKLVNLRHLTY  627 (673)
Q Consensus       565 l-p~----~i~~L-~~Lr~L~L~~~~i~~-----LP~~i~~L-~~L~~L~l~~c~~l~~lP-----~~i~~L~~Lr~L~l  627 (673)
                      . +.    .+..+ .+|++|+|++|.+..     +|..+..+ ++|++|+|++|. +...+     ..+..+++|++|++
T Consensus       182 ~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~~~~l~~~~~~l~~L~~L~L  260 (362)
T 3goz_A          182 KNCAELAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCLNC-LHGPSLENLKLLKDSLKHLQTVYL  260 (362)
T ss_dssp             SCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCSSC-CCCCCHHHHHHTTTTTTTCSEEEE
T ss_pred             hhHHHHHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcCCC-CCcHHHHHHHHHHhcCCCccEEEe
Confidence            2 22    22333 467777777776665     66666654 367777777654 54433     22355666777777


Q ss_pred             cccc
Q 005860          628 DDSC  631 (673)
Q Consensus       628 ~~~~  631 (673)
                      ++|.
T Consensus       261 ~~n~  264 (362)
T 3goz_A          261 DYDI  264 (362)
T ss_dssp             EHHH
T ss_pred             ccCC
Confidence            6665

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.44  E-value=5.6e-07  Score=90.81  Aligned_cols=114  Identities=11%  Similarity=-0.000  Sum_probs=75.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccc------cCCeEEEEEcCCcccHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFE------YFDKRMWVCVSDPFDEL  242 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~------~F~~~~wv~vs~~~~~~  242 (673)
                      ..+.|||+++++|...|...-.   ......+.|+|++|+|||++|+.|.+......      .| ..++|....-.+..
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i~---~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~-~~v~INc~~~~t~~   95 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSLM---SSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIF-DYIHIDALELAGMD   95 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH---TTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCE-EEEEEETTCCC--H
T ss_pred             cccCCHHHHHHHHHHHHHHHhc---CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCce-EEEEEeccccCCHH
Confidence            3489999999999988754321   13456789999999999999999998632111      12 35667766777888


Q ss_pred             HHHHHHHHHhhCCCCCcC-cHHHHHHHHHHH--hCCCeEEEEEcCCC
Q 005860          243 RIAKAIIEALEGFVPTVG-ELNSLLESIRAS--LVGKKFLLILDDMW  286 (673)
Q Consensus       243 ~~~~~i~~~l~~~~~~~~-~~~~~~~~l~~~--l~~kr~LlVLDdvw  286 (673)
                      .++..|++++.+...... ..+.+...+...  -.+++++|+||++.
T Consensus        96 ~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d  142 (318)
T 3te6_A           96 ALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPE  142 (318)
T ss_dssp             HHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCS
T ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHH
Confidence            999999999976532222 223333333322  25678999999993

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.43  E-value=5.5e-07  Score=92.40  Aligned_cols=148  Identities=13%  Similarity=0.108  Sum_probs=89.2

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|++..++.+..++....       ...+.|+|++|+||||+|+.+++... ...+ ...+.+..++......+ +.
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKT~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~~~-~~   95 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTGS-------MPHLLFAGPPGVGKTTAALALARELF-GENWRHNFLELNASDERGINVI-RE   95 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC-------CCEEEEESCTTSSHHHHHHHHHHHHH-GGGHHHHEEEEETTCHHHHHTT-HH
T ss_pred             HHhhCCHHHHHHHHHHHHcCC-------CCeEEEECcCCCCHHHHHHHHHHHhc-CCcccCceEEeeccccCchHHH-HH
Confidence            569999999999999886543       33489999999999999999988521 1111 12344444432221111 11


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhH-HH-hcccc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETV-AR-MMESI  325 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v-~~-~~~~~  325 (673)
                      .+..+...              .....+++.+||+||+..-....++.+...+.....++++|+||....- .. .....
T Consensus        96 ~~~~~~~~--------------~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~  161 (327)
T 1iqp_A           96 KVKEFART--------------KPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRC  161 (327)
T ss_dssp             HHHHHHHS--------------CCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTE
T ss_pred             HHHHHHhh--------------CCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhC
Confidence            11111000              0011257889999999665555666677666666677889988876431 11 11123


Q ss_pred             ceeecCCCCccccc
Q 005860          326 HVISIKELSEQECW  339 (673)
Q Consensus       326 ~~~~l~~L~~~~~~  339 (673)
                      ..+.+.+++.++..
T Consensus       162 ~~~~~~~l~~~~~~  175 (327)
T 1iqp_A          162 AIFRFRPLRDEDIA  175 (327)
T ss_dssp             EEEECCCCCHHHHH
T ss_pred             cEEEecCCCHHHHH
Confidence            46788888877643

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.43  E-value=3.1e-08  Score=103.60  Aligned_cols=150  Identities=12%  Similarity=0.115  Sum_probs=98.6

Q ss_pred             CceEEEEEEcCCCCccccc-----cccc-cccchhhhccchhhhhhhhhHHHHhhhC-Cccceeeeccccccccccchh-
Q 005860          492 EKLRHSMLVLGYEASFPIS-----IFKA-KNLRSLFINNTLIQVSLTHVLQSLFDQL-KCLRALRIATLMNTWDVNSTN-  563 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~-----~~~~-~~Lr~L~l~~~~~~~~~~~~~~~~~~~l-~~L~~L~L~~~~~~~~~~~~~-  563 (673)
                      ..++.+.+..+........     +..+ ++|++|++.++.........+...+..+ +.|+.|++++       |.+. 
T Consensus        80 ~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~-------N~l~~  152 (362)
T 3goz_A           80 ANVTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRG-------NDLGI  152 (362)
T ss_dssp             TTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTT-------SCGGG
T ss_pred             CCccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccC-------CcCCH
Confidence            6788888877765433322     2333 6888888888775333333344445553 5888888888       6655 


Q ss_pred             ----hhcccccccc-ccccceecCCCCcccc-hh----hhcC-CCccEEEeccCCCCcc-----cccccccc-ccCCeee
Q 005860          564 ----KILKGIEKLI-HLRYLRLVGLGTEELP-ET----CCEL-LNLQVLEIEQCTSLKR-----LPLGIGKL-VNLRHLT  626 (673)
Q Consensus       564 ----~lp~~i~~L~-~Lr~L~L~~~~i~~LP-~~----i~~L-~~L~~L~l~~c~~l~~-----lP~~i~~L-~~Lr~L~  626 (673)
                          .++..+..+. +|++|+|++|.+...+ ..    +..+ ++|++|+|++|. +..     +|..+..+ ++|++|+
T Consensus       153 ~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~  231 (362)
T 3goz_A          153 KSSDELIQILAAIPANVNSLNLRGNNLASKNCAELAKFLASIPASVTSLDLSANL-LGLKSYAELAYIFSSIPNHVVSLN  231 (362)
T ss_dssp             SCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSC-GGGSCHHHHHHHHHHSCTTCCEEE
T ss_pred             HHHHHHHHHHhcCCccccEeeecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCC-CChhHHHHHHHHHhcCCCCceEEE
Confidence                4555666665 8999999998876544 33    3444 589999999876 666     77777664 4899999


Q ss_pred             ccccccccccc-----cCCCCCCCCcCC
Q 005860          627 YDDSCLEFIPK-----GIQRLTNLRTLS  649 (673)
Q Consensus       627 l~~~~l~~lP~-----~i~~L~~L~~L~  649 (673)
                      +++|.+...+.     .+..+++|++|.
T Consensus       232 Ls~N~l~~~~~~~l~~~~~~l~~L~~L~  259 (362)
T 3goz_A          232 LCLNCLHGPSLENLKLLKDSLKHLQTVY  259 (362)
T ss_dssp             CCSSCCCCCCHHHHHHTTTTTTTCSEEE
T ss_pred             CcCCCCCcHHHHHHHHHHhcCCCccEEE
Confidence            98888776432     235555555553

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=98.39  E-value=2.5e-07  Score=96.10  Aligned_cols=145  Identities=20%  Similarity=0.181  Sum_probs=97.3

Q ss_pred             cCceEEEEEEcCCCCccccc-cccccccchhhhccchhhhhhhhhHHHHhhhC-Cccceeeeccccccccccchhhhccc
Q 005860          491 QEKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQL-KCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l-~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      ..+++.+.+..+.....++. +....++..|.+.++..   +....+..|..+ ..++.|++++       +.+..+|..
T Consensus       103 l~~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~---i~~l~~~~f~~~~~~l~~L~L~~-------N~i~~i~~~  172 (350)
T 4ay9_X          103 LPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNIN---IHTIERNSFVGLSFESVILWLNK-------NGIQEIHNS  172 (350)
T ss_dssp             CTTCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTT---CCEECTTSSTTSBSSCEEEECCS-------SCCCEECTT
T ss_pred             ccccccccccccccccCCchhhcccchhhhhhhccccc---cccccccchhhcchhhhhhcccc-------ccccCCChh
Confidence            45677788777766554432 23445555665544321   122233334444 3588899988       888888888


Q ss_pred             cccccccccceecCC-CCcccch-hhhcCCCccEEEeccCCCCccccccccccccCCeee-ccccccccccccCCCCCCC
Q 005860          569 IEKLIHLRYLRLVGL-GTEELPE-TCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLT-YDDSCLEFIPKGIQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~-~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~-l~~~~l~~lP~~i~~L~~L  645 (673)
                      +....+|+.|++.++ .++.+|. .+..+++|++|+++++. +..+|..  .+.+|++|. +..+.++.+|. +.+|++|
T Consensus       173 ~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~-l~~lp~~--~~~~L~~L~~l~~~~l~~lP~-l~~l~~L  248 (350)
T 4ay9_X          173 AFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPSY--GLENLKKLRARSTYNLKKLPT-LEKLVAL  248 (350)
T ss_dssp             SSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSC-CCCCCSS--SCTTCCEEECTTCTTCCCCCC-TTTCCSC
T ss_pred             hccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCC-cCccChh--hhccchHhhhccCCCcCcCCC-chhCcCh
Confidence            888888999999764 4899986 46889999999999875 8899864  244555555 44566778873 6677777


Q ss_pred             CcCC
Q 005860          646 RTLS  649 (673)
Q Consensus       646 ~~L~  649 (673)
                      +.+.
T Consensus       249 ~~l~  252 (350)
T 4ay9_X          249 MEAS  252 (350)
T ss_dssp             CEEE
T ss_pred             hhCc
Confidence            6654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.35  E-value=1.5e-06  Score=81.30  Aligned_cols=45  Identities=24%  Similarity=0.296  Sum_probs=38.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++||+++++++.+.+....       .+.+.|+|++|+||||||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRRT-------KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS-------SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcCC-------CCceEEECCCCCCHHHHHHHHHHH
Confidence            579999999999999986543       345789999999999999998874

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=98.33  E-value=1.1e-07  Score=102.76  Aligned_cols=133  Identities=14%  Similarity=0.141  Sum_probs=86.6

Q ss_pred             cCceEEEEEEcCCCC-----ccccccccccccchhhhccchhhhhhhhhHHHHhhhCC----ccceeeeccccccccccc
Q 005860          491 QEKLRHSMLVLGYEA-----SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLK----CLRALRIATLMNTWDVNS  561 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~-----~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~----~L~~L~L~~~~~~~~~~~  561 (673)
                      .++++.+.+..+...     .++..+..+++|++|++.++....   ..+..++..++    +|+.|++++       +.
T Consensus        27 ~~~L~~L~L~~~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~---~~~~~l~~~l~~~~~~L~~L~L~~-------n~   96 (461)
T 1z7x_W           27 LQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGD---VGVHCVLQGLQTPSCKIQKLSLQN-------CC   96 (461)
T ss_dssp             HTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHH---HHHHHHHHTTCSTTCCCCEEECTT-------SC
T ss_pred             cCCccEEEccCCCCCHHHHHHHHHHHHhCCCcCEEeCCCCcCCh---HHHHHHHHHHhhCCCceeEEEccC-------CC
Confidence            356777777777654     234445566788888887765311   12233344455    688888887       66


Q ss_pred             hh-----hhccccccccccccceecCCCCccc-chhhhc-----CCCccEEEeccCCCCcc-----ccccccccccCCee
Q 005860          562 TN-----KILKGIEKLIHLRYLRLVGLGTEEL-PETCCE-----LLNLQVLEIEQCTSLKR-----LPLGIGKLVNLRHL  625 (673)
Q Consensus       562 ~~-----~lp~~i~~L~~Lr~L~L~~~~i~~L-P~~i~~-----L~~L~~L~l~~c~~l~~-----lP~~i~~L~~Lr~L  625 (673)
                      +.     .+|..+..+++|++|+|++|.+... +..+..     +++|++|++++|. +..     +|..+..+++|++|
T Consensus        97 i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~-l~~~~~~~l~~~l~~~~~L~~L  175 (461)
T 1z7x_W           97 LTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCS-LSAASCEPLASVLRAKPDFKEL  175 (461)
T ss_dssp             CBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSC-CBGGGHHHHHHHHHHCTTCCEE
T ss_pred             CCHHHHHHHHHHHccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcceEEECCCCC-CCHHHHHHHHHHHhhCCCCCEE
Confidence            44     4677778888888888888876532 233322     4578888888875 543     46667778888888


Q ss_pred             ecccccccc
Q 005860          626 TYDDSCLEF  634 (673)
Q Consensus       626 ~l~~~~l~~  634 (673)
                      ++++|.+..
T Consensus       176 ~L~~n~i~~  184 (461)
T 1z7x_W          176 TVSNNDINE  184 (461)
T ss_dssp             ECCSSBCHH
T ss_pred             ECcCCCcch
Confidence            888877653

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=98.30  E-value=2.1e-07  Score=100.54  Aligned_cols=134  Identities=16%  Similarity=0.160  Sum_probs=89.2

Q ss_pred             CceEEEEEEcCCCCc-----cccccccccccchhhhccchhhhhhhhhHHHHh-hhCCccceeeeccccccccccchh--
Q 005860          492 EKLRHSMLVLGYEAS-----FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLF-DQLKCLRALRIATLMNTWDVNSTN--  563 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~-----~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~-~~l~~L~~L~L~~~~~~~~~~~~~--  563 (673)
                      .+++++.+..+....     ++..+..+++|++|++.++.........+...+ ...+.|+.|++++       |.+.  
T Consensus       256 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~-------n~l~~~  328 (461)
T 1z7x_W          256 SRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLWVKS-------CSFTAA  328 (461)
T ss_dssp             CCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHHHHTSTTCCCCEEECTT-------SCCBGG
T ss_pred             CCceEEECcCCCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHHHHHHHHhccCCccceeeEcCC-------CCCchH
Confidence            467777777665543     344455678888888887764222222222222 2335788888888       6543  


Q ss_pred             ---hhccccccccccccceecCCCCccc-chhhhc-----CCCccEEEeccCCCCc-----cccccccccccCCeeeccc
Q 005860          564 ---KILKGIEKLIHLRYLRLVGLGTEEL-PETCCE-----LLNLQVLEIEQCTSLK-----RLPLGIGKLVNLRHLTYDD  629 (673)
Q Consensus       564 ---~lp~~i~~L~~Lr~L~L~~~~i~~L-P~~i~~-----L~~L~~L~l~~c~~l~-----~lP~~i~~L~~Lr~L~l~~  629 (673)
                         .+|..+..+++|++|+|++|.+... +..++.     .++|++|++++|. +.     .+|..+..+++|++|++++
T Consensus       329 ~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~-i~~~~~~~l~~~l~~~~~L~~L~l~~  407 (461)
T 1z7x_W          329 CCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADCD-VSDSSCSSLAATLLANHSLRELDLSN  407 (461)
T ss_dssp             GHHHHHHHHHHCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSC-CCHHHHHHHHHHHHHCCCCCEEECCS
T ss_pred             HHHHHHHHHhhCCCccEEEccCCccccccHHHHHHHHcCCCCceEEEECCCCC-CChhhHHHHHHHHHhCCCccEEECCC
Confidence               3566777778888888888876554 344443     5688888888876 65     6788888888888888888


Q ss_pred             cccc
Q 005860          630 SCLE  633 (673)
Q Consensus       630 ~~l~  633 (673)
                      |.+.
T Consensus       408 N~i~  411 (461)
T 1z7x_W          408 NCLG  411 (461)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8765

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.29  E-value=5.7e-07  Score=93.24  Aligned_cols=96  Identities=25%  Similarity=0.176  Sum_probs=75.1

Q ss_pred             CCCccccccccccccchhhhcc-chhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcc-cccccccccccee
Q 005860          503 YEASFPISIFKAKNLRSLFINN-TLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRL  580 (673)
Q Consensus       503 ~~~~~~~~~~~~~~Lr~L~l~~-~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L  580 (673)
                      ....+|. +..+++|+.|++++ +.    +....+..|.++.+|+.|+|++       +.+..+|+ .+..|.+|++|+|
T Consensus        20 ~l~~ip~-l~~~~~L~~L~l~~~n~----l~~~~~~~~~~l~~L~~L~l~~-------N~l~~~~~~~~~~l~~L~~L~l   87 (347)
T 2ifg_A           20 ALDSLHH-LPGAENLTELYIENQQH----LQHLELRDLRGLGELRNLTIVK-------SGLRFVAPDAFHFTPRLSRLNL   87 (347)
T ss_dssp             CCTTTTT-SCSCSCCSEEECCSCSS----CCEECGGGSCSCCCCSEEECCS-------SCCCEECTTGGGSCSCCCEEEC
T ss_pred             CCCccCC-CCCCCCeeEEEccCCCC----CCCcChhHhccccCCCEEECCC-------CccceeCHHHhcCCcCCCEEeC
Confidence            3456677 77888999999985 65    3344556788899999999999       88887765 5788999999999


Q ss_pred             cCCCCcccchhhhcCCCccEEEeccCCCCcc
Q 005860          581 VGLGTEELPETCCELLNLQVLEIEQCTSLKR  611 (673)
Q Consensus       581 ~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~  611 (673)
                      ++|.+..+|+.+.....|++|+|.+++ +..
T Consensus        88 ~~N~l~~~~~~~~~~~~L~~l~l~~N~-~~c  117 (347)
T 2ifg_A           88 SFNALESLSWKTVQGLSLQELVLSGNP-LHC  117 (347)
T ss_dssp             CSSCCSCCCSTTTCSCCCCEEECCSSC-CCC
T ss_pred             CCCccceeCHHHcccCCceEEEeeCCC-ccC
Confidence            999999998776655559999998865 543

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=98.27  E-value=1.1e-07  Score=106.40  Aligned_cols=109  Identities=16%  Similarity=0.075  Sum_probs=57.8

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCC-C---cccchhhhcCCCccEEEeccCCCCc
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG-T---EELPETCCELLNLQVLEIEQCTSLK  610 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~-i---~~LP~~i~~L~~L~~L~l~~c~~l~  610 (673)
                      ++..+.++++|+.|++++       +.+..+|..+..+++|++|+++++. .   ...+..+..+++|+.|+++++. ..
T Consensus       212 l~~~~~~~~~L~~L~L~~-------~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~-~~  283 (592)
T 3ogk_B          212 LETIARNCRSLVSVKVGD-------FEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMG-PN  283 (592)
T ss_dssp             HHHHHHHCTTCCEEECSS-------CBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCC-TT
T ss_pred             HHHHHhhCCCCcEEeccC-------ccHHHHHHHHhhhhHHHhhcccccccccchHHHHHHhhccccccccCccccc-hh
Confidence            333444455555555555       4444444445555555555554322 1   2233344455555555555532 45


Q ss_pred             cccccccccccCCeeecccccccc--ccccCCCCCCCCcCCee
Q 005860          611 RLPLGIGKLVNLRHLTYDDSCLEF--IPKGIQRLTNLRTLSEF  651 (673)
Q Consensus       611 ~lP~~i~~L~~Lr~L~l~~~~l~~--lP~~i~~L~~L~~L~~~  651 (673)
                      .+|..+..+++|++|++++|.+..  ++..++.+++|+.|...
T Consensus       284 ~l~~~~~~~~~L~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~  326 (592)
T 3ogk_B          284 EMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCPNLEVLETR  326 (592)
T ss_dssp             TGGGGGGGGGGCCEEEETTCCCCHHHHHHHHTTCTTCCEEEEE
T ss_pred             HHHHHHhhcCCCcEEecCCCcCCHHHHHHHHHhCcCCCEEecc
Confidence            567667777788888877766432  22224566666666543

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=98.21  E-value=7.9e-08  Score=107.53  Aligned_cols=149  Identities=16%  Similarity=0.110  Sum_probs=95.2

Q ss_pred             cCceEEEEEEcCCCCcc-ccccc-cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----
Q 005860          491 QEKLRHSMLVLGYEASF-PISIF-KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----  563 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~-~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----  563 (673)
                      ..+++++.+..+..... +..+. .+++|++|.+.++...  ....++..+.++++|+.|++++       |.+.     
T Consensus       104 ~~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~~~--~~~~l~~~~~~~~~L~~L~L~~-------~~i~~~~~~  174 (594)
T 2p1m_B          104 YTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGF--STDGLAAIAATCRNLKELDLRE-------SDVDDVSGH  174 (594)
T ss_dssp             CTTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCEEE--EHHHHHHHHHHCTTCCEEECTT-------CEEECCCGG
T ss_pred             CCCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcCCC--CHHHHHHHHHhCCCCCEEeCcC-------CccCCcchH
Confidence            34677888877654322 22232 5788999988877310  1123556667888999999988       5532     


Q ss_pred             hhccccccccccccceecCCC--C--cccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccc-------cc
Q 005860          564 KILKGIEKLIHLRYLRLVGLG--T--EELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDS-------CL  632 (673)
Q Consensus       564 ~lp~~i~~L~~Lr~L~L~~~~--i--~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~-------~l  632 (673)
                      .++.....+++|++|+|++|.  +  ..++.-+..+++|++|++++|..+..+|..+.++++|++|+++.+       .+
T Consensus       175 ~l~~~~~~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~  254 (594)
T 2p1m_B          175 WLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVY  254 (594)
T ss_dssp             GGGGSCTTCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHHHHHCTTCSEEECSBCCCCCCHHHH
T ss_pred             HHHHHhhcCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHHHhcCCcceEcccccccCccchhhH
Confidence            234444567788999998886  2  223344456789999999988667778888888888888874332       23


Q ss_pred             ccccccCCCCCCCCcC
Q 005860          633 EFIPKGIQRLTNLRTL  648 (673)
Q Consensus       633 ~~lP~~i~~L~~L~~L  648 (673)
                      ..+|..++++++|+.|
T Consensus       255 ~~l~~~l~~~~~L~~L  270 (594)
T 2p1m_B          255 SGLSVALSGCKELRCL  270 (594)
T ss_dssp             HHHHHHHHTCTTCCEE
T ss_pred             HHHHHHHhcCCCcccc
Confidence            3344444455555444

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.20  E-value=5.8e-06  Score=86.47  Aligned_cols=157  Identities=13%  Similarity=0.180  Sum_probs=86.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|++..++.+...+....      ....+.|+|+.|+||||+|+.+.+.......+..   ..+....    ....+
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~------~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~---~~~~~~~----~~~~~   82 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR------IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA---TPCGVCD----NCREI   82 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC------CCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS---SCCSSSH----HHHHH
T ss_pred             hhccCcHHHHHHHHHHHHhCC------CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC---CCCcccH----HHHHH
Confidence            469999999999999886543      1346889999999999999998874221111100   0000000    00111


Q ss_pred             HHHh-------hCC-CCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-H
Q 005860          249 IEAL-------EGF-VPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-V  318 (673)
Q Consensus       249 ~~~l-------~~~-~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v  318 (673)
                      ....       ... .....+...+...+... ..+++.+||+||+..-+....+.+...+.....+..+|++|.... +
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l  162 (373)
T 1jr3_A           83 EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  162 (373)
T ss_dssp             HTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGS
T ss_pred             hccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhC
Confidence            1000       000 01112222222222111 235678999999965555556677777766556777777776432 1


Q ss_pred             -HHhccccceeecCCCCcccc
Q 005860          319 -ARMMESIHVISIKELSEQEC  338 (673)
Q Consensus       319 -~~~~~~~~~~~l~~L~~~~~  338 (673)
                       .........+++.+++.++.
T Consensus       163 ~~~l~sr~~~i~~~~l~~~~~  183 (373)
T 1jr3_A          163 PVTILSRCLQFHLKALDVEQI  183 (373)
T ss_dssp             CHHHHTTSEEEECCCCCHHHH
T ss_pred             cHHHHhheeEeeCCCCCHHHH
Confidence             11112246788888887764

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=98.17  E-value=3.7e-07  Score=101.99  Aligned_cols=150  Identities=11%  Similarity=-0.003  Sum_probs=83.4

Q ss_pred             eEEEEEEcCCCC---ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----hh
Q 005860          494 LRHSMLVLGYEA---SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KI  565 (673)
Q Consensus       494 ~r~l~l~~~~~~---~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~l  565 (673)
                      ++++.+..+...   .++.....+++|++|.+.++.........++..+..++.|+.|++++       +.+.     .+
T Consensus       140 L~~L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~~~~~~~l~~~~~~~~~L~~L~L~~-------n~~~~~~~~~l  212 (592)
T 3ogk_B          140 LETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYM-------TEFAKISPKDL  212 (592)
T ss_dssp             CCEEEEESCEEEEHHHHHHHHHHCTTCSEEECTTCEEECCCSHHHHHHHHHCCCCCEEECTT-------CCCSSCCHHHH
T ss_pred             CcEEECcCCCCcCHHHHHHHHhhCCCCCEEECccccccCcchhHHHHHHhcCCCccEEEeec-------cCCCccCHHHH
Confidence            666666554310   11111224566666666665421111112344455666666666666       4432     34


Q ss_pred             ccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCC---ccccccccccccCCeeeccccccccccccCCCC
Q 005860          566 LKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSL---KRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRL  642 (673)
Q Consensus       566 p~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l---~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L  642 (673)
                      +..+..+++|++|+|++|.+..+|..+.++++|+.|+++.+...   ...+..+..+++|+.|++..+....+|..+..+
T Consensus       213 ~~~~~~~~~L~~L~L~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~  292 (592)
T 3ogk_B          213 ETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFA  292 (592)
T ss_dssp             HHHHHHCTTCCEEECSSCBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGG
T ss_pred             HHHHhhCCCCcEEeccCccHHHHHHHHhhhhHHHhhcccccccccchHHHHHHhhccccccccCccccchhHHHHHHhhc
Confidence            44555666777777777666667777777777777777653322   234445666677777776655555666666666


Q ss_pred             CCCCcCCe
Q 005860          643 TNLRTLSE  650 (673)
Q Consensus       643 ~~L~~L~~  650 (673)
                      ++|+.|..
T Consensus       293 ~~L~~L~L  300 (592)
T 3ogk_B          293 AQIRKLDL  300 (592)
T ss_dssp             GGCCEEEE
T ss_pred             CCCcEEec
Confidence            66666543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.13  E-value=5.3e-06  Score=84.64  Aligned_cols=143  Identities=15%  Similarity=0.150  Sum_probs=85.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|++..++.+.+++....       ...+.|+|++|+||||+|+.+.+... ...+ ...+.+..+.....      
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~------   82 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN-------IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGI------   82 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC-------CCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTCT------
T ss_pred             HHHhCCHHHHHHHHHHHhCCC-------CCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccCh------
Confidence            469999999999998886543       23389999999999999999887411 1111 11233444332111      


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHH--h-CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHH-hc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRAS--L-VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VAR-MM  322 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~--l-~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~-~~  322 (673)
                                  .........+...  + .+++.+||+|++..-.....+.+...+.....+.++|+||.... +.. ..
T Consensus        83 ------------~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~  150 (319)
T 2chq_A           83 ------------DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQ  150 (319)
T ss_dssp             ------------TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHH
T ss_pred             ------------HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHH
Confidence                        1111111111111  1 25688999999955444455667666666566788888876543 111 11


Q ss_pred             cccceeecCCCCccc
Q 005860          323 ESIHVISIKELSEQE  337 (673)
Q Consensus       323 ~~~~~~~l~~L~~~~  337 (673)
                      .....+++.+++.++
T Consensus       151 sr~~~i~~~~~~~~~  165 (319)
T 2chq_A          151 SRCAVFRFKPVPKEA  165 (319)
T ss_dssp             TTCEEEECCCCCHHH
T ss_pred             hhCeEEEecCCCHHH
Confidence            223467788887665

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.04  E-value=5.5e-06  Score=76.93  Aligned_cols=120  Identities=18%  Similarity=0.232  Sum_probs=64.3

Q ss_pred             hhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          175 DEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       175 ~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      ...++.+.+++..-..    .....+.|+|++|+||||||+.+++.......+ .++++      +..++...+......
T Consensus        20 ~~~~~~~~~~~~~~~~----~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~-~~~~~------~~~~~~~~~~~~~~~   88 (180)
T 3ec2_A           20 NRALLTIRVFVHNFNP----EEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGI-RGYFF------DTKDLIFRLKHLMDE   88 (180)
T ss_dssp             HHHHHHHHHHHHSCCG----GGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCC-CCCEE------EHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccc----cCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCC-eEEEE------EHHHHHHHHHHHhcC
Confidence            3444555554433221    224689999999999999999999853212222 23444      344555555544433


Q ss_pred             CCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchh--hhhhhccC-CCCCeEEEEEcCC
Q 005860          255 FVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWE--PFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       255 ~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~--~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      ....     .....    +. +.-+|||||++......|.  .+...+.. ...|..||+||..
T Consensus        89 ~~~~-----~~~~~----~~-~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A           89 GKDT-----KFLKT----VL-NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             TCCS-----HHHHH----HH-TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             chHH-----HHHHH----hc-CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence            2211     11222    22 4568999999743333333  23332322 1246788888874

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.99  E-value=6.9e-06  Score=76.32  Aligned_cols=45  Identities=22%  Similarity=0.221  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++||+.+++.+.+.+....       .+.+.|+|++|+||||||+.+.+.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~-------~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRRT-------KNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS-------SCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCCC-------CCceEEECCCCCCHHHHHHHHHHH
Confidence            579999999999999986533       345689999999999999998874

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=97.96  E-value=2.7e-06  Score=88.83  Aligned_cols=135  Identities=16%  Similarity=0.078  Sum_probs=95.7

Q ss_pred             CceEEEEEEcCCCCcc-cccc-ccccccchhhhccchhhhhhhhhHHHHh-hhCCccceeeeccccccccccchhh----
Q 005860          492 EKLRHSMLVLGYEASF-PISI-FKAKNLRSLFINNTLIQVSLTHVLQSLF-DQLKCLRALRIATLMNTWDVNSTNK----  564 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~-~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~-~~l~~L~~L~L~~~~~~~~~~~~~~----  564 (673)
                      ..++.+.+..+..... ...+ ..+++|+.|++++|.........+...+ .....|+.|+|++       |.+..    
T Consensus       101 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~-------n~l~~~~~~  173 (372)
T 3un9_A          101 HALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSN-------NPLTAAGVA  173 (372)
T ss_dssp             SCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECCS-------SCCHHHHHH
T ss_pred             CCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCCC-------CCCChHHHH
Confidence            4677888877665321 1122 2357889999998875333333333334 3467899999999       77543    


Q ss_pred             -hccccccccccccceecCCCCcc-----cchhhhcCCCccEEEeccCCCCc-----cccccccccccCCeeeccccccc
Q 005860          565 -ILKGIEKLIHLRYLRLVGLGTEE-----LPETCCELLNLQVLEIEQCTSLK-----RLPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       565 -lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~L~l~~c~~l~-----~lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                       ++..+..+++|++|+|++|.+..     ++..+...++|++|+|++|. +.     .++..+...++|++|++++|.+.
T Consensus       174 ~l~~~L~~~~~L~~L~Ls~N~l~~~g~~~L~~~L~~~~~L~~L~Ls~N~-i~~~g~~~l~~~L~~~~~L~~L~Ls~N~i~  252 (372)
T 3un9_A          174 VLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNG-AGDTAALALARAAREHPSLELLHLYFNELS  252 (372)
T ss_dssp             HHHHHHHTCSSCCEEECTTSSCHHHHHHHHHHHGGGCSCCCEEECCSSC-CCHHHHHHHHHHHHHCSSCCEEECTTSSCC
T ss_pred             HHHHHHhcCCCcCEEeCCCCCCCcHHHHHHHHHHhcCCCcCeEECCCCC-CCHHHHHHHHHHHHhCCCCCEEeccCCCCC
Confidence             56666788899999999998753     46677788899999999986 64     35556667789999999999876


Q ss_pred             c
Q 005860          634 F  634 (673)
Q Consensus       634 ~  634 (673)
                      .
T Consensus       253 ~  253 (372)
T 3un9_A          253 S  253 (372)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.89  E-value=2.8e-05  Score=82.94  Aligned_cols=102  Identities=19%  Similarity=0.207  Sum_probs=60.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCC--eEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD--KRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      ...+.|+|++|+||||||+.+++.  ....|.  .+++++.      ..+..++...+....         ...+...+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~--l~~~~~~~~v~~v~~------~~~~~~~~~~~~~~~---------~~~~~~~~~  192 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYITS------EKFLNDLVDSMKEGK---------LNEFREKYR  192 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHH--HHHHCCSSCEEEEEH------HHHHHHHHHHHHTTC---------HHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEeeH------HHHHHHHHHHHHccc---------HHHHHHHhc
Confidence            457899999999999999999985  333332  2455543      334455555544321         123344444


Q ss_pred             CCeEEEEEcCCCCCCc--cchhhhhhhccC-CCCCeEEEEEcCC
Q 005860          275 GKKFLLILDDMWTDDY--SKWEPFHYCLKN-GVRGSKILVTTRK  315 (673)
Q Consensus       275 ~kr~LlVLDdvw~~~~--~~~~~l~~~l~~-~~~gs~iivTtr~  315 (673)
                      .+.-+|+|||+..-..  ...+.+...+.. ...|..||+||.+
T Consensus       193 ~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          193 KKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             TTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4667999999954322  122333333321 2356788888875

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.89  E-value=1.3e-05  Score=71.49  Aligned_cols=113  Identities=16%  Similarity=0.063  Sum_probs=65.1

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc-cccCCeEEEEEcCCcccHHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV-FEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      +++|+...++++.+.+..-..    . ..-|.|+|..|+|||++|+.+++...- ...|   + +..+...+.       
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~----~-~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~---v-~~~~~~~~~-------   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE----T-DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEF---V-YRELTPDNA-------   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT----C-CSCEEEESSTTSSHHHHHHHHHHSSTTTTSCC---E-EEECCTTTS-------
T ss_pred             CceeCCHHHHHHHHHHHHHhC----C-CCCEEEECCCCCCHHHHHHHHHHhCCccCCCE---E-EECCCCCcc-------
Confidence            578999999999887744221    1 123689999999999999999985211 1222   3 554432211       


Q ss_pred             HHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC
Q 005860          249 IEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       249 ~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~  315 (673)
                                 ...   ...+...   ..-.|+||++..-.......+...+.......+||.||..
T Consensus        66 -----------~~~---~~~~~~a---~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           66 -----------PQL---NDFIALA---QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             -----------SCH---HHHHHHH---TTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             -----------hhh---hcHHHHc---CCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCc
Confidence                       011   1111111   2246899999654444445555555444445577777764

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=97.88  E-value=1.2e-06  Score=91.51  Aligned_cols=146  Identities=15%  Similarity=0.096  Sum_probs=98.5

Q ss_pred             CceEEEEEEcCCCCcc-----ccccc-cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-
Q 005860          492 EKLRHSMLVLGYEASF-----PISIF-KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-  564 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~-----~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-  564 (673)
                      ..++.+.+..+.....     ...+. ..++|++|++.+|....   .....+...+++|+.|+|++       |.+.. 
T Consensus        72 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~~---~~~~~l~~~L~~L~~L~Ls~-------n~l~~~  141 (372)
T 3un9_A           72 SSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDP---AGLRTLLPVFLRARKLGLQL-------NSLGPE  141 (372)
T ss_dssp             TTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCCH---HHHHHTHHHHHTEEEEECCS-------SCCCHH
T ss_pred             hhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCCH---HHHHHHHHHHHhccHhhcCC-------CCCCHH
Confidence            3466677766654321     11122 23689999999987421   22334445567899999999       77543 


Q ss_pred             ----hcccc-ccccccccceecCCCCcc-----cchhhhcCCCccEEEeccCCCCc-----cccccccccccCCeeeccc
Q 005860          565 ----ILKGI-EKLIHLRYLRLVGLGTEE-----LPETCCELLNLQVLEIEQCTSLK-----RLPLGIGKLVNLRHLTYDD  629 (673)
Q Consensus       565 ----lp~~i-~~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~L~l~~c~~l~-----~lP~~i~~L~~Lr~L~l~~  629 (673)
                          +...+ ....+|++|+|++|.+..     ++..+..+++|++|+|++|. +.     .++..+...++|++|++++
T Consensus       142 ~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~-l~~~g~~~L~~~L~~~~~L~~L~Ls~  220 (372)
T 3un9_A          142 ACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTG-LGDEGLELLAAQLDRNRQLQELNVAY  220 (372)
T ss_dssp             HHHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSS-CHHHHHHHHHHHGGGCSCCCEEECCS
T ss_pred             HHHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCC-CCcHHHHHHHHHHhcCCCcCeEECCC
Confidence                22222 235789999999999754     66777889999999999987 64     3566778888999999999


Q ss_pred             ccccc-----ccccCCCCCCCCcC
Q 005860          630 SCLEF-----IPKGIQRLTNLRTL  648 (673)
Q Consensus       630 ~~l~~-----lP~~i~~L~~L~~L  648 (673)
                      |.+..     ++..+...++|++|
T Consensus       221 N~i~~~g~~~l~~~L~~~~~L~~L  244 (372)
T 3un9_A          221 NGAGDTAALALARAAREHPSLELL  244 (372)
T ss_dssp             SCCCHHHHHHHHHHHHHCSSCCEE
T ss_pred             CCCCHHHHHHHHHHHHhCCCCCEE
Confidence            98864     33334444555554

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=97.85  E-value=9.4e-06  Score=83.35  Aligned_cols=97  Identities=16%  Similarity=0.148  Sum_probs=71.6

Q ss_pred             ccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCC-eeecccccccccccc-CCCCCCCCc
Q 005860          572 LIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLR-HLTYDDSCLEFIPKG-IQRLTNLRT  647 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr-~L~l~~~~l~~lP~~-i~~L~~L~~  647 (673)
                      +.+|++|+|++|.++.+|+ .+.++.+|+.|++.++  +..+|. .|.++.+|+ .|.+.. .+..++.+ +.++++|+.
T Consensus       225 ~~~L~~l~L~~n~i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~~aF~~~~~L~~~l~l~~-~l~~I~~~aF~~c~~L~~  301 (329)
T 3sb4_A          225 MPNLVSLDISKTNATTIPDFTFAQKKYLLKIKLPHN--LKTIGQRVFSNCGRLAGTLELPA-SVTAIEFGAFMGCDNLRY  301 (329)
T ss_dssp             CTTCCEEECTTBCCCEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCEEEEECT-TCCEECTTTTTTCTTEEE
T ss_pred             cCCCeEEECCCCCcceecHhhhhCCCCCCEEECCcc--cceehHHHhhCChhccEEEEEcc-cceEEchhhhhCCccCCE
Confidence            5789999999888989985 5788899999999873  888875 578999999 998877 67777644 777888887


Q ss_pred             CCe--eEEccCCccCCCccccCCCCC
Q 005860          648 LSE--FVVVRGGSKYGGKACNLEGLR  671 (673)
Q Consensus       648 L~~--~~~~~~~~~~~~~~~~l~~L~  671 (673)
                      |..  -.+..-....+..+.+|+.|.
T Consensus       302 l~l~~n~i~~I~~~aF~~~~~L~~ly  327 (329)
T 3sb4_A          302 VLATGDKITTLGDELFGNGVPSKLIY  327 (329)
T ss_dssp             EEECSSCCCEECTTTTCTTCCCCEEE
T ss_pred             EEeCCCccCccchhhhcCCcchhhhc
Confidence            753  122222333467777887664

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.83  E-value=6.8e-06  Score=80.01  Aligned_cols=60  Identities=20%  Similarity=0.150  Sum_probs=38.8

Q ss_pred             Ccceech---hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          169 SEIRGRD---EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       169 ~~~vGr~---~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      ++++|.+   ..++.+..++...       ..+.+.|+|++|+||||||+.+++.  .......+.|+.+++
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~-------~~~~~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~   90 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD-------GVQAIYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLGI   90 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC-------SCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGGG
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC-------CCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHHH
Confidence            4577633   4455555555432       2457889999999999999999885  322334566776644

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.82  E-value=6.5e-05  Score=80.01  Aligned_cols=138  Identities=19%  Similarity=0.243  Sum_probs=75.6

Q ss_pred             CcceechhhH---HHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          169 SEIRGRDEEK---SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       169 ~~~vGr~~~~---~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      ++++|.+..+   ..+...+....       ...+.|+|++|+||||||+.+.+.  ....|   ..+.... .....+ 
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~~-------~~~vLL~GppGtGKTtlAr~ia~~--~~~~f---~~l~a~~-~~~~~i-   91 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAGH-------LHSMILWGPPGTGKTTLAEVIARY--ANADV---ERISAVT-SGVKEI-   91 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHTC-------CCEEEEECSTTSSHHHHHHHHHHH--TTCEE---EEEETTT-CCHHHH-
T ss_pred             HHhCCcHHHHhchHHHHHHHHcCC-------CcEEEEECCCCCcHHHHHHHHHHH--hCCCe---EEEEecc-CCHHHH-
Confidence            5789998887   66777665443       467899999999999999999985  22222   1222221 122211 


Q ss_pred             HHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh--H-HHhc
Q 005860          246 KAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET--V-ARMM  322 (673)
Q Consensus       246 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~--v-~~~~  322 (673)
                      +.++..                .......+++.+|+||++..-...+.+.+...+..+ .-.-|..||.+..  + ....
T Consensus        92 r~~~~~----------------a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~-~v~lI~att~n~~~~l~~aL~  154 (447)
T 3pvs_A           92 REAIER----------------ARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDG-TITFIGATTENPSFELNSALL  154 (447)
T ss_dssp             HHHHHH----------------HHHHHHTTCCEEEEEETTTCC------CCHHHHHTT-SCEEEEEESSCGGGSSCHHHH
T ss_pred             HHHHHH----------------HHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhcC-ceEEEecCCCCcccccCHHHh
Confidence            111111                011112567889999999665555566666666542 2222333555532  1 1112


Q ss_pred             cccceeecCCCCccc
Q 005860          323 ESIHVISIKELSEQE  337 (673)
Q Consensus       323 ~~~~~~~l~~L~~~~  337 (673)
                      .-..++.+++++.++
T Consensus       155 sR~~v~~l~~l~~ed  169 (447)
T 3pvs_A          155 SRARVYLLKSLSTED  169 (447)
T ss_dssp             TTEEEEECCCCCHHH
T ss_pred             CceeEEeeCCcCHHH
Confidence            224577788887665

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.80  E-value=6.5e-05  Score=75.23  Aligned_cols=53  Identities=23%  Similarity=0.263  Sum_probs=38.7

Q ss_pred             CCcceechhhHHHHHHHhccCCcc-c-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSE-E-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~-~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++++|.+..+++|.+.+...... .     +.....-+.|+|++|+||||||+.+++.
T Consensus        16 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           16 YEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            457999999999998887432000 0     0012345899999999999999999884

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.77  E-value=2.4e-05  Score=74.01  Aligned_cols=125  Identities=18%  Similarity=0.195  Sum_probs=64.4

Q ss_pred             cceech----hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHH
Q 005860          170 EIRGRD----EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIA  245 (673)
Q Consensus       170 ~~vGr~----~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  245 (673)
                      +|++.+    ..++.+..++.....   ......+.|+|++|+||||||+.+++.  .......++|++++      .+.
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~G~~GtGKT~la~~i~~~--~~~~~~~~~~~~~~------~~~   94 (202)
T 2w58_A           26 DVDLNDDGRIKAIRFAERFVAEYEP---GKKMKGLYLHGSFGVGKTYLLAAIANE--LAKRNVSSLIVYVP------ELF   94 (202)
T ss_dssp             SSCCSSHHHHHHHHHHHHHHHHCCS---SCCCCEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEEEHH------HHH
T ss_pred             hccCCChhHHHHHHHHHHHHHHhhh---ccCCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEhH------HHH
Confidence            455543    344455555543321   011267889999999999999999985  33334456677543      344


Q ss_pred             HHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhh--hhh-hccCC-CCCeEEEEEcCC
Q 005860          246 KAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEP--FHY-CLKNG-VRGSKILVTTRK  315 (673)
Q Consensus       246 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~--l~~-~l~~~-~~gs~iivTtr~  315 (673)
                      ..+......     .........+.    .. -+|||||++......|..  +.. .+... ..+.++|+||..
T Consensus        95 ~~~~~~~~~-----~~~~~~~~~~~----~~-~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A           95 RELKHSLQD-----QTMNEKLDYIK----KV-PVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             HHHHHC--------CCCHHHHHHHH----HS-SEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             HHHHHHhcc-----chHHHHHHHhc----CC-CEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence            444332211     11222222222    22 389999996544334322  222 22211 235568888774

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.74  E-value=7.3e-05  Score=75.80  Aligned_cols=51  Identities=22%  Similarity=0.143  Sum_probs=35.3

Q ss_pred             cceechhhHHHHHHHhccCCcc--------cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKLLCESSE--------EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~--------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++|.+..++.+.+++.....+        ........+.|+|++|+|||++|+.+.+.
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~   90 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGL   90 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            5889988888887665321000        00123456899999999999999988774

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.74  E-value=5.1e-05  Score=78.50  Aligned_cols=156  Identities=12%  Similarity=0.105  Sum_probs=84.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|+++.++.+..++....       ...+.|+|++|+||||+|+.+.+.......+. ..+.+..+.......+ .+
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~~-------~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~  108 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSAN-------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV-RE  108 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTT-------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH-TT
T ss_pred             HHhhCCHHHHHHHHHHHhcCC-------CCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHH-HH
Confidence            579999999999999986553       22388999999999999999988521111121 2333444432233222 22


Q ss_pred             HHHHhhCC-CCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHHh-ccc
Q 005860          248 IIEALEGF-VPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VARM-MES  324 (673)
Q Consensus       248 i~~~l~~~-~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~~-~~~  324 (673)
                      .+..+... .......     .....-.+++-+|++|++..-.....+.+...+.......++|++|.... +... ...
T Consensus       109 ~~~~~~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR  183 (353)
T 1sxj_D          109 KVKNFARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQ  183 (353)
T ss_dssp             HHHHHHHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHH
T ss_pred             HHHHHhhhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhcc
Confidence            22222111 0000000     00111124567999999854444445556665655555677777775432 1111 111


Q ss_pred             cceeecCCCCccc
Q 005860          325 IHVISIKELSEQE  337 (673)
Q Consensus       325 ~~~~~l~~L~~~~  337 (673)
                      ...+.+.+++.++
T Consensus       184 ~~~i~~~~~~~~~  196 (353)
T 1sxj_D          184 CSKFRFKALDASN  196 (353)
T ss_dssp             SEEEECCCCCHHH
T ss_pred             CceEEeCCCCHHH
Confidence            2356677766554

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=97.74  E-value=2.8e-06  Score=94.91  Aligned_cols=106  Identities=15%  Similarity=0.112  Sum_probs=57.5

Q ss_pred             hhhCCccceeeecccccccccc-chhhhccccccccccccceecCC-------CCcccchhhhcCCCccEE-EeccCCCC
Q 005860          539 FDQLKCLRALRIATLMNTWDVN-STNKILKGIEKLIHLRYLRLVGL-------GTEELPETCCELLNLQVL-EIEQCTSL  609 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~-~~~~lp~~i~~L~~Lr~L~L~~~-------~i~~LP~~i~~L~~L~~L-~l~~c~~l  609 (673)
                      +..+++|+.|++++       + .+..+|..+..+++|++|++.++       .+..+|..+.++++|+.| .+.+.. .
T Consensus       207 ~~~~~~L~~L~L~~-------~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~l~~~l~~~~~L~~Ls~~~~~~-~  278 (594)
T 2p1m_B          207 VTRCPNLKSLKLNR-------AVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVYSGLSVALSGCKELRCLSGFWDAV-P  278 (594)
T ss_dssp             HHHCTTCCEEECCT-------TSCHHHHHHHHHHCTTCSEEECSBCCCCCCHHHHHHHHHHHHTCTTCCEEECCBTCC-G
T ss_pred             HHhCCCCcEEecCC-------CCcHHHHHHHHhcCCcceEcccccccCccchhhHHHHHHHHhcCCCcccccCCcccc-h
Confidence            33445555555555       3 23334444555555555553322       233444455555555555 333322 3


Q ss_pred             ccccccccccccCCeeecccccccc--ccccCCCCCCCCcCCeeE
Q 005860          610 KRLPLGIGKLVNLRHLTYDDSCLEF--IPKGIQRLTNLRTLSEFV  652 (673)
Q Consensus       610 ~~lP~~i~~L~~Lr~L~l~~~~l~~--lP~~i~~L~~L~~L~~~~  652 (673)
                      ..+|..+..+++|++|++++|.+..  ++.-+.++++|++|....
T Consensus       279 ~~l~~~~~~~~~L~~L~L~~~~l~~~~l~~~~~~~~~L~~L~l~~  323 (594)
T 2p1m_B          279 AYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLD  323 (594)
T ss_dssp             GGGGGGHHHHTTCCEEECTTCCCCHHHHHHHHTTCTTCCEEEEEG
T ss_pred             hhHHHHHHhhCCCCEEEccCCCCCHHHHHHHHhcCCCcCEEeCcC
Confidence            4466556678999999988877553  223355677777776543

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.73  E-value=4.2e-05  Score=79.27  Aligned_cols=156  Identities=12%  Similarity=0.124  Sum_probs=79.3

Q ss_pred             CcceechhhHHHHHHHh-ccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc---ccc-ccCCe--------------
Q 005860          169 SEIRGRDEEKSSLKSKL-LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS---DVF-EYFDK--------------  229 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L-~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~---~~~-~~F~~--------------  229 (673)
                      .+++|.+..++.+..++ ....       ...+.|+|+.|+||||+|+.+.+..   ... -.++.              
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-------~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~   86 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-------LPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELN   86 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-------CCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------C
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-------CCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceee
Confidence            56899999999998887 4332       2228999999999999998876621   100 00110              


Q ss_pred             ------EEEEEcCCcc-cHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          230 ------RMWVCVSDPF-DELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       230 ------~~wv~vs~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                            .+.+..+... ......+++++.+.....- .   ... .+ ..+.+++-++|||++..-+....+.+...+..
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~---~~~-~l-s~l~~~~~vlilDE~~~L~~~~~~~L~~~le~  160 (354)
T 1sxj_E           87 VVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQV-D---FQD-SK-DGLAHRYKCVIINEANSLTKDAQAALRRTMEK  160 (354)
T ss_dssp             CEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHH
T ss_pred             eecccceEEecHhhcCCcchHHHHHHHHHHHHhccc-c---ccc-cc-cccCCCCeEEEEeCccccCHHHHHHHHHHHHh
Confidence                  1111111100 0000122233322211000 0   000 00 00234677999999966554455566666654


Q ss_pred             CCCCeEEEEEcCChh-HHH-hccccceeecCCCCccc
Q 005860          303 GVRGSKILVTTRKET-VAR-MMESIHVISIKELSEQE  337 (673)
Q Consensus       303 ~~~gs~iivTtr~~~-v~~-~~~~~~~~~l~~L~~~~  337 (673)
                      ...+..+|++|.+.. +.. ...-...+++++++.++
T Consensus       161 ~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~  197 (354)
T 1sxj_E          161 YSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSE  197 (354)
T ss_dssp             STTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHH
T ss_pred             hcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHH
Confidence            455778888877532 211 11223567778777665

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.73  E-value=5.1e-05  Score=77.63  Aligned_cols=139  Identities=17%  Similarity=0.168  Sum_probs=82.2

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      -++++|.+..++.+.+++....      ...++.+.|++|+||||+|+.+.+..  .   ...+.++.+.. ... ..+.
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~------~~~~~L~~G~~G~GKT~la~~la~~l--~---~~~~~i~~~~~-~~~-~i~~   91 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK------IPHIILHSPSPGTGKTTVAKALCHDV--N---ADMMFVNGSDC-KID-FVRG   91 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC------CCSEEEECSSTTSSHHHHHHHHHHHT--T---EEEEEEETTTC-CHH-HHHT
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC------CCeEEEeeCcCCCCHHHHHHHHHHHh--C---CCEEEEccccc-CHH-HHHH
Confidence            3579999999999999987543      23577888999999999999998842  1   23445554442 222 2222


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCC-ccchhhhhhhccCCCCCeEEEEEcCChh-----HHHh
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDD-YSKWEPFHYCLKNGVRGSKILVTTRKET-----VARM  321 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~-~~~~~~l~~~l~~~~~gs~iivTtr~~~-----v~~~  321 (673)
                      ++.......               ...+++.+|++|++..-. ....+.+...+.....+.++|+||....     +...
T Consensus        92 ~~~~~~~~~---------------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR  156 (324)
T 3u61_B           92 PLTNFASAA---------------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSR  156 (324)
T ss_dssp             HHHHHHHBC---------------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHH
T ss_pred             HHHHHHhhc---------------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhh
Confidence            221111000               012478899999995433 3344555555544344567888877543     1111


Q ss_pred             ccccceeecCCCCccc
Q 005860          322 MESIHVISIKELSEQE  337 (673)
Q Consensus       322 ~~~~~~~~l~~L~~~~  337 (673)
                         ...+++++++.++
T Consensus       157 ---~~~i~~~~~~~~e  169 (324)
T 3u61_B          157 ---CRVITFGQPTDED  169 (324)
T ss_dssp             ---SEEEECCCCCHHH
T ss_pred             ---CcEEEeCCCCHHH
Confidence               2356666665443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.72  E-value=1.8e-05  Score=70.37  Aligned_cols=47  Identities=11%  Similarity=0.174  Sum_probs=33.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.++|++..++++.+.+..-..    . ..-|.|+|..|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~----~-~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAK----R-TSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHT----C-SSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhC----C-CCcEEEECCCCccHHHHHHHHHHh
Confidence            3578999998888887753221    1 123779999999999999999985

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.70  E-value=2.4e-05  Score=72.92  Aligned_cols=115  Identities=16%  Similarity=0.097  Sum_probs=77.9

Q ss_pred             cccccccchhhhccc-hhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----hhccccccccccccceecCCC
Q 005860          511 IFKAKNLRSLFINNT-LIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KILKGIEKLIHLRYLRLVGLG  584 (673)
Q Consensus       511 ~~~~~~Lr~L~l~~~-~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~lp~~i~~L~~Lr~L~L~~~~  584 (673)
                      +...++|++|.+.++ .....-...+...+...+.|+.|+|++       +.+.     .+...+.....|++|+|++|.
T Consensus        32 l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~-------n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~  104 (185)
T 1io0_A           32 QNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVG-------TRSNDPVAFALAEMLKVNNTLKSLNVESNF  104 (185)
T ss_dssp             HTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTT-------SCCCHHHHHHHHHHHHHCSSCCEEECCSSC
T ss_pred             HhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcC-------CCCChHHHHHHHHHHHhCCCcCEEECcCCc
Confidence            345677888888877 543333344555666778888888888       6543     244555666788888888888


Q ss_pred             Ccc-----cchhhhcCCCccEEEe--ccCCCCcc-----ccccccccccCCeeeccccccc
Q 005860          585 TEE-----LPETCCELLNLQVLEI--EQCTSLKR-----LPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       585 i~~-----LP~~i~~L~~L~~L~l--~~c~~l~~-----lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      +..     +...+...++|++|+|  ++|. +..     +...+...++|++|+++.|.+.
T Consensus       105 i~~~g~~~l~~~L~~n~~L~~L~L~~~~N~-i~~~g~~~l~~~L~~n~~L~~L~L~~n~i~  164 (185)
T 1io0_A          105 ISGSGILALVEALQSNTSLIELRIDNQSQP-LGNNVEMEIANMLEKNTTLLKFGYHFTQQG  164 (185)
T ss_dssp             CCHHHHHHHHHGGGGCSSCCEEECCCCSSC-CCHHHHHHHHHHHHHCSSCCEEECCCSSHH
T ss_pred             CCHHHHHHHHHHHHhCCCceEEEecCCCCC-CCHHHHHHHHHHHHhCCCcCEEeccCCCCC
Confidence            654     5666777788888888  6554 532     4445566678888888777653

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.69  E-value=3.3e-05  Score=75.89  Aligned_cols=84  Identities=15%  Similarity=0.150  Sum_probs=53.1

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhh---hccccccccccccceecCCCCcccchhhhcCC--CccEEEeccCCCC
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNK---ILKGIEKLIHLRYLRLVGLGTEELPETCCELL--NLQVLEIEQCTSL  609 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~---lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~--~L~~L~l~~c~~l  609 (673)
                      ++....+++.|+.|+|++       |.+..   +|..+..+++|++|+|++|.+..+ ..+..|.  +|++|+|++++--
T Consensus       162 l~i~~~~l~~L~~L~Ls~-------N~l~~l~~l~~~~~~l~~L~~L~Ls~N~i~~~-~~l~~l~~l~L~~L~L~~Npl~  233 (267)
T 3rw6_A          162 LRIIEENIPELLSLNLSN-------NRLYRLDDMSSIVQKAPNLKILNLSGNELKSE-RELDKIKGLKLEELWLDGNSLC  233 (267)
T ss_dssp             HHHHHHHCTTCCEEECTT-------SCCCCCGGGTTHHHHSTTCCEEECTTSCCCSG-GGGGGGTTSCCSEEECTTSTTG
T ss_pred             HHHHHhhCCCCCEEECCC-------CCCCCCccchhHHhhCCCCCEEECCCCccCCc-hhhhhcccCCcceEEccCCcCc
Confidence            334445677788888887       76554   345566777788888877777766 3355555  7777777776622


Q ss_pred             ccccc-------cccccccCCeee
Q 005860          610 KRLPL-------GIGKLVNLRHLT  626 (673)
Q Consensus       610 ~~lP~-------~i~~L~~Lr~L~  626 (673)
                      ..+|.       .+..+++|+.||
T Consensus       234 ~~~~~~~~y~~~il~~~P~L~~LD  257 (267)
T 3rw6_A          234 DTFRDQSTYISAIRERFPKLLRLD  257 (267)
T ss_dssp             GGCSSHHHHHHHHHHHCTTCCEES
T ss_pred             cccCcchhHHHHHHHHCcccCeEC
Confidence            33442       245666666666

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.61  E-value=0.00021  Score=70.88  Aligned_cols=48  Identities=15%  Similarity=0.096  Sum_probs=34.7

Q ss_pred             CcceechhhHHHHHH-------HhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKS-------KLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~-------~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|....+++++.       .+....    ......+.|+|++|+|||+||+.+++.
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~----~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSD----RTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCS----SCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccC----CCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            357788777666665       232111    134678999999999999999999984

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.59  E-value=0.0001  Score=76.71  Aligned_cols=47  Identities=17%  Similarity=0.154  Sum_probs=35.7

Q ss_pred             CcceechhhHHH---HHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSS---LKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~---l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|++..++.   +...+....     ...+.+.|+|++|+|||++|+.+.+.
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~~-----~~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREGK-----IAGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTC-----CTTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHHHHHHcCC-----CCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            579999988766   444444333     22357899999999999999999985

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.59  E-value=0.00015  Score=74.16  Aligned_cols=122  Identities=21%  Similarity=0.199  Sum_probs=63.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGK  276 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~k  276 (673)
                      ...+.|+|++|+||||||+.+++..  ...-...++++.      ..+...+...+...     ...    .+...+. +
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~--~~~~~~~~~i~~------~~~~~~~~~~~~~~-----~~~----~~~~~~~-~   98 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEA--KKRGYRVIYSSA------DDFAQAMVEHLKKG-----TIN----EFRNMYK-S   98 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHH--HHTTCCEEEEEH------HHHHHHHHHHHHHT-----CHH----HHHHHHH-T
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH--HHCCCEEEEEEH------HHHHHHHHHHHHcC-----cHH----HHHHHhc-C
Confidence            4568899999999999999999852  111123455543      33344444443221     111    1222222 3


Q ss_pred             eEEEEEcCCCCCCc--cchhhhhhhccC-CCCCeEEEEEcCCh---------hHHHhccccceeecCCCCccc
Q 005860          277 KFLLILDDMWTDDY--SKWEPFHYCLKN-GVRGSKILVTTRKE---------TVARMMESIHVISIKELSEQE  337 (673)
Q Consensus       277 r~LlVLDdvw~~~~--~~~~~l~~~l~~-~~~gs~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~~  337 (673)
                      ..+|+|||+..-..  ...+.+...+.. ...|..||+||...         .+...+.....+++++ +.++
T Consensus        99 ~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e  170 (324)
T 1l8q_A           99 VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKT  170 (324)
T ss_dssp             CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHH
T ss_pred             CCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHH
Confidence            56999999944221  112233333321 13455788877532         1222222234567776 5544

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=97.55  E-value=0.00011  Score=75.38  Aligned_cols=101  Identities=14%  Similarity=0.073  Sum_probs=86.3

Q ss_pred             hhhCCccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcccc-hhhhcCCCcc-EEEeccCCCCcccc-c
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQ-VLEIEQCTSLKRLP-L  614 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~-~L~l~~c~~l~~lP-~  614 (673)
                      ...+..|+.|++++       +.+..+|+ .+..+.+|+.|+|..+ ++.+| ..+.++.+|+ .|++.+  ++..++ .
T Consensus       222 ~~~~~~L~~l~L~~-------n~i~~I~~~aF~~~~~L~~l~l~~n-i~~I~~~aF~~~~~L~~~l~l~~--~l~~I~~~  291 (329)
T 3sb4_A          222 RDYMPNLVSLDISK-------TNATTIPDFTFAQKKYLLKIKLPHN-LKTIGQRVFSNCGRLAGTLELPA--SVTAIEFG  291 (329)
T ss_dssp             HHHCTTCCEEECTT-------BCCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTTTCTTCCEEEEECT--TCCEECTT
T ss_pred             HHhcCCCeEEECCC-------CCcceecHhhhhCCCCCCEEECCcc-cceehHHHhhCChhccEEEEEcc--cceEEchh
Confidence            34588999999999       88888876 4788999999999987 88887 5688999999 999987  488887 5


Q ss_pred             cccccccCCeeecccccccccccc-CCCCCCCCcCC
Q 005860          615 GIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLS  649 (673)
Q Consensus       615 ~i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~  649 (673)
                      .|.++.+|+.|++..+.+..++.. +.++++|+.+.
T Consensus       292 aF~~c~~L~~l~l~~n~i~~I~~~aF~~~~~L~~ly  327 (329)
T 3sb4_A          292 AFMGCDNLRYVLATGDKITTLGDELFGNGVPSKLIY  327 (329)
T ss_dssp             TTTTCTTEEEEEECSSCCCEECTTTTCTTCCCCEEE
T ss_pred             hhhCCccCCEEEeCCCccCccchhhhcCCcchhhhc
Confidence            789999999999999999999875 78888888763

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.54  E-value=2e-05  Score=77.46  Aligned_cols=84  Identities=21%  Similarity=0.178  Sum_probs=66.7

Q ss_pred             ccccccccceecCCCCccc---chhhhcCCCccEEEeccCCCCccccccccccc--cCCeeecccccccc-cc-------
Q 005860          570 EKLIHLRYLRLVGLGTEEL---PETCCELLNLQVLEIEQCTSLKRLPLGIGKLV--NLRHLTYDDSCLEF-IP-------  636 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~L---P~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~--~Lr~L~l~~~~l~~-lP-------  636 (673)
                      .++++|+.|+|++|.+..+   |..+..+++|++|+|+++. +..++ ++..+.  +|+.|++++|.+.. +|       
T Consensus       167 ~~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~-i~~~~-~l~~l~~l~L~~L~L~~Npl~~~~~~~~~y~~  244 (267)
T 3rw6_A          167 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNE-LKSER-ELDKIKGLKLEELWLDGNSLCDTFRDQSTYIS  244 (267)
T ss_dssp             HHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSC-CCSGG-GGGGGTTSCCSEEECTTSTTGGGCSSHHHHHH
T ss_pred             hhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCc-cCCch-hhhhcccCCcceEEccCCcCccccCcchhHHH
Confidence            5678999999999997765   4677899999999999865 87773 566666  89999999998863 43       


Q ss_pred             ccCCCCCCCCcCCeeEEcc
Q 005860          637 KGIQRLTNLRTLSEFVVVR  655 (673)
Q Consensus       637 ~~i~~L~~L~~L~~~~~~~  655 (673)
                      .-+..+++|+.|++..+..
T Consensus       245 ~il~~~P~L~~LDg~~v~p  263 (267)
T 3rw6_A          245 AIRERFPKLLRLDGHELPP  263 (267)
T ss_dssp             HHHHHCTTCCEESSCBCCC
T ss_pred             HHHHHCcccCeECCcCCCC
Confidence            2357789999998876654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.53  E-value=3.9e-05  Score=68.57  Aligned_cols=38  Identities=21%  Similarity=0.170  Sum_probs=27.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      ..++|+|..|+|||||++.+++.... ..+ .++++...+
T Consensus        37 ~~~~l~G~~G~GKTtL~~~i~~~~~~-~g~-~~~~~~~~~   74 (149)
T 2kjq_A           37 QFIYVWGEEGAGKSHLLQAWVAQALE-AGK-NAAYIDAAS   74 (149)
T ss_dssp             SEEEEESSSTTTTCHHHHHHHHHHHT-TTC-CEEEEETTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHh-cCC-cEEEEcHHH
Confidence            47899999999999999999985322 111 256776544

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.52  E-value=0.00028  Score=71.07  Aligned_cols=140  Identities=14%  Similarity=0.006  Sum_probs=83.9

Q ss_pred             echhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc-cc-ccCCeEEEEEcCC-cccHHHHHHHHH
Q 005860          173 GRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD-VF-EYFDKRMWVCVSD-PFDELRIAKAII  249 (673)
Q Consensus       173 Gr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~-~~F~~~~wv~vs~-~~~~~~~~~~i~  249 (673)
                      |-++.++.+...+..+.       ...+.++|+.|+||||+|+.+.+... .. .+.+ ..++..++ ...+..+ ++++
T Consensus         1 g~~~~~~~L~~~i~~~~-------~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~i-r~li   71 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE-------GISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIK   71 (305)
T ss_dssp             ---CHHHHHHHHHHTCS-------SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHH
T ss_pred             ChHHHHHHHHHHHHCCC-------CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHHH-HHHH
Confidence            33455666777664432       56889999999999999999876310 11 1223 34444332 2233222 2333


Q ss_pred             HHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh-hHHHhcccccee
Q 005860          250 EALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE-TVARMMESIHVI  328 (673)
Q Consensus       250 ~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~-~v~~~~~~~~~~  328 (673)
                      +.+....                ..+++-++|+|++..-.....+.+...+......+.+|++|.+. .+...+.+. .+
T Consensus        72 ~~~~~~p----------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~  134 (305)
T 2gno_A           72 DFLNYSP----------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VF  134 (305)
T ss_dssp             HHHTSCC----------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SE
T ss_pred             HHHhhcc----------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eE
Confidence            3332211                12456789999996655566777888887766778888777543 343333445 88


Q ss_pred             ecCCCCcccc
Q 005860          329 SIKELSEQEC  338 (673)
Q Consensus       329 ~l~~L~~~~~  338 (673)
                      +++++++++.
T Consensus       135 ~f~~l~~~~i  144 (305)
T 2gno_A          135 RVVVNVPKEF  144 (305)
T ss_dssp             EEECCCCHHH
T ss_pred             eCCCCCHHHH
Confidence            8888887763

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.52  E-value=0.0001  Score=80.39  Aligned_cols=160  Identities=16%  Similarity=0.150  Sum_probs=82.4

Q ss_pred             CcceechhhHHHHHHHhccCCcc----------cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE----------EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP  238 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~----------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  238 (673)
                      .+++|++..++++..++......          .+....+.+.|+|++|+||||+|+.+.+..    .+ ..+.+..+..
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l----~~-~~i~in~s~~  113 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL----GY-DILEQNASDV  113 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT----TC-EEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc----CC-CEEEEeCCCc
Confidence            57999999999999998651100          000134689999999999999999999852    12 2345555554


Q ss_pred             ccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCcc---chhhhhhhccCCCCCeEEEEEcCC
Q 005860          239 FDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYS---KWEPFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       239 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~---~~~~l~~~l~~~~~gs~iivTtr~  315 (673)
                      .... +....+........-..-......  .....+++.+|++|++..-...   .+..+...+...  +..||+++.+
T Consensus       114 ~~~~-~~~~~i~~~~~~~~~~~~~~~~~~--~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~  188 (516)
T 1sxj_A          114 RSKT-LLNAGVKNALDNMSVVGYFKHNEE--AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNE  188 (516)
T ss_dssp             CCHH-HHHHTGGGGTTBCCSTTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESC
T ss_pred             chHH-HHHHHHHHHhccccHHHHHhhhhh--hhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcC
Confidence            4433 222222221111000000000000  0012367889999999432211   123343333322  2345555543


Q ss_pred             hh---HHHhccccceeecCCCCcccc
Q 005860          316 ET---VARMMESIHVISIKELSEQEC  338 (673)
Q Consensus       316 ~~---v~~~~~~~~~~~l~~L~~~~~  338 (673)
                      ..   +.........+.+++++.++.
T Consensus       189 ~~~~~l~~l~~r~~~i~f~~~~~~~~  214 (516)
T 1sxj_A          189 RNLPKMRPFDRVCLDIQFRRPDANSI  214 (516)
T ss_dssp             TTSSTTGGGTTTSEEEECCCCCHHHH
T ss_pred             CCCccchhhHhceEEEEeCCCCHHHH
Confidence            22   222112244677787777664

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.50  E-value=0.00021  Score=73.52  Aligned_cols=146  Identities=12%  Similarity=0.105  Sum_probs=79.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~  247 (673)
                      .+++|.+..++.+...+..+.       +..+.++|+.|+||||+|+.+.+... ...+. ....+..+.......+ ++
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~-------~~~~ll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~~~~~~~~~~~~~i-r~   95 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK-------LPHLLFYGPPGTGKTSTIVALAREIY-GKNYSNMVLELNASDDRGIDVV-RN   95 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC-------CCCEEEECSSSSSHHHHHHHHHHHHH-TTSHHHHEEEECTTSCCSHHHH-HT
T ss_pred             HHhcCcHHHHHHHHHHHhcCC-------CceEEEECCCCCCHHHHHHHHHHHHc-CCCccceEEEEcCcccccHHHH-HH
Confidence            467898888888888876543       22389999999999999999887421 11111 1223333332222211 11


Q ss_pred             HHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHHh-cccc
Q 005860          248 IIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VARM-MESI  325 (673)
Q Consensus       248 i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~~-~~~~  325 (673)
                      ++..+....              ..+.+.+-++|+|++..-.....+.+...+......+++|++|.... +... ..-.
T Consensus        96 ~i~~~~~~~--------------~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~  161 (340)
T 1sxj_C           96 QIKDFASTR--------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQC  161 (340)
T ss_dssp             HHHHHHHBC--------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             HHHHHHhhc--------------ccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhc
Confidence            111111000              00123467899999854333445556555554455677777765432 1111 1113


Q ss_pred             ceeecCCCCccc
Q 005860          326 HVISIKELSEQE  337 (673)
Q Consensus       326 ~~~~l~~L~~~~  337 (673)
                      ..+.+.+++.++
T Consensus       162 ~~~~~~~l~~~~  173 (340)
T 1sxj_C          162 TRFRFQPLPQEA  173 (340)
T ss_dssp             EEEECCCCCHHH
T ss_pred             eeEeccCCCHHH
Confidence            466777777655

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.46  E-value=0.00025  Score=72.91  Aligned_cols=51  Identities=24%  Similarity=0.309  Sum_probs=39.1

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++++|++..++.+..++......  ......|.|+|++|+|||+||+.+.+.
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~--~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKR--NECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHT--TSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhc--CCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            357999999999999888643100  122456899999999999999999874

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.43  E-value=0.00046  Score=67.87  Aligned_cols=52  Identities=19%  Similarity=0.181  Sum_probs=35.7

Q ss_pred             CcceechhhHHHHHHHhcc---CCc--ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLC---ESS--EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~---~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.+.+++..   ...  .-+....+-|.|+|++|+|||++|+.+++.
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            5789999888777665422   110  000122345789999999999999999884

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.37  E-value=0.00019  Score=74.30  Aligned_cols=138  Identities=17%  Similarity=0.188  Sum_probs=86.0

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHh-hhCCccceeeeccccccccc-cchhhhcc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLF-DQLKCLRALRIATLMNTWDV-NSTNKILK  567 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~-~~l~~L~~L~L~~~~~~~~~-~~~~~lp~  567 (673)
                      ..+.++.+.+..+....+++ + .+++|++|.+..+....   ....... ..+++|+.|+|+...+.... ..+..+.+
T Consensus       170 ~~P~L~~L~L~g~~~l~l~~-~-~~~~L~~L~L~~~~l~~---~~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~~  244 (362)
T 2ra8_A          170 AMPLLNNLKIKGTNNLSIGK-K-PRPNLKSLEIISGGLPD---SVVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFRP  244 (362)
T ss_dssp             TCTTCCEEEEECCBTCBCCS-C-BCTTCSEEEEECSBCCH---HHHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTGG
T ss_pred             cCCCCcEEEEeCCCCceecc-c-cCCCCcEEEEecCCCCh---HHHHHHHHccCCCCcEEEEeccccccccchhHHHHHH
Confidence            34678999987763233333 3 47899999987665311   1122221 36889999998531110000 11222222


Q ss_pred             cc--ccccccccceecCCCCcc-cchhhh---cCCCccEEEeccCCCCcc-----ccccccccccCCeeeccccccc
Q 005860          568 GI--EKLIHLRYLRLVGLGTEE-LPETCC---ELLNLQVLEIEQCTSLKR-----LPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       568 ~i--~~L~~Lr~L~L~~~~i~~-LP~~i~---~L~~L~~L~l~~c~~l~~-----lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                      .+  ..+++|++|+|++|.+.. .+..+.   .+++|++|+|+.|. +..     ++..+.++++|+.|+++.|.+.
T Consensus       245 ~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~-L~d~G~~~L~~~L~~l~~L~~L~L~~n~i~  320 (362)
T 2ra8_A          245 LFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGV-LTDEGARLLLDHVDKIKHLKFINMKYNYLS  320 (362)
T ss_dssp             GSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSC-CBHHHHHHHHTTHHHHTTCSEEECCSBBCC
T ss_pred             HHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCC-CChHHHHHHHhhcccCCcceEEECCCCcCC
Confidence            22  357899999999988642 233333   57899999998765 654     6666778899999999888765

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.32  E-value=0.001  Score=68.05  Aligned_cols=137  Identities=11%  Similarity=0.043  Sum_probs=76.5

Q ss_pred             hhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc--------------------ccCCeEEEEE
Q 005860          175 DEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF--------------------EYFDKRMWVC  234 (673)
Q Consensus       175 ~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~F~~~~wv~  234 (673)
                      ++..+.+...+..+.      -...+.++|+.|+||||+|+.+.+...-.                    .|++ ..++.
T Consensus         8 ~~~~~~l~~~i~~~~------~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~   80 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR------GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLA   80 (334)
T ss_dssp             HHHHHHHHHHHHTTC------CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEEC
T ss_pred             HHHHHHHHHHHHcCC------cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEe
Confidence            445666666665443      23468899999999999998887631100                    0122 12222


Q ss_pred             cCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEE
Q 005860          235 VSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKI  309 (673)
Q Consensus       235 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~i  309 (673)
                      ...                  .......++... +.+.+     .+++-++|+|++..-.....+.+...+.....++.+
T Consensus        81 ~~~------------------~~~~~~i~~ir~-l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~  141 (334)
T 1a5t_A           81 PEK------------------GKNTLGVDAVRE-VTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWF  141 (334)
T ss_dssp             CCT------------------TCSSBCHHHHHH-HHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEE
T ss_pred             ccc------------------cCCCCCHHHHHH-HHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEE
Confidence            110                  001112222222 22222     356778999999554445566677777666667787


Q ss_pred             EEEcCChh-HHH-hccccceeecCCCCccc
Q 005860          310 LVTTRKET-VAR-MMESIHVISIKELSEQE  337 (673)
Q Consensus       310 ivTtr~~~-v~~-~~~~~~~~~l~~L~~~~  337 (673)
                      |++|.+.+ +.. ...-...+++++++.++
T Consensus       142 Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~  171 (334)
T 1a5t_A          142 FLATREPERLLATLRSRCRLHYLAPPPEQY  171 (334)
T ss_dssp             EEEESCGGGSCHHHHTTSEEEECCCCCHHH
T ss_pred             EEEeCChHhCcHHHhhcceeeeCCCCCHHH
Confidence            77776643 222 12224567888887665

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.23  E-value=0.00013  Score=67.81  Aligned_cols=110  Identities=15%  Similarity=0.160  Sum_probs=80.7

Q ss_pred             hhhHHHHhhhCCccceeeecccccccccc-ch-----hhhccccccccccccceecCCCCcc-----cchhhhcCCCccE
Q 005860          532 THVLQSLFDQLKCLRALRIATLMNTWDVN-ST-----NKILKGIEKLIHLRYLRLVGLGTEE-----LPETCCELLNLQV  600 (673)
Q Consensus       532 ~~~~~~~~~~l~~L~~L~L~~~~~~~~~~-~~-----~~lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~  600 (673)
                      ...+...+...+.|+.|+|++       + .+     ..+...+....+|++|+|++|.+..     +...+...++|++
T Consensus        25 ~~~l~~~l~~~~~L~~L~L~~-------n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~   97 (185)
T 1io0_A           25 EETLKRIQNNDPDLEEVNLNN-------IMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKS   97 (185)
T ss_dssp             HHHHHHHHTTCTTCCEEECTT-------CTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCE
T ss_pred             HHHHHHHHhcCCCCCEEEecC-------CCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCE
Confidence            345566778889999999999       6 43     3456667778899999999998753     5566777789999


Q ss_pred             EEeccCCCCcc-----ccccccccccCCeeec--ccccccc-----ccccCCCCCCCCcCC
Q 005860          601 LEIEQCTSLKR-----LPLGIGKLVNLRHLTY--DDSCLEF-----IPKGIQRLTNLRTLS  649 (673)
Q Consensus       601 L~l~~c~~l~~-----lP~~i~~L~~Lr~L~l--~~~~l~~-----lP~~i~~L~~L~~L~  649 (673)
                      |+|++|. +..     +...+...++|++|++  ++|.+..     +...+...++|+.|.
T Consensus        98 L~L~~N~-i~~~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~g~~~l~~~L~~n~~L~~L~  157 (185)
T 1io0_A           98 LNVESNF-ISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFG  157 (185)
T ss_dssp             EECCSSC-CCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEE
T ss_pred             EECcCCc-CCHHHHHHHHHHHHhCCCceEEEecCCCCCCCHHHHHHHHHHHHhCCCcCEEe
Confidence            9999986 654     5667888889999999  7787753     333333344454443

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.22  E-value=0.00048  Score=79.98  Aligned_cols=45  Identities=27%  Similarity=0.357  Sum_probs=37.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.++.++...|....       ..-+.++|.+|+||||||+.+.+.
T Consensus       170 d~viGr~~~i~~l~~~l~~~~-------~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRRT-------KNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSS-------CCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHhcCC-------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            568999999999999986543       234689999999999999998874

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.22  E-value=0.00082  Score=68.44  Aligned_cols=52  Identities=21%  Similarity=0.286  Sum_probs=38.2

Q ss_pred             CcceechhhHHHHHHHhccCCc-----ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS-----EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~-----~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.|.+.+.....     .......+-|.|+|++|+|||+||+++++.
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             HHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            5799999999999887731100     000123456899999999999999999984

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.17  E-value=0.00027  Score=71.55  Aligned_cols=123  Identities=15%  Similarity=0.178  Sum_probs=64.5

Q ss_pred             cceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .++|.+..++.+...+......  ........+.|+|++|+||||+|+.+.+.  ....-...+.+..+...... ....
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~--~~~~~~~~~~~~~~~~~~~~-~~~~   94 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKH-AVSR   94 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHH--HHSCGGGEEEEEGGGCCSTT-HHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHH--HcCCCcceEEeecccccccc-cHHH
Confidence            5789999888888777543100  00122468999999999999999999884  21111234555554322211 1111


Q ss_pred             HHHHhhCCCCC--cCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhcc
Q 005860          248 IIEALEGFVPT--VGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLK  301 (673)
Q Consensus       248 i~~~l~~~~~~--~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~  301 (673)
                         .++.....  ......+...+.   ....-+|+||++..-+......+...+.
T Consensus        95 ---l~g~~~~~~~~~~~~~~~~~~~---~~~~~vl~lDEi~~l~~~~~~~Ll~~le  144 (311)
T 4fcw_A           95 ---LIGAPPGYVGYEEGGQLTEAVR---RRPYSVILFDAIEKAHPDVFNILLQMLD  144 (311)
T ss_dssp             ---HHCCCTTSTTTTTCCHHHHHHH---HCSSEEEEEETGGGSCHHHHHHHHHHHH
T ss_pred             ---hcCCCCccccccccchHHHHHH---hCCCeEEEEeChhhcCHHHHHHHHHHHh
Confidence               12211110  000012222222   2334699999995544444555555443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.14  E-value=0.00071  Score=72.67  Aligned_cols=45  Identities=22%  Similarity=0.295  Sum_probs=37.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.+++++...|....       ..-+.|+|.+|+|||++|+.+.+.
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~-------~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRT-------KNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS-------SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccC-------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999986543       123579999999999999998874

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.10  E-value=0.0011  Score=68.61  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=38.1

Q ss_pred             CcceechhhHHHHHHHhccC----Cc-ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS-EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~-~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.|.+.+...    .. .......+.|.|+|++|+|||+||+++++.
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~  140 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ  140 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999998877421    00 000123457889999999999999999884

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.09  E-value=0.00028  Score=69.75  Aligned_cols=47  Identities=15%  Similarity=0.105  Sum_probs=33.5

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|.+..+.++.+.+..-..     ...-|.|+|..|+|||++|+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~-----~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAP-----LDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTT-----SCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhC-----CCCCEEEECCCCCcHHHHHHHHHHh
Confidence            4589999998888876644221     1234779999999999999999985

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.08  E-value=0.0029  Score=64.30  Aligned_cols=52  Identities=23%  Similarity=0.293  Sum_probs=37.4

Q ss_pred             CcceechhhHHHHHHHhccC----Cc-ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS-EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~-~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..++.|.+.+...    .. .......+-|.|+|++|+|||+||+++++.
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~   68 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE   68 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH
Confidence            57899999888888766321    00 000123467889999999999999999984

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.08  E-value=0.0018  Score=67.77  Aligned_cols=53  Identities=25%  Similarity=0.320  Sum_probs=38.6

Q ss_pred             CCcceechhhHHHHHHHhccCCc-----ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESS-----EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~-----~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|.+..++.+..++.....     .......+-|.|+|.+|+|||+||+++.+.
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~  171 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE  171 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            35799999999999988732110     000122457899999999999999999874

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.02  E-value=0.0004  Score=63.28  Aligned_cols=85  Identities=12%  Similarity=0.210  Sum_probs=39.8

Q ss_pred             cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hhh-hccccccc----cccccceecCCC-Ccc
Q 005860          515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TNK-ILKGIEKL----IHLRYLRLVGLG-TEE  587 (673)
Q Consensus       515 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~-lp~~i~~L----~~Lr~L~L~~~~-i~~  587 (673)
                      .+|+.|+++++..    ...--..+.++++|+.|+|++       |. ++. -...+..+    ++|++|+|++|. ++.
T Consensus        61 ~~L~~LDLs~~~I----td~GL~~L~~~~~L~~L~L~~-------C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD  129 (176)
T 3e4g_A           61 YKIQAIDATDSCI----MSIGFDHMEGLQYVEKIRLCK-------CHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTD  129 (176)
T ss_dssp             CCEEEEEEESCCC----CGGGGGGGTTCSCCCEEEEES-------CTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCH
T ss_pred             ceEeEEeCcCCCc----cHHHHHHhcCCCCCCEEEeCC-------CCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCH
Confidence            3566666666542    111111234566666666666       32 221 12223332    246666666654 433


Q ss_pred             c-chhhhcCCCccEEEeccCCCCc
Q 005860          588 L-PETCCELLNLQVLEIEQCTSLK  610 (673)
Q Consensus       588 L-P~~i~~L~~L~~L~l~~c~~l~  610 (673)
                      - -..+.++++|++|+|++|+.+.
T Consensus       130 ~Gl~~L~~~~~L~~L~L~~c~~It  153 (176)
T 3e4g_A          130 KGIIALHHFRNLKYLFLSDLPGVK  153 (176)
T ss_dssp             HHHHHGGGCTTCCEEEEESCTTCC
T ss_pred             HHHHHHhcCCCCCEEECCCCCCCC
Confidence            1 1234455666666666665443

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=96.98  E-value=0.0029  Score=60.15  Aligned_cols=84  Identities=20%  Similarity=0.177  Sum_probs=51.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC-----------CC-CCcCcHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG-----------FV-PTVGELNS  264 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~-----------~~-~~~~~~~~  264 (673)
                      -.++.|+|.+|+||||||..+..     ..-..++|++....++...+.. +.+.++.           .. ....+...
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~-----~~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL-----LSGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH-----HHCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-----HcCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            45899999999999999988876     1224678888776555554433 3322211           11 11222233


Q ss_pred             HHHHHHHHhCCCeEEEEEcCCC
Q 005860          265 LLESIRASLVGKKFLLILDDMW  286 (673)
Q Consensus       265 ~~~~l~~~l~~kr~LlVLDdvw  286 (673)
                      ....++..+..+.-+||+|.+-
T Consensus        94 ~~~~~~~l~~~~~~lliiD~~~  115 (220)
T 2cvh_A           94 VIGSLKKTVDSNFALVVVDSIT  115 (220)
T ss_dssp             HHHHHHHHCCTTEEEEEEECCC
T ss_pred             HHHHHHHHhhcCCCEEEEcCcH
Confidence            4445555554457799999873

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.96  E-value=0.0025  Score=63.95  Aligned_cols=52  Identities=25%  Similarity=0.349  Sum_probs=38.2

Q ss_pred             CcceechhhHHHHHHHhccCCc-----ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS-----EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~-----~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.+.+.+.....     .......+.+.|+|++|+||||+|+.+.+.
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            5799999999999887743110     000122457899999999999999999884

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.94  E-value=0.00034  Score=70.62  Aligned_cols=47  Identities=19%  Similarity=0.190  Sum_probs=36.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|+...+.++.+.+..-..     ...-|.|+|.+|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~-----~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAP-----SDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCS-----TTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhC-----CCCcEEEECCCCchHHHHHHHHHHh
Confidence            4689999999988887754321     1234679999999999999999984

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=96.93  E-value=0.0015  Score=65.88  Aligned_cols=52  Identities=21%  Similarity=0.233  Sum_probs=37.1

Q ss_pred             CcceechhhHHHHHHHhccC--Cc--c---cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE--SS--E---EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~--~~--~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.+..++.+...+...  ..  .   .......-+.|+|++|+|||++|+.+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999988877541  00  0   00012345789999999999999999884

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=96.93  E-value=0.00018  Score=74.47  Aligned_cols=126  Identities=16%  Similarity=0.123  Sum_probs=76.6

Q ss_pred             cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh-hccccc--cccccccceecCC--C-
Q 005860          511 IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK-ILKGIE--KLIHLRYLRLVGL--G-  584 (673)
Q Consensus       511 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~-lp~~i~--~L~~Lr~L~L~~~--~-  584 (673)
                      +..+++|+.|.+.++.. .   . ++. + .+++|+.|++..       +.+.. ....+.  .+++|++|+|+.+  . 
T Consensus       168 l~~~P~L~~L~L~g~~~-l---~-l~~-~-~~~~L~~L~L~~-------~~l~~~~l~~l~~~~lp~L~~L~L~~~~~~~  233 (362)
T 2ra8_A          168 LDAMPLLNNLKIKGTNN-L---S-IGK-K-PRPNLKSLEIIS-------GGLPDSVVEDILGSDLPNLEKLVLYVGVEDY  233 (362)
T ss_dssp             HHTCTTCCEEEEECCBT-C---B-CCS-C-BCTTCSEEEEEC-------SBCCHHHHHHHHHSBCTTCCEEEEECBCGGG
T ss_pred             HhcCCCCcEEEEeCCCC-c---e-ecc-c-cCCCCcEEEEec-------CCCChHHHHHHHHccCCCCcEEEEecccccc
Confidence            44578899998877631 1   1 122 2 367888888877       55322 222333  6788999988531  1 


Q ss_pred             -----Ccccchhh--hcCCCccEEEeccCCCCccccccc---cccccCCeeecccccccc-----ccccCCCCCCCCcCC
Q 005860          585 -----TEELPETC--CELLNLQVLEIEQCTSLKRLPLGI---GKLVNLRHLTYDDSCLEF-----IPKGIQRLTNLRTLS  649 (673)
Q Consensus       585 -----i~~LP~~i--~~L~~L~~L~l~~c~~l~~lP~~i---~~L~~Lr~L~l~~~~l~~-----lP~~i~~L~~L~~L~  649 (673)
                           +..+.+.+  ..+++|++|+|++|......+..+   ..+++|++|+++.|.+..     ++.++.++++|+.|.
T Consensus       234 ~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~L~d~G~~~L~~~L~~l~~L~~L~  313 (362)
T 2ra8_A          234 GFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGVLTDEGARLLLDHVDKIKHLKFIN  313 (362)
T ss_dssp             TCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSCCBHHHHHHHHTTHHHHTTCSEEE
T ss_pred             ccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCCCChHHHHHHHhhcccCCcceEEE
Confidence                 22222222  357899999999876322223233   357899999998887764     455555666666664


Q ss_pred             e
Q 005860          650 E  650 (673)
Q Consensus       650 ~  650 (673)
                      .
T Consensus       314 L  314 (362)
T 2ra8_A          314 M  314 (362)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=96.93  E-value=0.0003  Score=70.25  Aligned_cols=67  Identities=18%  Similarity=0.439  Sum_probs=44.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEc--CCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCV--SDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  274 (673)
                      -+++.|+|++|+||||||.++...     .-..++|+++  .+..+.             .   ..+.+.....+.+.+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~v~~-------------~---~~~le~~l~~i~~~l~  181 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEPLSG-------------Y---NTDFNVFVDDIARAML  181 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCSSTT-------------C---BCCHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhhhhh-------------h---hcCHHHHHHHHHHHHh
Confidence            357789999999999999888763     1224567766  332110             0   0345555666666666


Q ss_pred             CCeEEEEEcCC
Q 005860          275 GKKFLLILDDM  285 (673)
Q Consensus       275 ~kr~LlVLDdv  285 (673)
                      ..+ +||+|++
T Consensus       182 ~~~-LLVIDsI  191 (331)
T 2vhj_A          182 QHR-VIVIDSL  191 (331)
T ss_dssp             HCS-EEEEECC
T ss_pred             hCC-EEEEecc
Confidence            556 9999999

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=96.93  E-value=0.0021  Score=64.74  Aligned_cols=52  Identities=23%  Similarity=0.242  Sum_probs=37.8

Q ss_pred             CcceechhhHHHHHHHhccCCc-c-----cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS-E-----EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~-~-----~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.+.+.+...-. +     -+....+.|.|+|++|+||||||+++++.
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            4699999998888887643200 0     00123457899999999999999999985

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.93  E-value=0.00037  Score=70.42  Aligned_cols=54  Identities=17%  Similarity=0.056  Sum_probs=34.0

Q ss_pred             hhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcccc-ccCCeEEEEEc
Q 005860          176 EEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVF-EYFDKRMWVCV  235 (673)
Q Consensus       176 ~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~v  235 (673)
                      ...+.+.+++.....    .....+.|+|+.|+|||+||+++++.  .. ..-..++++++
T Consensus       135 ~~~~~~~~~i~~~~~----~~~~~lll~G~~GtGKT~La~aia~~--~~~~~g~~v~~~~~  189 (308)
T 2qgz_A          135 EAFSAILDFVEQYPS----AEQKGLYLYGDMGIGKSYLLAAMAHE--LSEKKGVSTTLLHF  189 (308)
T ss_dssp             HHHHHHHHHHHHCSC----SSCCEEEEECSTTSSHHHHHHHHHHH--HHHHSCCCEEEEEH
T ss_pred             HHHHHHHHHHHhccc----cCCceEEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEH
Confidence            344455555543221    12356889999999999999999985  22 22234556654

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=96.93  E-value=0.0031  Score=67.14  Aligned_cols=52  Identities=23%  Similarity=0.293  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccC----Cc-ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS-EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~-~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..++.|.+.+...    .. .......+-|.|+|++|+|||+||+++++.
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999888876321    00 000123467889999999999999999984

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=96.92  E-value=0.0014  Score=67.75  Aligned_cols=52  Identities=21%  Similarity=0.277  Sum_probs=37.4

Q ss_pred             CcceechhhHHHHHHHhccC----Cc-ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS-EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~-~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++.|.+.+...    .. .......+-|.|+|++|+|||+||+++++.
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~  107 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE  107 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            47999999999998876321    00 000122345889999999999999999985

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=96.87  E-value=0.0014  Score=70.57  Aligned_cols=52  Identities=21%  Similarity=0.247  Sum_probs=37.9

Q ss_pred             CcceechhhHHHHHHHhccCCcc-c-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE-E-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~-~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+..++++.+++...... +     +....+-|.|+|++|+|||++|+++.+.
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~  261 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE  261 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHH
Confidence            46899999999998887532000 0     0022345889999999999999999884

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=96.85  E-value=0.00054  Score=62.36  Aligned_cols=81  Identities=19%  Similarity=0.215  Sum_probs=58.1

Q ss_pred             Cccceeeeccccccccccchhh-hccccccccccccceecCCC-Cccc-chhhhcC----CCccEEEeccCCCCcccc-c
Q 005860          543 KCLRALRIATLMNTWDVNSTNK-ILKGIEKLIHLRYLRLVGLG-TEEL-PETCCEL----LNLQVLEIEQCTSLKRLP-L  614 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~-lp~~i~~L~~Lr~L~L~~~~-i~~L-P~~i~~L----~~L~~L~l~~c~~l~~lP-~  614 (673)
                      -.|+.||+++       +.+.. =...+..+++|+.|+|++|. ++.- -..|+.+    ++|+.|+|++|.++..-= .
T Consensus        61 ~~L~~LDLs~-------~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~  133 (176)
T 3e4g_A           61 YKIQAIDATD-------SCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGII  133 (176)
T ss_dssp             CCEEEEEEES-------CCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHH
T ss_pred             ceEeEEeCcC-------CCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHH
Confidence            3689999999       66433 23456788999999999997 6542 1345554    379999999998775411 2


Q ss_pred             cccccccCCeeecccc
Q 005860          615 GIGKLVNLRHLTYDDS  630 (673)
Q Consensus       615 ~i~~L~~Lr~L~l~~~  630 (673)
                      .+.++++|++|+++++
T Consensus       134 ~L~~~~~L~~L~L~~c  149 (176)
T 3e4g_A          134 ALHHFRNLKYLFLSDL  149 (176)
T ss_dssp             HGGGCTTCCEEEEESC
T ss_pred             HHhcCCCCCEEECCCC
Confidence            4678899999997665

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=96.81  E-value=0.0014  Score=68.95  Aligned_cols=65  Identities=17%  Similarity=0.063  Sum_probs=34.0

Q ss_pred             cccccccccceecCCCCc-----ccc-hhhhcCCCccEEEeccCCCCccccc-cccccccCCeeecccccccccc
Q 005860          569 IEKLIHLRYLRLVGLGTE-----ELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~-----~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +..+.+|+.+.+.++.+.     .++ ..+..+++|+.++|..  ++..++. .|.++.+|+.+.+..+ +..++
T Consensus       267 F~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~~--~i~~I~~~aF~~c~~L~~l~lp~~-l~~I~  338 (401)
T 4fdw_A          267 FYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIPE--SIRILGQGLLGGNRKVTQLTIPAN-VTQIN  338 (401)
T ss_dssp             TTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCCT--TCCEECTTTTTTCCSCCEEEECTT-CCEEC
T ss_pred             hhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeCC--ceEEEhhhhhcCCCCccEEEECcc-ccEEc
Confidence            444556666666554433     333 3455566666666652  2555553 3555666666665333 44444

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=96.70  E-value=0.007  Score=69.33  Aligned_cols=45  Identities=24%  Similarity=0.245  Sum_probs=37.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.+++++...|....       ..-+.|+|.+|+||||+|+.+.+.
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~-------~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRR-------KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS-------SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccC-------CCCeEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999986543       234679999999999999998874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.68  E-value=0.00051  Score=78.73  Aligned_cols=125  Identities=18%  Similarity=0.252  Sum_probs=70.5

Q ss_pred             CcceechhhHHHHHHHhccCCccc--ccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEE--IINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~--~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|.+..++.+...+.......  .......+.++|++|+|||++|+.+.+.  ....-...+.++++.-.+..    
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~--l~~~~~~~i~i~~s~~~~~~----  564 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAES--IFGDEESMIRIDMSEYMEKH----  564 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHH--HHSCTTCEEEEEGGGGCSSC----
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH--hcCCCcceEEEechhccccc----
Confidence            468999999988888775432100  0123457999999999999999999884  21112234555544321100    


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCC-----------CCCeEEEEEcC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNG-----------VRGSKILVTTR  314 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~-----------~~gs~iivTtr  314 (673)
                                  ......+...++.   ....+|+||++..-+....+.+...+..+           ....+||+||.
T Consensus       565 ------------~~~~~~l~~~~~~---~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn  628 (758)
T 3pxi_A          565 ------------STSGGQLTEKVRR---KPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSN  628 (758)
T ss_dssp             ------------CCC---CHHHHHH---CSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEES
T ss_pred             ------------ccccchhhHHHHh---CCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCC
Confidence                        0000111112221   23348999999655544555555544431           13457888887

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.66  E-value=0.0021  Score=73.63  Aligned_cols=45  Identities=22%  Similarity=0.295  Sum_probs=37.7

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++||+.+++++...|....       ..-+.++|++|+|||++|+.+.+.
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~-------~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRT-------KNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS-------SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCCC-------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999986644       123679999999999999988874

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=96.65  E-value=0.0034  Score=61.45  Aligned_cols=53  Identities=25%  Similarity=0.241  Sum_probs=34.8

Q ss_pred             CCcceechhhHHHHHHHhc---cCCc-cc-ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLL---CESS-EE-IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~---~~~~-~~-~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++++|.+..++++.+.+.   .... .. +....+-+.|+|++|+||||||+.+.+.
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            3578999988777665432   1110 00 0011234889999999999999999884

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=96.51  E-value=0.002  Score=67.74  Aligned_cols=97  Identities=11%  Similarity=0.092  Sum_probs=45.7

Q ss_pred             cccccccceecCCCCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccc-----ccccc-CCCC
Q 005860          571 KLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLE-----FIPKG-IQRL  642 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~-----~lP~~-i~~L  642 (673)
                      .+.+|+.+.|..+ ++.++. .+.+ .+|+.+.+..  ++..++. .|.++.+|+.+.+.++.+.     .++.. +.++
T Consensus       224 ~~~~L~~l~l~~~-l~~I~~~aF~~-~~L~~i~lp~--~i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c  299 (401)
T 4fdw_A          224 KTSQLKTIEIPEN-VSTIGQEAFRE-SGITTVKLPN--GVTNIASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGC  299 (401)
T ss_dssp             TCTTCCCEECCTT-CCEECTTTTTT-CCCSEEEEET--TCCEECTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTC
T ss_pred             CCCCCCEEecCCC-ccCcccccccc-CCccEEEeCC--CccEEChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCC
Confidence            3444444444432 344432 2222 4555555532  2555543 4666777777776555443     34433 5556


Q ss_pred             CCCCcCCeeE-EccCCccCCCccccCCCCC
Q 005860          643 TNLRTLSEFV-VVRGGSKYGGKACNLEGLR  671 (673)
Q Consensus       643 ~~L~~L~~~~-~~~~~~~~~~~~~~l~~L~  671 (673)
                      ++|+.+..-. +..-....+..|.+|++|.
T Consensus       300 ~~L~~l~l~~~i~~I~~~aF~~c~~L~~l~  329 (401)
T 4fdw_A          300 PKLARFEIPESIRILGQGLLGGNRKVTQLT  329 (401)
T ss_dssp             TTCCEECCCTTCCEECTTTTTTCCSCCEEE
T ss_pred             ccCCeEEeCCceEEEhhhhhcCCCCccEEE
Confidence            6665553211 1111112355566666553

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.43  E-value=0.0044  Score=59.39  Aligned_cols=114  Identities=16%  Similarity=0.112  Sum_probs=60.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC--------------------
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP--------------------  257 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~--------------------  257 (673)
                      .+++|+|.+|+|||||++.+....  ...=..++|+....  ....+...+. .++....                    
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~--~~~~~~v~~~~~~~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKG--LRDGDPCIYVTTEE--SRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKEDQ   98 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH--HHHTCCEEEEESSS--CHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----CT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH--HHCCCeEEEEEccc--CHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCce
Confidence            589999999999999999888532  11223466766544  3344433332 3322110                    


Q ss_pred             ---CcCcHHHHHHHHHHHh---CCCeEEEEEcCCCCC---CccchhhhhhhccC--CCCCeEEEEEcCCh
Q 005860          258 ---TVGELNSLLESIRASL---VGKKFLLILDDMWTD---DYSKWEPFHYCLKN--GVRGSKILVTTRKE  316 (673)
Q Consensus       258 ---~~~~~~~~~~~l~~~l---~~kr~LlVLDdvw~~---~~~~~~~l~~~l~~--~~~gs~iivTtr~~  316 (673)
                         ...+.+++...+...+   .-+..+||+|..-..   +......+...+..  ...|..||+||...
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A           99 WSLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             TBCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             eeecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence               0113445555554444   223459999998421   22222333333322  13477899998865

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.37  E-value=0.0069  Score=58.50  Aligned_cols=89  Identities=21%  Similarity=0.139  Sum_probs=51.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC---------CcCcHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALEGFVP---------TVGELN  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---------~~~~~~  263 (673)
                      -.++.|+|.+|+|||||+..+........    .-..++|+.....++...+. .+++.++....         ...+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~  102 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNTD  102 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCHH
Confidence            35899999999999999988776311111    13578899877655554432 34444432210         011222


Q ss_pred             ---HHHHHHHHHhC-CCeEEEEEcCCC
Q 005860          264 ---SLLESIRASLV-GKKFLLILDDMW  286 (673)
Q Consensus       264 ---~~~~~l~~~l~-~kr~LlVLDdvw  286 (673)
                         .....+.+.+. .+.-+||||.+-
T Consensus       103 ~~~~~~~~~~~~~~~~~~~lliiD~~~  129 (243)
T 1n0w_A          103 HQTQLLYQASAMMVESRYALLIVDSAT  129 (243)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEeCch
Confidence               22333444443 467789999883

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.37  E-value=0.017  Score=59.07  Aligned_cols=58  Identities=17%  Similarity=0.201  Sum_probs=39.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhh
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALE  253 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~  253 (673)
                      ..-.++.|+|.+|+||||||..+........    .-..++|++....+++..+.. +++.++
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g  181 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFN  181 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcC
Confidence            3457999999999999999977765321111    224688999888777765543 444443

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.31  E-value=0.026  Score=54.02  Aligned_cols=23  Identities=30%  Similarity=0.599  Sum_probs=21.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999885

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.22  E-value=0.0042  Score=58.34  Aligned_cols=42  Identities=24%  Similarity=0.219  Sum_probs=32.9

Q ss_pred             chhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhc
Q 005860          174 RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       174 r~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      |++.++.+.+.+....    .....+|+|+|..|+||||+++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~----~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIK----TAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSC----CSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc----cCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            5566777777776543    13468999999999999999998876

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=96.21  E-value=0.0084  Score=61.28  Aligned_cols=83  Identities=20%  Similarity=0.208  Sum_probs=54.4

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  270 (673)
                      .-.++.|+|++|+||||||.++...  ....=..++|++....++..     .++.++....     ...+.++....+.
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~--~~~~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~  132 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAE--AQKMGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVD  132 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHH
Confidence            3479999999999999999888764  22222357889877766654     4555544311     2334555555555


Q ss_pred             HHhC-CCeEEEEEcCC
Q 005860          271 ASLV-GKKFLLILDDM  285 (673)
Q Consensus       271 ~~l~-~kr~LlVLDdv  285 (673)
                      ..++ .+.-++|+|.+
T Consensus       133 ~l~~~~~~dlvVIDSi  148 (356)
T 3hr8_A          133 ELVRSGVVDLIVVDSV  148 (356)
T ss_dssp             HHHHTSCCSEEEEECT
T ss_pred             HHhhhcCCCeEEehHh
Confidence            5543 45568999987

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=96.17  E-value=0.015  Score=56.08  Aligned_cols=24  Identities=25%  Similarity=0.429  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999885

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.13  E-value=0.012  Score=59.71  Aligned_cols=88  Identities=16%  Similarity=0.185  Sum_probs=52.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccccc----CCeEEEEEcCCcccHHHHHHHHHHHhhCCCC---------CcCcHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEY----FDKRMWVCVSDPFDELRIAKAIIEALEGFVP---------TVGELN  263 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---------~~~~~~  263 (673)
                      -.++.|+|.+|+||||||.++.........    -..++|++....++...+. ++++.++....         ...+.+
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~~  185 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINTD  185 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCHH
Confidence            358999999999999999777653211110    2468999988877776654 34455543210         111222


Q ss_pred             ---HHHHHHHHHhC--CCeEEEEEcCC
Q 005860          264 ---SLLESIRASLV--GKKFLLILDDM  285 (673)
Q Consensus       264 ---~~~~~l~~~l~--~kr~LlVLDdv  285 (673)
                         ++...+...++  .+.-+||+|.+
T Consensus       186 ~~~~~l~~l~~~~~~~~~~~lvVIDsl  212 (324)
T 2z43_A          186 HQIAIVDDLQELVSKDPSIKLIVVDSV  212 (324)
T ss_dssp             HHHHHHHHHHHHHHHCTTEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHhccCCCEEEEeCc
Confidence               23344444443  45668888887

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.13  E-value=0.0093  Score=60.52  Aligned_cols=88  Identities=17%  Similarity=0.168  Sum_probs=52.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccc---------cC-----CeEEEEEcCCcccHHHHHHHHHHHhhCCC------
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFE---------YF-----DKRMWVCVSDPFDELRIAKAIIEALEGFV------  256 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------  256 (673)
                      -.++.|+|.+|+||||||.++........         ..     ..++|++....+++..+.. +++.++...      
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~  176 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLDN  176 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhcC
Confidence            47999999999999999977765321111         11     4688999888877776653 345554321      


Q ss_pred             ---CCcCcHH---HHHHHHHHHhC--CCeEEEEEcCC
Q 005860          257 ---PTVGELN---SLLESIRASLV--GKKFLLILDDM  285 (673)
Q Consensus       257 ---~~~~~~~---~~~~~l~~~l~--~kr~LlVLDdv  285 (673)
                         ....+.+   ++...+.+.++  .+.-+||+|.+
T Consensus       177 l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl  213 (322)
T 2i1q_A          177 TFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSL  213 (322)
T ss_dssp             EEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECS
T ss_pred             EEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECc
Confidence               0111222   23334444443  34557888877

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.07  E-value=0.0042  Score=72.00  Aligned_cols=52  Identities=21%  Similarity=0.286  Sum_probs=38.0

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.+..++.+...+......  ........+.|+|+.|+|||++|+.+.+.
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~  611 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT  611 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            35799999888888777543210  00123468899999999999999999884

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.07  E-value=0.01  Score=61.26  Aligned_cols=52  Identities=19%  Similarity=0.187  Sum_probs=37.9

Q ss_pred             CcceechhhHHHHHHHhccCC--c----ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCES--S----EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~--~----~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+.-+-  +    .-+....+-|.++|++|.|||.||+++.+.
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            478899999888877664310  0    001233566889999999999999999985

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=96.04  E-value=0.014  Score=63.66  Aligned_cols=51  Identities=24%  Similarity=0.289  Sum_probs=35.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.+.-.+.+.+.+.-..-.. .....++.|+|++|+||||||+.+...
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~-~~~g~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTK-SLKGPILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSS-SCCSCEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcc-cCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            457888887777655442111000 113458999999999999999999884

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.04  E-value=0.0041  Score=59.16  Aligned_cols=112  Identities=15%  Similarity=0.010  Sum_probs=61.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCC--cCcHHHHHHHHHHHhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPT--VGELNSLLESIRASLV  274 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~  274 (673)
                      -.++.|+|..|+||||++..+...  ...+-..++.+.......   ....+++.++.....  .....++...+.+.+.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r--~~~~g~kVli~~~~~d~r---~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHR--LEYADVKYLVFKPKIDTR---SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHH--HHHTTCCEEEEEECCCGG---GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEEeccCch---HHHHHHHhcCCCccccccCCHHHHHHHHHHHhh
Confidence            478999999999999999666553  323333344443332211   112334444332111  2233455556665555


Q ss_pred             CCeE-EEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          275 GKKF-LLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       275 ~kr~-LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      +.++ +||+|.+..-+.++.+.+.. +.+  .|-.||+|-++.
T Consensus        87 ~~~~dvViIDEaQ~l~~~~ve~l~~-L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFDDRICEVANI-LAE--NGFVVIISGLDK  126 (223)
T ss_dssp             CTTCCEEEECSGGGSCTHHHHHHHH-HHH--TTCEEEEECCSB
T ss_pred             CCCCCEEEEecCccCcHHHHHHHHH-HHh--CCCeEEEEeccc
Confidence            5545 99999985433334444433 222  267899998853

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.04  E-value=0.011  Score=62.00  Aligned_cols=52  Identities=21%  Similarity=0.266  Sum_probs=38.2

Q ss_pred             CcceechhhHHHHHHHhccCCc------ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS------EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~------~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+...-.      .-+....+-|.++|++|+|||+||+++.+.
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            5788999998888876632110      001234567899999999999999999985

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.01  E-value=0.0056  Score=64.20  Aligned_cols=52  Identities=23%  Similarity=0.268  Sum_probs=38.2

Q ss_pred             CcceechhhHHHHHHHhccC---Cc---ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE---SS---EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~---~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+..+   +.   .-+....+-|.++|++|.|||.||+++.+.
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHH
Confidence            57899999998888765321   10   001234567899999999999999999995

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.97  E-value=0.012  Score=61.77  Aligned_cols=52  Identities=23%  Similarity=0.196  Sum_probs=38.1

Q ss_pred             CcceechhhHHHHHHHhccCCc------ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS------EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~------~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+..+-.      .-+....+-|.++|++|.|||+||+++.+.
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            5788999988888776643110      001234577899999999999999999995

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=95.93  E-value=0.016  Score=59.62  Aligned_cols=82  Identities=18%  Similarity=0.106  Sum_probs=53.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIRA  271 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~  271 (673)
                      -.++.|.|.+|+||||||.++...  ....-..++|++....++..     .++.++....     +..+.++....+..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~--~~~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQ--AQKAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHH--HHHCCCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            358889999999999999777654  22223468999988776654     2444443211     22355666666666


Q ss_pred             HhCC-CeEEEEEcCC
Q 005860          272 SLVG-KKFLLILDDM  285 (673)
Q Consensus       272 ~l~~-kr~LlVLDdv  285 (673)
                      ..+. ..-+||+|.+
T Consensus       147 l~~~~~~~lVVIDsl  161 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSV  161 (366)
T ss_dssp             HHTTTCCSEEEEECT
T ss_pred             HHhcCCCCEEEEeCh
Confidence            6543 4558999988

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=95.90  E-value=0.0096  Score=63.65  Aligned_cols=47  Identities=19%  Similarity=0.258  Sum_probs=35.1

Q ss_pred             CcceechhhHHHHHHHh---ccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKL---LCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L---~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..++.+..++   ....     ...+-+.++|++|+|||+||+.+.+.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~-----~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKK-----MAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTC-----CTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCC-----CCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            67999998877655443   3222     22345889999999999999999985

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.89  E-value=0.0064  Score=57.35  Aligned_cols=39  Identities=21%  Similarity=0.205  Sum_probs=29.1

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -+++|.+.+....     ....+|+|+|..|+|||||++.+...
T Consensus         7 ~~~~~~~~~~~~~-----~~g~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A            7 LCQGVLERLDPRQ-----PGRQLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             HHHHHHHHSCTTC-----CSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-----CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4455556554331     34679999999999999999998874

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=95.79  E-value=0.014  Score=58.17  Aligned_cols=24  Identities=29%  Similarity=0.239  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|.+|+||||++..+...
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~  128 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAI  128 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999887763

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=95.78  E-value=0.0093  Score=63.56  Aligned_cols=52  Identities=25%  Similarity=0.248  Sum_probs=34.9

Q ss_pred             CcceechhhHHHHHHHhccCCccc-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEE-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|.++.++++.+.+..-..+.     +....+-|.|+|++|+||||||+.+.+.
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~   72 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGE   72 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            478999988777766543210000     0011233789999999999999999984

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=95.77  E-value=0.024  Score=56.33  Aligned_cols=81  Identities=10%  Similarity=0.120  Sum_probs=52.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcCcccccc--CCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHH-HHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEY--FDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSL-LESIR  270 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~-~~~l~  270 (673)
                      ++-|.|.+|+||||||.++...  ....  =..++||+....++..     .+++++...+     ...+.++. ...+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~  102 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVN  102 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHH
Confidence            7899999999999999666553  2222  2468899988777753     3666665422     12344554 33333


Q ss_pred             HH--h-CCCeEEEEEcCCC
Q 005860          271 AS--L-VGKKFLLILDDMW  286 (673)
Q Consensus       271 ~~--l-~~kr~LlVLDdvw  286 (673)
                      ..  + .++.-+||+|-|-
T Consensus       103 ~l~~i~~~~~~lvVIDSI~  121 (333)
T 3io5_A          103 QLDAIERGEKVVVFIDSLG  121 (333)
T ss_dssp             HHHTCCTTCCEEEEEECST
T ss_pred             HHHHhhccCceEEEEeccc
Confidence            22  2 4578899999883

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=95.76  E-value=0.017  Score=65.37  Aligned_cols=97  Identities=15%  Similarity=0.215  Sum_probs=57.3

Q ss_pred             CcceechhhHHHHHHHhcc----CCc-c-cccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHH
Q 005860          169 SEIRGRDEEKSSLKSKLLC----ESS-E-EIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDEL  242 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~----~~~-~-~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  242 (673)
                      +++.|.++.+++|.+.+.-    +.- . -+....+-|.++|++|+|||+||+++++..  ..+|   +.|+.+      
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el--g~~~---~~v~~~------  272 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET--GAFF---FLINGP------  272 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT--TCEE---EEEEHH------
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh--CCeE---EEEEhH------
Confidence            4678899888888776532    110 0 012345678999999999999999999963  2232   334321      


Q ss_pred             HHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          243 RIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       243 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                      ++.        .... ......+...+....+..+.+|+||++
T Consensus       273 ~l~--------sk~~-gese~~lr~lF~~A~~~~PsIIfIDEi  306 (806)
T 3cf2_A          273 EIM--------SKLA-GESESNLRKAFEEAEKNAPAIIFIDEL  306 (806)
T ss_dssp             HHH--------SSCT-THHHHHHHHHHHHHTTSCSEEEEEESG
T ss_pred             Hhh--------cccc-hHHHHHHHHHHHHHHHcCCeEEEEehh
Confidence            111        1100 011122333444445677899999998

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.74  E-value=0.02  Score=60.06  Aligned_cols=52  Identities=23%  Similarity=0.224  Sum_probs=37.5

Q ss_pred             CcceechhhHHHHHHHhccC----Cc--ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS--EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+.-.    .-  .-+-...+-|.++|++|.|||+||+++.+.
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            46889999888887765321    00  001234567889999999999999999985

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=95.67  E-value=0.013  Score=60.18  Aligned_cols=82  Identities=18%  Similarity=0.132  Sum_probs=51.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIRA  271 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~  271 (673)
                      -+++.|.|.+|+||||||.++...  ....-..++|++....++..     .++.++....     +..+.++....++.
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~--~~~~g~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~~  135 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  135 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHHH
Confidence            458999999999999999777764  22222468899987776643     2344443211     11234444444444


Q ss_pred             HhC-CCeEEEEEcCC
Q 005860          272 SLV-GKKFLLILDDM  285 (673)
Q Consensus       272 ~l~-~kr~LlVLDdv  285 (673)
                      ..+ .+.-+||+|.+
T Consensus       136 l~~~~~~~lVVIDsl  150 (356)
T 1u94_A          136 LARSGAVDVIVVDSV  150 (356)
T ss_dssp             HHHHTCCSEEEEECG
T ss_pred             HHhccCCCEEEEcCH
Confidence            332 34558999987

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.64  E-value=0.0099  Score=54.85  Aligned_cols=115  Identities=19%  Similarity=0.101  Sum_probs=60.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC---cccHHHHHHHHHHHhh-------CCCCC------cCc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD---PFDELRIAKAIIEALE-------GFVPT------VGE  261 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~---~~~~~~~~~~i~~~l~-------~~~~~------~~~  261 (673)
                      ..|-|++-.|.||||.|-.+.-.  .-.+=..++++.+-.   ......++..+-  +.       -....      ...
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalR--A~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~--v~~~~~g~gf~~~~~~~~~~~~~  104 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAAR--AVGHGKNVGVVQFIKGTWPNGERNLLEPHG--VEFQVMATGFTWETQNREADTAA  104 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHH--HHHTTCCEEEEESSCCSSCCHHHHHHGGGT--CEEEECCTTCCCCGGGHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEeeCCCCCccHHHHHHhCC--cEEEEcccccccCCCCcHHHHHH
Confidence            45667777779999999554442  222222444554332   233444443331  10       00000      011


Q ss_pred             HHHHHHHHHHHhCCCeE-EEEEcCCCC---CCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          262 LNSLLESIRASLVGKKF-LLILDDMWT---DDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       262 ~~~~~~~l~~~l~~kr~-LlVLDdvw~---~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      ........++.+.+.+| |||||++-.   -..-..+.+...+.......-||+|+|..
T Consensus       105 a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          105 CMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            12334456666665555 999999811   11223455555665555667899999975

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=95.57  E-value=0.0081  Score=68.81  Aligned_cols=52  Identities=15%  Similarity=0.195  Sum_probs=37.2

Q ss_pred             CcceechhhHHHHHHHhccCCcc--cccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE--EIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.+..++.+...+......  ........+.++|++|+|||++|+.+.+.
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~  511 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHH
Confidence            35889998888887766432100  00123457899999999999999999884

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=95.56  E-value=0.024  Score=57.98  Aligned_cols=82  Identities=18%  Similarity=0.130  Sum_probs=52.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIRA  271 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~  271 (673)
                      -.++.|+|.+|+||||||.++...  ....=..++|++....++..     ..+.++....     ...+.++....+..
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~--~~~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~  133 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVAN--AQAAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADM  133 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            468999999999999999887753  22222468899988766653     2444443211     12345555555555


Q ss_pred             HhC-CCeEEEEEcCC
Q 005860          272 SLV-GKKFLLILDDM  285 (673)
Q Consensus       272 ~l~-~kr~LlVLDdv  285 (673)
                      ..+ .+.-+||+|.+
T Consensus       134 l~~~~~~~lIVIDsl  148 (349)
T 2zr9_A          134 LVRSGALDIIVIDSV  148 (349)
T ss_dssp             HHTTTCCSEEEEECG
T ss_pred             HHhcCCCCEEEEcCh
Confidence            543 34568999988

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=95.48  E-value=0.0063  Score=62.14  Aligned_cols=50  Identities=26%  Similarity=0.361  Sum_probs=35.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|.+..++.+...+......  ......+.|+|++|+||||||+.+.+.
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~--~~~~~~~ll~Gp~G~GKTTLa~~ia~~   74 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMR--GEVLDHVLLAGPPGLGKTTLAHIIASE   74 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHH--TCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhc--CCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            46788887777776665432100  122457899999999999999999984

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.45  E-value=0.012  Score=61.08  Aligned_cols=52  Identities=27%  Similarity=0.312  Sum_probs=37.8

Q ss_pred             CcceechhhHHHHHHHhccC---Cc---ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE---SS---EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~---~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++-|.++.+++|.+.+...   ..   .-+....+-|.++|++|.|||.||+++.+.
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH
Confidence            47889999888887765321   10   001233567899999999999999999985

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=95.42  E-value=0.0071  Score=54.97  Aligned_cols=20  Identities=40%  Similarity=0.722  Sum_probs=18.7

Q ss_pred             EEEEEEccCCChHHHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFA  217 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v  217 (673)
                      .+|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            37999999999999999999

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=95.38  E-value=0.0083  Score=55.57  Aligned_cols=24  Identities=33%  Similarity=0.373  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+|+|+|++|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999884

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.27  E-value=0.036  Score=55.78  Aligned_cols=45  Identities=18%  Similarity=0.145  Sum_probs=30.2

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhc
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +|-...+..+...+.....   .....+|+|.|..|+||||||+.+..
T Consensus        70 ~~~~~~l~~~~~~~l~~~~---~~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKPE---PKVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCCC---CCCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHhccCC---CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3333444444444443321   24578999999999999999988866

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.25  E-value=0.027  Score=55.57  Aligned_cols=51  Identities=22%  Similarity=0.347  Sum_probs=32.0

Q ss_pred             CcceechhhHHHHHHHhccCCcc-c-----c-cCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE-E-----I-INDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~-~-----~-~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.|.++.+++|.+.+...-.. .     + ..... +.|+|++|+||||||+.+...
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHHH
Confidence            45777777777776544211000 0     0 01122 999999999999999999984

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.23  E-value=0.024  Score=60.79  Aligned_cols=53  Identities=25%  Similarity=0.298  Sum_probs=34.8

Q ss_pred             CCcceechhhHHHHHHHhccCCccc-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEE-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|.++.++++.+....-..+.     +..-.+-|.|+|++|+||||||+++...
T Consensus        30 f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           30 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3579999988777665542110000     0001123899999999999999999985

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.13  E-value=0.0079  Score=61.33  Aligned_cols=43  Identities=23%  Similarity=0.018  Sum_probs=29.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCe-EEEEEcCCccc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDK-RMWVCVSDPFD  240 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~  240 (673)
                      -..++|+|..|+|||||++.+.+.... .+=+. ++++-+.+...
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i~~-~~~~v~~I~~lIGER~~  217 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSIAY-NHPDCVLMVLLIDERPE  217 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHHHH-HCTTSEEEEEEESSCHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHHhh-cCCCeeEEEEEecCChH
Confidence            357999999999999999988774211 11222 45677776543

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=95.12  E-value=0.0094  Score=54.47  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|+|++|+||||+|+.+.+.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~   26 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999999874

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.12  E-value=0.01  Score=54.57  Aligned_cols=24  Identities=13%  Similarity=0.402  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+...
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998763

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.11  E-value=0.012  Score=60.02  Aligned_cols=43  Identities=16%  Similarity=0.137  Sum_probs=36.0

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|++..++.+...+....         -+.++|.+|+|||+||+.+.+.
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~---------~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG---------HILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC---------CEEEESCCCHHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC---------eEEEECCCCCcHHHHHHHHHHH
Confidence            468999999988888776532         4889999999999999999884

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=95.10  E-value=0.055  Score=55.38  Aligned_cols=89  Identities=20%  Similarity=0.172  Sum_probs=50.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccC----CeEEEEEcCCcccHHHHHHHHHHHhhCCC------------CCc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF----DKRMWVCVSDPFDELRIAKAIIEALEGFV------------PTV  259 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------------~~~  259 (673)
                      .-.++.|+|..|+|||||+..+..........    ..++|++....+....+ ..+.+..+...            ...
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            45799999999999999998887642111111    24589987665544433 22333332110            001


Q ss_pred             CcHHHHHHHHHHHhC------CCeEEEEEcCC
Q 005860          260 GELNSLLESIRASLV------GKKFLLILDDM  285 (673)
Q Consensus       260 ~~~~~~~~~l~~~l~------~kr~LlVLDdv  285 (673)
                      ....++...+...+.      .+.-+||+|.+
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~  240 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSL  240 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETS
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCc
Confidence            112233344444443      46778999987

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=95.07  E-value=0.0097  Score=53.93  Aligned_cols=23  Identities=22%  Similarity=0.167  Sum_probs=20.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998763

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.04  E-value=0.022  Score=56.61  Aligned_cols=26  Identities=27%  Similarity=0.255  Sum_probs=22.9

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|+|+|..|+||||||+.+...
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999888774

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.01  E-value=0.011  Score=53.95  Aligned_cols=22  Identities=36%  Similarity=0.446  Sum_probs=20.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999887

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.00  E-value=0.0096  Score=55.69  Aligned_cols=24  Identities=33%  Similarity=0.372  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|+.|+||||+|+.+.+.
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~   48 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARK   48 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            358999999999999999999873

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=94.99  E-value=0.011  Score=58.15  Aligned_cols=53  Identities=23%  Similarity=0.226  Sum_probs=35.6

Q ss_pred             CCcceechhhHHHHHHHhccCCccc-----ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEE-----IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|.+..++.+.+.+..-..+.     +....+-+.|+|++|+|||+||+.+++.
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            3579999988888777653100000     0011223779999999999999999985

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.97  E-value=0.013  Score=53.37  Aligned_cols=23  Identities=26%  Similarity=0.677  Sum_probs=20.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -.+++|+|+.|+|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            46999999999999999997554

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=94.96  E-value=0.014  Score=54.65  Aligned_cols=24  Identities=33%  Similarity=0.349  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+||||+|+.+...
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            579999999999999999999874

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=94.96  E-value=0.054  Score=56.37  Aligned_cols=57  Identities=16%  Similarity=0.135  Sum_probs=36.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      -.++.|+|.+|+|||||+..++-......    .-..++|++....++...+ ..+.+.++.
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl  238 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGL  238 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTC
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCC
Confidence            35899999999999999986542111111    2346889987776665543 335555543

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=94.91  E-value=0.05  Score=57.31  Aligned_cols=49  Identities=18%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccC-CeEEEEEcCCccc-HHHHHHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYF-DKRMWVCVSDPFD-ELRIAKAII  249 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~-~~~~~~~i~  249 (673)
                      .++|+|..|+|||||++.+..+  ....+ +.++++-+.+..+ ..++..++.
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~iGerttev~el~~~l~  203 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAGVGERTREGNDLYHEMK  203 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEEESSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEeeeccCchHHHHHHHHhh
Confidence            5899999999999999988775  22222 4567777776543 334444443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=94.91  E-value=0.016  Score=62.23  Aligned_cols=43  Identities=16%  Similarity=0.115  Sum_probs=36.1

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.+..++.+...+..+.         -|.|+|++|+|||+||+.+.+.
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~---------~VLL~GpPGtGKT~LAraLa~~   64 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE---------SVFLLGPPGIAKSLIARRLKFA   64 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC---------EEEEECCSSSSHHHHHHHGGGG
T ss_pred             hhhHHHHHHHHHHHHHHhcCC---------eeEeecCchHHHHHHHHHHHHH
Confidence            358899999988887776443         4789999999999999999985

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.90  E-value=0.011  Score=53.82  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|+|+.|+||||+++.+...
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            46999999999999999998873

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.84  E-value=0.013  Score=54.83  Aligned_cols=23  Identities=26%  Similarity=0.385  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            58999999999999999998763

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.83  E-value=0.015  Score=54.88  Aligned_cols=25  Identities=40%  Similarity=0.329  Sum_probs=22.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|+.|+|||||++.+...
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999998873

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=94.78  E-value=0.016  Score=53.63  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+++|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            5799999999999999999975

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=94.77  E-value=0.016  Score=52.80  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|+|+.|+||||+++.+..
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            47899999999999999999876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=94.76  E-value=0.015  Score=53.28  Aligned_cols=22  Identities=41%  Similarity=0.513  Sum_probs=19.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|+|+.|+|||||++.+...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999988875

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=94.70  E-value=0.018  Score=54.11  Aligned_cols=25  Identities=40%  Similarity=0.412  Sum_probs=22.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|+.|+||||+|+.+...
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            4579999999999999999999874

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.70  E-value=0.025  Score=57.29  Aligned_cols=46  Identities=20%  Similarity=0.099  Sum_probs=32.2

Q ss_pred             eechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          172 RGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       172 vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+.+.-.+++++.+...-.   .+....|.|+|+.|+||||+++.+...
T Consensus         2 ~~~~~L~~~il~~l~~~i~---~g~~~~i~l~G~~G~GKTTl~~~la~~   47 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIE---DNYRVCVILVGSPGSGKSTIAEELCQI   47 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTT---TCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhc---cCCeeEEEEECCCCCcHHHHHHHHHHH
Confidence            4455566666666642211   134567999999999999999988874

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.65  E-value=0.013  Score=53.86  Aligned_cols=24  Identities=25%  Similarity=0.373  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+.|.|+|+.|+||||+|+.+.+.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~   28 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL   28 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            357889999999999999999773

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=94.62  E-value=0.02  Score=59.11  Aligned_cols=51  Identities=22%  Similarity=0.241  Sum_probs=35.8

Q ss_pred             cceechhhHHHHHHHhccC-------Cc-ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKLLCE-------SS-EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~-------~~-~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|.+..++.+...+...       .. .........|.++|++|+|||++|+.+.+.
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4789998888888777210       00 000112456899999999999999999984

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.62  E-value=0.016  Score=54.13  Aligned_cols=24  Identities=29%  Similarity=0.538  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+|||||++.+...
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~   52 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADE   52 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999773

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=94.60  E-value=0.022  Score=55.49  Aligned_cols=51  Identities=25%  Similarity=0.315  Sum_probs=33.1

Q ss_pred             CcceechhhHHHHHHHhccCCccc-----c-cCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEE-----I-INDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~-----~-~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..+.++.+....-....     + ..... +.|+|++|+||||||+.+++.
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHHH
Confidence            468898877666655432110000     0 01122 899999999999999999985

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=94.60  E-value=0.018  Score=53.21  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|++|+||||+|+.+.+.
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999998763

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=94.58  E-value=0.016  Score=54.54  Aligned_cols=24  Identities=29%  Similarity=0.546  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            468999999999999999999875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.58  E-value=0.016  Score=53.48  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999874

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.58  E-value=0.029  Score=55.79  Aligned_cols=25  Identities=24%  Similarity=0.352  Sum_probs=22.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....+|.|.|++|+||||+|+.+..
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999999876

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=94.52  E-value=0.079  Score=55.92  Aligned_cols=87  Identities=15%  Similarity=0.071  Sum_probs=54.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC--------------CCCcC--
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF--------------VPTVG--  260 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~--------------~~~~~--  260 (673)
                      .-++|+|..|+|||+|++.+.++. .+.+-+.++|+-+.+..+ ..++..++.+.=...              ..+..  
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d~p~~  244 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPG  244 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTTSCHH
T ss_pred             CeEEeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCCCCHH
Confidence            468999999999999998877741 123457888998888764 455666665431111              00000  


Q ss_pred             ---cHHHHHHHHHHHh---CCCeEEEEEcCC
Q 005860          261 ---ELNSLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       261 ---~~~~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                         -.....-.+.+++   +++.+||++||+
T Consensus       245 ~R~~~~~~altiAEyfrd~~G~dVLl~~Dsi  275 (498)
T 1fx0_B          245 ARMRVGLTALTMAEYFRDVNEQDVLLFIDNI  275 (498)
T ss_dssp             HHTTHHHHHHHTHHHHTTTSCCEEEEEEECS
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcEEEEeccH
Confidence               0112233344555   468999999998

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.50  E-value=0.014  Score=54.73  Aligned_cols=24  Identities=21%  Similarity=0.401  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999998774

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=94.49  E-value=0.02  Score=53.68  Aligned_cols=22  Identities=36%  Similarity=0.474  Sum_probs=20.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|+|+|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.48  E-value=0.028  Score=54.03  Aligned_cols=34  Identities=18%  Similarity=0.261  Sum_probs=26.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||.+.+..-   .....+.+++
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl---~~p~~G~I~~   64 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCL---DKPTEGEVYI   64 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC---CCCCceEEEE
Confidence            358999999999999999999884   2334455655

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=94.47  E-value=0.019  Score=53.54  Aligned_cols=26  Identities=35%  Similarity=0.320  Sum_probs=23.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +...+|+|+|+.|+||||+|+.+.+.
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            34689999999999999999999873

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.44  E-value=0.018  Score=53.91  Aligned_cols=24  Identities=29%  Similarity=0.520  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+||||+++.+...
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999998874

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=94.43  E-value=0.021  Score=57.44  Aligned_cols=26  Identities=27%  Similarity=0.206  Sum_probs=22.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|+|+|..|+|||||++.+..-
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gl  113 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQAL  113 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhh
Confidence            34679999999999999999998873

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=94.43  E-value=0.017  Score=54.06  Aligned_cols=21  Identities=38%  Similarity=0.442  Sum_probs=19.7

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +|+|+|+.|+||||+++.+..
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH
Confidence            699999999999999999876

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=94.43  E-value=0.09  Score=52.55  Aligned_cols=87  Identities=18%  Similarity=0.184  Sum_probs=45.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHH--HHHHHHHHHhhCC---CCCcCcHHHH-HHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDEL--RIAKAIIEALEGF---VPTVGELNSL-LESI  269 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~~~~~i~~~l~~~---~~~~~~~~~~-~~~l  269 (673)
                      ...+|.|+|.+|+||||++..+....  ...-..+.++.. +.+...  +-+...++..+..   .....+.... ...+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l--~~~g~kV~lv~~-D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al  179 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMF--VDEGKSVVLAAA-DTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV  179 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHH--HHTTCCEEEEEE-CTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHH--HhcCCEEEEEcc-ccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            46899999999999999998887642  222123444443 223322  2233344444322   1112222222 2334


Q ss_pred             HHHhCCCeEEEEEcCC
Q 005860          270 RASLVGKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~~kr~LlVLDdv  285 (673)
                      ...+....-++++|-.
T Consensus       180 ~~a~~~~~dvvIiDtp  195 (306)
T 1vma_A          180 AHALARNKDVVIIDTA  195 (306)
T ss_dssp             HHHHHTTCSEEEEEEC
T ss_pred             HHHHhcCCCEEEEECC
Confidence            4444444457888865

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.42  E-value=0.029  Score=53.48  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999884

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=94.39  E-value=0.018  Score=53.12  Aligned_cols=23  Identities=30%  Similarity=0.712  Sum_probs=20.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~   26 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDN   26 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999998873

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.37  E-value=0.015  Score=54.32  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ++++|+|+.|+|||||++.+..
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            5799999999999999998876

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.36  E-value=0.03  Score=55.14  Aligned_cols=33  Identities=27%  Similarity=0.356  Sum_probs=25.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||++.+..-   .....+.+++
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl---~~p~~G~I~~   67 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGI---LKPSSGRILF   67 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC---CCCCCeEEEE
Confidence            58999999999999999999884   2233445444

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.35  E-value=0.028  Score=54.76  Aligned_cols=41  Identities=20%  Similarity=0.189  Sum_probs=28.4

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++...+......  .....+|.|+|++|+||||+|+.+...
T Consensus        15 ~~~~~~~~~~~~~~--~~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           15 LARNLRSLTRGKKS--SKQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             HHHHHHHHHTTCCC--CSSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCc--ccCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34444444443321  244679999999999999999998763

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=94.35  E-value=0.018  Score=54.86  Aligned_cols=22  Identities=41%  Similarity=0.513  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|+|+|+.|+||||+|+.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999876

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=94.35  E-value=0.014  Score=53.68  Aligned_cols=23  Identities=35%  Similarity=0.546  Sum_probs=19.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|+|++|+|||||++.+...
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            34789999999999999998763

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.35  E-value=0.019  Score=53.69  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~   23 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKK   23 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            5899999999999999998873

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=94.33  E-value=0.021  Score=55.66  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=21.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....+|+|.|+.|+||||+|+.+..
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3467999999999999999998877

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.31  E-value=0.02  Score=55.74  Aligned_cols=23  Identities=26%  Similarity=0.195  Sum_probs=20.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|+|+.|+||||||+.+...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            47899999999999999998763

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.31  E-value=0.029  Score=54.03  Aligned_cols=33  Identities=12%  Similarity=0.169  Sum_probs=26.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||.+.+..-   .....+.+++
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl---~~p~~G~i~~   57 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGI---VKPDRGEVRL   57 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS---SCCSEEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC---CCCCceEEEE
Confidence            68999999999999999999984   2233455555

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=94.31  E-value=0.015  Score=59.55  Aligned_cols=45  Identities=24%  Similarity=0.234  Sum_probs=32.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..++.+...+....       ..-|.|+|.+|+|||+||+.+.+.
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~~-------~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDPG-------IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGG-------GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHhhCCC-------CceEEEECCCCccHHHHHHHHHHh
Confidence            468999886665544443322       123889999999999999999874

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=94.29  E-value=0.11  Score=54.36  Aligned_cols=24  Identities=33%  Similarity=0.275  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|.+|+||||++..+...
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999887764

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.28  E-value=0.027  Score=50.38  Aligned_cols=24  Identities=29%  Similarity=0.313  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        33 Ge~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            469999999999999999998873

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=94.28  E-value=0.022  Score=53.61  Aligned_cols=24  Identities=17%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            458999999999999999998773

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=94.26  E-value=0.024  Score=53.01  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=22.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|+|.|+.|+||||+|+.+.+.
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34679999999999999999998863

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.24  E-value=0.015  Score=54.49  Aligned_cols=25  Identities=28%  Similarity=0.499  Sum_probs=21.8

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|+|++|+|||||++.+...
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3568999999999999999998764

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.23  E-value=0.033  Score=54.47  Aligned_cols=34  Identities=24%  Similarity=0.247  Sum_probs=26.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||.+.+..-   .....+.+++
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl---~~p~~G~i~~   65 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFL---EKPSEGAIIV   65 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC---CCCCCcEEEE
Confidence            358999999999999999999984   2334456655

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.21  E-value=0.088  Score=53.29  Aligned_cols=52  Identities=13%  Similarity=0.079  Sum_probs=36.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      -.++.|.|.+|+||||||..+....  ..+=..++|++.-  .+..++...++...
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~--a~~g~~Vl~fSlE--ms~~ql~~Rlls~~   97 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSA--LNDDRGVAVFSLE--MSAEQLALRALSDL   97 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHH--HHTTCEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHH--HHcCCeEEEEeCC--CCHHHHHHHHHHHh
Confidence            3588999999999999998777642  2222456777653  45667777776554

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.20  E-value=0.023  Score=52.61  Aligned_cols=24  Identities=21%  Similarity=0.254  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+.+.
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999988763

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.19  E-value=0.026  Score=54.70  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|.|+.|+|||||++.+..
T Consensus        25 g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           25 PFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998876

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.19  E-value=0.027  Score=55.65  Aligned_cols=52  Identities=25%  Similarity=0.310  Sum_probs=34.0

Q ss_pred             CCcceechhhHHHHHHHhccCCccc-----c-cCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEE-----I-INDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~-----~-~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++++|.++.++++.+....-....     + ..... +.|+|++|+||||||+.+...
T Consensus        39 ~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           39 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             GGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHH
Confidence            3578998887766665442110000     0 01123 899999999999999999985

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=94.19  E-value=0.016  Score=53.09  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|++|+||||+|+.+.+.
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            457889999999999999998863

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=94.18  E-value=0.021  Score=52.60  Aligned_cols=23  Identities=35%  Similarity=0.391  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|+|+.|+||||+|+.+.+
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999999999877

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.16  E-value=0.038  Score=54.18  Aligned_cols=33  Identities=21%  Similarity=0.366  Sum_probs=26.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||++.+..-   .....+.+++
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl---~~p~~G~I~~   70 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGY---LSPSHGECHL   70 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSS---SCCSSCEEEE
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC---CCCCCcEEEE
Confidence            58999999999999999999984   2334566665

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.15  E-value=0.022  Score=51.37  Aligned_cols=24  Identities=33%  Similarity=0.427  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|+.|+||||+|+.+.+.
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~   30 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLA   30 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999998773

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=94.14  E-value=0.17  Score=52.99  Aligned_cols=25  Identities=40%  Similarity=0.251  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.++|.+|+||||++..+...
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~  120 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF  120 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999877764

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.14  E-value=0.027  Score=51.89  Aligned_cols=25  Identities=28%  Similarity=0.319  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|+|++|+||||+++.+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999874

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=94.12  E-value=0.024  Score=54.97  Aligned_cols=23  Identities=30%  Similarity=0.319  Sum_probs=20.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|+|+.|+|||||++.+.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999984

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=94.10  E-value=0.026  Score=56.81  Aligned_cols=25  Identities=28%  Similarity=0.503  Sum_probs=20.4

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+.+||+|.|-|||||||.|-.+.-
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~   70 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSA   70 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHH
Confidence            4579999999999999999855544

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.10  E-value=0.019  Score=52.30  Aligned_cols=22  Identities=41%  Similarity=0.551  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|.|+|++|+||||+|+.+...
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            5899999999999999999873

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.05  E-value=0.028  Score=51.61  Aligned_cols=23  Identities=30%  Similarity=0.254  Sum_probs=20.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|.|.|+.|+||||+|+.+.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999876

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.05  E-value=0.039  Score=53.21  Aligned_cols=33  Identities=27%  Similarity=0.330  Sum_probs=26.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||.+.+..-   .....+.+++
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl---~~p~~G~i~~   65 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL---VRAQKGKIIF   65 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC---CCCCCceEEE
Confidence            58999999999999999999984   2333455555

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.04  E-value=0.033  Score=52.55  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=21.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999999884

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=94.03  E-value=0.051  Score=55.08  Aligned_cols=108  Identities=14%  Similarity=0.120  Sum_probs=57.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      .+++|+|..|+|||||++.+....   ..-.+.+.+.-......... .   +.+..-. +  .-......+...|..++
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~---~~~~g~i~i~~~~e~~~~~~-~---~~i~~~~-g--gg~~~r~~la~aL~~~p  241 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFI---PKEERIISIEDTEEIVFKHH-K---NYTQLFF-G--GNITSADCLKSCLRMRP  241 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGS---CTTSCEEEEESSCCCCCSSC-S---SEEEEEC-B--TTBCHHHHHHHHTTSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---cCCCcEEEECCeeccccccc-h---hEEEEEe-C--CChhHHHHHHHHhhhCC
Confidence            479999999999999999998842   12245555542211110000 0   0000000 0  11223456667777788


Q ss_pred             EEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHH
Q 005860          278 FLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR  320 (673)
Q Consensus       278 ~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~  320 (673)
                      =+|++|.+.+  ...++.+. .+..+  +.-+|+||...+...
T Consensus       242 ~ilildE~~~--~e~~~~l~-~~~~g--~~tvi~t~H~~~~~~  279 (330)
T 2pt7_A          242 DRIILGELRS--SEAYDFYN-VLCSG--HKGTLTTLHAGSSEE  279 (330)
T ss_dssp             SEEEECCCCS--THHHHHHH-HHHTT--CCCEEEEEECSSHHH
T ss_pred             CEEEEcCCCh--HHHHHHHH-HHhcC--CCEEEEEEcccHHHH
Confidence            8999999954  23344333 23222  223777777655443

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.02  E-value=0.025  Score=51.09  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++++|+|..|+|||||+..+...
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            578999999999999999888874

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.01  E-value=0.022  Score=52.77  Aligned_cols=24  Identities=33%  Similarity=0.369  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+.+.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998763

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.01  E-value=0.039  Score=53.90  Aligned_cols=34  Identities=15%  Similarity=0.335  Sum_probs=25.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||++.+..-.   ....+.+++
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl~---~p~~G~I~~   83 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLLE---DFDEGEIII   83 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS---CCSEEEEEE
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcCC---CCCCcEEEE
Confidence            3589999999999999999998842   233445554

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=93.98  E-value=0.04  Score=53.32  Aligned_cols=33  Identities=27%  Similarity=0.359  Sum_probs=25.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||++.+..-.   ....+.+++
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl~---~p~~G~I~i   68 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRFY---IPENGQVLI   68 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS---CCSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC---CCCCcEEEE
Confidence            589999999999999999998842   233455554

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=93.96  E-value=0.04  Score=53.69  Aligned_cols=33  Identities=24%  Similarity=0.346  Sum_probs=25.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||.+.+..-.   ....+.+++
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~---~p~~G~i~~   66 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFL---KADEGRVYF   66 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS---CCSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCCcEEEE
Confidence            589999999999999999998842   233455555

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.95  E-value=0.041  Score=53.54  Aligned_cols=24  Identities=29%  Similarity=0.362  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999884

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=93.92  E-value=0.024  Score=52.66  Aligned_cols=25  Identities=12%  Similarity=0.470  Sum_probs=21.8

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|+|+|+.|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            3568999999999999999988763

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.92  E-value=0.042  Score=52.23  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=21.8

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|+|.+|+|||||+..+...
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3688999999999999999887764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=93.91  E-value=0.042  Score=53.07  Aligned_cols=24  Identities=29%  Similarity=0.310  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999874

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.91  E-value=0.023  Score=53.91  Aligned_cols=24  Identities=38%  Similarity=0.538  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+...
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998773

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=93.89  E-value=0.028  Score=54.96  Aligned_cols=24  Identities=29%  Similarity=0.534  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|++|+||||+|+.+...
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999998873

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=93.89  E-value=0.087  Score=50.05  Aligned_cols=45  Identities=22%  Similarity=0.262  Sum_probs=30.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccc--c-c-cCCeEEEEEcCCcccH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDV--F-E-YFDKRMWVCVSDPFDE  241 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~--~-~-~F~~~~wv~vs~~~~~  241 (673)
                      -.+++|+|++|+|||||++.+......  . . .-...+|+.-...+..
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~   73 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRP   73 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCH
Confidence            479999999999999999998752111  1 1 1345788876544333

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.88  E-value=0.042  Score=53.98  Aligned_cols=24  Identities=33%  Similarity=0.451  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999884

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=93.87  E-value=0.16  Score=51.81  Aligned_cols=54  Identities=20%  Similarity=0.052  Sum_probs=34.1

Q ss_pred             HHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCe-EEEEEcCCcc
Q 005860          179 SSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDK-RMWVCVSDPF  239 (673)
Q Consensus       179 ~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~  239 (673)
                      -++++.|..-.      .-..++|+|..|+|||+|++.+.+.... .+=+. ++++-+.+..
T Consensus       163 iraID~l~Pig------rGQR~lIfg~~g~GKT~Ll~~Ia~~i~~-~~~dv~~V~~lIGER~  217 (427)
T 3l0o_A          163 TRLIDLFAPIG------KGQRGMIVAPPKAGKTTILKEIANGIAE-NHPDTIRIILLIDERP  217 (427)
T ss_dssp             HHHHHHHSCCB------TTCEEEEEECTTCCHHHHHHHHHHHHHH-HCTTSEEEEEECSCCH
T ss_pred             chhhhhccccc------CCceEEEecCCCCChhHHHHHHHHHHhh-cCCCeEEEEEEeccCc
Confidence            45566664322      2346899999999999999888874211 12232 3566666643

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.86  E-value=0.029  Score=54.63  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|+|+.|+||||+++.+.+
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999985

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.85  E-value=0.15  Score=54.04  Aligned_cols=42  Identities=26%  Similarity=0.301  Sum_probs=29.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD  240 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  240 (673)
                      ...+++|+|.+|+|||||++.+....  . .-.+.+++.-.+.+.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll--~-~~~G~V~l~g~D~~r  333 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQF--E-QQGKSVMLAAGDTFR  333 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHH--H-HTTCCEEEECCCTTC
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHh--h-hcCCeEEEecCcccc
Confidence            45799999999999999999888742  1 224555555444444

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=93.85  E-value=0.024  Score=56.61  Aligned_cols=25  Identities=24%  Similarity=0.327  Sum_probs=22.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.+.++|++|+|||+||+++++.
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3567889999999999999999985

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.85  E-value=0.29  Score=49.10  Aligned_cols=52  Identities=15%  Similarity=0.075  Sum_probs=36.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      -.++.|.|.+|+||||||..+..+.... . ..++|++..  .+..++...++...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~-g-~~vl~~slE--~s~~~l~~R~~~~~  119 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDN-D-DVVNLHSLE--MGKKENIKRLIVTA  119 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTT-T-CEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHc-C-CeEEEEECC--CCHHHHHHHHHHHH
Confidence            4689999999999999997776542111 2 567888765  35666777766553

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=93.83  E-value=0.021  Score=52.41  Aligned_cols=22  Identities=27%  Similarity=0.431  Sum_probs=19.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|.|+|++|+||||+|+.+...
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKA   25 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998773

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=93.82  E-value=0.029  Score=51.70  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|+.|+||||+|+.+.+.
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998773

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.80  E-value=0.027  Score=52.27  Aligned_cols=23  Identities=35%  Similarity=0.411  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|.|+.|+||||+|+.+.+.
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998873

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=93.79  E-value=0.031  Score=51.80  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .-.+|+|+|+.|+||||+|+.+.+
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHH
Confidence            367999999999999999999877

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.79  E-value=0.03  Score=52.58  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=21.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            58999999999999999999874

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.79  E-value=0.029  Score=50.57  Aligned_cols=22  Identities=23%  Similarity=0.342  Sum_probs=19.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS   23 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998873

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.78  E-value=0.0048  Score=56.96  Aligned_cols=22  Identities=27%  Similarity=0.101  Sum_probs=17.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .++.|+|+.|+||||++..+..
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~   25 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVE   25 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4788999999999999844443

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=93.77  E-value=0.032  Score=50.93  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|+|+.|+||||+++.+...
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~   28 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEY   28 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998773

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.75  E-value=0.046  Score=53.56  Aligned_cols=34  Identities=24%  Similarity=0.215  Sum_probs=25.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||.+.+..-   .....+.+++
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl---~~p~~G~I~~   66 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGL---IEPTSGDVLY   66 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC---CCCCCcEEEE
Confidence            358999999999999999999884   2233455554

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=93.74  E-value=0.029  Score=53.23  Aligned_cols=25  Identities=20%  Similarity=0.272  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-.+++|+|+.|+|||||.+.+...
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3468999999999999999998774

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=93.71  E-value=0.18  Score=50.20  Aligned_cols=24  Identities=33%  Similarity=0.275  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+++|+|.+|+||||++..+...
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999888874

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.68  E-value=0.042  Score=52.01  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|+|.+|+|||||+..+...
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            4689999999999999999887764

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=93.67  E-value=0.026  Score=51.17  Aligned_cols=23  Identities=30%  Similarity=0.348  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|+.|+||||+|+.+.+.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            36899999999999999998773

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.67  E-value=0.03  Score=51.70  Aligned_cols=22  Identities=41%  Similarity=0.591  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~   23 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEY   23 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999873

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=93.66  E-value=0.036  Score=52.39  Aligned_cols=26  Identities=23%  Similarity=0.314  Sum_probs=23.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+||.|.|++|+||||.|+.+.+.
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998874

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.65  E-value=0.028  Score=51.93  Aligned_cols=22  Identities=36%  Similarity=0.428  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++|+|+.|+|||||++.+...
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhh
Confidence            6899999999999999888874

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=93.63  E-value=0.031  Score=52.15  Aligned_cols=24  Identities=25%  Similarity=0.202  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+.+.
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999998773

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=93.60  E-value=0.27  Score=51.69  Aligned_cols=53  Identities=21%  Similarity=0.201  Sum_probs=38.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEA  251 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~  251 (673)
                      .-++|+|..|+|||+|++.+.+.. .+.+-+.++++-+.+..+ +.++.+++.+.
T Consensus       154 Qr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          154 GKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             CeeeeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            468999999999999998877641 123446788888887654 45566666654

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=93.60  E-value=0.03  Score=56.00  Aligned_cols=25  Identities=28%  Similarity=0.384  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|++|+|||||++.+..-
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagl  125 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRY  125 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            3569999999999999999988864

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.57  E-value=0.052  Score=53.56  Aligned_cols=33  Identities=21%  Similarity=0.220  Sum_probs=26.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||.+.+..-.   ....+.+++
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~---~p~~G~I~~   80 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYE---PATSGTVNL   80 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS---CCSEEEEEE
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC---CCCCeEEEE
Confidence            589999999999999999999842   233456655

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=93.55  E-value=0.066  Score=46.03  Aligned_cols=46  Identities=15%  Similarity=0.154  Sum_probs=32.8

Q ss_pred             cchh--hhccccccccccccceecCCCCcccchh-hhcCCCccEEEeccCC
Q 005860          560 NSTN--KILKGIEKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCT  607 (673)
Q Consensus       560 ~~~~--~lp~~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~  607 (673)
                      ..++  .+|..+.  .+|++|+|++|.|..||.. +..|++|++|+|++++
T Consensus        18 ~~L~~~~vP~~lp--~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~NP   66 (130)
T 3rfe_A           18 RGLTWASLPTAFP--VDTTELVLTGNNLTALPPGLLDALPALRTAHLGANP   66 (130)
T ss_dssp             SCCCTTTSCSCCC--TTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSC
T ss_pred             CCCccccCCCCCC--cCCCEEECCCCcCCccChhhhhhccccCEEEecCCC
Confidence            5565  6676543  3578888888888888754 5667888888888755

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.51  E-value=0.17  Score=50.27  Aligned_cols=87  Identities=18%  Similarity=0.045  Sum_probs=44.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc-ccHHHHHHHHHHHhhCC---CCCcCcHHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP-FDELRIAKAIIEALEGF---VPTVGELNSLLESIRAS  272 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~---~~~~~~~~~~~~~l~~~  272 (673)
                      ..+|+++|.+|+||||++..+....  ...-..+.++..... ....+.+....+..+..   .....+..++.....+.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~--~~~g~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~  175 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFY--KKKGFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEK  175 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHH--HHTTCCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHH
Confidence            5789999999999999998877642  222223555554321 12223333344443332   11112333333333333


Q ss_pred             hC-CCeEEEEEcCC
Q 005860          273 LV-GKKFLLILDDM  285 (673)
Q Consensus       273 l~-~kr~LlVLDdv  285 (673)
                      ++ ..-=++++|-.
T Consensus       176 ~~~~~~D~ViIDTp  189 (297)
T 1j8m_F          176 FLSEKMEIIIVDTA  189 (297)
T ss_dssp             HHHTTCSEEEEECC
T ss_pred             HHhCCCCEEEEeCC
Confidence            43 22236777764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=93.51  E-value=0.025  Score=51.76  Aligned_cols=24  Identities=38%  Similarity=0.311  Sum_probs=17.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999998763

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=93.50  E-value=0.2  Score=52.57  Aligned_cols=24  Identities=33%  Similarity=0.407  Sum_probs=21.1

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ...+|.++|.+|+||||++..+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            468999999999999999877765

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=93.48  E-value=0.041  Score=54.48  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=21.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999873

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=93.47  E-value=0.051  Score=52.48  Aligned_cols=25  Identities=20%  Similarity=0.092  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|.|+.|+||||+|+.+.+.
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999998763

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.45  E-value=0.042  Score=54.96  Aligned_cols=25  Identities=36%  Similarity=0.361  Sum_probs=22.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++|+|+.|+||||+++.+...
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~  123 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHR  123 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            3579999999999999999888874

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=93.44  E-value=0.057  Score=55.97  Aligned_cols=23  Identities=35%  Similarity=0.413  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.++|++|+|||++|+.+.+.
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
Confidence            45889999999999999999884

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.43  E-value=0.031  Score=52.50  Aligned_cols=23  Identities=35%  Similarity=0.310  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.+..-
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999988763

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.41  E-value=0.023  Score=51.54  Aligned_cols=23  Identities=39%  Similarity=0.407  Sum_probs=20.8

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|..|+|||||++.+..-
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999988874

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=93.36  E-value=0.043  Score=55.12  Aligned_cols=24  Identities=33%  Similarity=0.339  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ...+|+|+|..|+|||||++.+..
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999887

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=93.32  E-value=0.035  Score=52.23  Aligned_cols=24  Identities=21%  Similarity=0.270  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|+.|+||||+|+.+.+.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999874

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.27  E-value=0.19  Score=52.90  Aligned_cols=25  Identities=24%  Similarity=0.239  Sum_probs=21.4

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.|+|.+|+||||++..+...
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~  123 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKF  123 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999777653

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.26  E-value=0.061  Score=52.06  Aligned_cols=23  Identities=35%  Similarity=0.472  Sum_probs=21.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            48999999999999999999984

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.25  E-value=0.029  Score=53.74  Aligned_cols=23  Identities=30%  Similarity=0.406  Sum_probs=16.0

Q ss_pred             EEEEEEccCCChHHHHHHHHh-cC
Q 005860          198 QIITIVGMGGIGKTTLAQFAY-ND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~-~~  220 (673)
                      .+++|+|+.|+|||||++.+. ..
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC--
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcC
Confidence            589999999999999999998 53

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=93.22  E-value=0.039  Score=51.84  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|+.|+||||+|+.+.+.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999874

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=93.19  E-value=0.05  Score=51.47  Aligned_cols=23  Identities=30%  Similarity=0.348  Sum_probs=20.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999865

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=93.19  E-value=0.41  Score=48.64  Aligned_cols=119  Identities=9%  Similarity=-0.038  Sum_probs=71.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHH-HHhCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIR-ASLVG  275 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~-~~l~~  275 (673)
                      ..+..++|..|.||++.|+.+.+... ...|+....+.+....+++++                     ...+. .-+-+
T Consensus        18 ~~~yl~~G~e~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~l---------------------~~~~~~~plf~   75 (343)
T 1jr3_D           18 RAAYLLLGNDPLLLQESQDAVRQVAA-AQGFEEHHTFSIDPNTDWNAI---------------------FSLCQAMSLFA   75 (343)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHHH-HHTCCEEEEEECCTTCCHHHH---------------------HHHHHHHHHCC
T ss_pred             CcEEEEECCcHHHHHHHHHHHHHHHH-hCCCCeeEEEEecCCCCHHHH---------------------HHHhcCcCCcc
Confidence            46889999999999999988877421 123433222233333333332                     22222 12345


Q ss_pred             CeEEEEEcCCCC-CCccchhhhhhhccCCCCCeEEEEEcCC-------hhHHHhc-cccceeecCCCCccc
Q 005860          276 KKFLLILDDMWT-DDYSKWEPFHYCLKNGVRGSKILVTTRK-------ETVARMM-ESIHVISIKELSEQE  337 (673)
Q Consensus       276 kr~LlVLDdvw~-~~~~~~~~l~~~l~~~~~gs~iivTtr~-------~~v~~~~-~~~~~~~l~~L~~~~  337 (673)
                      ++-++|+|++.. -....++.+...+....+++.+|++|..       ..+...+ .....++..+++.++
T Consensus        76 ~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~  146 (343)
T 1jr3_D           76 SRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQ  146 (343)
T ss_dssp             SCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTH
T ss_pred             CCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHH
Confidence            566888999854 3445677888888766678888776643       2344332 234667777777654

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=93.19  E-value=0.047  Score=51.41  Aligned_cols=24  Identities=29%  Similarity=0.253  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999998874

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=93.17  E-value=0.023  Score=53.51  Aligned_cols=22  Identities=36%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|+|.|..|+||||+|+.+...
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~   23 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGA   23 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            6899999999999999998774

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=93.12  E-value=0.089  Score=45.19  Aligned_cols=54  Identities=20%  Similarity=0.235  Sum_probs=43.8

Q ss_pred             ccceecCCCCc--ccchhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccc
Q 005860          576 RYLRLVGLGTE--ELPETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCL  632 (673)
Q Consensus       576 r~L~L~~~~i~--~LP~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l  632 (673)
                      ..++.++..++  .+|..+.  .+|++|+|+++. |..+|.+ +..+.+|+.|++++|.+
T Consensus        11 ~~v~Cs~~~L~~~~vP~~lp--~~l~~L~Ls~N~-l~~l~~~~f~~l~~L~~L~L~~NP~   67 (130)
T 3rfe_A           11 TLVDCGRRGLTWASLPTAFP--VDTTELVLTGNN-LTALPPGLLDALPALRTAHLGANPW   67 (130)
T ss_dssp             TEEECCSSCCCTTTSCSCCC--TTCSEEECTTSC-CSSCCTTTGGGCTTCCEEECCSSCC
T ss_pred             CEEEeCCCCCccccCCCCCC--cCCCEEECCCCc-CCccChhhhhhccccCEEEecCCCe
Confidence            36778888888  8886533  479999999966 9999875 68899999999988764

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=93.08  E-value=0.046  Score=53.04  Aligned_cols=23  Identities=30%  Similarity=0.588  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999984

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.07  E-value=0.043  Score=51.80  Aligned_cols=22  Identities=32%  Similarity=0.459  Sum_probs=19.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998763

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.05  E-value=0.042  Score=52.39  Aligned_cols=24  Identities=25%  Similarity=0.307  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|.|+.|+||||+|+.+.+.
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            357999999999999999998863

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.03  E-value=0.058  Score=53.86  Aligned_cols=24  Identities=29%  Similarity=0.504  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl  103 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRF  103 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcC
Confidence            358999999999999999999874

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=93.02  E-value=0.087  Score=54.06  Aligned_cols=25  Identities=24%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....+|+|+|.+|+|||||+..+..
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999987764

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=93.00  E-value=0.22  Score=53.78  Aligned_cols=52  Identities=12%  Similarity=-0.017  Sum_probs=36.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCcccccc-CCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEY-FDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      -.++.|.|.+|+||||||..+..+  .... =..++|++...  +..++...++...
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~--~a~~~g~~vl~~s~E~--s~~~l~~r~~~~~  294 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQ--WGTAMGKKVGLAMLEE--SVEETAEDLIGLH  294 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHH--HTTTSCCCEEEEESSS--CHHHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHH--HHHhcCCcEEEEeccC--CHHHHHHHHHHHH
Confidence            468899999999999999777664  2222 23577887654  4567777665544

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=92.96  E-value=0.046  Score=50.99  Aligned_cols=23  Identities=26%  Similarity=0.325  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|.|+.|+||||+++.+.+.
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            57999999999999999999885

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=92.96  E-value=0.049  Score=53.43  Aligned_cols=24  Identities=29%  Similarity=0.375  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999984

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=92.95  E-value=0.045  Score=51.85  Aligned_cols=23  Identities=26%  Similarity=0.276  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999998773

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=92.93  E-value=0.057  Score=54.60  Aligned_cols=25  Identities=36%  Similarity=0.334  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++|+|+.|+||||+++.+...
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999888874

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=92.90  E-value=0.047  Score=51.55  Aligned_cols=21  Identities=24%  Similarity=0.408  Sum_probs=19.1

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .|+|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999876

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=92.88  E-value=0.051  Score=53.07  Aligned_cols=23  Identities=35%  Similarity=0.566  Sum_probs=21.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.+..-
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            58999999999999999999985

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=92.88  E-value=0.04  Score=52.20  Aligned_cols=24  Identities=25%  Similarity=0.458  Sum_probs=20.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999999998774

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=92.85  E-value=0.077  Score=51.80  Aligned_cols=32  Identities=25%  Similarity=0.425  Sum_probs=25.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|+|||||.+.+..-   . ...+.+++
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl---~-p~~G~I~~   62 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGL---L-PYSGNIFI   62 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS---S-CCEEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC---C-CCCcEEEE
Confidence            48999999999999999999984   2 34555555

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=92.80  E-value=0.04  Score=53.35  Aligned_cols=23  Identities=35%  Similarity=0.525  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|+|+.|+||||+++.+...
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~   71 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARS   71 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999999873

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=92.79  E-value=0.058  Score=55.18  Aligned_cols=25  Identities=36%  Similarity=0.361  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++|+|..|+||||+++.+...
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~  180 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHR  180 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhh
Confidence            4579999999999999999888874

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=92.76  E-value=0.05  Score=50.83  Aligned_cols=21  Identities=33%  Similarity=0.428  Sum_probs=19.9

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +|+|.|+.|+||||+|+.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999877

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=92.75  E-value=0.054  Score=52.64  Aligned_cols=23  Identities=30%  Similarity=0.575  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999884

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.73  E-value=0.053  Score=54.72  Aligned_cols=23  Identities=35%  Similarity=0.351  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|+|.|+.|+||||||+.+...
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~   30 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKK   30 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHHH
Confidence            58999999999999999998873

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=92.69  E-value=0.053  Score=49.30  Aligned_cols=24  Identities=29%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+++|+|..|+|||||++.+...
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHh
Confidence            578999999999999999888874

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=92.61  E-value=0.042  Score=52.22  Aligned_cols=24  Identities=21%  Similarity=0.198  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999998874

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=92.57  E-value=0.065  Score=57.21  Aligned_cols=22  Identities=41%  Similarity=0.596  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+.|.|.+|+||||++.++...
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~   68 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEA   68 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            8999999999999999888774

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=92.47  E-value=0.58  Score=50.04  Aligned_cols=25  Identities=32%  Similarity=0.400  Sum_probs=20.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ...++|.|+|.+|+||||++..+..
T Consensus        99 ~~~~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W           99 GKQNVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             S--EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999977774

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=92.44  E-value=0.31  Score=51.53  Aligned_cols=84  Identities=19%  Similarity=0.162  Sum_probs=50.0

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccccccCCe-EEEEEcCCccc-HHHHHHHHHHHhhC-------CCCCcC-cHH---
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDVFEYFDK-RMWVCVSDPFD-ELRIAKAIIEALEG-------FVPTVG-ELN---  263 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~-------~~~~~~-~~~---  263 (673)
                      .-++|+|..|+|||+|| ..+.|..    .-+. ++++-+.+..+ +.++.+.+.+.=..       ...+.. ...   
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~----~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  251 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQK----GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIA  251 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTT----TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHH
Confidence            46899999999999995 6888853    3453 57888887654 34555555432110       011111 000   


Q ss_pred             -HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 -SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 -~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                       .....+.+++  +++.+||++||+
T Consensus       252 ~~~a~tiAEyfrd~G~dVLli~Dsl  276 (515)
T 2r9v_A          252 PYAGCAMGEYFAYSGRDALVVYDDL  276 (515)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEeccH
Confidence             1111233333  589999999998

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=92.38  E-value=0.067  Score=51.07  Aligned_cols=24  Identities=17%  Similarity=0.319  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~   32 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARA   32 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999998763

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=92.36  E-value=0.094  Score=53.46  Aligned_cols=23  Identities=39%  Similarity=0.522  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl   53 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGF   53 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCchHHHHHHHHhcC
Confidence            58999999999999999999884

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=92.36  E-value=0.12  Score=53.97  Aligned_cols=86  Identities=14%  Similarity=0.202  Sum_probs=51.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCC----eEEEEEcCCccc-HHHHHHHHHHH--hhC-----CCCCcCcH---
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFD----KRMWVCVSDPFD-ELRIAKAIIEA--LEG-----FVPTVGEL---  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~----~~~wv~vs~~~~-~~~~~~~i~~~--l~~-----~~~~~~~~---  262 (673)
                      .-++|.|..|+|||+|+.++.+....  +-+    .++++-+.+..+ +.++..++.+.  +..     ...+..-.   
T Consensus       152 Qr~~Ifgg~G~GKt~L~~~Ia~~~~~--~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~  229 (465)
T 3vr4_D          152 QKLPVFSGSGLPHKELAAQIARQATV--LDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERI  229 (465)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBC--SSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHH
T ss_pred             CEEEEeCCCCcChHHHHHHHHHHHHh--ccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHH
Confidence            34789999999999999988886332  223    567777776543 44555555443  110     01111111   


Q ss_pred             --HHHHHHHHHHh---CCCeEEEEEcCC
Q 005860          263 --NSLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       263 --~~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                        ......+.+++   +++.+||++||+
T Consensus       230 ~a~~~a~tiAEyfrd~~G~~VLl~~Dsl  257 (465)
T 3vr4_D          230 ATPRMALTAAEYLAYEKGMHVLVIMTDM  257 (465)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEcCh
Confidence              11222344444   379999999998

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=92.36  E-value=0.18  Score=53.83  Aligned_cols=47  Identities=15%  Similarity=0.121  Sum_probs=35.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH-HHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE-LRIAKAI  248 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~~~~~i  248 (673)
                      ..++|.|..|+|||+|++.+.+.    .+-+.++++-+.+..+. .++..++
T Consensus       228 qr~~I~g~~g~GKT~L~~~ia~~----~~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          228 GTAAIPGPAGSGKTVTQHQLAKW----SDAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             CEEEECSCCSHHHHHHHHHHHHH----SSCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             CeEEeecCCCCCHHHHHHHHHhc----cCCCEEEEEEecccHHHHHHHHHHH
Confidence            46899999999999999998774    23367888988887654 3444443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.34  E-value=0.071  Score=52.04  Aligned_cols=110  Identities=16%  Similarity=0.184  Sum_probs=56.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHHHHHH--HhhCCCCCcCcHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAKAIIE--ALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~--~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      -.+++|+|+.|+|||||++.+...  ....+.+.+++.-.. .+-.... ..++.  .++.   +.   ..+...+...+
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~--~~~~~~G~I~~~g~~i~~~~~~~-~~~v~q~~~gl---~~---~~l~~~la~aL   95 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDY--INQTKSYHIITIEDPIEYVFKHK-KSIVNQREVGE---DT---KSFADALRAAL   95 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHH--HHHHCCCEEEEEESSCCSCCCCS-SSEEEEEEBTT---TB---SCHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHHh--CCCCCCCEEEEcCCcceeecCCc-ceeeeHHHhCC---CH---HHHHHHHHHHH
Confidence            469999999999999999988873  211223444332100 0000000 00000  0000   11   12345566666


Q ss_pred             CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChhHHH
Q 005860          274 VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR  320 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~  320 (673)
                      ...+=+|++|...  +......+....   ..|.-|++||.+.++..
T Consensus        96 ~~~p~illlDEp~--D~~~~~~~l~~~---~~g~~vl~t~H~~~~~~  137 (261)
T 2eyu_A           96 REDPDVIFVGEMR--DLETVETALRAA---ETGHLVFGTLHTNTAID  137 (261)
T ss_dssp             HHCCSEEEESCCC--SHHHHHHHHHHH---HTTCEEEEEECCSSHHH
T ss_pred             hhCCCEEEeCCCC--CHHHHHHHHHHH---ccCCEEEEEeCcchHHH
Confidence            5566788999985  333322222222   24667899998866544

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=92.33  E-value=0.062  Score=51.38  Aligned_cols=25  Identities=28%  Similarity=0.147  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|.|..|+|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            4579999999999999999998873

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=92.27  E-value=0.1  Score=53.35  Aligned_cols=24  Identities=33%  Similarity=0.391  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL   77 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLL   77 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcC
Confidence            358999999999999999999874

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=92.25  E-value=0.074  Score=52.75  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|..|+|||||.+.+..-
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999885

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=92.24  E-value=0.097  Score=46.84  Aligned_cols=23  Identities=22%  Similarity=0.365  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999998874

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=92.22  E-value=0.071  Score=49.17  Aligned_cols=24  Identities=21%  Similarity=0.427  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|+|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            567999999999999999988775

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=92.20  E-value=0.079  Score=58.68  Aligned_cols=43  Identities=19%  Similarity=0.303  Sum_probs=35.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.++|.+..++.+...+..+         ..+.|+|++|+||||||+.+...
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g---------~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK---------RHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT---------CCEEEECCTTSSHHHHHHHHHHT
T ss_pred             ceEECchhhHhhccccccCC---------CEEEEEeCCCCCHHHHHHHHhcc
Confidence            46899998888877777543         36899999999999999999885

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.18  E-value=0.27  Score=52.21  Aligned_cols=50  Identities=10%  Similarity=0.115  Sum_probs=33.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAII  249 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  249 (673)
                      -.++.|.|.+|+||||||..+....... .-..++|++...  +...+...++
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~-~g~~Vl~~s~E~--s~~~l~~r~~  252 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATK-TNENVAIFSLEM--SAQQLVMRML  252 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHH-SSCCEEEEESSS--CHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEECCC--CHHHHHHHHH
Confidence            3589999999999999998877752211 123577877554  4455555554

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=92.15  E-value=0.072  Score=48.73  Aligned_cols=22  Identities=45%  Similarity=0.496  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|+|+|.+|+|||||++.+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998874

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.12  E-value=0.067  Score=50.84  Aligned_cols=22  Identities=32%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~   23 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDK   23 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998763

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=92.10  E-value=0.091  Score=52.87  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|+.|+||||||..+.+.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999885

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=92.09  E-value=0.072  Score=53.07  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl  149 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHF  149 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhh
Confidence            468999999999999999998873

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=92.08  E-value=0.068  Score=50.38  Aligned_cols=22  Identities=36%  Similarity=0.424  Sum_probs=19.6

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEK   23 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999998773

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=91.98  E-value=0.088  Score=53.04  Aligned_cols=25  Identities=36%  Similarity=0.461  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|+|+|.+|+||||++..+...
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~  128 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANY  128 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999887764

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=91.95  E-value=0.31  Score=51.47  Aligned_cols=84  Identities=19%  Similarity=0.136  Sum_probs=49.6

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccccccCCe-EEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcCcHH----
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDVFEYFDK-RMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVGELN----  263 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~~----  263 (673)
                      .-++|+|..|+|||+|| ..+.|..    .-+. ++++-+.+..+ +.++.+.+.+.=...       ..+..-..    
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a  238 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLA  238 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHH
Confidence            46899999999999995 6888852    3453 57888887654 344555554321110       11111011    


Q ss_pred             -HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          264 -SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       264 -~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                       .....+.+++  +++.+||++||+
T Consensus       239 ~~~a~tiAEyfrd~G~dVLl~~Dsl  263 (502)
T 2qe7_A          239 PYAGCAMGEYFMYKGKHALVVYDDL  263 (502)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEEecH
Confidence             0111233333  589999999998

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=91.94  E-value=0.4  Score=50.76  Aligned_cols=53  Identities=9%  Similarity=-0.023  Sum_probs=35.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      -.++.|.|.+|+||||||..+..+... .+=..++|++...  +...+...++...
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~-~~g~~vl~~slE~--~~~~l~~R~~~~~  252 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAAL-KEGVGVGIYSLEM--PAAQLTLRMMCSE  252 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHH-TTCCCEEEEESSS--CHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHH-hCCCeEEEEECCC--CHHHHHHHHHHHH
Confidence            358999999999999999777764211 1123577877654  4566776666543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=91.93  E-value=0.077  Score=53.19  Aligned_cols=23  Identities=30%  Similarity=0.319  Sum_probs=21.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|+|+.|+||||||+.+.+.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998873

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=91.87  E-value=0.089  Score=51.23  Aligned_cols=25  Identities=36%  Similarity=0.348  Sum_probs=21.9

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....++.+.|.||+||||++..+..
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHH
Confidence            4578999999999999999988874

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.84  E-value=0.12  Score=52.67  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999874

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=91.81  E-value=0.086  Score=48.87  Aligned_cols=37  Identities=19%  Similarity=0.115  Sum_probs=26.6

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +..+..++..-      +.-..+.|+|++|+||||+|..+.+.
T Consensus        45 ~~~l~~~~~~i------Pkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           45 LGALKSFLKGT------PKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHTC------TTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC------CcccEEEEECCCCCCHHHHHHHHHHH
Confidence            55555655432      22346899999999999999888774

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=91.78  E-value=0.086  Score=52.36  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|+.|+||||||..+...
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHh
Confidence            368999999999999999998874

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=91.78  E-value=0.42  Score=50.36  Aligned_cols=82  Identities=24%  Similarity=0.257  Sum_probs=50.3

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccccccCC-eEEEEEcCCccc-HHHHHHHHHHHhhCC-------CCCcC-cH----
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDVFEYFD-KRMWVCVSDPFD-ELRIAKAIIEALEGF-------VPTVG-EL----  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~-~~----  262 (673)
                      .-++|.|..|+|||+|| ..+.|.    .+-+ .++++-+.+..+ +.++...+.+.=...       ..+.. -.    
T Consensus       163 QR~~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a  238 (513)
T 3oaa_A          163 QRELIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLA  238 (513)
T ss_dssp             CBCEEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHH
Confidence            45899999999999996 677774    2334 467888888654 445555544431111       11111 00    


Q ss_pred             ----HHHHHHHHHHhCCCeEEEEEcCC
Q 005860          263 ----NSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       263 ----~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                          -...+.+++  +++.+||++||+
T Consensus       239 ~~~a~tiAEyfrd--~G~dVLli~Dsl  263 (513)
T 3oaa_A          239 PYAGCAMGEYFRD--RGEDALIIYDDL  263 (513)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHh--cCCCEEEEecCh
Confidence                122333443  689999999998

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=91.75  E-value=0.23  Score=46.09  Aligned_cols=49  Identities=20%  Similarity=0.155  Sum_probs=31.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAII  249 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  249 (673)
                      .|+|=|.-|+||||.++.+.+.  ....-..+++..-.......+..++++
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~--L~~~g~~v~~treP~~t~~~~~ir~~l   50 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQY--LEKRGKKVILKREPGGTETGEKIRKIL   50 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCCcHHHHHHHHh
Confidence            3778899999999999999885  333333445554444333444444444

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=91.74  E-value=0.11  Score=53.01  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl   49 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGF   49 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCccHHHHHHHHHcC
Confidence            58999999999999999999984

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=91.73  E-value=0.081  Score=55.54  Aligned_cols=52  Identities=21%  Similarity=0.218  Sum_probs=35.6

Q ss_pred             CcceechhhHHHHHHHhccC-------CcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE-------SSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~-------~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.++.++.+...+...       ..-......+-|.++|++|+||||+|+.+...
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            46889888888877666321       00000012355889999999999999999884

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=91.70  E-value=0.043  Score=54.56  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=18.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+|+|.|..|+||||+|+.+.+
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999877

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=91.69  E-value=0.083  Score=49.49  Aligned_cols=22  Identities=32%  Similarity=0.431  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|.|.|++|+||||.|+.+.+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998874

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=91.68  E-value=0.13  Score=52.60  Aligned_cols=34  Identities=18%  Similarity=0.223  Sum_probs=26.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||.+.+..-.   ....+.+++
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~---~p~~G~I~i   62 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAGIY---KPTSGEIYF   62 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS---CCSEEEEEE
T ss_pred             CCEEEEEcCCCchHHHHHHHHHCCC---CCCccEEEE
Confidence            3589999999999999999999842   233455554

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=91.68  E-value=0.084  Score=51.78  Aligned_cols=22  Identities=36%  Similarity=0.668  Sum_probs=20.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|+|..|+|||||.+.++.-
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999998873

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=91.68  E-value=0.084  Score=52.70  Aligned_cols=22  Identities=36%  Similarity=0.446  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999887

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=91.67  E-value=0.09  Score=47.96  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=19.4

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +.+|+|..|+|||||+.+++-
T Consensus        28 ~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            889999999999999998865

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=91.64  E-value=0.13  Score=47.09  Aligned_cols=25  Identities=32%  Similarity=0.312  Sum_probs=21.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....|.|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4457899999999999999888775

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=91.62  E-value=0.082  Score=50.58  Aligned_cols=24  Identities=25%  Similarity=0.167  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|.|+.|+||||+|+.+.+.
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999874

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.61  E-value=0.13  Score=52.59  Aligned_cols=24  Identities=25%  Similarity=0.301  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl   52 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAGI   52 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcC
Confidence            358999999999999999999884

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=91.58  E-value=0.13  Score=52.85  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcC
Confidence            58999999999999999999884

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=91.57  E-value=0.089  Score=53.06  Aligned_cols=25  Identities=36%  Similarity=0.553  Sum_probs=22.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+.+++|+|+.|+|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4789999999999999999999864

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=91.56  E-value=0.13  Score=52.76  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            358999999999999999999884

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=91.56  E-value=0.13  Score=52.78  Aligned_cols=23  Identities=30%  Similarity=0.485  Sum_probs=21.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~llGpsGsGKSTLLr~iaGl   52 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAGL   52 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEEcCCCchHHHHHHHHHcC
Confidence            58999999999999999999984

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=91.55  E-value=0.1  Score=46.13  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|+|.+|+|||||+..+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45899999999999999888765

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=91.53  E-value=0.22  Score=53.31  Aligned_cols=46  Identities=17%  Similarity=0.118  Sum_probs=33.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKA  247 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~  247 (673)
                      ..++|.|..|+|||+|+..+.+..    +-+.++++-+.+..+ +.++..+
T Consensus       233 qr~~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER~~Ev~e~~~~  279 (600)
T 3vr4_A          233 GAAAVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGERGNEMTDVVNE  279 (600)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECHHHHHHHHHH
T ss_pred             CEEeeecCCCccHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHH
Confidence            568999999999999999988742    336788888877643 3344433

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=91.52  E-value=0.1  Score=48.28  Aligned_cols=24  Identities=21%  Similarity=0.427  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            467899999999999999988875

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=91.48  E-value=0.31  Score=51.60  Aligned_cols=88  Identities=23%  Similarity=0.203  Sum_probs=50.5

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccc----cccCC-eEEEEEcCCccc-HHHHHHHHHHHhhC-------CCCCcC-cH
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDV----FEYFD-KRMWVCVSDPFD-ELRIAKAIIEALEG-------FVPTVG-EL  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~----~~~F~-~~~wv~vs~~~~-~~~~~~~i~~~l~~-------~~~~~~-~~  262 (673)
                      .-++|+|..|+|||+|| ..+.|....    ..+-+ .++++-+.+..+ +.++.+.+.+.=..       ...+.. ..
T Consensus       163 QR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~  242 (510)
T 2ck3_A          163 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  242 (510)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHH
Confidence            46899999999999995 677775321    01244 477888887654 34555555432100       011111 00


Q ss_pred             H----HHHHHHHHHh--CCCeEEEEEcCC
Q 005860          263 N----SLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       263 ~----~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .    .....+.+++  +++.+||++||+
T Consensus       243 r~~a~~~a~tiAEyfrd~G~dVLli~Dsl  271 (510)
T 2ck3_A          243 QYLAPYSGCSMGEYFRDNGKHALIIYDDL  271 (510)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcEEEEEcCH
Confidence            0    1111233333  589999999998

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=91.43  E-value=0.12  Score=47.07  Aligned_cols=25  Identities=20%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....|+|+|.+|+|||||...+...
T Consensus         6 ~~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            6 KSYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999998874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=91.42  E-value=0.24  Score=61.24  Aligned_cols=81  Identities=19%  Similarity=0.151  Sum_probs=0.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIRAS  272 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~  272 (673)
                      ++|-|+|++|+|||+||.++...  ....=..++|+++...++...     ++.++..-.     .....++....++..
T Consensus      1428 ~~vll~GppGtGKT~LA~ala~e--a~~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~l 1500 (2050)
T 3cmu_A         1428 RIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDAL 1500 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH--HHTTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHHHH


Q ss_pred             h-CCCeEEEEEcCC
Q 005860          273 L-VGKKFLLILDDM  285 (673)
Q Consensus       273 l-~~kr~LlVLDdv  285 (673)
                      . ..+.-+||+|.+
T Consensus      1501 vr~~~~~lVVIDsi 1514 (2050)
T 3cmu_A         1501 ARSGAVDVIVVDSV 1514 (2050)
T ss_dssp             HHHTCCSEEEESCG
T ss_pred             HhcCCCCEEEEcCh

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=91.35  E-value=0.089  Score=50.47  Aligned_cols=25  Identities=28%  Similarity=0.284  Sum_probs=22.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ....+|+|+|+.|+||||+++.+..
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4456899999999999999999876

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=91.29  E-value=0.098  Score=51.61  Aligned_cols=22  Identities=32%  Similarity=0.380  Sum_probs=19.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .++.|+|.+|+|||||+..+..
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            5899999999999999987775

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=91.24  E-value=0.099  Score=52.06  Aligned_cols=51  Identities=16%  Similarity=0.126  Sum_probs=32.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKAIIEA  251 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~  251 (673)
                      -.+++|+|.+|+|||||++.+....  ...-. .++|+....  +..++...+...
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~~--~~~~G~~v~~~~~e~--~~~~~~~r~~~~   86 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQW--GTAMGKKVGLAMLEE--SVEETAEDLIGL   86 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHHH--HHTSCCCEEEEESSS--CHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH--HHHcCCeEEEEeCcC--CHHHHHHHHHHH
Confidence            3589999999999999998887742  22212 466766443  344444444443

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=91.13  E-value=0.1  Score=54.85  Aligned_cols=25  Identities=28%  Similarity=0.452  Sum_probs=22.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|+|++|+||||+|+.+...
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4679999999999999999998874

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=91.11  E-value=0.11  Score=54.22  Aligned_cols=25  Identities=16%  Similarity=0.274  Sum_probs=22.4

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++|+|..|+|||||.+.+..-
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhCC
Confidence            3569999999999999999999883

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=91.08  E-value=0.12  Score=51.23  Aligned_cols=24  Identities=29%  Similarity=0.191  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+|.|+|+.|+||||||..+.+.
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCccCHHHHHHHHHHh
Confidence            578999999999999999998873

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=91.08  E-value=0.11  Score=53.09  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999874

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=91.07  E-value=0.2  Score=52.29  Aligned_cols=88  Identities=14%  Similarity=0.092  Sum_probs=50.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcccc--------ccCC-eEEEEEcCCccc-HHHHHHHHHHH--hhC-----CCCCcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVF--------EYFD-KRMWVCVSDPFD-ELRIAKAIIEA--LEG-----FVPTVG  260 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~--------~~F~-~~~wv~vs~~~~-~~~~~~~i~~~--l~~-----~~~~~~  260 (673)
                      .-++|.|..|+|||+|+..+.+.....        ++=+ .++++-+.+..+ +.++..++.+.  +..     ...+..
T Consensus       148 Qr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~d~p  227 (464)
T 3gqb_B          148 QKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDP  227 (464)
T ss_dssp             CBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEETTSC
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECCCCC
Confidence            357899999999999999888864331        1112 567777776543 34455544332  100     011111


Q ss_pred             cHH-----HHHHHHHHHh---CCCeEEEEEcCC
Q 005860          261 ELN-----SLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       261 ~~~-----~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                      -..     .....+.+++   +++.+||++||+
T Consensus       228 ~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~Ddl  260 (464)
T 3gqb_B          228 TIERILTPRMALTVAEYLAFEHDYHVLVILTDM  260 (464)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTCCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcCh
Confidence            111     1222344444   379999999998

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.05  E-value=0.13  Score=49.43  Aligned_cols=39  Identities=18%  Similarity=0.296  Sum_probs=27.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      -.++.|.|.+|+||||||..+...  ....=..++|++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~--~~~~~~~v~~~~~e~   61 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWN--GLKMGEPGIYVALEE   61 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEESSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEccC
Confidence            358999999999999998766543  212224677887654

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=90.95  E-value=0.16  Score=52.22  Aligned_cols=23  Identities=30%  Similarity=0.166  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..+++|+|+.|+|||||++.+..
T Consensus       169 ~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          169 KRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999987

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=90.94  E-value=0.1  Score=46.13  Aligned_cols=22  Identities=32%  Similarity=0.643  Sum_probs=19.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||+..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999888764

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=90.93  E-value=0.21  Score=52.78  Aligned_cols=82  Identities=20%  Similarity=0.143  Sum_probs=49.5

Q ss_pred             EEEEEEccCCChHHHHH-HHHhcCccccccCC-eEEEEEcCCccc-HHHHHHHHHHHhhC--------C-CCC-cCc---
Q 005860          198 QIITIVGMGGIGKTTLA-QFAYNDSDVFEYFD-KRMWVCVSDPFD-ELRIAKAIIEALEG--------F-VPT-VGE---  261 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~vs~~~~-~~~~~~~i~~~l~~--------~-~~~-~~~---  261 (673)
                      .-++|+|..|+|||+|| ..+.|..    .-+ .++++-+.+..+ +.++.+.+.+.=..        . +.+ ...   
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  239 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQQ----GQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  239 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCC----TTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             CEEEEecCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHH
Confidence            46899999999999995 6888863    245 457888887654 33444444331000        0 111 110   


Q ss_pred             ---HHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          262 ---LNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       262 ---~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                         .-...+.++.  +++.+||++||+
T Consensus       240 ~~~a~tiAEyfrd--~G~dVLli~Dsl  264 (507)
T 1fx0_A          240 PYTGAALAEYFMY--RERHTLIIYDDL  264 (507)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEECH
T ss_pred             HHHHHHHHHHHHH--cCCcEEEEEecH
Confidence               1123344444  589999999998

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=90.89  E-value=0.17  Score=55.44  Aligned_cols=23  Identities=22%  Similarity=0.380  Sum_probs=20.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.|.+|.||||++..+...
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~  227 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADL  227 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            47889999999999999888763

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=90.82  E-value=0.13  Score=49.08  Aligned_cols=25  Identities=36%  Similarity=0.417  Sum_probs=22.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+|.|.|+.|+||||+++.+.+.
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999885

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=90.81  E-value=0.29  Score=56.43  Aligned_cols=21  Identities=24%  Similarity=0.135  Sum_probs=19.6

Q ss_pred             eEEEEEEccCCChHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFA  217 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v  217 (673)
                      -.+++|+|+.|.||||+.+.+
T Consensus       662 g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            479999999999999999988

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=90.81  E-value=0.12  Score=46.58  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999998875

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=90.74  E-value=0.15  Score=45.30  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=20.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456889999999999999988764

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=90.72  E-value=0.14  Score=47.07  Aligned_cols=23  Identities=26%  Similarity=0.267  Sum_probs=20.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|.|+.|+||||||..+...
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            56899999999999999988774

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.68  E-value=0.13  Score=49.54  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|.|..|+||||+++.+.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999998874

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=90.64  E-value=0.13  Score=45.77  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=19.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4789999999999999988764

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=90.61  E-value=0.1  Score=57.47  Aligned_cols=22  Identities=32%  Similarity=0.407  Sum_probs=20.2

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||+||+.+.+.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTT
T ss_pred             ceEEECCCchHHHHHHHHHHHh
Confidence            4789999999999999999985

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=90.61  E-value=0.16  Score=45.68  Aligned_cols=25  Identities=32%  Similarity=0.353  Sum_probs=21.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999988774

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=90.51  E-value=0.19  Score=44.99  Aligned_cols=24  Identities=29%  Similarity=0.513  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            456899999999999999988775

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=90.50  E-value=0.7  Score=43.97  Aligned_cols=89  Identities=18%  Similarity=0.196  Sum_probs=45.4

Q ss_pred             EEEEEEccCCChHHHHHHHH-hcCccccccC-CeEEEEEcCCcccHHHHHHHHHHHhhCCCC---------------C--
Q 005860          198 QIITIVGMGGIGKTTLAQFA-YNDSDVFEYF-DKRMWVCVSDPFDELRIAKAIIEALEGFVP---------------T--  258 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v-~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---------------~--  258 (673)
                      +.+.|+|..|+||||+...+ .+........ ...+.+......-...+...+...++....               .  
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  156 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHA  156 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSS
T ss_pred             CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCC
Confidence            36899999999999876433 3221111112 223333334433344455555544432200               0  


Q ss_pred             ---cCcHHHHHHHHHHHhCCCeEEEEEcCCCC
Q 005860          259 ---VGELNSLLESIRASLVGKKFLLILDDMWT  287 (673)
Q Consensus       259 ---~~~~~~~~~~l~~~l~~kr~LlVLDdvw~  287 (673)
                         ....+.+...+...+.+-+ +||+|.+..
T Consensus       157 ~Ivv~Tpg~l~~~l~~~l~~~~-~lVlDEah~  187 (235)
T 3llm_A          157 SIMFCTVGVLLRKLEAGIRGIS-HVIVDEIHE  187 (235)
T ss_dssp             EEEEEEHHHHHHHHHHCCTTCC-EEEECCTTS
T ss_pred             eEEEECHHHHHHHHHhhhcCCc-EEEEECCcc
Confidence               0133455555555444443 789999943

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=90.48  E-value=0.14  Score=52.78  Aligned_cols=24  Identities=21%  Similarity=0.234  Sum_probs=21.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...++|+|..|+|||||++.+..-
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999988773

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=90.48  E-value=0.22  Score=50.56  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ...+++|+|.+|+|||||.+.+..
T Consensus        54 ~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           54 RAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999875

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=90.47  E-value=0.12  Score=47.26  Aligned_cols=23  Identities=30%  Similarity=0.590  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999888764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=90.40  E-value=0.59  Score=49.34  Aligned_cols=51  Identities=16%  Similarity=0.091  Sum_probs=33.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEA  251 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  251 (673)
                      -.++.|.|.+|+||||+|..+..+..  ..=..++|++.-.  +..++...++..
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a--~~g~~vl~fSlEm--s~~ql~~R~~~~  247 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMS--DNDDVVNLHSLEM--GKKENIKRLIVT  247 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHH--HTTCEEEEECSSS--CTTHHHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHH--HcCCEEEEEECCC--CHHHHHHHHHHH
Confidence            45899999999999999977766422  2223567765543  444555555544

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=90.35  E-value=0.18  Score=45.89  Aligned_cols=24  Identities=29%  Similarity=0.369  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        16 ~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           16 EVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            467899999999999999998875

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=90.33  E-value=0.21  Score=53.28  Aligned_cols=38  Identities=24%  Similarity=0.079  Sum_probs=30.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPF  239 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  239 (673)
                      .-++|.|..|+|||+|+..+.+..    +-+.++++-+.+..
T Consensus       222 qr~~Ifg~~g~GKT~l~~~ia~~~----~~~v~V~~~iGER~  259 (578)
T 3gqb_A          222 GTAAIPGPFGSGKSVTQQSLAKWS----NADVVVYVGSGERG  259 (578)
T ss_dssp             CEEEECCCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECH
T ss_pred             CEEeeeCCCCccHHHHHHHHHhcc----CCCEEEEEEecccH
Confidence            468999999999999999988742    33678888887763

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=90.32  E-value=0.29  Score=46.26  Aligned_cols=25  Identities=32%  Similarity=0.403  Sum_probs=22.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....|.|.|+.|+||||+++.+.+.
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~   44 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEY   44 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999885

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=90.32  E-value=0.27  Score=55.66  Aligned_cols=97  Identities=16%  Similarity=0.255  Sum_probs=56.7

Q ss_pred             CcceechhhHHHHHHHhccCCcc-c-----ccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSE-E-----IINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDEL  242 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~-~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  242 (673)
                      .++.|.++.+++|.+.+.-.-.. +     +....+-|.++|++|.|||.||+++.+...  ..     ++.++.    .
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~--~~-----f~~v~~----~  545 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ--AN-----FISIKG----P  545 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTT--CE-----EEECCH----H
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhC--Cc-----eEEecc----c
Confidence            46778888888887766432110 0     112344578999999999999999999622  22     333332    1


Q ss_pred             HHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          243 RIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       243 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                      +    ++....+     .....+...+...-+..++.|++|++
T Consensus       546 ~----l~s~~vG-----ese~~vr~lF~~Ar~~~P~IifiDEi  579 (806)
T 3cf2_A          546 E----LLTMWFG-----ESEANVREIFDKARQAAPCVLFFDEL  579 (806)
T ss_dssp             H----HHTTTCS-----SCHHHHHHHHHHHHTTCSEEEECSCG
T ss_pred             h----hhccccc-----hHHHHHHHHHHHHHHcCCceeechhh
Confidence            1    1111111     11223333344444567899999998

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=90.30  E-value=0.14  Score=45.63  Aligned_cols=23  Identities=26%  Similarity=0.502  Sum_probs=20.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999888764

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=90.24  E-value=0.2  Score=44.60  Aligned_cols=22  Identities=36%  Similarity=0.453  Sum_probs=19.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      --|.|+|.+|+|||||...+..
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4589999999999999998865

---

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	673
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	6e-40

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  145 bits (367), Expect = 6e-40
 Identities = 42/285 (14%), Positives = 79/285 (27%), Gaps = 55/285 (19%)

Query: 157 SERIQSTSLIDVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQF 216
             ++   ++        R+     +  KL          D   + + G  G GK+ +A  
Sbjct: 8   DRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCD----LDSFFLFLHGRAGSGKSVIASQ 63

Query: 217 AYNDSDVFE--YFDKRMWVCVSDPFDELRIAKAIIEALEGF----------VPTVGELNS 264
           A + SD      +D  +W+  S    +          L             V  V  +  
Sbjct: 64  ALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVL 123

Query: 265 LLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKETVAR-MME 323
                 A +     L + DD+  ++  +W              + LVTTR   ++    +
Sbjct: 124 KRMICNALIDRPNTLFVFDDVVQEETIRWAQEL--------RLRCLVTTRDVEISNAASQ 175

Query: 324 SIHVISIKELSEQECW--------------------------CKGLPLAAKTIGSLLRFK 357
           +   I +  L   EC+                            G P             
Sbjct: 176 TCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCE-P 234

Query: 358 RTREEWESILDSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQY 402
           +T E+   + +           G+      SY  L   ++RC + 
Sbjct: 235 KTFEKMAQLNN---KLESRGLVGVECITPYSYKSLAMALQRCVEV 276

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	673
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.23
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.19
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.11
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.11
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.1
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.07
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.03
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.03
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	98.99
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	98.93
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.92
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	98.88
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	98.83
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.82
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.8
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.8
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.78
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.75
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	98.74
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.73
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	98.73
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.69
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.69
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	98.66
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	98.61
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.47
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.47
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.43
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.43
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.28
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.25
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.24
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.23
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.22
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.2
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.2
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.07
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.05
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.04
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.01
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.01
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.0
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.0
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.84
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.8
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.77
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.68
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.65
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.53
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.43
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.34
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.28
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.14
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.06
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.89
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.85
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	96.72
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.72
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	96.67
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.64
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.62
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.6
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.57
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.55
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.5
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.43
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.42
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.38
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.37
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	96.36
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.35
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.21
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.15
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.06
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.04
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.03
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.01
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.98
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.96
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.9
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.9
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.86
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.86
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.79
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.79
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.77
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.76
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	95.66
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.65
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.63
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.62
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.58
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.57
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.56
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.52
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.52
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.44
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.44
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.39
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.38
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.36
d1okkd2	207	GTPase domain of the signal recognition particle r	95.34
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.21
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.18
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.16
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.01
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.96
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.95
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	94.94
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.77
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.74
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	94.72
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.69
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.65
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	94.57
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.49
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	94.44
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	94.41
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.32
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.3
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.3
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.26
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.24
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.23
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.23
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.23
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.22
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.22
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.18
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.17
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.08
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.05
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	93.99
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	93.96
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.88
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	93.86
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	93.75
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.69
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.67
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	93.62
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.59
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	93.58
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.57
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	93.44
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.33
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	93.32
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.23
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.23
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.16
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	93.13
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	92.93
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	92.91
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	92.91
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	92.87
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	92.79
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.57
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.53
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.48
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.46
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.45
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	92.45
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.39
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.31
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.28
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	92.08
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	92.07
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.04
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.02
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	92.01
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.88
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	91.75
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	91.7
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	91.68
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	91.61
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.49
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	91.48
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.45
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	91.43
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.42
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.39
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	91.37
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.32
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.29
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.29
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.28
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	91.25
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	91.23
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	91.2
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	91.03
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	91.02
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.86
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	90.78
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	90.77
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	90.76
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.75
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	90.73
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	90.68
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	90.67
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	90.6
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	90.43
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	90.27
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	90.25
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	90.24
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	90.2
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	90.19
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.14
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	90.08
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	90.06
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.96
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	89.96
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	89.89
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	89.88
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.88
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.88
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	89.73
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	89.65
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	89.62
d1nrjb_	209	Signal recognition particle receptor beta-subunit	89.59
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	89.55
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.46
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	89.45
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	89.33
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	89.25
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	89.21
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	89.18
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	89.12
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	89.11
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	89.1
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	89.05
d2fh5b1	207	Signal recognition particle receptor beta-subunit	88.94
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	88.93
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	88.9
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	88.87
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.81
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	88.76
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.7
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	88.7
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	88.58
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	88.51
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	88.46
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	88.31
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	88.31
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	88.15
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	88.0
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	87.9
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	87.85
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	87.37
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	87.17
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	87.16
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	87.13
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	86.89
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.73
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	86.49
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	86.33
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.26
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	85.8
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	85.69
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	85.37
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	85.04
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	84.99
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	84.35
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	84.34
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	84.34
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	83.91
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	83.63
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	83.51
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	82.93
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	82.88
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	82.45
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	81.88
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	81.88
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	80.89

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=2.4e-37  Score=309.54  Aligned_cols=220  Identities=19%  Similarity=0.122  Sum_probs=174.5

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc--ccccCCeEEEEEcCCcccHHHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD--VFEYFDKRMWVCVSDPFDELRI  244 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~~  244 (673)
                      ..+.++||+.++++|+++|....    +.+.++|+|+||||+||||||+++|++..  +..+|++++||++++.++...+
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~----~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l   93 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMC----DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTF   93 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHT----TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHH
T ss_pred             CCCceeCcHHHHHHHHHHHHhcc----CCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHH
Confidence            45678999999999999997644    24578999999999999999999998643  6778999999999999887777


Q ss_pred             HHHHHHHhh---CCCC-------CcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcC
Q 005860          245 AKAIIEALE---GFVP-------TVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       245 ~~~i~~~l~---~~~~-------~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                      ...+...+.   ....       ...........+.+.+.++|+|+||||||+.  .+|+.+.      ..|||||||||
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~--~~~~~~~------~~~srilvTTR  165 (277)
T d2a5yb3          94 DLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE--ETIRWAQ------ELRLRCLVTTR  165 (277)
T ss_dssp             HHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH--HHHHHHH------HTTCEEEEEES
T ss_pred             HHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHH--hhhhhhc------ccCceEEEEee
Confidence            666655442   2110       1122233455678889999999999999965  4454432      25899999999


Q ss_pred             ChhHHHhccc-cceeecCCCCccccc--------------------------cCCchhhHHHHhhhhccCCCHHHHHHHH
Q 005860          315 KETVARMMES-IHVISIKELSEQECW--------------------------CKGLPLAAKTIGSLLRFKRTREEWESIL  367 (673)
Q Consensus       315 ~~~v~~~~~~-~~~~~l~~L~~~~~~--------------------------c~GlPLai~~~~~~L~~~~~~~~w~~~l  367 (673)
                      ++.++..+.. .+.|+|++|+.+|||                          |+|+|||++++|+.|+.+ +.+.|....
T Consensus       166 ~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k-~~~~~~~~~  244 (277)
T d2a5yb3         166 DVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-TFEKMAQLN  244 (277)
T ss_dssp             BGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-SHHHHHHHH
T ss_pred             hHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccC-CHHHHHHHH
Confidence            9999988665 478999999999998                          999999999999999755 688888766


Q ss_pred             hhhcccchhhhhccchhhhhcccCCChhhhhhhch
Q 005860          368 DSELWQLEEFEKGLLAPLLLSYNDLPPMIKRCFQY  402 (673)
Q Consensus       368 ~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cfl~  402 (673)
                      +....   ....++.+++.+||++||+++|.||-+
T Consensus       245 ~~L~~---~~~~~v~~il~~sY~~L~~~lk~c~~~  276 (277)
T d2a5yb3         245 NKLES---RGLVGVECITPYSYKSLAMALQRCVEV  276 (277)
T ss_dssp             HHHHH---HCSSTTCCCSSSSSSSHHHHHHHHHHT
T ss_pred             HHHhc---CcHHHHHHHHHHHHhcccHHHHHHHHh
Confidence            54321   234679999999999999999999954

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.9e-12  Score=116.55  Aligned_cols=131  Identities=21%  Similarity=0.128  Sum_probs=109.4

Q ss_pred             cccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccch
Q 005860          511 IFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPE  590 (673)
Q Consensus       511 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~  590 (673)
                      +.++.++|.|++.++.+     ..++..+..++.|++|++++       +.+..++ .+..+++|++|++++|.+..+|+
T Consensus        14 ~~n~~~lr~L~L~~n~I-----~~i~~~~~~l~~L~~L~Ls~-------N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~   80 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKI-----PVIENLGATLDQFDAIDFSD-------NEIRKLD-GFPLLRRLKTLLVNNNRICRIGE   80 (162)
T ss_dssp             EECTTSCEEEECTTSCC-----CSCCCGGGGTTCCSEEECCS-------SCCCEEC-CCCCCSSCCEEECCSSCCCEECS
T ss_pred             ccCcCcCcEEECCCCCC-----CccCccccccccCCEEECCC-------CCCCccC-CcccCcchhhhhcccccccCCCc
Confidence            44677889999998874     22345567889999999999       9988884 58999999999999999999987


Q ss_pred             hh-hcCCCccEEEeccCCCCccccc--cccccccCCeeeccccccccccc----cCCCCCCCCcCCeeEEcc
Q 005860          591 TC-CELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIPK----GIQRLTNLRTLSEFVVVR  655 (673)
Q Consensus       591 ~i-~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP~----~i~~L~~L~~L~~~~~~~  655 (673)
                      .+ ..+++|++|++++|. +..+|.  .+..+++|++|++++|.+..+|.    .+..+++|+.|++-.+..
T Consensus        81 ~~~~~l~~L~~L~L~~N~-i~~~~~l~~l~~l~~L~~L~l~~N~i~~~~~~r~~~i~~lp~L~~LD~~~i~~  151 (162)
T d1a9na_          81 GLDQALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCILRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKL  151 (162)
T ss_dssp             CHHHHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECCSSGGGGSTTHHHHHHHHCTTCSEETTEECCH
T ss_pred             cccccccccccceecccc-ccccccccccccccccchhhcCCCccccccchHHHHHHHCCCcCeeCCCCCCH
Confidence            65 579999999999976 888874  67889999999999999988874    377899999999877754

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.19  E-value=2.1e-11  Score=104.13  Aligned_cols=74  Identities=22%  Similarity=0.289  Sum_probs=37.7

Q ss_pred             cchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccccc
Q 005860          560 NSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       560 ~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +.+..++ .++.+.+|++|++++|.++.+|+.++.+++|++|+++++. +..+| +++++++|++|++++|.+..+|
T Consensus         8 n~l~~l~-~l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N~-i~~l~-~~~~l~~L~~L~l~~N~i~~~~   81 (124)
T d1dcea3           8 KDLTVLC-HLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNA-LENVD-GVANLPRLQELLLCNNRLQQSA   81 (124)
T ss_dssp             SCCSSCC-CGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSC-CCCCG-GGTTCSSCCEEECCSSCCCSSS
T ss_pred             CCCCCCc-ccccCCCCCEEECCCCccCcchhhhhhhhccccccccccc-ccccC-ccccccccCeEECCCCccCCCC
Confidence            4444443 2455555555555555555555555555555555555533 55554 3555555555555555554443

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.11  E-value=2.9e-11  Score=103.22  Aligned_cols=89  Identities=18%  Similarity=0.143  Sum_probs=80.4

Q ss_pred             hhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccc--cc
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL--GI  616 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~--~i  616 (673)
                      +..+..|+.|++++       +.+..+|+.++.+++|++|++++|.++.+|. ++.+++|++|+++++. +..+|.  .+
T Consensus        16 l~~l~~L~~L~ls~-------N~l~~lp~~~~~l~~L~~L~l~~N~i~~l~~-~~~l~~L~~L~l~~N~-i~~~~~~~~l   86 (124)
T d1dcea3          16 LEQLLLVTHLDLSH-------NRLRALPPALAALRCLEVLQASDNALENVDG-VANLPRLQELLLCNNR-LQQSAAIQPL   86 (124)
T ss_dssp             GGGGTTCCEEECCS-------SCCCCCCGGGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSSC-CCSSSTTGGG
T ss_pred             cccCCCCCEEECCC-------CccCcchhhhhhhhcccccccccccccccCc-cccccccCeEECCCCc-cCCCCCchhh
Confidence            57888999999999       9999999999999999999999999999985 9999999999999976 888873  68


Q ss_pred             cccccCCeeecccccccccc
Q 005860          617 GKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       617 ~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      +.+++|++|++++|.+..+|
T Consensus        87 ~~~~~L~~L~l~~N~i~~~~  106 (124)
T d1dcea3          87 VSCPRLVLLNLQGNSLCQEE  106 (124)
T ss_dssp             GGCTTCCEEECTTSGGGGSS
T ss_pred             cCCCCCCEEECCCCcCCcCc
Confidence            89999999999999887665

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.11  E-value=3.9e-11  Score=112.02  Aligned_cols=137  Identities=19%  Similarity=0.235  Sum_probs=67.6

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      +++.+.+..+....+. .+..+++|++|+++++..    ... +. +.++++|+.|++++       +.+..++ .++.+
T Consensus        41 ~l~~L~l~~~~i~~l~-~l~~l~nL~~L~Ls~N~l----~~~-~~-l~~l~~L~~L~l~~-------n~~~~~~-~l~~l  105 (199)
T d2omxa2          41 QVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQL----TDI-TP-LKNLTKLVDILMNN-------NQIADIT-PLANL  105 (199)
T ss_dssp             TCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCC----CCC-GG-GTTCTTCCEEECCS-------SCCCCCG-GGTTC
T ss_pred             CCCEEECCCCCCCCcc-ccccCCCcCcCccccccc----cCc-cc-ccCCcccccccccc-------ccccccc-ccccc
Confidence            4444544444433322 234455566666655542    111 11 45555566666655       4444443 25555


Q ss_pred             cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          573 IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      .+|++|+++++.+..++ .+..+++|+.|++++|. +..+| .+..+++|+.|++.+|.++.+| .++++++|+.|
T Consensus       106 ~~L~~L~l~~~~~~~~~-~~~~l~~L~~L~l~~n~-l~~~~-~l~~~~~L~~L~l~~n~l~~l~-~l~~l~~L~~L  177 (199)
T d2omxa2         106 TNLTGLTLFNNQITDID-PLKNLTNLNRLELSSNT-ISDIS-ALSGLTSLQQLNFSSNQVTDLK-PLANLTTLERL  177 (199)
T ss_dssp             TTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSSC-CCCCG-GGTTCTTCSEEECCSSCCCCCG-GGTTCTTCCEE
T ss_pred             ccccccccccccccccc-ccchhhhhHHhhhhhhh-hcccc-cccccccccccccccccccCCc-cccCCCCCCEE
Confidence            55555555555544433 24555555566555543 44444 3555555555555555555553 24444444444

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.10  E-value=7.1e-11  Score=110.16  Aligned_cols=140  Identities=21%  Similarity=0.269  Sum_probs=115.3

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ..++++.+.+..+.....++ +..+++|++|.+.++..     ..++ .+.+++.|+.|++++       +....++ .+
T Consensus        60 ~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n~~-----~~~~-~l~~l~~L~~L~l~~-------~~~~~~~-~~  124 (199)
T d2omxa2          60 YLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQI-----ADIT-PLANLTNLTGLTLFN-------NQITDID-PL  124 (199)
T ss_dssp             GCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCC-----CCCG-GGTTCTTCSEEECCS-------SCCCCCG-GG
T ss_pred             cCCCcCcCccccccccCccc-ccCCccccccccccccc-----cccc-ccccccccccccccc-------ccccccc-cc
Confidence            35789999999887766554 77899999999998763     1122 267899999999998       7655543 47


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTL  648 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L  648 (673)
                      ..+++|++|++++|.+..+| .+..+++|+.|++++|. +..+| .++++++|++|++++|.++.+| .+++|++|++|
T Consensus       125 ~~l~~L~~L~l~~n~l~~~~-~l~~~~~L~~L~l~~n~-l~~l~-~l~~l~~L~~L~ls~N~i~~i~-~l~~L~~L~~L  199 (199)
T d2omxa2         125 KNLTNLNRLELSSNTISDIS-ALSGLTSLQQLNFSSNQ-VTDLK-PLANLTTLERLDISSNKVSDIS-VLAKLTNLESL  199 (199)
T ss_dssp             TTCTTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSSC-CCCCG-GGTTCTTCCEEECCSSCCCCCG-GGGGCTTCSEE
T ss_pred             chhhhhHHhhhhhhhhcccc-ccccccccccccccccc-ccCCc-cccCCCCCCEEECCCCCCCCCc-cccCCCCCCcC
Confidence            88999999999999998876 58899999999999976 88887 5899999999999999999986 57888888865

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.07  E-value=1.6e-10  Score=108.77  Aligned_cols=143  Identities=22%  Similarity=0.306  Sum_probs=103.7

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccc
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGI  569 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i  569 (673)
                      ...+++.+.+..+....++ .+..+++|+.|.+.++..    . .++ .+..++.|+.|++++       +.+..++ .+
T Consensus        66 ~l~~L~~L~L~~n~i~~l~-~~~~l~~L~~L~l~~n~i----~-~l~-~l~~l~~L~~L~l~~-------~~~~~~~-~l  130 (210)
T d1h6ta2          66 YLPNVTKLFLNGNKLTDIK-PLANLKNLGWLFLDENKV----K-DLS-SLKDLKKLKSLSLEH-------NGISDIN-GL  130 (210)
T ss_dssp             GCTTCCEEECCSSCCCCCG-GGTTCTTCCEEECCSSCC----C-CGG-GGTTCTTCCEEECTT-------SCCCCCG-GG
T ss_pred             hCCCCCEEeCCCccccCcc-ccccCccccccccccccc----c-ccc-ccccccccccccccc-------ccccccc-cc
Confidence            3557788888777665554 356778888888877753    1 122 356778888888887       6655543 47


Q ss_pred             ccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          570 EKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      ..+++|++++++++.+..++ .+..+++|+++++++|. +..+| .+++|++|++|++++|.++.+| ++.+|++|+.|+
T Consensus       131 ~~l~~l~~l~~~~n~l~~~~-~~~~l~~L~~l~l~~n~-l~~i~-~l~~l~~L~~L~Ls~N~i~~l~-~l~~l~~L~~L~  206 (210)
T d1h6ta2         131 VHLPQLESLYLGNNKITDIT-VLSRLTKLDTLSLEDNQ-ISDIV-PLAGLTKLQNLYLSKNHISDLR-ALAGLKNLDVLE  206 (210)
T ss_dssp             GGCTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSSC-CCCCG-GGTTCTTCCEEECCSSCCCBCG-GGTTCTTCSEEE
T ss_pred             cccccccccccccccccccc-ccccccccccccccccc-ccccc-cccCCCCCCEEECCCCCCCCCh-hhcCCCCCCEEE
Confidence            77788888888888777655 46778888888888875 77776 4788888888888888888876 577777777776


Q ss_pred             ee
Q 005860          650 EF  651 (673)
Q Consensus       650 ~~  651 (673)
                      .+
T Consensus       207 Ls  208 (210)
T d1h6ta2         207 LF  208 (210)
T ss_dssp             EE
T ss_pred             cc
Confidence            54

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=1.3e-10  Score=113.76  Aligned_cols=146  Identities=24%  Similarity=0.253  Sum_probs=117.9

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccc
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKG  568 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~  568 (673)
                      .+.+++.+.+..+....+++ .+..+++|+.|.+.++.+    . .++ .+..+++|+.|++++       +.+...+..
T Consensus        29 lp~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l----~-~l~-~~~~l~~L~~L~Ls~-------N~l~~~~~~   95 (266)
T d1p9ag_          29 LPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAEL----T-KLQ-VDGTLPVLGTLDLSH-------NQLQSLPLL   95 (266)
T ss_dssp             CCTTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCC----C-EEE-CCSCCTTCCEEECCS-------SCCSSCCCC
T ss_pred             cCcCCCEEECcCCcCCCcCHHHhhccccccccccccccc----c-ccc-ccccccccccccccc-------ccccccccc
Confidence            45678899998888777664 467799999999998864    1 122 246788999999999       888888888


Q ss_pred             cccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCcccccc-ccccccCCeeecccccccccccc-CCCCCCC
Q 005860          569 IEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL  645 (673)
Q Consensus       569 i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L  645 (673)
                      +..+++|++|+++++.+..++ ..+..+.+|++|+++++. +..+|.. +..+.+|+.|++++|.++.+|.+ ++.+++|
T Consensus        96 ~~~l~~L~~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~-l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~~l~~L  174 (266)
T d1p9ag_          96 GQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENL  174 (266)
T ss_dssp             TTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTC
T ss_pred             cccccccccccccccccceeeccccccccccccccccccc-cceeccccccccccchhcccccccccccCcccccccccc
Confidence            999999999999999977765 566788999999999876 8888764 57789999999999999988865 6777777


Q ss_pred             CcCC
Q 005860          646 RTLS  649 (673)
Q Consensus       646 ~~L~  649 (673)
                      ++|.
T Consensus       175 ~~L~  178 (266)
T d1p9ag_         175 DTLL  178 (266)
T ss_dssp             CEEE
T ss_pred             ceee
Confidence            7764

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.03  E-value=9.1e-11  Score=110.44  Aligned_cols=140  Identities=21%  Similarity=0.271  Sum_probs=111.7

Q ss_pred             CceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhcccccc
Q 005860          492 EKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEK  571 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~  571 (673)
                      ..++++.+..+....++ .+..+++|++|.+.++..    .. ++ .+..+++|++|++++       +.+..+| .++.
T Consensus        46 ~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~L~~n~i----~~-l~-~~~~l~~L~~L~l~~-------n~i~~l~-~l~~  110 (210)
T d1h6ta2          46 NSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKL----TD-IK-PLANLKNLGWLFLDE-------NKVKDLS-SLKD  110 (210)
T ss_dssp             HTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCC----CC-CG-GGTTCTTCCEEECCS-------SCCCCGG-GGTT
T ss_pred             cCccEEECcCCCCCCch-hHhhCCCCCEEeCCCccc----cC-cc-ccccCcccccccccc-------ccccccc-cccc
Confidence            35667777666655443 467799999999999864    12 22 257899999999999       8888877 5888


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCe
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~  650 (673)
                      +++|++|++++|.+..+| .+..+++|+.++++++. +..++ .++++++|+++++++|.+..+|. ++++++|+.|..
T Consensus       111 l~~L~~L~l~~~~~~~~~-~l~~l~~l~~l~~~~n~-l~~~~-~~~~l~~L~~l~l~~n~l~~i~~-l~~l~~L~~L~L  185 (210)
T d1h6ta2         111 LKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNK-ITDIT-VLSRLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYL  185 (210)
T ss_dssp             CTTCCEEECTTSCCCCCG-GGGGCTTCCEEECCSSC-CCCCG-GGGGCTTCSEEECCSSCCCCCGG-GTTCTTCCEEEC
T ss_pred             cccccccccccccccccc-ccccccccccccccccc-ccccc-ccccccccccccccccccccccc-ccCCCCCCEEEC
Confidence            999999999999988776 58899999999999876 76655 67899999999999999988864 778888887643

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=1.8e-10  Score=112.75  Aligned_cols=145  Identities=22%  Similarity=0.191  Sum_probs=110.6

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-ccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KGI  569 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~i  569 (673)
                      ..+++.+.+..+....++. +..+++|++|++.++..     ...+..+..++.|+.|++++       +.+..++ ..+
T Consensus        54 l~~L~~L~L~~N~l~~l~~-~~~l~~L~~L~Ls~N~l-----~~~~~~~~~l~~L~~L~l~~-------~~~~~~~~~~~  120 (266)
T d1p9ag_          54 YTRLTQLNLDRAELTKLQV-DGTLPVLGTLDLSHNQL-----QSLPLLGQTLPALTVLDVSF-------NRLTSLPLGAL  120 (266)
T ss_dssp             CTTCCEEECTTSCCCEEEC-CSCCTTCCEEECCSSCC-----SSCCCCTTTCTTCCEEECCS-------SCCCCCCSSTT
T ss_pred             ccccccccccccccccccc-ccccccccccccccccc-----cccccccccccccccccccc-------cccceeecccc
Confidence            4578888888777665543 45788899999988764     22344567888899999988       7766654 456


Q ss_pred             ccccccccceecCCCCcccchh-hhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccccCCCCCCCCc
Q 005860          570 EKLIHLRYLRLVGLGTEELPET-CCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRT  647 (673)
Q Consensus       570 ~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~  647 (673)
                      ..+.+|++|++.+|.+..+|+. +..+++|++|++++|. +..+|. .++.+++|++|++++|.++.+|+++..+++|+.
T Consensus       121 ~~l~~l~~L~l~~n~l~~l~~~~~~~l~~l~~l~l~~N~-l~~~~~~~~~~l~~L~~L~Ls~N~L~~lp~~~~~~~~L~~  199 (266)
T d1p9ag_         121 RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNN-LTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPF  199 (266)
T ss_dssp             TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSC-CSCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCCCSE
T ss_pred             ccccccccccccccccceeccccccccccchhccccccc-ccccCccccccccccceeecccCCCcccChhHCCCCCCCE
Confidence            7778888999988888888754 4568889999998865 777775 478888899999888888888888888877776


Q ss_pred             CC
Q 005860          648 LS  649 (673)
Q Consensus       648 L~  649 (673)
                      |.
T Consensus       200 L~  201 (266)
T d1p9ag_         200 AF  201 (266)
T ss_dssp             EE
T ss_pred             EE
Confidence            53

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=4.1e-10  Score=100.84  Aligned_cols=108  Identities=17%  Similarity=0.190  Sum_probs=88.8

Q ss_pred             hhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccc-c
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGI-G  617 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i-~  617 (673)
                      |.++..||.|+|++       +.+..+|.....+.+|++|+|++|.+..+| .+..+++|++|++++|. +..+|..+ .
T Consensus        14 ~~n~~~lr~L~L~~-------n~I~~i~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~-i~~l~~~~~~   84 (162)
T d1a9na_          14 YTNAVRDRELDLRG-------YKIPVIENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNR-ICRIGEGLDQ   84 (162)
T ss_dssp             EECTTSCEEEECTT-------SCCCSCCCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSC-CCEECSCHHH
T ss_pred             ccCcCcCcEEECCC-------CCCCccCccccccccCCEEECCCCCCCccC-CcccCcchhhhhccccc-ccCCCccccc
Confidence            45667899999999       999999877788999999999999999996 58999999999999987 99998765 6


Q ss_pred             ccccCCeeeccccccccccccCCCCCCCCcCCeeEEccC
Q 005860          618 KLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVVRG  656 (673)
Q Consensus       618 ~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~~~~~~  656 (673)
                      .+++|++|++++|.+..+|. +..+..+..|..+.+..+
T Consensus        85 ~l~~L~~L~L~~N~i~~~~~-l~~l~~l~~L~~L~l~~N  122 (162)
T d1a9na_          85 ALPDLTELILTNNSLVELGD-LDPLASLKSLTYLCILRN  122 (162)
T ss_dssp             HCTTCCEEECCSCCCCCGGG-GGGGGGCTTCCEEECCSS
T ss_pred             cccccccceecccccccccc-ccccccccccchhhcCCC
Confidence            79999999999999988864 444445555555555543

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.92  E-value=8.3e-12  Score=116.30  Aligned_cols=138  Identities=20%  Similarity=0.169  Sum_probs=109.3

Q ss_pred             CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCC
Q 005860          505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLG  584 (673)
Q Consensus       505 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~  584 (673)
                      ..++..+..+++|+.|.+.++..    .. ++ .+..+++|+.|++++       |.+..+|.....+.+|++|++++|.
T Consensus        38 ~~l~~sl~~L~~L~~L~Ls~n~I----~~-i~-~l~~l~~L~~L~Ls~-------N~i~~i~~~~~~~~~L~~L~l~~N~  104 (198)
T d1m9la_          38 EKMDATLSTLKACKHLALSTNNI----EK-IS-SLSGMENLRILSLGR-------NLIKKIENLDAVADTLEELWISYNQ  104 (198)
T ss_dssp             CCCHHHHHHTTTCCEEECSEEEE----SC-CC-CHHHHTTCCEEECCE-------EEECSCSSHHHHHHHCCEEECSEEE
T ss_pred             hhhhhHHhcccccceeECcccCC----CC-cc-cccCCccccChhhcc-------ccccccccccccccccccccccccc
Confidence            34455677889999999998874    12 22 367889999999999       8888888766777789999999999


Q ss_pred             CcccchhhhcCCCccEEEeccCCCCccccc--cccccccCCeeecccccccccccc-----------CCCCCCCCcCCee
Q 005860          585 TEELPETCCELLNLQVLEIEQCTSLKRLPL--GIGKLVNLRHLTYDDSCLEFIPKG-----------IQRLTNLRTLSEF  651 (673)
Q Consensus       585 i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~--~i~~L~~Lr~L~l~~~~l~~lP~~-----------i~~L~~L~~L~~~  651 (673)
                      ++.+| .+..+++|++|++++|. +..+|.  .+..|++|++|++++|.+...+..           +.++++|+.|++.
T Consensus       105 i~~l~-~~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~~~~r~~vi~~lp~L~~LD~~  182 (198)
T d1m9la_         105 IASLS-GIEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGM  182 (198)
T ss_dssp             CCCHH-HHHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEECSSHHHHHHCTTTTHHHHHHHHHHHCSSCCEESSG
T ss_pred             ccccc-cccccccccccccccch-hccccccccccCCCccceeecCCCccccCcccccchhhHHHHHHHHCCCcCEeCCc
Confidence            99886 48899999999999876 888773  688999999999999887655433           4568889988877


Q ss_pred             EEccCC
Q 005860          652 VVVRGG  657 (673)
Q Consensus       652 ~~~~~~  657 (673)
                      .|....
T Consensus       183 ~I~~~e  188 (198)
T d1m9la_         183 PVDVDE  188 (198)
T ss_dssp             GGTTTT
T ss_pred             cCCHHH
Confidence            665443

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=98.88  E-value=6.8e-10  Score=111.30  Aligned_cols=36  Identities=22%  Similarity=0.173  Sum_probs=24.6

Q ss_pred             cCceEEEEEEc-CCC-Cccccccccccccchhhhccch
Q 005860          491 QEKLRHSMLVL-GYE-ASFPISIFKAKNLRSLFINNTL  526 (673)
Q Consensus       491 ~~~~r~l~l~~-~~~-~~~~~~~~~~~~Lr~L~l~~~~  526 (673)
                      ...++.+.+.. +.. ..+|+.+.++++|++|++.++.
T Consensus        75 L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~  112 (313)
T d1ogqa_          75 LPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTN  112 (313)
T ss_dssp             CTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEEC
T ss_pred             Cccccccccccccccccccccccccccccchhhhcccc
Confidence            45677777764 333 3567777778888888877665

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=98.83  E-value=2.3e-09  Score=107.38  Aligned_cols=131  Identities=18%  Similarity=0.158  Sum_probs=106.3

Q ss_pred             CceEEEEEEcCCCC---ccccccccccccchhhhcc-chhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-c
Q 005860          492 EKLRHSMLVLGYEA---SFPISIFKAKNLRSLFINN-TLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-L  566 (673)
Q Consensus       492 ~~~r~l~l~~~~~~---~~~~~~~~~~~Lr~L~l~~-~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p  566 (673)
                      .++..+.+..+...   .+|+.+.++++|++|++.+ +.    +...+|..|.++++|++|++++       +.+..+ |
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~----l~g~iP~~i~~L~~L~~L~Ls~-------N~l~~~~~  118 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINN----LVGPIPPAIAKLTQLHYLYITH-------TNVSGAIP  118 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETT----EESCCCGGGGGCTTCSEEEEEE-------ECCEEECC
T ss_pred             EEEEEEECCCCCCCCCCCCChHHhcCccccccccccccc----cccccccccccccccchhhhcc-------cccccccc
Confidence            35888888877654   4678899999999999986 33    2234677789999999999999       887665 5


Q ss_pred             cccccccccccceecCCC-CcccchhhhcCCCccEEEeccCCCCccccccccccccC-Ceeeccccccc
Q 005860          567 KGIEKLIHLRYLRLVGLG-TEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNL-RHLTYDDSCLE  633 (673)
Q Consensus       567 ~~i~~L~~Lr~L~L~~~~-i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L-r~L~l~~~~l~  633 (673)
                      ..+..+.+|++++++.|. ...+|.+++++++|++++++++.....+|..++.+.+| +.+++++|.++
T Consensus       119 ~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~  187 (313)
T d1ogqa_         119 DFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLT  187 (313)
T ss_dssp             GGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEE
T ss_pred             ccccchhhhcccccccccccccCchhhccCcccceeecccccccccccccccccccccccccccccccc
Confidence            568889999999999998 67789999999999999999987455789988888876 67777776654

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.82  E-value=3.8e-09  Score=103.54  Aligned_cols=176  Identities=13%  Similarity=0.191  Sum_probs=98.7

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-----cccH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-----PFDE  241 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-----~~~~  241 (673)
                      ...+||||++++++|.+..           -++|.|+|++|+|||||++++.+.  ...   ...|+.+..     ....
T Consensus        10 ~~~~f~GR~~el~~l~~~~-----------~~~i~i~G~~G~GKTsLl~~~~~~--~~~---~~~~i~~~~~~~~~~~~~   73 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGLR-----------APITLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLRKFEERNYISY   73 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHTC-----------SSEEEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGGGGTTCSCCCH
T ss_pred             ChhhCCChHHHHHHHHhcc-----------CCEEEEEcCCCCcHHHHHHHHHHH--CCC---CeEEEEeccccccccccH
Confidence            3578999999999987631           257889999999999999998774  222   234554321     2223


Q ss_pred             HHHHHHHHHHhhC--------------C---------------CCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCC---
Q 005860          242 LRIAKAIIEALEG--------------F---------------VPTVGELNSLLESIRASLVGKKFLLILDDMWTDD---  289 (673)
Q Consensus       242 ~~~~~~i~~~l~~--------------~---------------~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~---  289 (673)
                      ..+...+......              .               ......+.++...+. ...++++++|+|++..-.   
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~i~id~~~~~~~~~  152 (283)
T d2fnaa2          74 KDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFE-QASKDNVIIVLDEAQELVKLR  152 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHH-HTCSSCEEEEEETGGGGGGCT
T ss_pred             HHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHH-hhcccccccccchhhhhcccc
Confidence            3344333333210              0               001122333333332 345789999999872210   


Q ss_pred             -ccchhhhhhhccCCCCCeEEEEEcCChhHHHhcc------------ccceeecCCCCccccc-----------------
Q 005860          290 -YSKWEPFHYCLKNGVRGSKILVTTRKETVARMME------------SIHVISIKELSEQECW-----------------  339 (673)
Q Consensus       290 -~~~~~~l~~~l~~~~~gs~iivTtr~~~v~~~~~------------~~~~~~l~~L~~~~~~-----------------  339 (673)
                       ..-+..+..... .......+++.+.......+.            ....+.|.+++.+++.                 
T Consensus       153 ~~~~~~~l~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~~  231 (283)
T d2fnaa2         153 GVNLLPALAYAYD-NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY  231 (283)
T ss_dssp             TCCCHHHHHHHHH-HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH
T ss_pred             hHHHHHHHHHHHH-hhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHHHH
Confidence             011112222211 223445555555443322211            1345789999988864                 


Q ss_pred             ------cCCchhhHHHHhhhhccCCCH
Q 005860          340 ------CKGLPLAAKTIGSLLRFKRTR  360 (673)
Q Consensus       340 ------c~GlPLai~~~~~~L~~~~~~  360 (673)
                            ++|+|..+..+|..+......
T Consensus       232 ~~i~~~~~G~P~~L~~~~~~~~~~~~~  258 (283)
T d2fnaa2         232 EVVYEKIGGIPGWLTYFGFIYLDNKNL  258 (283)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccH
Confidence                  899999999988766544433

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.80  E-value=3.4e-09  Score=109.05  Aligned_cols=138  Identities=19%  Similarity=0.260  Sum_probs=86.5

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      +++.+.+..+.....+ .+..+++|++|.+.++..    .. .+ .+..+..++.+++..       +.+..+ ..+..+
T Consensus       242 ~L~~L~l~~n~l~~~~-~~~~~~~L~~L~l~~~~l----~~-~~-~~~~~~~l~~l~~~~-------n~l~~~-~~~~~~  306 (384)
T d2omza2         242 NLTDLDLANNQISNLA-PLSGLTKLTELKLGANQI----SN-IS-PLAGLTALTNLELNE-------NQLEDI-SPISNL  306 (384)
T ss_dssp             TCSEEECCSSCCCCCG-GGTTCTTCSEEECCSSCC----CC-CG-GGTTCTTCSEEECCS-------SCCSCC-GGGGGC
T ss_pred             ccchhccccCccCCCC-cccccccCCEeeccCccc----CC-CC-ccccccccccccccc-------cccccc-cccchh
Confidence            4444444444333322 233445555555544432    01 11 133445555555555       444443 346777


Q ss_pred             cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCC
Q 005860          573 IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLS  649 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~  649 (673)
                      .++++|++++|.+..+|+ +..+++|++|++++|. +..+| .++++++|++|++++|.++.+|+ ++++++|++|.
T Consensus       307 ~~l~~L~ls~n~l~~l~~-l~~l~~L~~L~L~~n~-l~~l~-~l~~l~~L~~L~l~~N~l~~l~~-l~~l~~L~~L~  379 (384)
T d2omza2         307 KNLTYLTLYFNNISDISP-VSSLTKLQRLFFANNK-VSDVS-SLANLTNINWLSAGHNQISDLTP-LANLTRITQLG  379 (384)
T ss_dssp             TTCSEEECCSSCCSCCGG-GGGCTTCCEEECCSSC-CCCCG-GGGGCTTCCEEECCSSCCCBCGG-GTTCTTCSEEE
T ss_pred             cccCeEECCCCCCCCCcc-cccCCCCCEEECCCCC-CCCCh-hHcCCCCCCEEECCCCcCCCChh-hccCCCCCEee
Confidence            788888888888888764 7888888888888875 77777 68888888888888888888764 77777777664

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.80  E-value=1.7e-09  Score=102.88  Aligned_cols=149  Identities=14%  Similarity=0.213  Sum_probs=100.4

Q ss_pred             ccCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecccccccc-----------
Q 005860          490 YQEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWD-----------  558 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~-----------  558 (673)
                      ..++++.+.+..+...... .+..+++|+++.+.++..     ..++ .+..++.|+.+++++......           
T Consensus        61 ~l~~L~~L~ls~n~i~~~~-~l~~l~~l~~l~~~~n~~-----~~i~-~l~~l~~L~~l~l~~~~~~~~~~~~~~~~~~~  133 (227)
T d1h6ua2          61 YLNNLIGLELKDNQITDLA-PLKNLTKITELELSGNPL-----KNVS-AIAGLQSIKTLDLTSTQITDVTPLAGLSNLQV  133 (227)
T ss_dssp             GCTTCCEEECCSSCCCCCG-GGTTCCSCCEEECCSCCC-----SCCG-GGTTCTTCCEEECTTSCCCCCGGGTTCTTCCE
T ss_pred             cCCCCcEeecCCceeeccc-cccccccccccccccccc-----cccc-cccccccccccccccccccccchhccccchhh
Confidence            4567888888777665443 366778888888877653     1122 356788888888877321100           


Q ss_pred             ----ccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeecccccccc
Q 005860          559 ----VNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       559 ----~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~  634 (673)
                          .+.+.. ...+..+.+|++|++++|.+...+. ++++++|+.|++++|. +..+| .++++++|++|++++|.++.
T Consensus       134 l~~~~~~~~~-~~~~~~~~~L~~L~l~~n~~~~~~~-l~~l~~L~~L~Ls~n~-l~~l~-~l~~l~~L~~L~Ls~N~lt~  209 (227)
T d1h6ua2         134 LYLDLNQITN-ISPLAGLTNLQYLSIGNAQVSDLTP-LANLSKLTTLKADDNK-ISDIS-PLASLPNLIEVHLKNNQISD  209 (227)
T ss_dssp             EECCSSCCCC-CGGGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSC-CCCCG-GGGGCTTCCEEECTTSCCCB
T ss_pred             hhchhhhhch-hhhhccccccccccccccccccchh-hcccccceecccCCCc-cCCCh-hhcCCCCCCEEECcCCcCCC
Confidence                000111 1235666778888888888776654 7888889999998875 77777 47888889999988888888


Q ss_pred             ccccCCCCCCCCcCCe
Q 005860          635 IPKGIQRLTNLRTLSE  650 (673)
Q Consensus       635 lP~~i~~L~~L~~L~~  650 (673)
                      +|+ ++++++|+.|+.
T Consensus       210 i~~-l~~l~~L~~L~l  224 (227)
T d1h6ua2         210 VSP-LANTSNLFIVTL  224 (227)
T ss_dssp             CGG-GTTCTTCCEEEE
T ss_pred             Ccc-cccCCCCCEEEe
Confidence            863 666766666543

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.78  E-value=2.1e-09  Score=99.27  Aligned_cols=116  Identities=19%  Similarity=0.231  Sum_probs=73.6

Q ss_pred             CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-ccccccccccccceecCC
Q 005860          505 ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEKLIHLRYLRLVGL  583 (673)
Q Consensus       505 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~  583 (673)
                      ..+|..+.  +++++|+++++.+.   ....+..|.++++|+.|++++       +.+..+ +..+..+.+|++|+|++|
T Consensus        21 ~~iP~~lp--~~l~~L~Ls~N~i~---~~~~~~~f~~l~~L~~L~L~~-------N~i~~~~~~~~~~~~~L~~L~Ls~N   88 (192)
T d1w8aa_          21 KEIPRDIP--LHTTELLLNDNELG---RISSDGLFGRLPHLVKLELKR-------NQLTGIEPNAFEGASHIQELQLGEN   88 (192)
T ss_dssp             SSCCSCCC--TTCSEEECCSCCCC---SBCCSCSGGGCTTCCEEECCS-------SCCCCBCTTTTTTCTTCCEEECCSC
T ss_pred             CccCCCCC--CCCCEEEeCCCCCc---ccccccccCCCceEeeeeccc-------cccccccccccccccccceeeeccc
Confidence            34444332  46677777766531   012234566777777777777       665554 345666777777777777


Q ss_pred             CCcccch-hhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccc
Q 005860          584 GTEELPE-TCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       584 ~i~~LP~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~  633 (673)
                      .+..+|+ .+.+|++|++|+|+++. +..+|. .+..+++|++|++++|.+.
T Consensus        89 ~l~~l~~~~F~~l~~L~~L~L~~N~-l~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          89 KIKEISNKMFLGLHQLKTLNLYDNQ-ISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             CCCEECSSSSTTCTTCCEEECCSSC-CCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cccccCHHHHhCCCcccccccCCcc-ccccCHHHhcCCcccccccccccccc
Confidence            7777754 46677777777777755 777654 3567777777777666554

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.75  E-value=8.1e-09  Score=97.99  Aligned_cols=79  Identities=16%  Similarity=0.217  Sum_probs=68.6

Q ss_pred             hhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccc
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGK  618 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  618 (673)
                      +..+++|+.|++.+       +.+...+. ++.+++|++|+|++|.++.+|. ++++++|++|++++|+ +..+| .+++
T Consensus       147 ~~~~~~L~~L~l~~-------n~~~~~~~-l~~l~~L~~L~Ls~n~l~~l~~-l~~l~~L~~L~Ls~N~-lt~i~-~l~~  215 (227)
T d1h6ua2         147 LAGLTNLQYLSIGN-------AQVSDLTP-LANLSKLTTLKADDNKISDISP-LASLPNLIEVHLKNNQ-ISDVS-PLAN  215 (227)
T ss_dssp             GGGCTTCCEEECCS-------SCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-GGGCTTCCEEECTTSC-CCBCG-GGTT
T ss_pred             hccccccccccccc-------cccccchh-hcccccceecccCCCccCCChh-hcCCCCCCEEECcCCc-CCCCc-cccc
Confidence            56778899999988       77655443 8889999999999999999876 8999999999999986 99998 5899


Q ss_pred             cccCCeeecc
Q 005860          619 LVNLRHLTYD  628 (673)
Q Consensus       619 L~~Lr~L~l~  628 (673)
                      +++|+.|+++
T Consensus       216 l~~L~~L~ls  225 (227)
T d1h6ua2         216 TSNLFIVTLT  225 (227)
T ss_dssp             CTTCCEEEEE
T ss_pred             CCCCCEEEee
Confidence            9999999975

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.74  E-value=3.7e-09  Score=104.14  Aligned_cols=175  Identities=21%  Similarity=0.229  Sum_probs=123.4

Q ss_pred             ccCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhh---------------------hhhhhHHHHhhhCCccce
Q 005860          490 YQEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQV---------------------SLTHVLQSLFDQLKCLRA  547 (673)
Q Consensus       490 ~~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~---------------------~~~~~~~~~~~~l~~L~~  547 (673)
                      .+..++.+.+..+....+++ .+..+++|+.|++.++....                     ......+..|.++++|++
T Consensus        30 ip~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~  109 (284)
T d1ozna_          30 IPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHT  109 (284)
T ss_dssp             CCTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCE
T ss_pred             CCCCCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccccccccchhhcccccCCE
Confidence            34567888888887776665 46678888888887654310                     011223556788889999


Q ss_pred             eeeccccccccccchhhhc-cccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccccccCCe
Q 005860          548 LRIATLMNTWDVNSTNKIL-KGIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRH  624 (673)
Q Consensus       548 L~L~~~~~~~~~~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~  624 (673)
                      |++++       +.+..++ ..+..+.+|+++++++|.++.+| ..+..+++|+.|+++++. +..+|. .+..+++|+.
T Consensus       110 L~l~~-------n~~~~~~~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~-l~~l~~~~f~~l~~L~~  181 (284)
T d1ozna_         110 LHLDR-------CGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNR-ISSVPERAFRGLHSLDR  181 (284)
T ss_dssp             EECTT-------SCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCE
T ss_pred             EecCC-------cccccccccccchhcccchhhhccccccccChhHhccccchhhcccccCc-ccccchhhhccccccch
Confidence            99988       7766654 35667888999999999988886 456788899999999876 888764 5788999999


Q ss_pred             eeccccccccc-cccCCCCCCCCcCCeeEEc--cCCccCCCccccCCCCCC
Q 005860          625 LTYDDSCLEFI-PKGIQRLTNLRTLSEFVVV--RGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       625 L~l~~~~l~~l-P~~i~~L~~L~~L~~~~~~--~~~~~~~~~~~~l~~L~~  672 (673)
                      |+++.|.+..+ |..|+++++|++|....-.  ...+..+..+.+|+.|.+
T Consensus       182 l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~i~~~~~~~~~~~~~L~~L~l  232 (284)
T d1ozna_         182 LLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRL  232 (284)
T ss_dssp             EECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTCCEEEC
T ss_pred             hhhhhccccccChhHhhhhhhcccccccccccccccccccccccccCEEEe
Confidence            99988888776 5667888877776433222  111123455666766654

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.73  E-value=3.3e-10  Score=105.24  Aligned_cols=105  Identities=26%  Similarity=0.287  Sum_probs=89.2

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccc
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPL  614 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~  614 (673)
                      ++..+..+++|+.|+|++       +.+..++ .+..+++|++|+|++|.++.+|..+..+.+|++|++++|. +..+| 
T Consensus        40 l~~sl~~L~~L~~L~Ls~-------n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N~-i~~l~-  109 (198)
T d1m9la_          40 MDATLSTLKACKHLALST-------NNIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQ-IASLS-  109 (198)
T ss_dssp             CHHHHHHTTTCCEEECSE-------EEESCCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEEE-CCCHH-
T ss_pred             hhhHHhcccccceeECcc-------cCCCCcc-cccCCccccChhhccccccccccccccccccccccccccc-ccccc-
Confidence            345678899999999999       9888875 6999999999999999999999877777899999999976 88886 


Q ss_pred             cccccccCCeeeccccccccccc--cCCCCCCCCcCC
Q 005860          615 GIGKLVNLRHLTYDDSCLEFIPK--GIQRLTNLRTLS  649 (673)
Q Consensus       615 ~i~~L~~Lr~L~l~~~~l~~lP~--~i~~L~~L~~L~  649 (673)
                      .+.++++|++|++++|.++.+|.  .++.+++|+.|.
T Consensus       110 ~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~  146 (198)
T d1m9la_         110 GIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLL  146 (198)
T ss_dssp             HHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEE
T ss_pred             cccccccccccccccchhccccccccccCCCccceee
Confidence            68899999999999999988763  466666666654

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.73  E-value=7.2e-09  Score=103.15  Aligned_cols=58  Identities=19%  Similarity=0.138  Sum_probs=32.6

Q ss_pred             cCceEEEEEEcCCCCcccc-ccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecc
Q 005860          491 QEKLRHSMLVLGYEASFPI-SIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIAT  552 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~  552 (673)
                      +.+++++.+..+....+++ .+.++++|++|.+.++..    ....+..|.+++.|+.|++++
T Consensus        30 ~~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n~~----~~i~~~~f~~l~~L~~L~l~~   88 (305)
T d1xkua_          30 PPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKI----SKISPGAFAPLVKLERLYLSK   88 (305)
T ss_dssp             CTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCC----CCBCTTTTTTCTTCCEEECCS
T ss_pred             CCCCCEEECcCCcCCCcChhHhhccccccccccccccc----cccchhhhhCCCccCEecccC
Confidence            3556777776666655554 355666677776666542    223344455555555555543

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.69  E-value=9.1e-09  Score=105.74  Aligned_cols=163  Identities=19%  Similarity=0.189  Sum_probs=116.0

Q ss_pred             cCceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccc
Q 005860          491 QEKLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIE  570 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~  570 (673)
                      ..+++.+.+..+....++ .+..+++|+.|.+.++..    .. ++ .+..++.|+.|++++       +.+..+++ +.
T Consensus       218 ~~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~l~~n~l----~~-~~-~~~~~~~L~~L~l~~-------~~l~~~~~-~~  282 (384)
T d2omza2         218 LTNLDELSLNGNQLKDIG-TLASLTNLTDLDLANNQI----SN-LA-PLSGLTKLTELKLGA-------NQISNISP-LA  282 (384)
T ss_dssp             CTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSSCC----CC-CG-GGTTCTTCSEEECCS-------SCCCCCGG-GT
T ss_pred             cCCCCEEECCCCCCCCcc-hhhcccccchhccccCcc----CC-CC-cccccccCCEeeccC-------cccCCCCc-cc
Confidence            456777777766654443 456778888888887753    11 11 256778888888888       77666653 66


Q ss_pred             cccccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCCCCCCcCCe
Q 005860          571 KLIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSE  650 (673)
Q Consensus       571 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~  650 (673)
                      .+..++++.+..|.+..++ .+..+++|+.|+++++. +..+| .+..+++|+.|++++|.++.+| .++++++|++|+.
T Consensus       283 ~~~~l~~l~~~~n~l~~~~-~~~~~~~l~~L~ls~n~-l~~l~-~l~~l~~L~~L~L~~n~l~~l~-~l~~l~~L~~L~l  358 (384)
T d2omza2         283 GLTALTNLELNENQLEDIS-PISNLKNLTYLTLYFNN-ISDIS-PVSSLTKLQRLFFANNKVSDVS-SLANLTNINWLSA  358 (384)
T ss_dssp             TCTTCSEEECCSSCCSCCG-GGGGCTTCSEEECCSSC-CSCCG-GGGGCTTCCEEECCSSCCCCCG-GGGGCTTCCEEEC
T ss_pred             ccccccccccccccccccc-ccchhcccCeEECCCCC-CCCCc-ccccCCCCCEEECCCCCCCCCh-hHcCCCCCCEEEC
Confidence            7788888988888887765 48899999999999976 88887 4899999999999999998886 5777777776654


Q ss_pred             eEEccCCccCCCccccCCCCCC
Q 005860          651 FVVVRGGSKYGGKACNLEGLRY  672 (673)
Q Consensus       651 ~~~~~~~~~~~~~~~~l~~L~~  672 (673)
                      -...-.+-.-+..+.+|++|.+
T Consensus       359 ~~N~l~~l~~l~~l~~L~~L~L  380 (384)
T d2omza2         359 GHNQISDLTPLANLTRITQLGL  380 (384)
T ss_dssp             CSSCCCBCGGGTTCTTCSEEEC
T ss_pred             CCCcCCCChhhccCCCCCEeeC
Confidence            3211111011355667777765

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.69  E-value=1.2e-08  Score=94.00  Aligned_cols=99  Identities=18%  Similarity=0.178  Sum_probs=84.0

Q ss_pred             Cccceeeeccccccccccchhh-h-ccccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccc-cccc
Q 005860          543 KCLRALRIATLMNTWDVNSTNK-I-LKGIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGK  618 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~-l-p~~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~  618 (673)
                      ..++.|+|++       +.+.. + +..+..+.+|+.|+|++|.+..+| ..+..+++|++|+++++. +..+|. .|.+
T Consensus        29 ~~l~~L~Ls~-------N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~N~-l~~l~~~~F~~  100 (192)
T d1w8aa_          29 LHTTELLLND-------NELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENK-IKEISNKMFLG  100 (192)
T ss_dssp             TTCSEEECCS-------CCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCC-CCEECSSSSTT
T ss_pred             CCCCEEEeCC-------CCCcccccccccCCCceEeeeeccccccccccccccccccccceeeecccc-ccccCHHHHhC
Confidence            5799999999       99865 4 345789999999999999977765 678889999999999976 888876 5899


Q ss_pred             cccCCeeecccccccccccc-CCCCCCCCcCC
Q 005860          619 LVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLS  649 (673)
Q Consensus       619 L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~  649 (673)
                      |++|++|++++|.++.+|++ +..+++|++|.
T Consensus       101 l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~  132 (192)
T d1w8aa_         101 LHQLKTLNLYDNQISCVMPGSFEHLNSLTSLN  132 (192)
T ss_dssp             CTTCCEEECCSSCCCEECTTSSTTCTTCCEEE
T ss_pred             CCcccccccCCccccccCHHHhcCCccccccc
Confidence            99999999999999999876 66777777664

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.66  E-value=1.5e-08  Score=100.84  Aligned_cols=127  Identities=17%  Similarity=0.180  Sum_probs=71.1

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhh-cccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKI-LKGIEK  571 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l-p~~i~~  571 (673)
                      +++.+.+..+....++..+  +++|+.|.+.++..    ....+..|.+++.+++|++++       +.+..+ +..+..
T Consensus       151 ~L~~l~l~~n~l~~l~~~~--~~~L~~L~l~~n~~----~~~~~~~~~~~~~l~~L~~s~-------n~l~~~~~~~~~~  217 (305)
T d1xkua_         151 KLSYIRIADTNITTIPQGL--PPSLTELHLDGNKI----TKVDAASLKGLNNLAKLGLSF-------NSISAVDNGSLAN  217 (305)
T ss_dssp             TCCEEECCSSCCCSCCSSC--CTTCSEEECTTSCC----CEECTGGGTTCTTCCEEECCS-------SCCCEECTTTGGG
T ss_pred             ccCccccccCCccccCccc--CCccCEEECCCCcC----CCCChhHhhcccccccccccc-------ccccccccccccc
Confidence            4445555444443333322  35566666655442    122334455666666666666       655554 334566


Q ss_pred             ccccccceecCCCCcccchhhhcCCCccEEEeccCCCCcccccc-------ccccccCCeeeccccccc
Q 005860          572 LIHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLG-------IGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       572 L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~-------i~~L~~Lr~L~l~~~~l~  633 (673)
                      +++|++|+|++|.++.+|+++.++++|++|+|++|+ ++.+|..       ...+.+|+.|++++|.+.
T Consensus       218 l~~L~~L~L~~N~L~~lp~~l~~l~~L~~L~Ls~N~-i~~i~~~~f~~~~~~~~~~~L~~L~L~~N~~~  285 (305)
T d1xkua_         218 TPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNN-ISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQ  285 (305)
T ss_dssp             STTCCEEECCSSCCSSCCTTTTTCSSCCEEECCSSC-CCCCCTTSSSCSSCCTTSCCCSEEECCSSSSC
T ss_pred             cccceeeecccccccccccccccccCCCEEECCCCc-cCccChhhccCcchhcccCCCCEEECCCCcCc
Confidence            666666666666666666666666666666666654 6655432       234556666666666554

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.61  E-value=1e-08  Score=100.89  Aligned_cols=91  Identities=23%  Similarity=0.227  Sum_probs=41.4

Q ss_pred             hhhCCccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccccccc
Q 005860          539 FDQLKCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRLPLGI  616 (673)
Q Consensus       539 ~~~l~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~lP~~i  616 (673)
                      +..+..|+.+++++       +.+..+|+ .+..+.+|+.|+|++|.+..+| ..+.++++|+.|+++++....-.|..|
T Consensus       125 ~~~~~~L~~l~l~~-------N~l~~i~~~~f~~~~~L~~L~l~~N~l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f  197 (284)
T d1ozna_         125 FRGLAALQYLYLQD-------NALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAF  197 (284)
T ss_dssp             TTTCTTCCEEECCS-------SCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTT
T ss_pred             cchhcccchhhhcc-------ccccccChhHhccccchhhcccccCcccccchhhhccccccchhhhhhccccccChhHh
Confidence            33444455555554       44444432 2334444555555555544443 233444555555555443222223444


Q ss_pred             cccccCCeeecccccccccc
Q 005860          617 GKLVNLRHLTYDDSCLEFIP  636 (673)
Q Consensus       617 ~~L~~Lr~L~l~~~~l~~lP  636 (673)
                      .++++|++|+++.|.+..+|
T Consensus       198 ~~l~~L~~L~l~~N~i~~~~  217 (284)
T d1ozna_         198 RDLGRLMTLYLFANNLSALP  217 (284)
T ss_dssp             TTCTTCCEEECCSSCCSCCC
T ss_pred             hhhhhccccccccccccccc
Confidence            55555555555555444444

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.47  E-value=1.3e-06  Score=84.65  Aligned_cols=118  Identities=16%  Similarity=0.084  Sum_probs=80.1

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHH
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIA  245 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~  245 (673)
                      .+..++||+.+++.+..+|...-... ....+.+.|+|++|+||||+|+.+.+.  ....+. ..+|+..........+.
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~-~~~~~~lll~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~   90 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNP-GHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAII   90 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHST-TSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCC-CCCCCceEEECCCCCCHHHHHHHHHHH--HhcccCCcEEEecchhhhhhhhhh
Confidence            34578999999999999885320000 134568899999999999999999985  333332 35677777777888888


Q ss_pred             HHHHHHhhCCCCC-cCcHHHHHHHHHHHh--CCCeEEEEEcCCCC
Q 005860          246 KAIIEALEGFVPT-VGELNSLLESIRASL--VGKKFLLILDDMWT  287 (673)
Q Consensus       246 ~~i~~~l~~~~~~-~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~  287 (673)
                      ..+....+..... ..........+.+.+  ......+++|++..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~  135 (276)
T d1fnna2          91 GEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFN  135 (276)
T ss_dssp             HHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGG
T ss_pred             hhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHH
Confidence            8888887765332 334445555555544  34567777887744

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=1.3e-07  Score=83.60  Aligned_cols=89  Identities=18%  Similarity=0.153  Sum_probs=69.9

Q ss_pred             HHHhhhCCccceeeeccccccccccc-hhhhcc-ccccccccccceecCCCCcccc-hhhhcCCCccEEEeccCCCCccc
Q 005860          536 QSLFDQLKCLRALRIATLMNTWDVNS-TNKILK-GIEKLIHLRYLRLVGLGTEELP-ETCCELLNLQVLEIEQCTSLKRL  612 (673)
Q Consensus       536 ~~~~~~l~~L~~L~L~~~~~~~~~~~-~~~lp~-~i~~L~~Lr~L~L~~~~i~~LP-~~i~~L~~L~~L~l~~c~~l~~l  612 (673)
                      +..+..+++|+.|++.+       +. ++.++. .+..|.+|+.|+|++|.++.+| ..+..+++|++|+|+++. +..+
T Consensus        24 p~~l~~l~~l~~L~l~~-------n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~-l~~l   95 (156)
T d2ifga3          24 LHHLPGAENLTELYIEN-------QQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNA-LESL   95 (156)
T ss_dssp             TTTSCSCSCCSEEECCS-------CSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSC-CSCC
T ss_pred             cccccCccccCeeecCC-------CccccccCchhhccccccCcceeeccccCCcccccccccccccceeccCCC-Cccc
Confidence            34456778888888876       54 777754 5788889999999999988885 557888999999999866 8888


Q ss_pred             cccccccccCCeeecccccc
Q 005860          613 PLGIGKLVNLRHLTYDDSCL  632 (673)
Q Consensus       613 P~~i~~L~~Lr~L~l~~~~l  632 (673)
                      |.++....+|++|++++|.+
T Consensus        96 ~~~~~~~~~l~~L~L~~Np~  115 (156)
T d2ifga3          96 SWKTVQGLSLQELVLSGNPL  115 (156)
T ss_dssp             CSTTTCSCCCCEEECCSSCC
T ss_pred             ChhhhccccccccccCCCcc
Confidence            88766666788998887765

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=1e-07  Score=84.28  Aligned_cols=97  Identities=23%  Similarity=0.130  Sum_probs=65.2

Q ss_pred             cCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhc-cccccccccccce
Q 005860          501 LGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKIL-KGIEKLIHLRYLR  579 (673)
Q Consensus       501 ~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp-~~i~~L~~Lr~L~  579 (673)
                      .......|..+..+++|+.|.+.++..   +....+..|.+++.|+.|++++       +.+..++ ..+..+++|++|+
T Consensus        17 ~~~~~~~p~~l~~l~~l~~L~l~~n~~---l~~i~~~~f~~l~~L~~L~Ls~-------N~l~~i~~~~f~~l~~L~~L~   86 (156)
T d2ifga3          17 RDGALDSLHHLPGAENLTELYIENQQH---LQHLELRDLRGLGELRNLTIVK-------SGLRFVAPDAFHFTPRLSRLN   86 (156)
T ss_dssp             SSCCCTTTTTSCSCSCCSEEECCSCSS---CCEECGGGSCSCCCCSEEECCS-------SCCCEECTTGGGSCSCCCEEE
T ss_pred             CCCCccCcccccCccccCeeecCCCcc---ccccCchhhccccccCcceeec-------cccCCccccccccccccccee
Confidence            333344455566677777777754421   2233445677778888888887       7777764 3467778888888


Q ss_pred             ecCCCCcccchhhhcCCCccEEEeccCC
Q 005860          580 LVGLGTEELPETCCELLNLQVLEIEQCT  607 (673)
Q Consensus       580 L~~~~i~~LP~~i~~L~~L~~L~l~~c~  607 (673)
                      |++|.++.+|.++....+|+.|+|++++
T Consensus        87 Ls~N~l~~l~~~~~~~~~l~~L~L~~Np  114 (156)
T d2ifga3          87 LSFNALESLSWKTVQGLSLQELVLSGNP  114 (156)
T ss_dssp             CCSSCCSCCCSTTTCSCCCCEEECCSSC
T ss_pred             ccCCCCcccChhhhccccccccccCCCc
Confidence            8888888887776666678888887754

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=8.6e-08  Score=91.55  Aligned_cols=160  Identities=18%  Similarity=0.150  Sum_probs=96.6

Q ss_pred             CceEEEEEEcCCCCccccc-cccccccchhhhccchhhh----------------------hhhhhHHHHhhhCCcccee
Q 005860          492 EKLRHSMLVLGYEASFPIS-IFKAKNLRSLFINNTLIQV----------------------SLTHVLQSLFDQLKCLRAL  548 (673)
Q Consensus       492 ~~~r~l~l~~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~----------------------~~~~~~~~~~~~l~~L~~L  548 (673)
                      .+++.+.+..+....++.. +.++++|++|++.++....                      ......+..|.++++|+.|
T Consensus        29 ~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~~l  108 (242)
T d1xwdc1          29 RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYL  108 (242)
T ss_dssp             SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEECCTTCCEE
T ss_pred             CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeecccccccccccccccccccccccccccccccccccccc
Confidence            4566666666665555442 4556667766665543210                      0112233456777888888


Q ss_pred             eecccccc--cc---c-------------cchhhhc-cccccc-cccccceecCCCCcccchhhhcCCCccEEEeccCCC
Q 005860          549 RIATLMNT--WD---V-------------NSTNKIL-KGIEKL-IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTS  608 (673)
Q Consensus       549 ~L~~~~~~--~~---~-------------~~~~~lp-~~i~~L-~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~  608 (673)
                      ++.+..-.  ..   .             ..+..++ ..+..+ ..+.+|++.++.+..+|.......+++.+....++.
T Consensus       109 ~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~~~~~~l~~L~l~~n~l~~i~~~~~~~~~l~~~~~l~~n~  188 (242)
T d1xwdc1         109 LISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNN  188 (242)
T ss_dssp             EEESCCCCSCCCCTTTCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEECTTTTTTCCEEEEECTTCTT
T ss_pred             ccchhhhcccccccccccccccccccccccccccccccccccccccceeeecccccccccccccccchhhhccccccccc
Confidence            88771000  00   0             0011111 112222 356777788877888887777777777776555556


Q ss_pred             Ccccccc-ccccccCCeeecccccccccccc-CCCCCCCCcCCee
Q 005860          609 LKRLPLG-IGKLVNLRHLTYDDSCLEFIPKG-IQRLTNLRTLSEF  651 (673)
Q Consensus       609 l~~lP~~-i~~L~~Lr~L~l~~~~l~~lP~~-i~~L~~L~~L~~~  651 (673)
                      +.++|.. +.++++|++|++++|.++.+|.. +.++++|++|...
T Consensus       189 l~~l~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~l~~~  233 (242)
T d1xwdc1         189 LEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTY  233 (242)
T ss_dssp             CCCCCTTTTTTSCCCSEEECTTSCCCCCCSSSCTTCCEEESSSEE
T ss_pred             cccccHHHhcCCCCCCEEECCCCcCCccCHHHHcCCcccccCcCC
Confidence            8888864 68888999999888888888764 6677777776654

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.28  E-value=9.2e-07  Score=83.14  Aligned_cols=125  Identities=18%  Similarity=0.158  Sum_probs=77.9

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccC--CeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYF--DKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~  246 (673)
                      ++++|.++.++.|..++....       ..-+-++|++|+||||+|+.+.+.  +...+  ..++-+..++......+..
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~~-------~~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~~~i~~   85 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDGN-------MPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVVRN   85 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC-------CCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHHHT
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-------CCeEEEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCceehhh
Confidence            579999999999999997654       334679999999999999988774  22211  1244455555554444333


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      .+.........              ...++.-++|+|++..-.......+...+......+++++||.+.
T Consensus        86 ~~~~~~~~~~~--------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          86 QIKHFAQKKLH--------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             HHHHHHHBCCC--------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHHHHHhhcc--------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            33222221111              012355688899995544445555655555556677777777653

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.25  E-value=1.1e-06  Score=82.84  Aligned_cols=146  Identities=12%  Similarity=0.101  Sum_probs=83.1

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|.++.++.|.+++....       ...+-++|+.|+||||+|+.+.+..........+.-+..+...+........
T Consensus        14 ~divg~~~~~~~L~~~i~~~~-------~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~   86 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK-------LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQI   86 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC-------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC-------CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecch
Confidence            579999999999999996554       3336799999999999999998852111111223333444433333222111


Q ss_pred             HHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHH-hccccc
Q 005860          249 IEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VAR-MMESIH  326 (673)
Q Consensus       249 ~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~-~~~~~~  326 (673)
                      .......               ....+++-.+|+|++.......-..+...+......++++++|.... +.. ......
T Consensus        87 ~~~~~~~---------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~  151 (227)
T d1sxjc2          87 KDFASTR---------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCT  151 (227)
T ss_dssp             HHHHHBC---------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             hhccccc---------------cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHh
Confidence            1111110               11123455888999954444444556666666667788888877532 111 112234


Q ss_pred             eeecCCCCcc
Q 005860          327 VISIKELSEQ  336 (673)
Q Consensus       327 ~~~l~~L~~~  336 (673)
                      .+.+++++.+
T Consensus       152 ~i~~~~~~~~  161 (227)
T d1sxjc2         152 RFRFQPLPQE  161 (227)
T ss_dssp             EEECCCCCHH
T ss_pred             hhcccccccc
Confidence            4555555433

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.24  E-value=9.2e-07  Score=83.86  Aligned_cols=157  Identities=12%  Similarity=0.059  Sum_probs=87.4

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc-cccCCeEEEEEcCCcccHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV-FEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      -++++|.++.++.+..++....       ...+.++|++|+||||+|+.+++...- .........+..+.......+..
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~-------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSAN-------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVRE   83 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT-------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTT
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHH
Confidence            3569999999999999986544       334789999999999999999885211 11123344455555555544333


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-H-HHhccc
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-V-ARMMES  324 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v-~~~~~~  324 (673)
                      .+-......... ..    ...+.....++.-++|+|++..-....+..+...+.......++|+||.... + ......
T Consensus        84 ~~~~~~~~~~~~-~~----~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr  158 (237)
T d1sxjd2          84 KVKNFARLTVSK-PS----KHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQ  158 (237)
T ss_dssp             HHHHHHHSCCCC-CC----TTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHH
T ss_pred             HHHHHhhhhhhh-hh----HHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccch
Confidence            332222221111 11    1122233344455789999854444455555555555556677777765432 1 111111


Q ss_pred             cceeecCCCCcc
Q 005860          325 IHVISIKELSEQ  336 (673)
Q Consensus       325 ~~~~~l~~L~~~  336 (673)
                      ...+++++++.+
T Consensus       159 ~~~i~f~~~~~~  170 (237)
T d1sxjd2         159 CSKFRFKALDAS  170 (237)
T ss_dssp             SEEEECCCCCHH
T ss_pred             hhhhcccccccc
Confidence            344555555543

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.23  E-value=2.6e-07  Score=90.44  Aligned_cols=148  Identities=16%  Similarity=0.126  Sum_probs=82.9

Q ss_pred             cCceEEEEEEcCCCCc--cccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccc-hh--hh
Q 005860          491 QEKLRHSMLVLGYEAS--FPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNS-TN--KI  565 (673)
Q Consensus       491 ~~~~r~l~l~~~~~~~--~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~-~~--~l  565 (673)
                      ..+++++.+..+....  +...+..+++|++|.+.++..    .......+.++++|+.|++++       +. ++  .+
T Consensus        45 ~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l----~~~~~~~l~~~~~L~~L~Ls~-------c~~itd~~l  113 (284)
T d2astb2          45 PFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRL----SDPIVNTLAKNSNLVRLNLSG-------CSGFSEFAL  113 (284)
T ss_dssp             CBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBC----CHHHHHHHTTCTTCSEEECTT-------CBSCCHHHH
T ss_pred             CCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCC----CcHHHHHHhcCCCCcCccccc-------ccccccccc
Confidence            3467888876654322  233355789999999998753    233445567889999999998       43 32  23


Q ss_pred             ccccccccccccceecCCC-Cc--ccchhhhcC-CCccEEEeccCC-CCc--cccccccccccCCeeecccc-ccc-ccc
Q 005860          566 LKGIEKLIHLRYLRLVGLG-TE--ELPETCCEL-LNLQVLEIEQCT-SLK--RLPLGIGKLVNLRHLTYDDS-CLE-FIP  636 (673)
Q Consensus       566 p~~i~~L~~Lr~L~L~~~~-i~--~LP~~i~~L-~~L~~L~l~~c~-~l~--~lP~~i~~L~~Lr~L~l~~~-~l~-~lP  636 (673)
                      ..-...+++|++|++++|. +.  .++..+..+ ++|+.|++++|. .+.  .++.-..++++|++|+++++ .++ ..+
T Consensus       114 ~~l~~~~~~L~~L~ls~c~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~  193 (284)
T d2astb2         114 QTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCF  193 (284)
T ss_dssp             HHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGG
T ss_pred             chhhHHHHhccccccccccccccccchhhhcccccccchhhhcccccccccccccccccccccccccccccccCCCchhh
Confidence            3334567889999998875 42  223333333 456666666543 121  12222344555666665432 232 222


Q ss_pred             ccCCCCCCCCcCC
Q 005860          637 KGIQRLTNLRTLS  649 (673)
Q Consensus       637 ~~i~~L~~L~~L~  649 (673)
                      ..++++++|++|.
T Consensus       194 ~~l~~~~~L~~L~  206 (284)
T d2astb2         194 QEFFQLNYLQHLS  206 (284)
T ss_dssp             GGGGGCTTCCEEE
T ss_pred             hhhcccCcCCEEE
Confidence            3344444444443

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.22  E-value=3.2e-06  Score=75.95  Aligned_cols=148  Identities=18%  Similarity=0.195  Sum_probs=83.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc---cc-cccCCeEEEEEcCCcccHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS---DV-FEYFDKRMWVCVSDPFDELRI  244 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~---~~-~~~F~~~~wv~vs~~~~~~~~  244 (673)
                      +.++||+++++++...|.....       .-+.+||.+|+|||++++.+....   ++ ...-+..+|.-     +...+
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k-------~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-----d~~~L   89 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTK-------NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-----DMGAL   89 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSS-------CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-----CHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccCC-------CCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe-----eHHHH
Confidence            3589999999999999976541       235799999999999986666531   12 22334555542     22211


Q ss_pred             HHHHHHHhhCCCCCcCcHHHHHHHHHHHh--CCCeEEEEEcCCCCC--------CccchhhhhhhccCCCCCeEEEEEcC
Q 005860          245 AKAIIEALEGFVPTVGELNSLLESIRASL--VGKKFLLILDDMWTD--------DYSKWEPFHYCLKNGVRGSKILVTTR  314 (673)
Q Consensus       245 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l--~~kr~LlVLDdvw~~--------~~~~~~~l~~~l~~~~~gs~iivTtr  314 (673)
                      .        .......++++....+.+.+  ...+.++++|++..-        ..+.-+.+...+..  ..-++|.||.
T Consensus        90 i--------Ag~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT  159 (195)
T d1jbka_          90 V--------AGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATT  159 (195)
T ss_dssp             H--------TTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEEC
T ss_pred             h--------ccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhC--CCceEEecCC
Confidence            1        11111223444333333333  345899999998431        00111223333332  2346888887


Q ss_pred             ChhHHHhccc-------cceeecCCCCcccc
Q 005860          315 KETVARMMES-------IHVISIKELSEQEC  338 (673)
Q Consensus       315 ~~~v~~~~~~-------~~~~~l~~L~~~~~  338 (673)
                      .+........       ...+.+++++.+++
T Consensus       160 ~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t  190 (195)
T d1jbka_         160 LDEYRQYIEKDAALERRFQKVFVAEPSVEDT  190 (195)
T ss_dssp             HHHHHHHTTTCHHHHTTEEEEECCCCCHHHH
T ss_pred             HHHHHHHHHcCHHHHhcCCEeecCCCCHHHH
Confidence            6665554332       46677888776653

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.20  E-value=3.3e-07  Score=89.72  Aligned_cols=59  Identities=20%  Similarity=0.096  Sum_probs=27.0

Q ss_pred             CceEEEEEEcCCCC-ccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecc
Q 005860          492 EKLRHSMLVLGYEA-SFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIAT  552 (673)
Q Consensus       492 ~~~r~l~l~~~~~~-~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~  552 (673)
                      ++++++.+..+... ..+..+.++++|++|.++++...  ....+...+..+++|+.|++++
T Consensus        71 ~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c~~i--td~~l~~l~~~~~~L~~L~ls~  130 (284)
T d2astb2          71 SKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGF--SEFALQTLLSSCSRLDELNLSW  130 (284)
T ss_dssp             CCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSC--CHHHHHHHHHHCTTCCEEECCC
T ss_pred             CCcccccccccCCCcHHHHHHhcCCCCcCccccccccc--cccccchhhHHHHhcccccccc
Confidence            34555555544321 12233445556666666554210  0112233344555666666655

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.20  E-value=9.5e-06  Score=77.14  Aligned_cols=149  Identities=19%  Similarity=0.196  Sum_probs=87.6

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCc---ccccc-CCeEEEE-EcCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDS---DVFEY-FDKRMWV-CVSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~---~~~~~-F~~~~wv-~vs~~~~~~~  243 (673)
                      +.++||+++++++...|.....       .-+.+||.+|+|||++++.+....   .+... .+..+|. +++.      
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k-------~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~------   84 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRK-------NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS------   84 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSS-------CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------
T ss_pred             CcccChHHHHHHHHHHHhcCcc-------CCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech------
Confidence            3589999999999999975541       235599999999999987666531   12222 2445554 2211      


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHh-CCCeEEEEEcCCCCC----C-ccchhhhhhhccC-CCC-CeEEEEEcCC
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASL-VGKKFLLILDDMWTD----D-YSKWEPFHYCLKN-GVR-GSKILVTTRK  315 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-~~kr~LlVLDdvw~~----~-~~~~~~l~~~l~~-~~~-gs~iivTtr~  315 (673)
                              +-.......++++....+.+.+ +.++.++++|++..-    . ...-.++...+.+ -.. .-++|.||..
T Consensus        85 --------liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~  156 (268)
T d1r6bx2          85 --------LLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTY  156 (268)
T ss_dssp             ----------CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECH
T ss_pred             --------HhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCH
Confidence                    1111223455666555555555 457799999998431    0 0000112222321 122 3578888887


Q ss_pred             hhHHHhccc-------cceeecCCCCcccc
Q 005860          316 ETVARMMES-------IHVISIKELSEQEC  338 (673)
Q Consensus       316 ~~v~~~~~~-------~~~~~l~~L~~~~~  338 (673)
                      ++.......       ...+++++++.+++
T Consensus       157 eey~~~~e~d~al~rrF~~I~V~Eps~e~t  186 (268)
T d1r6bx2         157 QEFSNIFEKDRALARRFQKIDITEPSIEET  186 (268)
T ss_dssp             HHHHCCCCCTTSSGGGEEEEECCCCCHHHH
T ss_pred             HHHHHHHhhcHHHHhhhcccccCCCCHHHH
Confidence            776665432       45678888887763

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=98.07  E-value=1e-06  Score=88.59  Aligned_cols=101  Identities=23%  Similarity=0.214  Sum_probs=54.9

Q ss_pred             ceEEEEEEcCCCCccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccc
Q 005860          493 KLRHSMLVLGYEASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKL  572 (673)
Q Consensus       493 ~~r~l~l~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L  572 (673)
                      +++.+.+..+....+|..   +++|++|+++++..    . .+|.   .+.+|+.|++++       +.+..++.-.   
T Consensus        39 ~l~~LdLs~~~L~~lp~~---~~~L~~L~Ls~N~l----~-~lp~---~~~~L~~L~l~~-------n~l~~l~~lp---   97 (353)
T d1jl5a_          39 QAHELELNNLGLSSLPEL---PPHLESLVASCNSL----T-ELPE---LPQSLKSLLVDN-------NNLKALSDLP---   97 (353)
T ss_dssp             TCSEEECTTSCCSCCCSC---CTTCSEEECCSSCC----S-SCCC---CCTTCCEEECCS-------SCCSCCCSCC---
T ss_pred             CCCEEEeCCCCCCCCCCC---CCCCCEEECCCCCC----c-cccc---chhhhhhhhhhh-------cccchhhhhc---
Confidence            355666665555555532   35666666666542    1 1222   234566666666       5544443211   


Q ss_pred             cccccceecCCCCcccchhhhcCCCccEEEeccCCCCccccccc
Q 005860          573 IHLRYLRLVGLGTEELPETCCELLNLQVLEIEQCTSLKRLPLGI  616 (673)
Q Consensus       573 ~~Lr~L~L~~~~i~~LP~~i~~L~~L~~L~l~~c~~l~~lP~~i  616 (673)
                      ..|++|++++|.+..+|. ++.+++|++|+++++. +...|..+
T Consensus        98 ~~L~~L~L~~n~l~~lp~-~~~l~~L~~L~l~~~~-~~~~~~~~  139 (353)
T d1jl5a_          98 PLLEYLGVSNNQLEKLPE-LQNSSFLKIIDVDNNS-LKKLPDLP  139 (353)
T ss_dssp             TTCCEEECCSSCCSSCCC-CTTCTTCCEEECCSSC-CSCCCCCC
T ss_pred             cccccccccccccccccc-hhhhccceeecccccc-cccccccc
Confidence            246667777666666664 4666777777776654 55555443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.05  E-value=8.6e-06  Score=77.03  Aligned_cols=135  Identities=13%  Similarity=0.148  Sum_probs=72.8

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAI  248 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  248 (673)
                      .+++|.++.++.+..++.....      ...+-|+|+.|+||||+|+.+.+..........       ...........+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~------~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~-------~~~~~~~~~~~i   78 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRI------HHAYLFSGTRGVGKTSIARLLAKGLNCETGITA-------TPCGVCDNCREI   78 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCC------CSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCS-------SCCSCSHHHHHH
T ss_pred             HHccChHHHHHHHHHHHHcCCC------CeeEEEECCCCCcHHHHHHHHHHHhcCcccccc-------CccccchHHHHH
Confidence            5799999999999999866542      345779999999999999887653110000000       000000011111


Q ss_pred             HHHhhC-----CCCCcCcHHHHHHHHHHH----hCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          249 IEALEG-----FVPTVGELNSLLESIRAS----LVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       249 ~~~l~~-----~~~~~~~~~~~~~~l~~~----l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      ...-..     ...+....++....+...    ..++.-++|||++..-+...-+.|...+......+++|+||.+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~  155 (239)
T d1njfa_          79 EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDP  155 (239)
T ss_dssp             HHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCG
T ss_pred             HcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCc
Confidence            111000     000111122222222111    12456689999995444444456666676666778888887753

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.04  E-value=3.3e-06  Score=79.62  Aligned_cols=125  Identities=15%  Similarity=0.073  Sum_probs=74.1

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHH
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~  246 (673)
                      -++++|.+..++.+..++....       .+.+.++|++|+||||+|+.+.+... ...+. ..+-+..+...+...+..
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~-------~~~lll~Gp~G~GKTtla~~iak~l~-~~~~~~~~~e~n~s~~~~~~~~~~   94 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGS-------MPHLLFAGPPGVGKTTAALALARELF-GENWRHNFLELNASDERGINVIRE   94 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC-------CCEEEEESCTTSSHHHHHHHHHHHHH-GGGHHHHEEEEETTCHHHHHTTHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-------CCeEEEECCCCCcHHHHHHHHHHHHH-hcccCCCeeEEecCcccchhHHHH
Confidence            3579999999999999996544       44578999999999999999987421 11222 123344444322222111


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCC
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRK  315 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~  315 (673)
                      .+.......               .....++.++++|++.......+..+...+........+|.||..
T Consensus        95 ~~~~~~~~~---------------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~  148 (231)
T d1iqpa2          95 KVKEFARTK---------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNY  148 (231)
T ss_dssp             HHHHHHHSC---------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHHHhhh---------------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCC
Confidence            111111110               111346778999999555555566666666544445566666654

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=98.01  E-value=2.7e-06  Score=85.40  Aligned_cols=105  Identities=20%  Similarity=0.221  Sum_probs=72.1

Q ss_pred             cccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCcccchhhhc
Q 005860          515 KNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTEELPETCCE  594 (673)
Q Consensus       515 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~  594 (673)
                      .+++.|+++++..    . .+|+   .+++|+.|++++       +.++.+|..++   +|+.|++++|.++.+|.-   
T Consensus        38 ~~l~~LdLs~~~L----~-~lp~---~~~~L~~L~Ls~-------N~l~~lp~~~~---~L~~L~l~~n~l~~l~~l---   96 (353)
T d1jl5a_          38 RQAHELELNNLGL----S-SLPE---LPPHLESLVASC-------NSLTELPELPQ---SLKSLLVDNNNLKALSDL---   96 (353)
T ss_dssp             HTCSEEECTTSCC----S-CCCS---CCTTCSEEECCS-------SCCSSCCCCCT---TCCEEECCSSCCSCCCSC---
T ss_pred             cCCCEEEeCCCCC----C-CCCC---CCCCCCEEECCC-------CCCcccccchh---hhhhhhhhhcccchhhhh---
Confidence            4677788877653    1 2332   346788888888       88888887654   456667777776666531   


Q ss_pred             CCCccEEEeccCCCCccccccccccccCCeeeccccccccccccCCCC
Q 005860          595 LLNLQVLEIEQCTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKGIQRL  642 (673)
Q Consensus       595 L~~L~~L~l~~c~~l~~lP~~i~~L~~Lr~L~l~~~~l~~lP~~i~~L  642 (673)
                      .++|++|++++|. +..+| .++++++|++|+++++.+...|..+..+
T Consensus        97 p~~L~~L~L~~n~-l~~lp-~~~~l~~L~~L~l~~~~~~~~~~~~~~l  142 (353)
T d1jl5a_          97 PPLLEYLGVSNNQ-LEKLP-ELQNSSFLKIIDVDNNSLKKLPDLPPSL  142 (353)
T ss_dssp             CTTCCEEECCSSC-CSSCC-CCTTCTTCCEEECCSSCCSCCCCCCTTC
T ss_pred             ccccccccccccc-ccccc-chhhhccceeeccccccccccccccccc
Confidence            1468889998866 88888 4678889999998887777666544333

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.01  E-value=3.2e-06  Score=80.23  Aligned_cols=104  Identities=16%  Similarity=0.238  Sum_probs=82.9

Q ss_pred             Cccceeeeccccccccccchhhhcc-ccccccccccceecCCCCcc-cc-hhhhcCCCccEEEeccCCCCccccc-cccc
Q 005860          543 KCLRALRIATLMNTWDVNSTNKILK-GIEKLIHLRYLRLVGLGTEE-LP-ETCCELLNLQVLEIEQCTSLKRLPL-GIGK  618 (673)
Q Consensus       543 ~~L~~L~L~~~~~~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~-LP-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~  618 (673)
                      ++++.|++++       +.+..+|. .+..+++|++|+|++|.+.. +| ..+..+++++.|.+..++++..+|. .+.+
T Consensus        29 ~~l~~L~Ls~-------n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~  101 (242)
T d1xwdc1          29 RNAIELRFVL-------TKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQN  101 (242)
T ss_dssp             SCCSEEEEES-------CCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEEC
T ss_pred             CCCCEEECcC-------CcCCccChhHhhccchhhhhhhccccccceeeccccccccccccccccccccccccccccccc
Confidence            5789999999       99988887 47899999999999998655 43 4678899999999988777777664 5799


Q ss_pred             cccCCeeeccccccccccccCCCCCCCCcCCeeEEc
Q 005860          619 LVNLRHLTYDDSCLEFIPKGIQRLTNLRTLSEFVVV  654 (673)
Q Consensus       619 L~~Lr~L~l~~~~l~~lP~~i~~L~~L~~L~~~~~~  654 (673)
                      +++|++|+++++.+...|. ...+.+++.+......
T Consensus       102 l~~L~~l~l~~~~l~~~~~-~~~~~~l~~l~~~~~~  136 (242)
T d1xwdc1         102 LPNLQYLLISNTGIKHLPD-VHKIHSLQKVLLDIQD  136 (242)
T ss_dssp             CTTCCEEEEESCCCCSCCC-CTTTCBSSCEEEEEES
T ss_pred             cccccccccchhhhccccc-cccccccccccccccc
Confidence            9999999999998877653 5556666666554443

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.00  E-value=1.2e-05  Score=78.00  Aligned_cols=117  Identities=23%  Similarity=0.216  Sum_probs=76.7

Q ss_pred             cCCcceechhhHHHHHHHhcc----CCcccccCCeEEEEEEccCCChHHHHHHHHhcCccc----cccCCeEEEEEcCCc
Q 005860          167 DVSEIRGRDEEKSSLKSKLLC----ESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDV----FEYFDKRMWVCVSDP  238 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~----~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~vs~~  238 (673)
                      .++.++||+.++++|.+.+..    +..+  .+...++.|+|++|+||||+|+++.+...-    ........++.....
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~~--~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~   91 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAGL--SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA   91 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCB--CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCCC--CCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccc
Confidence            457899999999999887632    2211  123446778899999999999999985211    111234567777777


Q ss_pred             ccHHHHHHHHHHHhhCCCCC-cCcHHHHHHHHHHHh--CCCeEEEEEcCC
Q 005860          239 FDELRIAKAIIEALEGFVPT-VGELNSLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       239 ~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      .........+...++..... ..........+.+..  .+...++++|.+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~  141 (287)
T d1w5sa2          92 PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEF  141 (287)
T ss_dssp             CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEEST
T ss_pred             cchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEE
Confidence            77888888888887765332 233344444444444  356777888876

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.00  E-value=2.4e-06  Score=81.70  Aligned_cols=47  Identities=21%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             CCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++++|.++..+.|..++....      ...-+.|+|++|+||||+|+++.+.
T Consensus        10 ~~diig~~~~~~~L~~~~~~~~------~~~~lll~Gp~G~GKTt~~~~la~~   56 (252)
T d1sxje2          10 LNALSHNEELTNFLKSLSDQPR------DLPHLLLYGPNGTGKKTRCMALLES   56 (252)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTT------CCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC------CCCeEEEECCCCCCHHHHHHHHHHh
Confidence            3579999998888888875443      2334679999999999999988774

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.84  E-value=3.8e-05  Score=70.84  Aligned_cols=120  Identities=23%  Similarity=0.239  Sum_probs=69.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCe
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKK  277 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr  277 (673)
                      ..+.|+|..|+|||.|++++++.  .......+++++      ..++...+...+....     ..    .+.+.+++ -
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~------~~~~~~~~~~~~~~~~-----~~----~~~~~~~~-~   98 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSS------ADDFAQAMVEHLKKGT-----IN----EFRNMYKS-V   98 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEE------HHHHHHHHHHHHHHTC-----HH----HHHHHHHT-C
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH--hccCccceEEec------hHHHHHHHHHHHHccc-----hh----hHHHHHhh-c
Confidence            34789999999999999999996  444555677774      3445555555543321     11    22222332 3


Q ss_pred             EEEEEcCCCCCC-ccchhh-hhhhccC-CCCCeEEEEEcCCh---------hHHHhccccceeecCCCCcc
Q 005860          278 FLLILDDMWTDD-YSKWEP-FHYCLKN-GVRGSKILVTTRKE---------TVARMMESIHVISIKELSEQ  336 (673)
Q Consensus       278 ~LlVLDdvw~~~-~~~~~~-l~~~l~~-~~~gs~iivTtr~~---------~v~~~~~~~~~~~l~~L~~~  336 (673)
                      -+|+|||+.... ...|+. +...+.. ...|.+||+||+..         ++...+.....+.++ ++++
T Consensus        99 dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~  168 (213)
T d1l8qa2          99 DLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNK  168 (213)
T ss_dssp             SEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHH
T ss_pred             cchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcH
Confidence            589999994321 234544 3322322 24677899998843         233334455667775 3443

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.80  E-value=6.1e-05  Score=75.66  Aligned_cols=147  Identities=18%  Similarity=0.237  Sum_probs=78.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHh----cCccccccCCeEEEEE-cCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAY----NDSDVFEYFDKRMWVC-VSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~----~~~~~~~~F~~~~wv~-vs~~~~~~~  243 (673)
                      +.++||+.++++++..|.....    +   -+.+||.+|||||+++..+.    +..-...-.+.++|.- ++.      
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k----~---n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~------   88 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTK----N---NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS------   88 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSC----C---CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------
T ss_pred             CCCcCcHHHHHHHHHHHhcCCC----C---CCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh------
Confidence            3589999999999999975542    1   23678999999999874444    4321222335566542 221      


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHh-CC-CeEEEEEcCCCCC--------CccchhhhhhhccCCCCCeEEEEEc
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASL-VG-KKFLLILDDMWTD--------DYSKWEPFHYCLKNGVRGSKILVTT  313 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-~~-kr~LlVLDdvw~~--------~~~~~~~l~~~l~~~~~gs~iivTt  313 (673)
                      ++        ......+++++....+...+ .. .+++|++|++..-        ..+.-+.|...|..+  .-++|.+|
T Consensus        89 l~--------ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg--~~~~I~~t  158 (387)
T d1qvra2          89 LL--------AGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARG--ELRLIGAT  158 (387)
T ss_dssp             -----------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTT--CCCEEEEE
T ss_pred             hh--------cccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCC--Ccceeeec
Confidence            10        01111234444444444333 33 4799999999431        011122333334332  23567776


Q ss_pred             CChhHHHhccc-------cceeecCCCCccccc
Q 005860          314 RKETVARMMES-------IHVISIKELSEQECW  339 (673)
Q Consensus       314 r~~~v~~~~~~-------~~~~~l~~L~~~~~~  339 (673)
                      ..+.... +..       ...+.+++++.+++.
T Consensus       159 T~~ey~~-~e~d~al~rrF~~v~v~ep~~~~~~  190 (387)
T d1qvra2         159 TLDEYRE-IEKDPALERRFQPVYVDEPTVEETI  190 (387)
T ss_dssp             CHHHHHH-HTTCTTTCSCCCCEEECCCCHHHHH
T ss_pred             CHHHHHH-hcccHHHHHhcccccCCCCcHHHHH
Confidence            6655543 222       466788888888765

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.77  E-value=2.6e-06  Score=75.35  Aligned_cols=66  Identities=20%  Similarity=0.222  Sum_probs=38.0

Q ss_pred             HHHHhhhCCccceeeeccccccccccchhhh---ccccccccccccceecCCCCcccch-hhhcCCCccEEEeccCC
Q 005860          535 LQSLFDQLKCLRALRIATLMNTWDVNSTNKI---LKGIEKLIHLRYLRLVGLGTEELPE-TCCELLNLQVLEIEQCT  607 (673)
Q Consensus       535 ~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~l---p~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~L~l~~c~  607 (673)
                      ++..+..++.|++|+|++       +.+..+   +..+..+++|++|+|++|.++.+++ ...+..+|+.|++++++
T Consensus        57 l~~~~~~~~~L~~L~Ls~-------N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Np  126 (162)
T d1koha1          57 LRIIEENIPELLSLNLSN-------NRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNS  126 (162)
T ss_dssp             HHHHHHHCTTCCCCCCCS-------SCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTST
T ss_pred             hHHHHHhCCCCCEeeCCC-------ccccCCchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCC
Confidence            444455666777777777       665543   3345556666666666666666654 22223456666666654

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.68  E-value=4.2e-05  Score=72.70  Aligned_cols=111  Identities=20%  Similarity=0.189  Sum_probs=63.5

Q ss_pred             CCcceechhhHHHHHHHhccCC----------cccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC
Q 005860          168 VSEIRGRDEEKSSLKSKLLCES----------SEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       168 ~~~~vGr~~~~~~l~~~L~~~~----------~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      -.+++|.++.+++|.++|..-.          ...+....+.+.++|++|+||||+|+++++..     .-..+++..+.
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~-----~~~~~~~~~~~   87 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL-----GYDILEQNASD   87 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT-----TCEEEEECTTS
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH-----Hhhhhcccccc
Confidence            3589999999999999885310          00012345678999999999999999999842     22345666665


Q ss_pred             cccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCCC
Q 005860          238 PFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDMW  286 (673)
Q Consensus       238 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdvw  286 (673)
                      ..+...+-. ..+.............  .........++..++++|++-
T Consensus        88 ~~~~~~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~vi~ide~~  133 (253)
T d1sxja2          88 VRSKTLLNA-GVKNALDNMSVVGYFK--HNEEAQNLNGKHFVIIMDEVD  133 (253)
T ss_dssp             CCCHHHHHH-TGGGGTTBCCSTTTTT--C----CCSSTTSEEEEECSGG
T ss_pred             chhhHHHHH-HHHHHhhcchhhhhhh--hhhhcccccccceEEEeeecc
Confidence            544443322 2222221111100000  011122345678899999983

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.65  E-value=0.00011  Score=67.37  Aligned_cols=152  Identities=9%  Similarity=-0.005  Sum_probs=79.1

Q ss_pred             chhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCcc--ccccCCeEEEEEcCCcccHHHHHHHHHHH
Q 005860          174 RDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSD--VFEYFDKRMWVCVSDPFDELRIAKAIIEA  251 (673)
Q Consensus       174 r~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  251 (673)
                      -+...+++.+.+.....      ...+-++|+.|+||||+|+.+.+..-  ......     ......+...+.......
T Consensus         7 ~~~~~~~l~~~~~~~~l------~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~-----~~~~~~~~~~i~~~~~~~   75 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGRG------HHALLIQALPGMGDDALIYALSRYLLCQQPQGHK-----SCGHCRGCQLMQAGTHPD   75 (207)
T ss_dssp             GHHHHHHHHHHHHTTCC------CSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTB-----CCSCSHHHHHHHHTCCTT
T ss_pred             cHHHHHHHHHHHHcCCc------CeEEEEECCCCCcHHHHHHHHHHhcccccccccc-----cccccchhhhhhhccccc
Confidence            34556777777765442      34588999999999999987765210  000000     000011111111000000


Q ss_pred             hhC----CCCCcCcHHHHHHHHHHHh-----CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCChh-HHHh
Q 005860          252 LEG----FVPTVGELNSLLESIRASL-----VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKET-VARM  321 (673)
Q Consensus       252 l~~----~~~~~~~~~~~~~~l~~~l-----~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~~-v~~~  321 (673)
                      +..    ........++... +.+.+     .+++-++|+||+..-.......+...+......+.+|+||++.+ +...
T Consensus        76 ~~~~~~~~~~~~i~~~~ir~-l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~t  154 (207)
T d1a5ta2          76 YYTLAPEKGKNTLGVDAVRE-VTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLAT  154 (207)
T ss_dssp             EEEECCCTTCSSBCHHHHHH-HHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHH
T ss_pred             cchhhhhhcccccccchhhH-HhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhh
Confidence            000    0011112233222 22222     35677999999966566667778888877778889888887653 3222


Q ss_pred             c-cccceeecCCCCccc
Q 005860          322 M-ESIHVISIKELSEQE  337 (673)
Q Consensus       322 ~-~~~~~~~l~~L~~~~  337 (673)
                      + .-...+.+.+++.++
T Consensus       155 I~SRc~~i~~~~~~~~~  171 (207)
T d1a5ta2         155 LRSRCRLHYLAPPPEQY  171 (207)
T ss_dssp             HHTTSEEEECCCCCHHH
T ss_pred             hcceeEEEecCCCCHHH
Confidence            2 224566666665443

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=2.5e-05  Score=68.83  Aligned_cols=89  Identities=20%  Similarity=0.089  Sum_probs=68.5

Q ss_pred             hccccccccccccceecCCCCccc---chhhhcCCCccEEEeccCCCCccccc-cccccccCCeeeccccccccccc---
Q 005860          565 ILKGIEKLIHLRYLRLVGLGTEEL---PETCCELLNLQVLEIEQCTSLKRLPL-GIGKLVNLRHLTYDDSCLEFIPK---  637 (673)
Q Consensus       565 lp~~i~~L~~Lr~L~L~~~~i~~L---P~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~Lr~L~l~~~~l~~lP~---  637 (673)
                      ++.....+++|++|+|++|.++.+   +..+..+++|++|+++++. +..++. ......+|+.|++.+|.+.....   
T Consensus        57 l~~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~-i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~  135 (162)
T d1koha1          57 LRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNE-LKSERELDKIKGLKLEELWLDGNSLSDTFRDQS  135 (162)
T ss_dssp             HHHHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSC-CCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHH
T ss_pred             hHHHHHhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCc-cccchhhhhhhccccceeecCCCCcCcCcccch
Confidence            333345788999999999998876   4567889999999999966 888885 33344578999999998865432   


Q ss_pred             -----cCCCCCCCCcCCeeEEc
Q 005860          638 -----GIQRLTNLRTLSEFVVV  654 (673)
Q Consensus       638 -----~i~~L~~L~~L~~~~~~  654 (673)
                           -+..+++|+.|++-.+.
T Consensus       136 ~y~~~i~~~~P~L~~LDg~~v~  157 (162)
T d1koha1         136 TYISAIRERFPKLLRLDGHELP  157 (162)
T ss_dssp             HHHHHHHTTSTTCCEETTEECC
T ss_pred             hHHHHHHHHCCCCCEECcCCCc
Confidence                 24678999999988773

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.43  E-value=0.00017  Score=67.68  Aligned_cols=50  Identities=26%  Similarity=0.361  Sum_probs=38.3

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.+..++.|..++......  ....+-+.++|++|+||||+|+.+.+.
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~--~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMR--GEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHH--TCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHHHHhc--CCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            57999999999999888532110  122345779999999999999999884

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.34  E-value=0.00027  Score=66.45  Aligned_cols=48  Identities=15%  Similarity=0.063  Sum_probs=35.1

Q ss_pred             CcceechhhHHHHHHHhc-------cCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLL-------CESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~-------~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|..++++.++....       ...    ....+-|.++|++|+|||++|+++++.
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~----~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSD----RTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCS----SCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccC----CCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            458888777766665442       111    234677889999999999999999985

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.28  E-value=4.6e-05  Score=78.89  Aligned_cols=40  Identities=8%  Similarity=0.071  Sum_probs=17.1

Q ss_pred             cccccchhhhccchhhhhhhhhHHHHhhhCCccceeeecc
Q 005860          513 KAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIAT  552 (673)
Q Consensus       513 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~  552 (673)
                      .++++++|.+.+|.....-...+...+...++|+.|+|++
T Consensus        25 ~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~   64 (460)
T d1z7xw1          25 LLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRS   64 (460)
T ss_dssp             HHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTT
T ss_pred             hCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcC
Confidence            3445555555544321111122333344445555555554

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.14  E-value=0.0012  Score=59.58  Aligned_cols=102  Identities=14%  Similarity=-0.046  Sum_probs=63.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccc--cccCCeEEEEEcC-CcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHh
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDV--FEYFDKRMWVCVS-DPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASL  273 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~vs-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  273 (673)
                      ..-+.++|.+|+||||+|..+.+....  ..|.| .+++.-. ....++++ +++.+.+....                .
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~~~----------------~   76 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSP----------------E   76 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCC----------------S
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhhCc----------------c
Confidence            678999999999999999887764211  12333 3333221 12223322 22333332211                1


Q ss_pred             CCCeEEEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          274 VGKKFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       274 ~~kr~LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      .+++=++|+|++..-+...++.+...+.....++.+|++|.+.
T Consensus        77 ~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          77 LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCCh
Confidence            2455589999997777778888888888777788887777764

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.06  E-value=0.00032  Score=65.71  Aligned_cols=50  Identities=26%  Similarity=0.401  Sum_probs=38.4

Q ss_pred             CcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++||-++.++++..++......  ...++-+-++|++|+||||+|+.+++.
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~--~~~~~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKAR--KEPLEHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTS--SSCCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhc--CCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999988887532210  123455779999999999999999884

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=96.89  E-value=0.00083  Score=63.29  Aligned_cols=97  Identities=18%  Similarity=0.158  Sum_probs=55.5

Q ss_pred             CcceechhhHHHHHHH---hccCCc-cc-ccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHH
Q 005860          169 SEIRGRDEEKSSLKSK---LLCESS-EE-IINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~---L~~~~~-~~-~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      ++++|.++.+++|.+.   +..... .. +....+-+.++|++|+|||++|+.+.+..  ..+   .+.+..++-.+   
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~--~~~---~~~i~~~~l~~---   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA--KVP---FFTISGSDFVE---   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH--TCC---EEEECSCSSTT---
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc--CCC---EEEEEhHHhhh---
Confidence            5799999888777554   322110 00 11234668899999999999999999842  212   23333322111   


Q ss_pred             HHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeEEEEEcCC
Q 005860          244 IAKAIIEALEGFVPTVGELNSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       244 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                                 .. .......+...+...-+..+++|++||+
T Consensus        84 -----------~~-~g~~~~~l~~~f~~A~~~~P~il~iDei  113 (256)
T d1lv7a_          84 -----------MF-VGVGASRVRDMFEQAKKAAPCIIFIDEI  113 (256)
T ss_dssp             -----------SC-CCCCHHHHHHHHHHHHTTCSEEEEETTH
T ss_pred             -----------cc-hhHHHHHHHHHHHHHHHcCCEEEEEECh
Confidence                       00 0111233334444444678899999998

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.85  E-value=0.0007  Score=64.09  Aligned_cols=52  Identities=19%  Similarity=0.229  Sum_probs=37.2

Q ss_pred             CcceechhhHHHHHHHhcc----CCc--ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLC----ESS--EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~----~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.+..+++|.+.+..    ...  ..+....+-|.++|++|+|||++|+++.+.
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~   61 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE   61 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHH
Confidence            4689999999888886421    100  001123456889999999999999999984

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=96.72  E-value=0.00075  Score=66.89  Aligned_cols=115  Identities=17%  Similarity=0.170  Sum_probs=64.8

Q ss_pred             ccccccchhhhccchhhhh-hhhhHHHHhhhCCccceeeeccccccccccchh-----hhccccccccccccceecCCCC
Q 005860          512 FKAKNLRSLFINNTLIQVS-LTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KILKGIEKLIHLRYLRLVGLGT  585 (673)
Q Consensus       512 ~~~~~Lr~L~l~~~~~~~~-~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~lp~~i~~L~~Lr~L~L~~~~i  585 (673)
                      ...++|++|.+.++..... ....+...+...++|+.|++++       +.+.     .+...+...++|++|+|++|.+
T Consensus       183 ~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~-------N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n~i  255 (344)
T d2ca6a1         183 QSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQD-------NTFTHLGSSALAIALKSWPNLRELGLNDCLL  255 (344)
T ss_dssp             HHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCS-------SCCHHHHHHHHHHHGGGCTTCCEEECTTCCC
T ss_pred             hhhhhhcccccccccccccccccchhhhhcchhhhccccccc-------ccccccccccccccccccccchhhhhhcCcc
Confidence            3456677777766653211 1222344456667777777776       5432     2445566667777777777765


Q ss_pred             ccc-----chhhhc--CCCccEEEeccCCCCcc-----cccccc-ccccCCeeecccccccc
Q 005860          586 EEL-----PETCCE--LLNLQVLEIEQCTSLKR-----LPLGIG-KLVNLRHLTYDDSCLEF  634 (673)
Q Consensus       586 ~~L-----P~~i~~--L~~L~~L~l~~c~~l~~-----lP~~i~-~L~~Lr~L~l~~~~l~~  634 (673)
                      ..-     -..+..  .+.|++|++++|. +..     +...+. ++++|++|++++|.+..
T Consensus       256 ~~~g~~~l~~~l~~~~~~~L~~L~ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~l~~N~~~~  316 (344)
T d2ca6a1         256 SARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNRFSE  316 (344)
T ss_dssp             CHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSBSCT
T ss_pred             CchhhHHHHHHhhhccCCCCCEEECCCCc-CChHHHHHHHHHHHccCCCCCEEECCCCcCCC
Confidence            432     122222  2457777777754 432     344442 56677777777766543

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.72  E-value=0.0016  Score=60.88  Aligned_cols=52  Identities=29%  Similarity=0.350  Sum_probs=35.2

Q ss_pred             CcceechhhHHHHHHHh---ccCCc-cc-ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKL---LCESS-EE-IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L---~~~~~-~~-~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++|.++.++.|.+.+   ..... .+ +....+-|.++|++|+|||+||+++.+.
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH
Confidence            47899998877665533   21110 00 0122456889999999999999999984

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=96.67  E-value=0.00063  Score=67.46  Aligned_cols=112  Identities=20%  Similarity=0.263  Sum_probs=75.8

Q ss_pred             ccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchhh------hccccccccccccceecCCCCc-
Q 005860          514 AKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTNK------ILKGIEKLIHLRYLRLVGLGTE-  586 (673)
Q Consensus       514 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~------lp~~i~~L~~Lr~L~L~~~~i~-  586 (673)
                      .+.|+.+.+.++.........+...+...+.|+.|++++       +.+..      +...+...++|++|+|++|.+. 
T Consensus       157 ~~~L~~l~l~~n~i~~~~~~~l~~~l~~~~~L~~L~L~~-------n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~  229 (344)
T d2ca6a1         157 APPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQ-------NGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTH  229 (344)
T ss_dssp             CCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCS-------SCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHH
T ss_pred             Ccccceeecccccccccccccccchhhhhhhhccccccc-------ccccccccccchhhhhcchhhhcccccccccccc
Confidence            455666666665432223334556677788899999888       65432      3456778888999999988753 


Q ss_pred             ----ccchhhhcCCCccEEEeccCCCCcc-----ccccccc--cccCCeeeccccccc
Q 005860          587 ----ELPETCCELLNLQVLEIEQCTSLKR-----LPLGIGK--LVNLRHLTYDDSCLE  633 (673)
Q Consensus       587 ----~LP~~i~~L~~L~~L~l~~c~~l~~-----lP~~i~~--L~~Lr~L~l~~~~l~  633 (673)
                          .+...+...++|++|+|++|. +..     +=..+..  ..+|++|++++|.+.
T Consensus       230 ~g~~~L~~~l~~~~~L~~L~Ls~n~-i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~i~  286 (344)
T d2ca6a1         230 LGSSALAIALKSWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNEIE  286 (344)
T ss_dssp             HHHHHHHHHGGGCTTCCEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSCCB
T ss_pred             cccccccccccccccchhhhhhcCc-cCchhhHHHHHHhhhccCCCCCEEECCCCcCC
Confidence                356677788999999999886 543     2122322  356899999888765

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.64  E-value=0.004  Score=56.96  Aligned_cols=56  Identities=23%  Similarity=0.236  Sum_probs=34.4

Q ss_pred             HHHHHHHhCCCeEEEEEcCCCCC-CccchhhhhhhccC--CCCCeEEEEEcCChhHHHh
Q 005860          266 LESIRASLVGKKFLLILDDMWTD-DYSKWEPFHYCLKN--GVRGSKILVTTRKETVARM  321 (673)
Q Consensus       266 ~~~l~~~l~~kr~LlVLDdvw~~-~~~~~~~l~~~l~~--~~~gs~iivTtr~~~v~~~  321 (673)
                      +-.+.+.|..++-+|++|.--.. |...-..+...+..  ...|..||++|.+.+++..
T Consensus       153 RvaIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~~~a~~  211 (230)
T d1l2ta_         153 RVAIARALANNPPIILADQPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDINVARF  211 (230)
T ss_dssp             HHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHTT
T ss_pred             HHHHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCHHHHHh
Confidence            44566677778889999986321 12222223333332  2457889999999888853

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.62  E-value=0.00077  Score=60.63  Aligned_cols=40  Identities=25%  Similarity=0.228  Sum_probs=29.5

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++.|.+......    ..+.-+|+|.|..|+||||||+.+...
T Consensus         6 ~~~~~~~~~~~~~----~~~~~iIgI~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_           6 RIDFLCKTILAIK----TAGRLVLGIDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             HHHHHHHHHHTSC----CSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc----CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3455555554433    245779999999999999999999874

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=96.60  E-value=0.00085  Score=65.44  Aligned_cols=122  Identities=12%  Similarity=0.137  Sum_probs=64.8

Q ss_pred             CcceechhhHHHHHHHhccCCc--ccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHH
Q 005860          169 SEIRGRDEEKSSLKSKLLCESS--EEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAK  246 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  246 (673)
                      ..++|-++.++.+...+.....  ........++.++|+.|+|||.||+.+..-  +   +...+-++.+.-.+...   
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~--l---~~~~i~~d~s~~~~~~~---   93 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA--L---GIELLRFDMSEYMERHT---   93 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH--H---TCEEEEEEGGGCSSSSC---
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh--c---cCCeeEeccccccchhh---
Confidence            4678888888888766531100  000234668899999999999999999873  2   23334444332111000   


Q ss_pred             HHHHHhhCCCCCcCcHHHHHHHHHHH-hCCCeEEEEEcCCCCCCccchhhhhhhcc
Q 005860          247 AIIEALEGFVPTVGELNSLLESIRAS-LVGKKFLLILDDMWTDDYSKWEPFHYCLK  301 (673)
Q Consensus       247 ~i~~~l~~~~~~~~~~~~~~~~l~~~-l~~kr~LlVLDdvw~~~~~~~~~l~~~l~  301 (673)
                        ...+-+..+....... ...+... .+....+++||++...+...|+.+...+.
T Consensus        94 --~~~l~g~~~gy~g~~~-~~~l~~~~~~~~~~vvl~DeieKa~~~V~~~lLqild  146 (315)
T d1r6bx3          94 --VSRLIGAPPGYVGFDQ-GGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMD  146 (315)
T ss_dssp             --CSSSCCCCSCSHHHHH-TTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHH
T ss_pred             --hhhhcccCCCcccccc-CChhhHHHHhCccchhhhcccccccchHhhhhHHhhc
Confidence              0011111111000000 0111122 23556789999997666666777666654

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.57  E-value=0.00046  Score=61.48  Aligned_cols=24  Identities=21%  Similarity=0.234  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++.|.|.|+.|+||||||+.+.+.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            688999999999999999998873

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.55  E-value=0.0035  Score=56.51  Aligned_cols=88  Identities=19%  Similarity=0.126  Sum_probs=51.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH--HHHHHHHHHHhhCCC---CCcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE--LRIAKAIIEALEGFV---PTVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~---~~~~~~~~~~~~l  269 (673)
                      ....||.++|+.|+||||.+-++...  .+ .....+.+-..+.+.+  .+-++...+.++.+-   .+..+........
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~--~~-~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~   83 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQ--FE-QQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDA   83 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHH--HH-TTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HH-HCCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHH
Confidence            45789999999999999987555553  22 2234555555566665  456667777777652   2333443333333


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      .+..+ ...=+|++|=.
T Consensus        84 ~~~a~~~~~d~ilIDTa  100 (211)
T d2qy9a2          84 IQAAKARNIDVLIADTA  100 (211)
T ss_dssp             HHHHHHTTCSEEEECCC
T ss_pred             HHHHHHcCCCEEEeccC
Confidence            32222 22336777755

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=96.50  E-value=0.00045  Score=60.57  Aligned_cols=24  Identities=29%  Similarity=0.414  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|++|+|..|+|||||++++.+.
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~   25 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPA   25 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999999873

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.43  E-value=0.00066  Score=58.33  Aligned_cols=22  Identities=36%  Similarity=0.446  Sum_probs=19.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ++|.|+|++|+||||||+.+..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999998765

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.42  E-value=0.0022  Score=60.79  Aligned_cols=52  Identities=23%  Similarity=0.262  Sum_probs=36.0

Q ss_pred             CcceechhhHHHHHHHhccC----Cc--ccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLCE----SS--EEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~~----~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++.|.++.+++|.+.+...    +.  ..+....+-|-++|++|.|||+||+++++.
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~   64 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   64 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHH
Confidence            45888888877777665311    00  001133456889999999999999999985

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.38  E-value=0.00079  Score=59.49  Aligned_cols=37  Identities=14%  Similarity=-0.014  Sum_probs=27.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccc-cCCeEEEE
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFE-YFDKRMWV  233 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv  233 (673)
                      ....+|.|+|++|+||||+|+.+...  ... +++...++
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~--L~~~~~~~~~~~   41 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVT--LNQQGGRSVSLL   41 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHH--HHHHCSSCEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HhhcCCCchhhh
Confidence            34579999999999999999999884  333 34555554

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.00049  Score=59.84  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|+|++|+||||+|+.+.+.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            35888899999999999999884

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.36  E-value=0.0011  Score=67.86  Aligned_cols=107  Identities=19%  Similarity=0.205  Sum_probs=70.8

Q ss_pred             ccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----hhccccccccccccceecCCCCcc---
Q 005860          516 NLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KILKGIEKLIHLRYLRLVGLGTEE---  587 (673)
Q Consensus       516 ~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~lp~~i~~L~~Lr~L~L~~~~i~~---  587 (673)
                      +|++|++.++..   ....+...+..++++++|+|++       |.+.     .++..+..+++|++|+|++|.+..   
T Consensus         3 ~l~~ld~~~~~i---~~~~~~~l~~~l~~l~~L~L~~-------~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~   72 (460)
T d1z7xw1           3 DIQSLDIQCEEL---SDARWAELLPLLQQCQVVRLDD-------CGLTEARCKDISSALRVNPALAELNLRSNELGDVGV   72 (460)
T ss_dssp             EEEEEEEESCCC---CHHHHHHHHHHHTTCSEEEEES-------SCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHH
T ss_pred             CCCEEEeeCCcC---ChHHHHHHHHhCCCCCEEEeCC-------CCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHH
Confidence            566777766653   1233445566778888888888       5432     455666778888888888887643   


Q ss_pred             --cchhhhc-CCCccEEEeccCCCCcc-----ccccccccccCCeeeccccccc
Q 005860          588 --LPETCCE-LLNLQVLEIEQCTSLKR-----LPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       588 --LP~~i~~-L~~L~~L~l~~c~~l~~-----lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                        +...+.. ..+|++|++++|. +..     ++..+..+++|++|++++|.+.
T Consensus        73 ~~l~~~l~~~~~~L~~L~L~~n~-it~~~~~~l~~~l~~~~~L~~L~L~~N~i~  125 (460)
T d1z7xw1          73 HCVLQGLQTPSCKIQKLSLQNCC-LTGAGCGVLSSTLRTLPTLQELHLSDNLLG  125 (460)
T ss_dssp             HHHHHTTCSTTCCCCEEECTTSC-CBGGGHHHHHHHTTSCTTCCEEECCSSBCH
T ss_pred             HHHHHHHhcCCCCCCEEECCCCC-ccccccccccchhhccccccccccccccch
Confidence              2222222 2468888888876 533     5666777888888888777654

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.35  E-value=0.00077  Score=59.13  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999876

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.21  E-value=0.0029  Score=61.37  Aligned_cols=123  Identities=17%  Similarity=0.255  Sum_probs=61.6

Q ss_pred             cceechhhHHHHHHHhccCCc--ccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHH
Q 005860          170 EIRGRDEEKSSLKSKLLCESS--EEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKA  247 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  247 (673)
                      .++|.++.++.+...+.....  ........++.++|+.|+|||.||+.+.+.  +-..-...+-+..+.-.+...+   
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~--l~~~~~~~~~~~~~~~~~~~~~---   98 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKHAV---   98 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH--HHSSGGGEEEECTTTCCSSGGG---
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHH--hcCCCcceEEEeccccccchhh---
Confidence            567888888777665532110  000133568899999999999999888773  2111112233333322111110   


Q ss_pred             HHHHhhCCCCC---cCcHHHHHHHHHHHhCCCeEEEEEcCCCCCCccchhhhhhhccC
Q 005860          248 IIEALEGFVPT---VGELNSLLESIRASLVGKKFLLILDDMWTDDYSKWEPFHYCLKN  302 (673)
Q Consensus       248 i~~~l~~~~~~---~~~~~~~~~~l~~~l~~kr~LlVLDdvw~~~~~~~~~l~~~l~~  302 (673)
                        ..+.+..+.   ......+...++   +....+|+||++...+...++.+...+..
T Consensus        99 --~~L~g~~~gyvG~~~~~~l~~~~~---~~p~~Vvl~DEieK~~~~v~~~ll~~l~~  151 (315)
T d1qvra3          99 --SRLIGAPPGYVGYEEGGQLTEAVR---RRPYSVILFDEIEKAHPDVFNILLQILDD  151 (315)
T ss_dssp             --GGC--------------CHHHHHH---HCSSEEEEESSGGGSCHHHHHHHHHHHTT
T ss_pred             --hhhcCCCCCCcCcccCChHHHHHH---hCCCcEEEEehHhhcCHHHHHHHHHHhcc
Confidence              001111000   001111222232   24578999999966566666666665543

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.15  E-value=0.014  Score=53.77  Aligned_cols=23  Identities=39%  Similarity=0.586  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|+|+|..|+|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            58999999999999999999884

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.06  E-value=0.0011  Score=57.99  Aligned_cols=23  Identities=35%  Similarity=0.457  Sum_probs=20.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|.|.|++|+||||+|+.+.+.
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            34779999999999999999873

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.04  E-value=0.00091  Score=59.31  Aligned_cols=23  Identities=35%  Similarity=0.431  Sum_probs=20.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|+|++|+|||||++++...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            46899999999999999999875

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.03  E-value=0.0015  Score=57.12  Aligned_cols=26  Identities=27%  Similarity=0.493  Sum_probs=23.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+++.|.|++|+||||+|+.+...
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998873

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.01  E-value=0.0016  Score=58.57  Aligned_cols=26  Identities=23%  Similarity=0.317  Sum_probs=23.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.+|.|+|++|+||||+|+.+.+.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999874

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.98  E-value=0.0017  Score=58.48  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=23.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +..+||.|.|++|+||||+|+.+.+.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            56899999999999999999999874

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=95.96  E-value=0.0026  Score=60.29  Aligned_cols=42  Identities=17%  Similarity=0.255  Sum_probs=29.0

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...+.++.+.....+  ...++.|.++|++|+||||||+.+++.
T Consensus        14 ~~~~~~~~~~~~~~~--~~~P~~ilL~GpPGtGKT~la~~la~~   55 (273)
T d1gvnb_          14 RLNDNLEELIQGKKA--VESPTAFLLGGQPGSGKTSLRSAIFEE   55 (273)
T ss_dssp             HHHHHHHHHHTTCCC--CSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccC--CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            333444444443321  245677899999999999999999984

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.90  E-value=0.0092  Score=55.97  Aligned_cols=84  Identities=18%  Similarity=0.114  Sum_probs=58.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESI  269 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l  269 (673)
                      +.-+++-|+|..|+||||||.+++..  ....-..++|++.-..++.+.     +++++...+     +....++..+.+
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~--~q~~g~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~  130 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIA  130 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHH--HHHTTCEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHH--HhcCCCEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHH
Confidence            45689999999999999999766664  333345689999988888764     455655422     224456656555


Q ss_pred             HHHhC-CCeEEEEEcCC
Q 005860          270 RASLV-GKKFLLILDDM  285 (673)
Q Consensus       270 ~~~l~-~kr~LlVLDdv  285 (673)
                      ....+ ++.-|||+|.+
T Consensus       131 ~~l~~~~~~~liIiDSi  147 (269)
T d1mo6a1         131 DMLIRSGALDIVVIDSV  147 (269)
T ss_dssp             HHHHHTTCEEEEEEECS
T ss_pred             HHHHhcCCCCEEEEecc
Confidence            55554 45779999988

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.90  E-value=0.0014  Score=58.69  Aligned_cols=35  Identities=17%  Similarity=0.023  Sum_probs=25.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      ..+|.++|++|+||||+|+.+...  ....+....++
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~--l~~~~~~~~~~   53 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEY--LVCHGIPCYTL   53 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHH--HHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhcCCCccch
Confidence            468899999999999999999874  33344334443

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=95.86  E-value=0.0022  Score=56.20  Aligned_cols=24  Identities=33%  Similarity=0.373  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -++|.|.|++|+||||+|+.+.+.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            479999999999999999999874

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.86  E-value=0.0017  Score=56.70  Aligned_cols=23  Identities=30%  Similarity=0.317  Sum_probs=21.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|++|+|..|+|||||+.++...
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~   24 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAA   24 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            58999999999999999988874

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=95.79  E-value=0.0017  Score=57.05  Aligned_cols=24  Identities=17%  Similarity=0.271  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|.|.|.+|+||||+|+.+.+.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998883

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.79  E-value=0.0017  Score=57.68  Aligned_cols=23  Identities=30%  Similarity=0.712  Sum_probs=21.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|.|.|+.|+||||+++.+.+.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999998763

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=95.77  E-value=0.0018  Score=56.25  Aligned_cols=21  Identities=43%  Similarity=0.621  Sum_probs=19.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+||+|+||||+|+.+.+.
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678899999999999999885

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.76  E-value=0.0021  Score=58.34  Aligned_cols=24  Identities=25%  Similarity=0.319  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.+|.++|.+|+||||+|+++.+.
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999874

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.66  E-value=0.0025  Score=55.95  Aligned_cols=25  Identities=28%  Similarity=0.433  Sum_probs=22.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +...+|.++|++|+||||+|+.+..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999998866

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.65  E-value=0.0022  Score=55.96  Aligned_cols=21  Identities=29%  Similarity=0.485  Sum_probs=18.1

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++||+|+||||+|+.+.+.
T Consensus         4 IvliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            445699999999999999874

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=95.63  E-value=0.0023  Score=56.00  Aligned_cols=25  Identities=32%  Similarity=0.403  Sum_probs=21.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..-.|.|.|++|+||||+|+.+.+.
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4457889999999999999999873

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=95.62  E-value=0.011  Score=56.62  Aligned_cols=79  Identities=16%  Similarity=0.160  Sum_probs=46.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCC--eEEEEEcCCcccHHHHHHHHHHHhhC--CCCCcCcHHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD--KRMWVCVSDPFDELRIAKAIIEALEG--FVPTVGELNSLLESIR  270 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~~i~~~l~~--~~~~~~~~~~~~~~l~  270 (673)
                      ..+-+|||.|..|+||||+|+.+...  ....+.  .+.-|+..+=+-..+.+..  +.+..  ..+..-+.+.+...+.
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~l--L~~~~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~g~Pes~D~~~L~~~L~  153 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQAL--LSRWPEHRRVELITTDGFLHPNQVLKE--RGLMKKKGFPESYDMHRLVKFVS  153 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHH--HTTSTTCCCEEEEEGGGGBCCHHHHHH--HTCTTCTTSGGGBCHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHH--HhhhcCCCceEEEeeeeeECCchHHHH--hcCCccCCchHhhhHHHHHHHHH
Confidence            56789999999999999999888763  333231  2334443332222222211  11111  1234567778888777


Q ss_pred             HHhCCCe
Q 005860          271 ASLVGKK  277 (673)
Q Consensus       271 ~~l~~kr  277 (673)
                      ....++.
T Consensus       154 ~lk~g~~  160 (308)
T d1sq5a_         154 DLKSGVP  160 (308)
T ss_dssp             HHTTTCS
T ss_pred             HHHcCCC
Confidence            7776654

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.58  E-value=0.0026  Score=56.03  Aligned_cols=21  Identities=43%  Similarity=0.570  Sum_probs=19.6

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|+|++|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            899999999999999999874

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.57  E-value=0.011  Score=55.45  Aligned_cols=83  Identities=18%  Similarity=0.108  Sum_probs=58.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIR  270 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  270 (673)
                      .-+++-|+|.+|+||||||.++....  ...=..++|++.-..++++     +++.++...+     +..+.++..+.+.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~a--qk~g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQA--QKAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHH--HhCCCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHH
Confidence            35699999999999999997766642  2222458999998888874     5677766432     2345566666666


Q ss_pred             HHhCC-CeEEEEEcCC
Q 005860          271 ASLVG-KKFLLILDDM  285 (673)
Q Consensus       271 ~~l~~-kr~LlVLDdv  285 (673)
                      ...+. ..-|||+|-+
T Consensus       129 ~l~~~~~~~liIiDSi  144 (268)
T d1xp8a1         129 LLVRSGAIDVVVVDSV  144 (268)
T ss_dssp             HHHTTTCCSEEEEECT
T ss_pred             HHHhcCCCcEEEEecc
Confidence            65543 4568999988

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=95.56  E-value=0.0077  Score=56.49  Aligned_cols=82  Identities=18%  Similarity=0.132  Sum_probs=54.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCC-----CcCcHHHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVP-----TVGELNSLLESIRA  271 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~  271 (673)
                      -+++-|+|.+|+||||||-++...  ....=..++|++....++..     .++.++...+     ...+.++..+.+..
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~--~q~~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~  126 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  126 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHH--HHcCCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHH
Confidence            469999999999999999777765  33333568999988888764     3556655422     22344555555555


Q ss_pred             HhC-CCeEEEEEcCC
Q 005860          272 SLV-GKKFLLILDDM  285 (673)
Q Consensus       272 ~l~-~kr~LlVLDdv  285 (673)
                      ..+ +..-|||+|-+
T Consensus       127 l~~~~~~~liViDSi  141 (263)
T d1u94a1         127 LARSGAVDVIVVDSV  141 (263)
T ss_dssp             HHHHTCCSEEEEECG
T ss_pred             HHhcCCCCEEEEECc
Confidence            443 33458888887

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=95.52  E-value=0.029  Score=50.25  Aligned_cols=57  Identities=21%  Similarity=0.081  Sum_probs=36.0

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc--HHHHHHHHHHHhhCC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD--ELRIAKAIIEALEGF  255 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~  255 (673)
                      +.+||.++|+.|+||||.+-++...  .+..-..+..+++ +.+.  ..+.++...+.++.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~--~~~~g~kV~lit~-Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY--YKGKGRRPLLVAA-DTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH--HHHTTCCEEEEEC-CSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEec-ccccchHHHHHHHHHHhcCCc
Confidence            4589999999999999887555543  2233234555554 3333  345566666666654

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=95.52  E-value=0.0089  Score=53.83  Aligned_cols=59  Identities=19%  Similarity=-0.023  Sum_probs=32.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHHHHHHHhhCC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAKAIIEALEGF  255 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~  255 (673)
                      ....||.++|+.|+||||.+-++....+ ... ..+..|++.. .....+-++...+.++.+
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~-~~g-~kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYK-KKG-FKVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHH-HTT-CCEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-HCC-CceEEEEeeccccchhHHHHHhccccCcc
Confidence            3578999999999999998655544322 122 2456665532 233445556666666654

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.44  E-value=0.016  Score=54.71  Aligned_cols=24  Identities=29%  Similarity=0.499  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+...
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            358999999999999999999874

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=95.44  E-value=0.018  Score=51.80  Aligned_cols=88  Identities=16%  Similarity=0.063  Sum_probs=50.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcC-CcccHHHHHHHHHHHhhCC---CCCcCcHHHHHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS-DPFDELRIAKAIIEALEGF---VPTVGELNSLLESIR  270 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~~~~~i~~~l~~~---~~~~~~~~~~~~~l~  270 (673)
                      ..+.||.++|+.|+||||.+-++....  ..+=..+..+++. ......+-++...+.++..   ..+..+.........
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~--~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~   86 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMF--VDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV   86 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHH--HHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH--HHCCCceEEEeecccccchhHHHHHHhhhcCccccccCCCCcHHHHHHHHH
Confidence            457899999999999999875555432  2222456666553 2334456677777777654   222234433332222


Q ss_pred             --HHhCCCeEEEEEcCC
Q 005860          271 --ASLVGKKFLLILDDM  285 (673)
Q Consensus       271 --~~l~~kr~LlVLDdv  285 (673)
                        ...++.. +|++|=.
T Consensus        87 ~~~~~~~~d-~ilIDTa  102 (213)
T d1vmaa2          87 AHALARNKD-VVIIDTA  102 (213)
T ss_dssp             HHHHHTTCS-EEEEEEC
T ss_pred             HHHHHcCCC-EEEEecc
Confidence              2223333 6677754

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.39  E-value=0.017  Score=54.05  Aligned_cols=87  Identities=17%  Similarity=0.106  Sum_probs=54.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCccc-HHHHHHHHHHHhhCC-------------CCCcCcH-
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFD-ELRIAKAIIEALEGF-------------VPTVGEL-  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------------~~~~~~~-  262 (673)
                      .-++|.|..|+|||+|+..+.++. .+.+=+.++++-+.+... ..++.+++.+.-...             ..+..-. 
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~  147 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGA  147 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHH
Confidence            358999999999999998887641 123345678888887643 456666666642110             0011101 


Q ss_pred             ----HHHHHHHHHHh---CCCeEEEEEcCC
Q 005860          263 ----NSLLESIRASL---VGKKFLLILDDM  285 (673)
Q Consensus       263 ----~~~~~~l~~~l---~~kr~LlVLDdv  285 (673)
                          ....-.+.+++   +++++|+++||+
T Consensus       148 r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsl  177 (276)
T d2jdid3         148 RARVALTGLTVAEYFRDQEGQDVLLFIDNI  177 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCEEEEEECT
T ss_pred             HHHHHHHHHHHHHHHHhcCCCeEEEEEcch
Confidence                11223355555   379999999999

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.38  E-value=0.0027  Score=61.64  Aligned_cols=52  Identities=23%  Similarity=0.222  Sum_probs=35.3

Q ss_pred             CcceechhhHHHHHHHhcc----C-Cccc--ccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          169 SEIRGRDEEKSSLKSKLLC----E-SSEE--IINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       169 ~~~vGr~~~~~~l~~~L~~----~-~~~~--~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|-++.++.+...+..    . -...  .....+-+.++|++|+|||.||+++.+.
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhc
Confidence            3678988888877665511    0 0000  0123466789999999999999999984

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=95.36  E-value=0.0031  Score=55.18  Aligned_cols=21  Identities=33%  Similarity=0.395  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|++|+||||+|+.+.+.
T Consensus         5 Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568899999999999999874

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.34  E-value=0.011  Score=53.19  Aligned_cols=59  Identities=17%  Similarity=0.028  Sum_probs=39.1

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCC-cccHHHHHHHHHHHhhCC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSD-PFDELRIAKAIIEALEGF  255 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~  255 (673)
                      +..+||.++|+.|+||||.+-++....  ..+=..+..|+... .....+-++...+.++.+
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~--~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYY--QNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHH--HTTTCCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH--HHCCCcEEEEEeccccccchhhHhhcccccCce
Confidence            346799999999999999876665532  22223466665432 345566777777777665

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.21  E-value=0.0043  Score=56.47  Aligned_cols=24  Identities=17%  Similarity=0.137  Sum_probs=21.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +-||||.|..|+||||+|+.+.+.
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999988764

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=95.18  E-value=0.0043  Score=55.08  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|.|.|+.|+||||+|+.+...
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999774

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.16  E-value=0.0045  Score=55.37  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=21.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|.|++|+||||.|+.+++.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999874

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.01  E-value=0.0091  Score=55.30  Aligned_cols=41  Identities=20%  Similarity=0.241  Sum_probs=32.9

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCc
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDP  238 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  238 (673)
                      .-.++.|+|.+|+|||++|.++..+  ...+...++|++....
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~   65 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEES   65 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCC
Confidence            4579999999999999999777775  5566777889887653

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.96  E-value=0.022  Score=53.70  Aligned_cols=81  Identities=15%  Similarity=0.069  Sum_probs=46.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCC-eEEEEEcCCcccHHHHHHHHHHHhhC-------CCCCcCcHHHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFD-KRMWVCVSDPFDELRIAKAIIEALEG-------FVPTVGELNSLL  266 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l~~-------~~~~~~~~~~~~  266 (673)
                      ..+-+|||-|..|+||||||..+......+..+. .++.++..+=+-..+-...+.+....       ..+...+.+.+.
T Consensus        25 ~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll~  104 (286)
T d1odfa_          25 KCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQ  104 (286)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHHH
T ss_pred             CCCEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHHHH
Confidence            4577999999999999999988876421111222 34555544432222222334443321       235566777766


Q ss_pred             HHHHHHhCC
Q 005860          267 ESIRASLVG  275 (673)
Q Consensus       267 ~~l~~~l~~  275 (673)
                      +.+....++
T Consensus       105 ~~l~~l~~~  113 (286)
T d1odfa_         105 EVLNTIFNN  113 (286)
T ss_dssp             HHHHHHTC-
T ss_pred             HHHHHHHhh
Confidence            666666554

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=94.95  E-value=0.0058  Score=54.42  Aligned_cols=24  Identities=25%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++| |+|++|+||||+|+.+.+.
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHH
Confidence            46777 7899999999999998873

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=94.94  E-value=0.0044  Score=56.68  Aligned_cols=42  Identities=29%  Similarity=0.303  Sum_probs=30.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHh
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEAL  252 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  252 (673)
                      +||+|.|++|+||||+|+.+.++.    .|   .++      +.-+++++++...
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~----gl---~~i------StGdLlR~~a~~~   45 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEAL----QW---HLL------DSGAIYRVLALAA   45 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH----TC---EEE------EHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh----CC---cEE------CHHHHHHHHHHHH
Confidence            599999999999999999998852    22   123      4456777666543

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=94.77  E-value=0.021  Score=53.69  Aligned_cols=96  Identities=16%  Similarity=0.063  Sum_probs=51.5

Q ss_pred             HHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEE-cCCcccHHHHHHHHHHHhhCC---
Q 005860          180 SLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVC-VSDPFDELRIAKAIIEALEGF---  255 (673)
Q Consensus       180 ~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~~~~~i~~~l~~~---  255 (673)
                      ++++.|..-.      .-..++|+|..|+|||+|+..+.+... ..+-+.++.+. +.+..  ++ ..++.+.....   
T Consensus        32 r~ID~l~Pig------rGQr~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~~~iger~--~e-v~~~~~~~~~~vv~  101 (289)
T d1xpua3          32 RVLDLASPIG------RGQRGLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMVLLIDERP--EE-VTEMQRLVKGEVVA  101 (289)
T ss_dssp             HHHHHHSCCB------TTCEEEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEEEEEEECH--HH-HHHHHHHCSSEEEE
T ss_pred             eeeeeccccc------CCCeeeEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEeeceeH--HH-HHhHHhhcceEEEe
Confidence            5667665432      234689999999999999988887522 23344444443 33322  22 22333332111   


Q ss_pred             -CCCcCc-----HHHHHHHHHHHh--CCCeEEEEEcCC
Q 005860          256 -VPTVGE-----LNSLLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       256 -~~~~~~-----~~~~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                       ..+...     .....-.+.+++  +++.+||++||+
T Consensus       102 ~t~d~~~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsl  139 (289)
T d1xpua3         102 STFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSI  139 (289)
T ss_dssp             EETTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEESCH
T ss_pred             ccCCCchhHHHHHHHHHHHHHHHHHHhccCceeecCcH
Confidence             111110     011222333433  579999999998

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.74  E-value=0.009  Score=53.56  Aligned_cols=24  Identities=33%  Similarity=0.404  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.++.-
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            358999999999999999999984

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=94.72  E-value=0.014  Score=50.74  Aligned_cols=86  Identities=15%  Similarity=0.118  Sum_probs=40.6

Q ss_pred             ccccchhhhccc-hhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----hhccccccccccccceecCCCCcc
Q 005860          514 AKNLRSLFINNT-LIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KILKGIEKLIHLRYLRLVGLGTEE  587 (673)
Q Consensus       514 ~~~Lr~L~l~~~-~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~lp~~i~~L~~Lr~L~L~~~~i~~  587 (673)
                      .++|+.|.++++ .........+...+...+.|+.|+|++       +.+.     .+...+...+.|+.|+|++|.+..
T Consensus        14 ~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~-------n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~   86 (167)
T d1pgva_          14 DTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLAN-------TAISDSEARGLIELIETSPSLRVLNVESNFLTP   86 (167)
T ss_dssp             CSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTT-------SCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCH
T ss_pred             CCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccc-------cccchhHHHHHhhhhhhcccccceeeehhhcch
Confidence            345556655542 121111122333344555666666666       4322     222334444556666666665432


Q ss_pred             -----cchhhhcCCCccEEEeccC
Q 005860          588 -----LPETCCELLNLQVLEIEQC  606 (673)
Q Consensus       588 -----LP~~i~~L~~L~~L~l~~c  606 (673)
                           +-..+..-++|+.|+++++
T Consensus        87 ~g~~~l~~aL~~n~sL~~L~l~~n  110 (167)
T d1pgva_          87 ELLARLLRSTLVTQSIVEFKADNQ  110 (167)
T ss_dssp             HHHHHHHHHTTTTCCCSEEECCCC
T ss_pred             HHHHHHHHHHHhCCcCCEEECCCC
Confidence                 2223444455666666554

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=94.69  E-value=0.0079  Score=54.40  Aligned_cols=26  Identities=27%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....||-+.|++|+||||||+.+...
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~   47 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQ   47 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34679999999999999999998863

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=94.65  E-value=0.0072  Score=53.81  Aligned_cols=23  Identities=39%  Similarity=0.419  Sum_probs=20.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +-+|||+|+.|+||||+|+.+-+
T Consensus         3 p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            56999999999999999998743

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=94.57  E-value=0.013  Score=50.75  Aligned_cols=99  Identities=14%  Similarity=0.120  Sum_probs=67.0

Q ss_pred             hhHHHHhhhCCccceeeeccccccccccchhhhccccccccccccceecCCCCc-----ccchhhhcCCCccEEEeccCC
Q 005860          533 HVLQSLFDQLKCLRALRIATLMNTWDVNSTNKILKGIEKLIHLRYLRLVGLGTE-----ELPETCCELLNLQVLEIEQCT  607 (673)
Q Consensus       533 ~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~-----~LP~~i~~L~~L~~L~l~~c~  607 (673)
                      ..+.....+.+.|+.|+|++... .....+..+-..+....+|++|+|++|.+.     .+-..+...+.|+.|+|++|.
T Consensus         5 ~~l~~l~~n~~~L~~L~L~~~~~-i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~   83 (167)
T d1pgva_           5 SCINRLREDDTDLKEVNINNMKR-VSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNF   83 (167)
T ss_dssp             HHHHHHHTTCSSCCEEECTTCCS-SCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSB
T ss_pred             HHHHHHHhCCCCCcEEEeCCCCC-CCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhh
Confidence            34455566778999999987110 000112334556777788999999999864     344556677899999999986


Q ss_pred             CCcc-----ccccccccccCCeeeccccccc
Q 005860          608 SLKR-----LPLGIGKLVNLRHLTYDDSCLE  633 (673)
Q Consensus       608 ~l~~-----lP~~i~~L~~Lr~L~l~~~~l~  633 (673)
                       +..     +-..+..-++|++|+++++.+.
T Consensus        84 -i~~~g~~~l~~aL~~n~sL~~L~l~~n~~~  113 (167)
T d1pgva_          84 -LTPELLARLLRSTLVTQSIVEFKADNQRQS  113 (167)
T ss_dssp             -CCHHHHHHHHHHTTTTCCCSEEECCCCSSC
T ss_pred             -cchHHHHHHHHHHHhCCcCCEEECCCCcCC
Confidence             543     3334666688999999877544

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.49  E-value=0.0074  Score=53.15  Aligned_cols=21  Identities=29%  Similarity=0.457  Sum_probs=19.0

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999999998773

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=94.44  E-value=0.008  Score=54.90  Aligned_cols=45  Identities=24%  Similarity=0.225  Sum_probs=31.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCC
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFV  256 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~  256 (673)
                      +|+|-|++|+||||+|+.+.....    |   .++      +.-++++.++.......
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg----~---~~i------stGdl~R~~a~~~~~~~   49 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFG----F---TYL------DTGAMYRAATYMALKNQ   49 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHC----C---EEE------EHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC----C---cEE------CHHHHHHHHHHHHHHcC
Confidence            688999999999999999988421    1   123      45567777665554443

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=94.41  E-value=0.0065  Score=54.04  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4779999999999999998874

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.32  E-value=0.015  Score=54.21  Aligned_cols=34  Identities=24%  Similarity=0.247  Sum_probs=27.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      -.+++|+|+.|+|||||++.+..-   ...-.+.+++
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl---~~p~~G~I~~   61 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFL---EKPSEGAIIV   61 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS---SCCSEEEEEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcC---ccCCCCCEEE
Confidence            358999999999999999999873   3344566665

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.30  E-value=0.016  Score=53.08  Aligned_cols=32  Identities=13%  Similarity=0.164  Sum_probs=26.1

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      +++|+|+.|+|||||.+.+..-   ...-.+.+|+
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl---~~p~~G~I~~   57 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGI---VKPDRGEVRL   57 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTS---SCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHHcC---CCCCceEEEE
Confidence            7889999999999999999994   3344566766

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.30  E-value=0.0083  Score=52.95  Aligned_cols=23  Identities=17%  Similarity=0.460  Sum_probs=20.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++|.|+|++|+|||||++.+.+.
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            57889999999999999998764

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=94.26  E-value=0.0084  Score=53.55  Aligned_cols=25  Identities=32%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++|.|.|++|+||||+|+.+.+.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999873

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.24  E-value=0.016  Score=53.81  Aligned_cols=24  Identities=33%  Similarity=0.454  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcc
Confidence            358999999999999999999884

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=94.23  E-value=0.017  Score=55.92  Aligned_cols=26  Identities=23%  Similarity=0.249  Sum_probs=22.5

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....+|+|.|++|+|||||..++...
T Consensus        49 ~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          49 GRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999777753

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=94.23  E-value=0.0091  Score=53.12  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=19.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.|.|.|++|+||||+|+.+...
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHHHHHH
Confidence            34557799999999999999884

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=94.23  E-value=0.011  Score=55.89  Aligned_cols=37  Identities=30%  Similarity=0.337  Sum_probs=25.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS  236 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  236 (673)
                      +.|+|+|-||+||||+|-.+...  ....-..++-|+..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~--LA~~G~rVllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSG--LHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEEEC
T ss_pred             CEEEEECCCcCCHHHHHHHHHHH--HHhCCCcEEEEecC
Confidence            68999999999999999666553  22222345566553

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=94.22  E-value=0.017  Score=55.86  Aligned_cols=26  Identities=19%  Similarity=0.188  Sum_probs=22.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+..+|+|+|.+|+|||||...+...
T Consensus        52 ~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          52 GNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999877653

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.22  E-value=0.017  Score=53.05  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.++.-
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcC
Confidence            58999999999999999999874

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.18  E-value=0.0094  Score=52.48  Aligned_cols=21  Identities=29%  Similarity=0.319  Sum_probs=19.1

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|.|++|+||||+|+.+++.
T Consensus         3 I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678899999999999999874

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.17  E-value=0.01  Score=52.30  Aligned_cols=21  Identities=33%  Similarity=0.496  Sum_probs=19.3

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999884

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.08  E-value=0.011  Score=52.71  Aligned_cols=26  Identities=27%  Similarity=0.148  Sum_probs=22.6

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ...-+|+|-|..|+||||+|+.+.+.
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999998763

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.05  E-value=0.018  Score=53.50  Aligned_cols=24  Identities=29%  Similarity=0.427  Sum_probs=21.5

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl   64 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRF   64 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            358999999999999999999873

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.99  E-value=0.02  Score=52.46  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|.|||||.+.+..-
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl   55 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGL   55 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            358999999999999999999884

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.96  E-value=0.0087  Score=53.27  Aligned_cols=21  Identities=29%  Similarity=0.594  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|++|+|||||++.+.+.
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            679999999999999998773

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=93.88  E-value=0.025  Score=48.77  Aligned_cols=109  Identities=17%  Similarity=0.128  Sum_probs=51.1

Q ss_pred             ccccchhhhccc-hhhhhhhhhHHHHhhhCCccceeeeccccccccccchh-----hhccccccccccccceecCCCC--
Q 005860          514 AKNLRSLFINNT-LIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNSTN-----KILKGIEKLIHLRYLRLVGLGT--  585 (673)
Q Consensus       514 ~~~Lr~L~l~~~-~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~-----~lp~~i~~L~~Lr~L~L~~~~i--  585 (673)
                      .++|+.|.+.+. .........+...+...++|+.|++++       +.+.     .+-..+.....|+++++++|.+  
T Consensus        16 ~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~-------n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~   88 (166)
T d1io0a_          16 DPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVG-------TRSNDPVAFALAEMLKVNNTLKSLNVESNFISG   88 (166)
T ss_dssp             CTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTT-------SCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCH
T ss_pred             CCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccC-------CcccHHHHHHHHHHHhhcccchhhhhccccccc
Confidence            345555555442 111112222333444556666666666       4321     2333344455666666666553  


Q ss_pred             ---cccchhhhcCCCccEEEeccCC-CCc-----cccccccccccCCeeeccc
Q 005860          586 ---EELPETCCELLNLQVLEIEQCT-SLK-----RLPLGIGKLVNLRHLTYDD  629 (673)
Q Consensus       586 ---~~LP~~i~~L~~L~~L~l~~c~-~l~-----~lP~~i~~L~~Lr~L~l~~  629 (673)
                         ..+-..+...++|+.++|+.|. .+.     .+-..+.+.++|++|+++.
T Consensus        89 ~g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~  141 (166)
T d1io0a_          89 SGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHF  141 (166)
T ss_dssp             HHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCC
T ss_pred             hhHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcC
Confidence               2233445555666665554332 121     2333444555666666543

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=93.86  E-value=0.045  Score=51.18  Aligned_cols=86  Identities=15%  Similarity=0.060  Sum_probs=48.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH-HHHHHHHHHHhhC---------CCCCcCc---HHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE-LRIAKAIIEALEG---------FVPTVGE---LNS  264 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~~~~~i~~~l~~---------~~~~~~~---~~~  264 (673)
                      .-++|+|..|+|||+|+..+...  ...+-+.++++-+.+.... .++..++.+.=..         .+.....   .-.
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~  145 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPY  145 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHH
T ss_pred             ceEeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHH
Confidence            34899999999999999764443  2344467788887775432 2333333222000         0111110   112


Q ss_pred             HHHHHHHHh--CCCeEEEEEcCC
Q 005860          265 LLESIRASL--VGKKFLLILDDM  285 (673)
Q Consensus       265 ~~~~l~~~l--~~kr~LlVLDdv  285 (673)
                      ....+.+++  +++++|+++||+
T Consensus       146 ~a~tiAEyfrd~G~~Vlll~Dsl  168 (276)
T d1fx0a3         146 TGAALAEYFMYRERHTLIIYDDL  168 (276)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEECH
T ss_pred             HHHHHHHHHHHcCCceeEEeecc
Confidence            223333444  489999999999

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.75  E-value=0.013  Score=51.95  Aligned_cols=22  Identities=36%  Similarity=0.548  Sum_probs=19.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|+.|+|||||++.+.+.
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            3789999999999999998774

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=93.69  E-value=0.015  Score=53.30  Aligned_cols=24  Identities=33%  Similarity=0.391  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+.--
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl   54 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLL   54 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            358999999999999999999985

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.67  E-value=0.025  Score=51.57  Aligned_cols=24  Identities=29%  Similarity=0.403  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~Gl   49 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAGL   49 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcC
Confidence            358999999999999999999874

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.62  E-value=0.014  Score=51.34  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=19.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++| |.|++|+||||+|+.+.+.
T Consensus         3 mrIv-l~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           3 IRMV-LIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             eEEE-EECCCCCCHHHHHHHHHHH
Confidence            4555 7799999999999999873

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=93.59  E-value=0.025  Score=52.10  Aligned_cols=24  Identities=29%  Similarity=0.310  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~gl   51 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLERF   51 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999763

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.58  E-value=0.014  Score=51.20  Aligned_cols=21  Identities=38%  Similarity=0.482  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999999874

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=93.57  E-value=0.017  Score=56.44  Aligned_cols=45  Identities=24%  Similarity=0.262  Sum_probs=32.2

Q ss_pred             cCCcceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHh
Q 005860          167 DVSEIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAY  218 (673)
Q Consensus       167 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  218 (673)
                      +-.+++|.+..+..|.-.+....       ..-|.|+|.+|+||||||+.+.
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~-------~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPG-------IGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGG-------GCCEEEECCGGGCTTHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccC-------CCeEEEECCCCccHHHHHHHHH
Confidence            44689999977665543333222       1247899999999999999875

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.44  E-value=0.015  Score=51.02  Aligned_cols=23  Identities=13%  Similarity=0.455  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|+|+.|+|||||++.+...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            46889999999999999988863

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.33  E-value=0.029  Score=52.97  Aligned_cols=35  Identities=34%  Similarity=0.492  Sum_probs=26.1

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhc
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      +..+.+.+..       ++.+||.+.|-||+||||+|-.+..
T Consensus         8 ~~~~~~~~~~-------~~~~iii~sGKGGVGKTT~a~nLA~   42 (279)
T d1ihua2           8 LSALVDDIAR-------NEHGLIMLMGKGGVGKTTMAAAIAV   42 (279)
T ss_dssp             HHHHHHHHHT-------TSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhhc-------CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4445555542       4579999999999999999866655

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=93.32  E-value=0.018  Score=53.04  Aligned_cols=21  Identities=43%  Similarity=0.498  Sum_probs=19.2

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ||+|+|+.|+|||||...+..
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            799999999999999988865

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=93.23  E-value=0.027  Score=51.17  Aligned_cols=24  Identities=25%  Similarity=0.288  Sum_probs=21.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl   49 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGF   49 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999884

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.23  E-value=0.031  Score=51.36  Aligned_cols=33  Identities=27%  Similarity=0.319  Sum_probs=26.0

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|.|||||.+.+..-.   ..-.+.+.+
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl~---~p~~G~I~~   65 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGLV---RAQKGKIIF   65 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS---CCSEEEEEE
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC---CCCccEEEe
Confidence            589999999999999999999842   333455554

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=93.16  E-value=0.021  Score=54.39  Aligned_cols=38  Identities=34%  Similarity=0.357  Sum_probs=24.8

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS  236 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  236 (673)
                      -+.|+|.|-||+||||+|..+...  ....=..++-|...
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~--LA~~G~rVLlID~D   39 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAA--LAEMGKKVMIVGCD   39 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEEEC
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEecC
Confidence            367889999999999988666542  22222235555553

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=93.13  E-value=0.059  Score=51.52  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=20.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++.++|++|+|||.||+.+...
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~  146 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEA  146 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHHH
Confidence            46667999999999999999984

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.93  E-value=0.036  Score=51.45  Aligned_cols=33  Identities=24%  Similarity=0.339  Sum_probs=25.7

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEE
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWV  233 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  233 (673)
                      .+++|+|+.|.|||||++.+.--.+   .-.+.+++
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl~~---p~~G~I~~   63 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGFLK---ADEGRVYF   63 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC---CSEEEEEE
T ss_pred             CEEEEECCCCCcHHHHHHHHHCCCc---CCCcEEEE
Confidence            5899999999999999999998532   23455554

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=92.91  E-value=0.029  Score=53.42  Aligned_cols=45  Identities=20%  Similarity=0.213  Sum_probs=30.0

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDE  241 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  241 (673)
                      +..++|.+.|-||+||||+|..+...  ....=..++-|+.....+.
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~--lA~~G~rVLlvD~Dp~~~l   50 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIR--LAEQGKRVLLVSTDPASNV   50 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEECCTTCCH
T ss_pred             CCCeEEEEECCCcChHHHHHHHHHHH--HHHCCCCEEEEeCCCCCCH
Confidence            34678899999999999988666653  2222235667766544443

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.91  E-value=0.048  Score=50.03  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=31.7

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcCccccc----cCCeEEEEEcCCcccH
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYNDSDVFE----YFDKRMWVCVSDPFDE  241 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~  241 (673)
                      .-+++-|+|.+|+||||||.++........    .-..++|++....++.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   82 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRP   82 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCG
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHH
Confidence            456999999999999999966654422221    1245788887666553

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=92.87  E-value=0.038  Score=50.66  Aligned_cols=24  Identities=29%  Similarity=0.362  Sum_probs=22.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            359999999999999999999985

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=92.79  E-value=0.027  Score=51.62  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=21.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+++|+|+.|+|||||++.+..-
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl   54 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGL   54 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcC
Confidence            58999999999999999999884

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.57  E-value=0.028  Score=51.80  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++.|+|-|+-|+||||+++.+.+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH
Confidence            579999999999999999998874

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=92.53  E-value=0.049  Score=47.39  Aligned_cols=23  Identities=30%  Similarity=0.517  Sum_probs=19.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|+|.+|+|||||...+...
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            34679999999999999888764

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=92.48  E-value=0.03  Score=49.68  Aligned_cols=26  Identities=19%  Similarity=0.388  Sum_probs=22.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ++++.|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            45678999999999999999999864

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=92.46  E-value=0.029  Score=50.45  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=19.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|||+|+.|+||||.|+.+-.
T Consensus         4 ~iIgitG~igSGKStv~~~l~~   25 (208)
T d1vhta_           4 YIVALTGGIGSGKSTVANAFAD   25 (208)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEECCCcCCHHHHHHHHHH
Confidence            3899999999999999987643

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.45  E-value=0.022  Score=52.42  Aligned_cols=24  Identities=29%  Similarity=0.302  Sum_probs=21.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+.|+|-|+.|+||||+|+.+.+.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999988774

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=92.45  E-value=0.028  Score=50.46  Aligned_cols=23  Identities=22%  Similarity=0.348  Sum_probs=20.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+|.|+|++|+|||||.+.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            57889999999999999988773

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=92.39  E-value=0.13  Score=50.15  Aligned_cols=52  Identities=19%  Similarity=0.150  Sum_probs=30.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCc-cccccCCeEEEEEcCCcccHHHHHHHHH
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDS-DVFEYFDKRMWVCVSDPFDELRIAKAII  249 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~vs~~~~~~~~~~~i~  249 (673)
                      ++..|.|.+|.||||++..+.... +....-...+.+.....--...+...+.
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~  216 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLG  216 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHT
T ss_pred             CeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHH
Confidence            578899999999999885543310 1111123467777665544444444433

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=92.31  E-value=0.038  Score=54.19  Aligned_cols=45  Identities=18%  Similarity=0.049  Sum_probs=30.8

Q ss_pred             ceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          171 IRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       171 ~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.+..+.+..+.+..+.     +.-+.+.++|++|+|||++|+.+.+.
T Consensus       133 ~~~~~~~i~~~l~~~~~~~-----~~~~~~~~~g~~~~gk~~~~~~~~~~  177 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNI-----PKKRYWLFKGPIDSGKTTLAAALLEL  177 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCC-----TTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhCC-----CCcCeEEEECCCCCCHHHHHHHHHHH
Confidence            4444444444444443333     34568999999999999999999984

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.28  E-value=0.029  Score=48.01  Aligned_cols=21  Identities=38%  Similarity=0.482  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|+|.+|+|||||.+.+.++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            779999999999999888775

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.08  E-value=0.16  Score=46.61  Aligned_cols=49  Identities=22%  Similarity=0.226  Sum_probs=33.2

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCcc----ccccCCeEEEEEcCCcccHHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDSD----VFEYFDKRMWVCVSDPFDELR  243 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~----~~~~F~~~~wv~vs~~~~~~~  243 (673)
                      +.-+++.|+|.+|+||||+|.++..+..    .......++|+......+...
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER   86 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHH
Confidence            3457999999999999999965543211    112235678888777666543

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.07  E-value=0.21  Score=45.65  Aligned_cols=48  Identities=17%  Similarity=0.068  Sum_probs=34.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcCc----cccccCCeEEEEEcCCcccHH
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYNDS----DVFEYFDKRMWVCVSDPFDEL  242 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~~----~~~~~F~~~~wv~vs~~~~~~  242 (673)
                      +.-+++.|+|.+|+|||++|.++....    .....+..+.|+.....+...
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            456899999999999999997665321    123355678888877766544

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=92.04  E-value=0.032  Score=47.35  Aligned_cols=21  Identities=33%  Similarity=0.366  Sum_probs=18.3

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|.+|+|||||...+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            669999999999999887654

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=92.02  E-value=0.036  Score=49.70  Aligned_cols=22  Identities=36%  Similarity=0.474  Sum_probs=19.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -+|||+|..|+||||+|+.+-.
T Consensus         3 ~iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999987743

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.01  E-value=0.034  Score=51.46  Aligned_cols=46  Identities=20%  Similarity=0.206  Sum_probs=34.9

Q ss_pred             cceechhhHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          170 EIRGRDEEKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       170 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +|||....++++.+.+..-..    .+. -|.|.|..|+|||++|+.++..
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~----~~~-pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISC----AEC-PVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT----CCS-CEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhC----CCC-CEEEECCCCcCHHHHHHHHHHh
Confidence            478888888888887755431    122 2688999999999999999873

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=91.88  E-value=0.04  Score=47.21  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            679999999999999988764

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.75  E-value=0.047  Score=49.74  Aligned_cols=37  Identities=27%  Similarity=0.262  Sum_probs=28.3

Q ss_pred             EEEEEE-ccCCChHHHHHHHHhcCccccccCCeEEEEEcC
Q 005860          198 QIITIV-GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS  236 (673)
Q Consensus       198 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  236 (673)
                      +||+|+ |-||+||||+|..+...  ....-..++.|...
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~--la~~g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVA--LAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHH--HHhCCCCEEEEeCC
Confidence            788998 88999999999887764  33344567888764

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=91.70  E-value=0.019  Score=54.08  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=17.7

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..||||.|.+|+||||+|+.+.+
T Consensus         4 ~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           4 HPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHHH
Confidence            45999999999999999988766

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.68  E-value=0.041  Score=50.93  Aligned_cols=24  Identities=33%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -..++|+|..|+|||||++.+..-
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhc
Confidence            358999999999999999988763

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=91.61  E-value=0.032  Score=51.01  Aligned_cols=22  Identities=36%  Similarity=0.539  Sum_probs=20.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+++|+|+.|.|||||.+.+..
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999887

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.49  E-value=0.041  Score=47.18  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=19.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||+..+.++
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999877764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.48  E-value=0.054  Score=46.98  Aligned_cols=25  Identities=32%  Similarity=0.388  Sum_probs=22.2

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -...|+|+|.+|+|||||..++.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999999999864

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.45  E-value=0.042  Score=49.44  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..|+|-|+.|+||||+++.+.+.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999998884

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.43  E-value=0.045  Score=49.74  Aligned_cols=25  Identities=36%  Similarity=0.553  Sum_probs=22.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++|..|.|.-|+|||||.+++.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5899999999999999999888774

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.42  E-value=0.043  Score=49.13  Aligned_cols=22  Identities=36%  Similarity=0.534  Sum_probs=19.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|-|+-|+||||+++.+.+.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~   23 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGA   23 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999988874

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=91.39  E-value=0.074  Score=46.35  Aligned_cols=25  Identities=32%  Similarity=0.501  Sum_probs=20.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..++ |.++|.+|+|||||...+...
T Consensus        16 k~~K-I~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          16 KELR-ILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             SCEE-EEEEEETTSSHHHHHHHTCCS
T ss_pred             ceEE-EEEECCCCCCHHHHHHHHhcC
Confidence            3455 559999999999999988664

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.37  E-value=0.049  Score=46.65  Aligned_cols=21  Identities=29%  Similarity=0.574  Sum_probs=18.0

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999876653

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=91.32  E-value=0.078  Score=45.80  Aligned_cols=24  Identities=29%  Similarity=0.562  Sum_probs=20.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++ |.|+|.+|+|||||...+...
T Consensus        16 ~~k-I~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          16 EVR-ILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             CEE-EEEEESTTSSHHHHHHHHCCS
T ss_pred             EEE-EEEECCCCCCHHHHHHHHhcC
Confidence            344 679999999999999988774

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.29  E-value=0.05  Score=46.91  Aligned_cols=21  Identities=29%  Similarity=0.615  Sum_probs=18.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999877764

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.29  E-value=0.052  Score=46.82  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=19.4

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .|+|+|..|+|||||..++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999988763

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.28  E-value=0.044  Score=47.49  Aligned_cols=22  Identities=27%  Similarity=0.362  Sum_probs=18.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||+..+.++
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3679999999999999887654

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.25  E-value=0.062  Score=46.69  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=22.0

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.|+|+|.+|+|||||...+.+.
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999998865

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.23  E-value=0.045  Score=47.02  Aligned_cols=22  Identities=27%  Similarity=0.348  Sum_probs=18.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||+..+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999877654

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.20  E-value=0.15  Score=47.69  Aligned_cols=86  Identities=22%  Similarity=0.188  Sum_probs=46.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCcc-ccccC-----CeEEEEEcCCcccH-HHHHHHHHHHhhCC-------CCCcCcH-
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSD-VFEYF-----DKRMWVCVSDPFDE-LRIAKAIIEALEGF-------VPTVGEL-  262 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F-----~~~~wv~vs~~~~~-~~~~~~i~~~l~~~-------~~~~~~~-  262 (673)
                      .-++|.|..|+|||+|+..+..... ....-     ..++++-+.+..+. .++...+...-...       ..+..-. 
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~  148 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  148 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCCCHHH
Confidence            4589999999999999865554311 11111     13567767765543 34444433321100       1111100 


Q ss_pred             --------HHHHHHHHHHhCCCeEEEEEcCC
Q 005860          263 --------NSLLESIRASLVGKKFLLILDDM  285 (673)
Q Consensus       263 --------~~~~~~l~~~l~~kr~LlVLDdv  285 (673)
                              -..++.+++  ++|++|+++||+
T Consensus       149 r~~~~~~a~tiAEyfrd--~G~~VLll~Dsl  177 (285)
T d2jdia3         149 QYLAPYSGCSMGEYFRD--NGKHALIIYDDL  177 (285)
T ss_dssp             HHHHHHHHHHHHHHHHH--TTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHHHHH--cCCcEEEEEcCh
Confidence                    122333432  689999999999

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.03  E-value=0.056  Score=46.54  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=19.2

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||++.+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3789999999999999888764

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.02  E-value=0.038  Score=48.23  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=19.3

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998764

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.86  E-value=0.057  Score=47.32  Aligned_cols=22  Identities=27%  Similarity=0.381  Sum_probs=19.2

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4779999999999999888764

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.78  E-value=0.22  Score=44.30  Aligned_cols=23  Identities=35%  Similarity=0.508  Sum_probs=20.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|+|-|+.|+||||+++.+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~   25 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET   25 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999988874

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=90.77  E-value=0.083  Score=45.32  Aligned_cols=109  Identities=12%  Similarity=0.073  Sum_probs=74.5

Q ss_pred             CceEEEEEEcCC-C-----CccccccccccccchhhhccchhhhhhhhhHHHHhhhCCccceeeeccccccccccch---
Q 005860          492 EKLRHSMLVLGY-E-----ASFPISIFKAKNLRSLFINNTLIQVSLTHVLQSLFDQLKCLRALRIATLMNTWDVNST---  562 (673)
Q Consensus       492 ~~~r~l~l~~~~-~-----~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~---  562 (673)
                      +.++++.+.... .     ..+...+...++|+.|.++++.........+...+...+.++.|++.+       +.+   
T Consensus        17 ~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~-------~~~~~~   89 (166)
T d1io0a_          17 PDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVES-------NFISGS   89 (166)
T ss_dssp             TTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCS-------SCCCHH
T ss_pred             CCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhcc-------ccccch
Confidence            467777765422 2     112233446788999999998764444455666778889999999988       543   


Q ss_pred             --hhhcccccccccccccee--cCCCCc-----ccchhhhcCCCccEEEeccCC
Q 005860          563 --NKILKGIEKLIHLRYLRL--VGLGTE-----ELPETCCELLNLQVLEIEQCT  607 (673)
Q Consensus       563 --~~lp~~i~~L~~Lr~L~L--~~~~i~-----~LP~~i~~L~~L~~L~l~~c~  607 (673)
                        ..+...+...+.|+.++|  +++.+.     .+...+.+.++|+.|+++.+.
T Consensus        90 g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          90 GILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             HHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             hHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcCCC
Confidence              345567777788886555  555553     466777889999999998754

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=90.76  E-value=0.053  Score=46.73  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=18.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999877653

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.75  E-value=0.052  Score=46.86  Aligned_cols=23  Identities=30%  Similarity=0.445  Sum_probs=19.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||.+.+.++
T Consensus         6 ~Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           6 FKIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34789999999999999887764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.73  E-value=0.053  Score=46.40  Aligned_cols=21  Identities=29%  Similarity=0.434  Sum_probs=18.4

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|.+|+|||||+..+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999877654

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.68  E-value=0.054  Score=46.52  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=18.3

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|.+|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999887764

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.67  E-value=0.055  Score=46.42  Aligned_cols=22  Identities=32%  Similarity=0.475  Sum_probs=19.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||...+.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999888764

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.60  E-value=0.056  Score=46.41  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=18.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||+..+.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4689999999999999877654

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.43  E-value=0.059  Score=46.26  Aligned_cols=22  Identities=27%  Similarity=0.561  Sum_probs=18.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|-+|+|||||...+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999877664

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.27  E-value=0.062  Score=46.30  Aligned_cols=22  Identities=18%  Similarity=0.357  Sum_probs=18.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999777654

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=90.25  E-value=0.07  Score=46.47  Aligned_cols=22  Identities=27%  Similarity=0.344  Sum_probs=19.8

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|+|+|.+|+|||||..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999998874

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.24  E-value=0.064  Score=46.40  Aligned_cols=22  Identities=41%  Similarity=0.610  Sum_probs=18.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||...+.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999887653

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=90.20  E-value=0.051  Score=47.57  Aligned_cols=20  Identities=30%  Similarity=0.572  Sum_probs=18.6

Q ss_pred             EEEEccCCChHHHHHHHHhc
Q 005860          200 ITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~  219 (673)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999865

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.19  E-value=0.062  Score=46.48  Aligned_cols=23  Identities=30%  Similarity=0.551  Sum_probs=19.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||+..+.++
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34679999999999999877654

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=90.14  E-value=0.14  Score=43.93  Aligned_cols=23  Identities=30%  Similarity=0.378  Sum_probs=19.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|+|.+|+|||||..++...
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34679999999999999877664

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.08  E-value=0.064  Score=46.37  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=18.2

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -|.++|.+|+|||||+..+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999977654

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.06  E-value=0.066  Score=46.04  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=18.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||+|.+.+.++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999877764

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.96  E-value=0.067  Score=46.13  Aligned_cols=22  Identities=32%  Similarity=0.554  Sum_probs=18.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||...+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999876654

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.96  E-value=0.08  Score=48.21  Aligned_cols=37  Identities=35%  Similarity=0.310  Sum_probs=26.5

Q ss_pred             EEEEEE-ccCCChHHHHHHHHhcCccccccCCeEEEEEcC
Q 005860          198 QIITIV-GMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVS  236 (673)
Q Consensus       198 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  236 (673)
                      +||+|+ +-||+||||+|..+...  ....-..++.+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~--la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA--LGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH--HHhCCCCEEEEeCC
Confidence            689999 67999999999877764  33333456666643

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=89.89  E-value=0.075  Score=48.76  Aligned_cols=22  Identities=32%  Similarity=0.507  Sum_probs=20.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+|||.|..|+||||+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999865

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.88  E-value=0.07  Score=45.73  Aligned_cols=21  Identities=33%  Similarity=0.707  Sum_probs=18.6

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999887764

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.88  E-value=0.07  Score=45.14  Aligned_cols=22  Identities=36%  Similarity=0.560  Sum_probs=19.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999877764

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.88  E-value=0.069  Score=46.24  Aligned_cols=23  Identities=22%  Similarity=0.405  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|..|+|||||+..+.++
T Consensus         5 ~Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           5 FKVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34889999999999999877654

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.73  E-value=0.074  Score=45.60  Aligned_cols=21  Identities=29%  Similarity=0.620  Sum_probs=18.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||+|...+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            679999999999999876654

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.65  E-value=0.33  Score=42.98  Aligned_cols=23  Identities=22%  Similarity=0.124  Sum_probs=19.6

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -.++.|.|.+|+||||||.++..
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~   45 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAV   45 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHH
Confidence            46999999999999999966654

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.62  E-value=0.092  Score=44.94  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|+|..|+|||||...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45789999999999999887654

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.59  E-value=0.071  Score=47.51  Aligned_cols=23  Identities=35%  Similarity=0.407  Sum_probs=20.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +.|.|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            36899999999999999888764

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=89.55  E-value=0.088  Score=51.53  Aligned_cols=23  Identities=35%  Similarity=0.377  Sum_probs=20.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ..-+..+|+.|+|||-||+.+..
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CcceeeeCCCCccHHHHHHHHHh
Confidence            45688899999999999998876

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.46  E-value=0.087  Score=46.50  Aligned_cols=23  Identities=26%  Similarity=0.417  Sum_probs=19.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||+..+.+.
T Consensus         7 ~KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           7 FKLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEEECCCCcCHHHHHHHHhhC
Confidence            45789999999999999877764

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=89.45  E-value=0.13  Score=43.45  Aligned_cols=24  Identities=29%  Similarity=0.313  Sum_probs=21.9

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-+|.+.|.=|+||||+++.+.+.
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEecCCCccHHHHHHHHHhh
Confidence            468999999999999999999885

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.33  E-value=0.079  Score=45.91  Aligned_cols=22  Identities=41%  Similarity=0.513  Sum_probs=18.5

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||...+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999777664

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=89.25  E-value=0.079  Score=45.72  Aligned_cols=24  Identities=25%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++ |.++|.+|+|||||...+.+.
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            466 558999999999999998775

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.21  E-value=0.21  Score=45.41  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=20.1

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -.++.|.|.+|+|||++|..+..
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~   56 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCV   56 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            47999999999999999966654

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.18  E-value=0.082  Score=47.58  Aligned_cols=24  Identities=33%  Similarity=0.498  Sum_probs=21.2

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -+.|+|-|+-|+||||+++.+.+.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~   26 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKK   26 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHH
Confidence            357999999999999999998874

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=89.12  E-value=0.087  Score=44.99  Aligned_cols=21  Identities=33%  Similarity=0.474  Sum_probs=17.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568899999999999877654

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.11  E-value=0.086  Score=45.29  Aligned_cols=21  Identities=14%  Similarity=0.425  Sum_probs=17.8

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.|+|..|+|||||...+.+.
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668999999999999776654

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.10  E-value=0.095  Score=45.19  Aligned_cols=22  Identities=32%  Similarity=0.546  Sum_probs=18.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      --|.++|.+|+|||||++.+..
T Consensus         4 ~Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           4 YRVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3478999999999999988765

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.05  E-value=0.085  Score=46.16  Aligned_cols=23  Identities=39%  Similarity=0.442  Sum_probs=19.5

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||...+.++
T Consensus        10 ~Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          10 LKCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhhC
Confidence            34889999999999999877664

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.94  E-value=0.085  Score=47.06  Aligned_cols=22  Identities=27%  Similarity=0.282  Sum_probs=19.4

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.|+|.+|+|||||..++.+.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999887764

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.93  E-value=0.09  Score=45.18  Aligned_cols=23  Identities=30%  Similarity=0.371  Sum_probs=19.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||+..+.+.
T Consensus         7 fKi~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           7 FKVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34899999999999999876553

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.90  E-value=0.093  Score=45.98  Aligned_cols=20  Identities=25%  Similarity=0.434  Sum_probs=17.4

Q ss_pred             EEEEccCCChHHHHHHHHhc
Q 005860          200 ITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~  219 (673)
                      |.++|-+|+|||+|.+.+..
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            67999999999999987654

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.87  E-value=0.069  Score=46.03  Aligned_cols=22  Identities=36%  Similarity=0.578  Sum_probs=17.7

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||...+.++
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778999999999999887664

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.81  E-value=0.095  Score=46.25  Aligned_cols=19  Identities=32%  Similarity=0.490  Sum_probs=17.0

Q ss_pred             EEEEEccCCChHHHHHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFA  217 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v  217 (673)
                      -|.|+|.+|+|||||...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3679999999999999877

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=88.76  E-value=0.11  Score=45.40  Aligned_cols=24  Identities=38%  Similarity=0.563  Sum_probs=20.3

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .++ |+|+|..|+|||||..++.+.
T Consensus         8 ~~k-V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           8 AIK-VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             CEE-EEEECSTTSSHHHHHHHHHTS
T ss_pred             CCE-EEEECCCCCCHHHHHHHHHCC
Confidence            344 799999999999999888764

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=88.70  E-value=0.5  Score=43.82  Aligned_cols=54  Identities=15%  Similarity=0.083  Sum_probs=34.1

Q ss_pred             EEEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEG  254 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  254 (673)
                      .++.|.|.+|+||||+|..+.-+.-.... ..+++++.-  .+..++...++.....
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g-~~v~~~s~E--~~~~~~~~r~~~~~~~   89 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMG-KKVGLAMLE--ESVEETAEDLIGLHNR   89 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSC-CCEEEEESS--SCHHHHHHHHHHHHTT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhcc-cceeEeeec--cchhhHHhHHHHHhhc
Confidence            47889999999999999666543111222 245566544  4566666666665543

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=88.70  E-value=0.1  Score=44.16  Aligned_cols=21  Identities=24%  Similarity=0.332  Sum_probs=18.4

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+|+|.+|+|||||..++...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999888653

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.58  E-value=0.17  Score=45.44  Aligned_cols=33  Identities=30%  Similarity=0.445  Sum_probs=26.0

Q ss_pred             HHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          178 KSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       178 ~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +++|.++|. +         +...++|..|+|||||..++..+
T Consensus        86 ~~~L~~~l~-~---------kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLK-G---------KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHS-S---------SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhc-C---------CeEEEECCCCCCHHHHHHhhcch
Confidence            567777662 2         35678999999999999999775

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.51  E-value=0.13  Score=44.84  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|.+|+|||||...+.++
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35889999999999999777664

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=88.46  E-value=0.087  Score=45.78  Aligned_cols=25  Identities=16%  Similarity=0.150  Sum_probs=21.6

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ....|+|+|.+++|||||..++...
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567999999999999999888664

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.31  E-value=0.1  Score=45.12  Aligned_cols=21  Identities=38%  Similarity=0.604  Sum_probs=18.4

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||||...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999877653

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.31  E-value=0.1  Score=45.45  Aligned_cols=22  Identities=36%  Similarity=0.548  Sum_probs=19.0

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999887764

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.15  E-value=0.11  Score=45.22  Aligned_cols=21  Identities=38%  Similarity=0.483  Sum_probs=18.2

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|..|+|||+|++.+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877664

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=88.00  E-value=0.17  Score=43.35  Aligned_cols=24  Identities=33%  Similarity=0.624  Sum_probs=20.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +--|.|+|.+|+|||||+..+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            456789999999999999886654

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.90  E-value=0.12  Score=44.46  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=19.4

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .--|.++|.+|+|||||+..+.++
T Consensus         6 ~~KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           6 LFKVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            445889999999999999766553

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.85  E-value=0.13  Score=44.07  Aligned_cols=22  Identities=32%  Similarity=0.653  Sum_probs=18.6

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      -|.++|..|+|||||+..+.++
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3668899999999999887764

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.37  E-value=0.13  Score=44.45  Aligned_cols=23  Identities=17%  Similarity=0.236  Sum_probs=19.2

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.++|.+|+|||||...+.+.
T Consensus         6 ~ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           6 LRLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            34789999999999999877664

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.17  E-value=0.13  Score=45.11  Aligned_cols=21  Identities=33%  Similarity=0.441  Sum_probs=17.7

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||+|+..+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999776654

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.16  E-value=0.15  Score=47.45  Aligned_cols=25  Identities=24%  Similarity=0.181  Sum_probs=21.3

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhc
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .++|-|+|+|.+|.|||||+.++..
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHH
Confidence            4588899999999999999966643

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.13  E-value=0.69  Score=41.71  Aligned_cols=23  Identities=22%  Similarity=0.173  Sum_probs=20.3

Q ss_pred             eEEEEEEccCCChHHHHHHHHhc
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -+++.|.|+...||||+.+.+.-
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHH
Confidence            46899999999999999988765

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=86.89  E-value=0.32  Score=44.89  Aligned_cols=39  Identities=23%  Similarity=0.342  Sum_probs=27.5

Q ss_pred             hHHHHHHHhccCCcccccCCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          177 EKSSLKSKLLCESSEEIINDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       177 ~~~~l~~~L~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+.++...+....     ...--|.++|..|+|||||...++..
T Consensus        17 ~l~e~~~~l~~~~-----~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQED-----VNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTT-----CCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcC-----CCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            3445555554433     23345779999999999999999875

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.73  E-value=0.15  Score=44.79  Aligned_cols=21  Identities=24%  Similarity=0.333  Sum_probs=18.1

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |.++|.+|+|||+|...+..+
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999887553

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.49  E-value=0.1  Score=44.93  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=9.3

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      --|.|+|-+|+|||||...+..+
T Consensus         7 ~Ki~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           7 FKLLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34789999999999999766653

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=86.33  E-value=0.16  Score=45.76  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=18.6

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .-|.++|.+|+|||||.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999987754

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=85.80  E-value=0.2  Score=44.68  Aligned_cols=22  Identities=18%  Similarity=0.224  Sum_probs=19.0

Q ss_pred             EEEEEEccC-CChHHHHHHHHhc
Q 005860          198 QIITIVGMG-GIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~g-GiGKTtLa~~v~~  219 (673)
                      +.+.|.|-| ||||||++-.+..
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~   24 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ   24 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHH
Confidence            568899998 9999999877766

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=85.69  E-value=0.22  Score=46.17  Aligned_cols=21  Identities=43%  Similarity=0.683  Sum_probs=18.9

Q ss_pred             eEEEEEEccCCChHHHHHHHH
Q 005860          197 IQIITIVGMGGIGKTTLAQFA  217 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v  217 (673)
                      +|-|+|+|..|.|||||+.++
T Consensus         2 iRNv~iiGh~~~GKTtL~e~l   22 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEAL   22 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHH
Confidence            578999999999999999766

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=85.37  E-value=0.2  Score=43.11  Aligned_cols=23  Identities=26%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|.|.+|+||||||..+...
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45889999999999999876663

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.04  E-value=0.075  Score=45.07  Aligned_cols=21  Identities=38%  Similarity=0.578  Sum_probs=18.9

Q ss_pred             EEEEccCCChHHHHHHHHhcC
Q 005860          200 ITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       200 i~I~G~gGiGKTtLa~~v~~~  220 (673)
                      |+++|.+|+|||||..++...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999888753

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=84.99  E-value=0.23  Score=42.65  Aligned_cols=23  Identities=30%  Similarity=0.333  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|.|.+|+||||||..+...
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45789999999999999777663

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=84.35  E-value=0.24  Score=46.09  Aligned_cols=22  Identities=32%  Similarity=0.380  Sum_probs=17.9

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      .+..|+|.+|+||||||..+.-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            3677999999999999965543

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=84.34  E-value=0.2  Score=50.28  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=19.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcC
Q 005860          199 IITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      =|.++|+.|+|||-||+.+...
T Consensus        51 NILliGPTGvGKTlLAr~LAk~   72 (443)
T d1g41a_          51 NILMIGPTGVGKTEIARRLAKL   72 (443)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999884

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.34  E-value=0.45  Score=44.22  Aligned_cols=26  Identities=23%  Similarity=0.342  Sum_probs=23.7

Q ss_pred             CCeEEEEEEccCCChHHHHHHHHhcC
Q 005860          195 NDIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       195 ~~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      ..+.||+|+|.-+.|||||+..++..
T Consensus        30 ~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          30 QPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             SBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            45999999999999999999998874

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=83.91  E-value=0.31  Score=46.70  Aligned_cols=25  Identities=32%  Similarity=0.391  Sum_probs=22.5

Q ss_pred             CeEEEEEEccCCChHHHHHHHHhcC
Q 005860          196 DIQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       196 ~~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .+-.|.|=|.-|+||||+++.+.+.
T Consensus         5 ~~~rI~iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_           5 TIVRIYLDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHSG
T ss_pred             ceEEEEEECCccCCHHHHHHHHHHH
Confidence            3667999999999999999999985

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=83.63  E-value=0.26  Score=42.05  Aligned_cols=23  Identities=30%  Similarity=0.289  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhcC
Q 005860          198 QIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      .-|.|.|.+|+||||||..+...
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999776663

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=83.51  E-value=0.27  Score=44.23  Aligned_cols=39  Identities=23%  Similarity=0.415  Sum_probs=26.3

Q ss_pred             eEEEEEEccCCChHHHHHHH-HhcCccccccCCeEEEEEcCC
Q 005860          197 IQIITIVGMGGIGKTTLAQF-AYNDSDVFEYFDKRMWVCVSD  237 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~-v~~~~~~~~~F~~~~wv~vs~  237 (673)
                      -.++-|.|.+|+|||+||.+ +++.  ....-..++|++...
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~--~~~~~~~~~~~s~e~   65 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNG--IIEFDEPGVFVTFEE   65 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH--HHHHCCCEEEEESSS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH--HHhcCCCcccccccC
Confidence            46899999999999999965 4442  222223566776544

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=82.93  E-value=0.3  Score=46.60  Aligned_cols=24  Identities=33%  Similarity=0.351  Sum_probs=21.0

Q ss_pred             eEEEEEEccCCChHHHHHHHHhcC
Q 005860          197 IQIITIVGMGGIGKTTLAQFAYND  220 (673)
Q Consensus       197 ~~vi~I~G~gGiGKTtLa~~v~~~  220 (673)
                      +..|+|=|.-|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHH
Confidence            567999999999999999999874

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=82.88  E-value=0.28  Score=46.85  Aligned_cols=103  Identities=16%  Similarity=0.151  Sum_probs=52.9

Q ss_pred             EEEEEccCCChHHHHHHHHhcCccccccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHHHHHHHHHhCCCeE
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSDVFEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSLLESIRASLVGKKF  278 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~kr~  278 (673)
                      -|.|.|..|+||||+++++.+.  +... ..++-+.-........- ..   ..........   ...+.++..++..+=
T Consensus       168 nili~G~tgSGKTT~l~al~~~--i~~~-~rivtiEd~~El~l~~~-~~---~~~~~~~~~~---~~~~ll~~~lR~~pd  237 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEF--IPKE-ERIISIEDTEEIVFKHH-KN---YTQLFFGGNI---TSADCLKSCLRMRPD  237 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGG--SCTT-CCEEEEESSCCCCCSSC-SS---EEEEECBTTB---CHHHHHHHHTTSCCS
T ss_pred             CEEEEeeccccchHHHHHHhhh--cccc-cceeeccchhhhhcccc-cc---cceeccccch---hHHHHHHHHhccCCC
Confidence            3789999999999999999884  2111 12222211111100000 00   0000000011   234456777777777


Q ss_pred             EEEEcCCCCCCccchhhhhhhccCCCCCeEEEEEcCCh
Q 005860          279 LLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTTRKE  316 (673)
Q Consensus       279 LlVLDdvw~~~~~~~~~l~~~l~~~~~gs~iivTtr~~  316 (673)
                      .||+..+..  .+.|+.+ .....++.|  ++-|..-.
T Consensus       238 ~iivgEiR~--~ea~~~l-~a~~tGh~g--~~tT~Ha~  270 (323)
T d1g6oa_         238 RIILGELRS--SEAYDFY-NVLCSGHKG--TLTTLHAG  270 (323)
T ss_dssp             EEEESCCCS--THHHHHH-HHHHTTCSC--EEEEECCS
T ss_pred             cccCCccCc--hhHHHHH-HHHHhcCCc--EEEEECCC
Confidence            899999953  3566544 344455555  45555433

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=82.45  E-value=1.9  Score=38.36  Aligned_cols=108  Identities=16%  Similarity=0.161  Sum_probs=55.3

Q ss_pred             EEEEEccCCChHHHHHHHHhcCcc------------c-cccCCeEEEEEcCCcccHHHHHHHHHHHhhCCCCCcCcHHHH
Q 005860          199 IITIVGMGGIGKTTLAQFAYNDSD------------V-FEYFDKRMWVCVSDPFDELRIAKAIIEALEGFVPTVGELNSL  265 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~~~~------------~-~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~  265 (673)
                      ++.|.|+...||||+.+.|.-..-            . -..|+ .++..+...-+...-....          ..++.++
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d-~I~~~~~~~d~~~~~~StF----------~~el~~~  105 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFD-GIYTRIGASDDLAGGKSTF----------MVEMEEV  105 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCS-EEEEECCC------CCSHH----------HHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecc-eEEEEECCCccccCCccHH----------HHhHHHH
Confidence            788999999999999987765310            0 12333 2344443322211100000          0112222


Q ss_pred             HHHHHHHhCCCeEEEEEcCCCCCCcc-ch----hhhhhhccCCCCCeEEEEEcCChhHHHh
Q 005860          266 LESIRASLVGKKFLLILDDMWTDDYS-KW----EPFHYCLKNGVRGSKILVTTRKETVARM  321 (673)
Q Consensus       266 ~~~l~~~l~~kr~LlVLDdvw~~~~~-~~----~~l~~~l~~~~~gs~iivTtr~~~v~~~  321 (673)
                      ...+..  .+++.|+++|.+...... +=    ..+...+.  ..++++++||...++...
T Consensus       106 ~~il~~--~~~~sLvliDE~~~gT~~~eg~ala~aile~L~--~~~~~~i~tTH~~eL~~l  162 (224)
T d1ewqa2         106 ALILKE--ATENSLVLLDEVGRGTSSLDGVAIATAVAEALH--ERRAYTLFATHYFELTAL  162 (224)
T ss_dssp             HHHHHH--CCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEECCCHHHHTC
T ss_pred             HHHhcc--CCCCcEEeecccccCcchhhhcchHHHHHHHHh--hcCcceEEeeechhhhhh
Confidence            222321  367899999999653221 11    11222222  246789999998877653

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=81.88  E-value=0.32  Score=43.92  Aligned_cols=22  Identities=32%  Similarity=0.446  Sum_probs=19.4

Q ss_pred             EEEEEEccCCChHHHHHHHHhc
Q 005860          198 QIITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       198 ~vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      ++|+|+|-.++|||||+.++..
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHh
Confidence            4699999999999999987765

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=80.89  E-value=0.39  Score=41.34  Aligned_cols=21  Identities=33%  Similarity=0.335  Sum_probs=19.3

Q ss_pred             EEEEEccCCChHHHHHHHHhc
Q 005860          199 IITIVGMGGIGKTTLAQFAYN  219 (673)
Q Consensus       199 vi~I~G~gGiGKTtLa~~v~~  219 (673)
                      -|+|+|..++|||||..++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            599999999999999998875