Psyllid ID: psy11422

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------
Protein Sequence
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccEEEEEEccccccEEEEEEcccEEEEEcccccccccccccccccccccccccccccccccEEEEccEEEccHHHHHHHHHHHHHccccccccccccccccccccccHHHHcccccEEEEEccccccccccccHHHHHHHHHHcccccccccEEEccHHHHHHHHHHHHHHcccccccccEEEEEEccHHHHHHHcccccccHHHHcccccccccEEEEEEEEEEcccccccccccEEEEEEEccEEEcccccccHHHHHHcccccccEEEEEEccccccEEcEEcccccccccccccccccccccccccccccccEEEEccccccccHHHHHcHHHHcccccccccccccHHHHHHHHHccccccccccccccHHHHcccccccHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHcccHHHHHcccHHHHHcccccHHHHHHHHHHHHccHHHHHHHHHHHHcccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHccccccccccccccEEEEcccccccHHHHHHccccEEcHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccHccccHHHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHHHHHHHHHHccccccccccccccccccHHHHcccEcccccccccccccHHHHHHHHHHHHHHccccccEEEEEEEcccEEEEEEEEEccEEEEEEEcccccccccHHHccccHcccccEccccccccEEEEEcEEEccHHHHHHHHHHHHHcccccccccHHHHHccHHccccHHEcccccEEEEEEEEEcccccccccHHHHHHHHHHccccccHHHHHcccHHHHHHHHHHHHHHHccccccccEEEEEEccHHHHHHHccccccccEEEEEcccHHHHHEEEEcEEEEEcccccEcccEEEcEEEEEEEEEcccccccHHHHHHcccEEccEEEEEEcccccHHHHHHHHHHccccccEEEcccccccccccEEEccccEEEEccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHcHHHHHHHHHHHHHHHcccHHHHHHHHccHHHHHHHHHHHHHHHccHHHHHHccHHHHHHccccHHHHHHHHHHHHHcHHHHHHHHHHHHcccccccccccccccccccccEEEEEccccHccHHHHHHHHHHcccEEEEEccccccEEEEcccccHHHHHHHHccccEEcHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
msfhakkkinfsklSFRVTELKKELHRHNIayylydnpiisdnkYDQLLFELKKIEEKYpelltkdsltqhvglvggenskyVHHTFKmmsldngfsdedVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGylkqastrgdgnigenittnihiihkiplvlnikyppeLLEVRCEVLIYKKDFIKLNKYRYhlglkkftnprnaAAGILRqlnpkinknKILHFFAHGvgelrgmnmpsshSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKInikrfnlpyeidgVVYKINCLStqkklgftsraPRFALAYKFLSKEALTKIKAINIQigrtgiitpvallkpvlidgititratlhneseiyrkniqigDTVVVHrsgnvipkITSSilslrpndskifkipnicpicnskiIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQllnipkigSTTVKAFIKFINQPLHRLLISQLRDVGIywlnnpntkgnknyLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYlvkgqkpgkKLEKAIKLNIKILDEKNFVKIVKgfstetki
Flexible Loop (DISEMBL)
msfhakkkinfsklsfRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLkqastrgdgniGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLglkkftnprnAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLStqkklgftsrAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITratlhneseiyrkniqigdtvvvHRSGNVIPKitssilslrpndskifkipnICPICNSKIIYIESNLIARCSGSWIECIAQRKaglqhfssrKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAiqksklttFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNnpntkgnknyLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNylvkgqkpgkklEKAIKLnikildeknfvkivkgfstetki
Low Complexity Region (SEG)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDgnigenittnihiihkiPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Disordered region (IsUnstruct)
********INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF******
Disordered Region (DISOPRED)
***************FRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL***********LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIV**F******
Disordered Region (DISEMBL)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Disordered Region (DISPRO)
********INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
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	687	2.2.26 [Sep-21-2011]
A6SZQ8	692	DNA ligase OS=Janthinobac	yes	N/A	0.975	0.968	0.505	0.0
A4G4R4	696	DNA ligase OS=Herminiimon	yes	N/A	0.981	0.968	0.500	0.0
Q470D2	711	DNA ligase OS=Cupriavidus	yes	N/A	0.962	0.929	0.465	0.0
B2JID1	683	DNA ligase OS=Burkholderi	yes	N/A	0.975	0.980	0.476	0.0
A4JF81	691	DNA ligase OS=Burkholderi	yes	N/A	0.972	0.966	0.465	0.0
Q13XB0	688	DNA ligase OS=Burkholderi	yes	N/A	0.972	0.970	0.470	0.0
B2T5K0	688	DNA ligase OS=Burkholderi	yes	N/A	0.972	0.970	0.473	0.0
A9AIK9	691	DNA ligase OS=Burkholderi	yes	N/A	0.972	0.966	0.462	0.0
Q2SX03	691	DNA ligase OS=Burkholderi	yes	N/A	0.967	0.962	0.461	0.0
Q0BE10	691	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.965	0.464	0.0

>sp|A6SZQ8|DNLJ_JANMA DNA ligase OS=Janthinobacterium sp. (strain Marseille) GN=ligA PE=3 SV=1

 Score =  736 bits (1899), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/672 (50%), Positives = 468/672 (69%), Gaps = 2/672 (0%)

Query: 7   KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKD 66
           ++ + S  + R   L+ EL+RHN +Y++ DNP I D +YD+L  EL+ +E  +PELL  D
Sbjct: 19  EEPDASNPAARAAWLRDELNRHNYSYHVLDNPSIPDAEYDKLFRELQALETSHPELLVFD 78

Query: 67  SLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKF 126
           S TQ VG +       V H+  M+SL NGF DED+I F+KR+++ L  T+ IEY  ELKF
Sbjct: 79  SPTQRVGALALSAFPQVTHSVPMLSLGNGFEDEDIIAFDKRVSDGLNSTE-IEYATELKF 137

Query: 127 DGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI 186
           DG+A+NLRYE G L +A+TRGDG  GEN+TTNI  +  IPL L+   PP++L+VR EV++
Sbjct: 138 DGLAINLRYEDGILVEAATRGDGATGENVTTNIRTVRAIPLRLHTATPPKVLDVRGEVMM 197

Query: 187 YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246
           YK D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FFA+G+G L G  MP
Sbjct: 198 YKADLAKLNARQRDAGGKEFANPRNAAAGSLRQLDSRITAQRTLRFFAYGIGMLEGAEMP 257

Query: 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
            SHS LL+WY ++GL +C E +V+ G   L+EFYK +  KR  LPYEIDGVVYK+N +  
Sbjct: 258 PSHSALLDWYAELGLPVCAERAVVKGAAGLLEFYKAVGQKRPTLPYEIDGVVYKVNRVEQ 317

Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
           Q++LGF SRAPR+A+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+T A
Sbjct: 318 QQQLGFVSRAPRYAIAHKFPAEEALTTVQGIEVQVGRTGAITPVARLAPVLVGGVTVTNA 377

Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
           TLHNE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP D++ F +P  CP+CNS I+
Sbjct: 378 TLHNEDEVRRKDIQIGDTVIVRRAGDVIPEVVAYVPEKRPVDAQPFVMPTNCPVCNSPIV 437

Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
            +E   IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA DLY
Sbjct: 438 KLEDEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAADLY 497

Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
           K+ F+ L  LDR+++K A N++ A++KSK TT +RFIYALGIRHVGE TAKELA +F NL
Sbjct: 498 KLGFRALAELDRMADKSAQNVMAALEKSKSTTLARFIYALGIRHVGEATAKELARHFGNL 557

Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNY 606
           E + +A+EEQLL +  IG    ++   F++ PL+  LI QL+  G+ W  +      K +
Sbjct: 558 EALLQASEEQLLEVADIGPVVAQSIRSFLSDPLNMELIEQLQAAGVRWPEHVVENKPKPF 617

Query: 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
              K FV TG+L    R++A   IE  GGKV   +SK T+Y+V G   G KL KA +L I
Sbjct: 618 AG-KTFVLTGTLPTLSRDQAAEKIEAAGGKVAGSVSKKTSYVVAGADAGSKLAKAEELGI 676

Query: 667 KILDEKNFVKIV 678
            ILDE   ++++
Sbjct: 677 TILDESALLQLL 688

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.
Janthinobacterium sp. (strain Marseille) (taxid: 375286)
EC: 6EC: .EC: 5EC: .EC: 1EC: .EC: 2

>sp|A4G4R4|DNLJ_HERAR DNA ligase OS=Herminiimonas arsenicoxydans GN=ligA PE=3 SV=1

 Score =  732 bits (1890), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 338/675 (50%), Positives = 462/675 (68%), Gaps = 1/675 (0%)

Query: 4   HAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELL 63
             K+  + S  S R   L+ EL+RHN AYY+ DNPI+ D +YDQL  EL+ +E  +PELL
Sbjct: 17  QPKEIPDASDPSARAAWLRSELNRHNYAYYVLDNPIVPDAEYDQLFRELQALEASHPELL 76

Query: 64  TKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAE 123
             DS TQ VG +       V H+  M+SL NGF DEDV+ F+KR++  L   + +EY  E
Sbjct: 77  VFDSPTQRVGALALTAFPPVTHSVPMLSLGNGFEDEDVLAFDKRVSEGLNSREEVEYATE 136

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A+NLRYE G L QA+TRGDG  GEN+T NI  +  IPL L+   PP++L+VR E
Sbjct: 137 LKFDGLAINLRYEDGVLVQAATRGDGATGENVTANIRTVRAIPLRLHTNNPPKVLDVRGE 196

Query: 184 VLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243
           V++YK D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FF++G+G L G 
Sbjct: 197 VMMYKADLAKLNARQRDAGAKEFANPRNAAAGSLRQLDSRITAQRSLRFFSYGIGLLEGA 256

Query: 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303
           +MP+SHS LL+WY ++G+ +C E +V+ GV  L+EFYK  + KR  LPYEIDGVVYK+N 
Sbjct: 257 DMPASHSALLDWYAELGIPVCSERAVVRGVQGLLEFYKATSEKRPQLPYEIDGVVYKVNR 316

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
           +  Q +LGF SRAPRFA+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+
Sbjct: 317 VDQQLQLGFVSRAPRFAIAHKFPAEEALTTVQDIEVQVGRTGAITPVARLAPVLVGGVTV 376

Query: 364 TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNS 423
           T ATLHNE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP  ++ F +P+ CP+C S
Sbjct: 377 TNATLHNEDEVRRKDIQIGDTVIVRRAGDVIPEVVAFVPERRPASARPFIMPSSCPVCGS 436

Query: 424 KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV 483
            I+ +E   IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA 
Sbjct: 437 PIVRLEDEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAA 496

Query: 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
           DLYK+ F+ L  LDR+++K A N+L A++KSK TT +RFIYALGIRHVGE TAKELA +F
Sbjct: 497 DLYKLGFRALAELDRMADKSAQNVLDALEKSKRTTLARFIYALGIRHVGEATAKELARHF 556

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGN 603
            NL+ + +A+ EQLL +  IG     +   F    ++  LI QLR  G+ W  +   +  
Sbjct: 557 GNLDALLQASPEQLLEVADIGPVVAASITAFFTDAMNIELIEQLRAAGVTWPEH-VVENR 615

Query: 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIK 663
              L  K FV TG+L    R+ A   IE  GGKV   +SK T+Y+V G + G KL KA +
Sbjct: 616 PRPLAGKTFVLTGTLPTLSRDAAAEKIEAAGGKVAGSVSKKTSYVVAGAEAGSKLAKAEE 675

Query: 664 LNIKILDEKNFVKIV 678
           L + ILDE   ++++
Sbjct: 676 LGVTILDETGLLQLL 690

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Herminiimonas arsenicoxydans (taxid: 204773)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|Q470D2|DNLJ_CUPPJ DNA ligase OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=ligA PE=3 SV=1

 Score =  673 bits (1737), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 315/676 (46%), Positives = 441/676 (65%), Gaps = 15/676 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           RV  L+ EL RHN  YY+ D P I D +YD L  EL+ +E ++PELLT DS TQ VG   
Sbjct: 27  RVQWLRDELDRHNYQYYVLDAPTIPDAEYDALFTELQALEAEHPELLTPDSPTQRVGGAP 86

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL-------------KLTKNIEYIAE 123
                 V H   M+SL+NGFSDEDV  F++R    L                + +EY  E
Sbjct: 87  LSAFDTVRHRVPMLSLNNGFSDEDVTGFDRRCAQGLGRSAAAGGEQDLFSAAEGVEYACE 146

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A++LRYE G L QA+TRGDG  GE++T N+  I  IPL L     P +LEVR E
Sbjct: 147 LKFDGLAMSLRYEDGRLVQAATRGDGETGEDVTVNVRTIKAIPLKLR-GAAPAVLEVRGE 205

Query: 184 VLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243
           V +Y++DF KLN  +   G K F NPRNAAAG LRQL+P+I   + L FFA+G+GEL+G+
Sbjct: 206 VFMYRRDFDKLNARQAEAGDKTFVNPRNAAAGSLRQLDPRITAKRPLSFFAYGLGELQGI 265

Query: 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303
             P++HS +L+ +  +GL +C E +V+ G   L++FY+K+  KR  LPY+IDGVVYK+N 
Sbjct: 266 ERPATHSAMLDGFATMGLPVCNERAVVKGAQGLLDFYRKVGEKRDQLPYDIDGVVYKVNA 325

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
           L+ Q++LGF SRAPRFALA+KF ++E  T ++ I +Q+GRTG ITPVA L+PV + G+T+
Sbjct: 326 LAEQEQLGFVSRAPRFALAHKFPAQEMTTIVEDIEVQVGRTGAITPVARLQPVFVGGVTV 385

Query: 364 TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNS 423
           T ATLHNE E+ RK++ IGDTV+V R+G+VIP++ + +L  RP+D++ F +P  CP+C S
Sbjct: 386 TNATLHNEDEVRRKDVHIGDTVIVRRAGDVIPEVVAVVLERRPDDARAFVMPTACPVCGS 445

Query: 424 KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV 483
            I  +E   IARC+G  I C AQRK  L HF+ R+AM+I GLG K++E+LV+  IV T  
Sbjct: 446 HIERLEDEAIARCTGGLI-CAAQRKQALLHFAQRRAMDIEGLGDKVVEQLVDQGIVRTPA 504

Query: 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
           DLYK+    L  LDR+++K A N++ AI+ S+ TTF+RFI++LGIRHVGE TAK+LA +F
Sbjct: 505 DLYKLGVAKLAALDRMADKSAGNLVAAIEASRSTTFNRFIFSLGIRHVGEATAKDLARHF 564

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGN 603
             L+ +  A E  LL +  +G    ++ + F  +P +  +I QLR  G++W  +      
Sbjct: 565 GKLDGLMVADEAALLEVNDVGPVVAQSIVNFFGEPHNVEVIEQLRAAGVHWPESEPVARA 624

Query: 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIK 663
              L  K FV TG+L +  R  A  ++E  G KV   +SK T+Y+V G + G KL+KA  
Sbjct: 625 PAPLAGKTFVLTGTLPSLSREAAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLDKAEA 684

Query: 664 LNIKILDEKNFVKIVK 679
           L + +LDE   + +++
Sbjct: 685 LGVPVLDEAGMLALLE 700

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (taxid: 264198)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|B2JID1|DNLJ_BURP8 DNA ligase OS=Burkholderia phymatum (strain DSM 17167 / STM815) GN=ligA PE=3 SV=1

 Score =  669 bits (1725), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/674 (47%), Positives = 453/674 (67%), Gaps = 4/674 (0%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S  + R   L+ EL R N AYY+ D P + D +YD+L  EL++IE ++P+L+T DS TQ 
Sbjct: 12  SAPAERALWLRDELERANYAYYVLDQPDLPDAEYDRLFKELQQIESEHPDLITPDSPTQR 71

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAV 131
           VG       + V H   M+SL+NGFSDED+  F+KR+++ L  T  ++Y  ELKFDG+A+
Sbjct: 72  VGGEVASGFRPVVHDMPMLSLNNGFSDEDIAAFDKRVSDTLHHTP-VDYACELKFDGLAI 130

Query: 132 NLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDF 191
           +LRY  G   QA+TRGDG  GE++T N+  I  IPL L  K  P+L++VR EVL++++DF
Sbjct: 131 SLRYVDGQFTQAATRGDGATGEDVTENVRTIRSIPLKLKGKRVPKLVDVRGEVLMFRRDF 190

Query: 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251
            KLN+ +   G ++F NPRNAAAG LRQL+PK+   + L FFA+G+G L G+ MP +HSE
Sbjct: 191 DKLNQRQRDAGQREFANPRNAAAGSLRQLDPKMTAQRPLSFFAYGIGVLDGIEMPGTHSE 250

Query: 252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
           LL+WY ++GL +  E +V+ G   ++ F+ K+  KR  LPY+IDGVVYK+N    Q  LG
Sbjct: 251 LLDWYHEMGLPVNSERAVVQGAEGVLGFFHKVGEKRDKLPYDIDGVVYKVNRRDEQDALG 310

Query: 312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
           F SRAPRFALA+KF ++EALTK+ AI++Q+GRTG ITPVA L+PV + G T+T ATLHNE
Sbjct: 311 FVSRAPRFALAHKFPAQEALTKLIAIDVQVGRTGAITPVARLEPVFVGGATVTNATLHNE 370

Query: 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
            E+ RK+I+IGDTV+V R+G+VIP++  ++L  RP D++ F +P  CP+C S I  +   
Sbjct: 371 DEVRRKDIRIGDTVIVRRAGDVIPEVVGALLERRPPDAREFVMPTQCPVCGSAIERLPDE 430

Query: 432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
            IARCSG    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  DL+ + F 
Sbjct: 431 AIARCSGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVELNLVRTPADLFNLGFA 489

Query: 492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
            L  LDR + K A N++ +++K+K TT +RFIYALGIRHVGE+TAK+LA +F +L+ +  
Sbjct: 490 TLAELDRFAEKSAQNLIDSLEKAKHTTLARFIYALGIRHVGESTAKDLARHFGSLDPIMS 549

Query: 552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-KGNKNYLKE 609
           AT E+LL +  +G    +A  +F  +  +R +I QLR  G + W   P   K  +  L  
Sbjct: 550 ATVEELLEVNDVGPIVAEAIHQFFAEEHNRTVIEQLRAPGKVTWAEGPPAPKAPQGVLAG 609

Query: 610 KIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKIL 669
           K  V TG+L    R+EA  L+E  G KV   +SK T+Y+V G + G KL KA +L I +L
Sbjct: 610 KTVVLTGTLPNMGRDEAKELLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKAEELGIPVL 669

Query: 670 DEKNFVKIVKGFST 683
           DE    K+++G +T
Sbjct: 670 DEDGMRKLLEGQTT 683

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia phymatum (strain DSM 17167 / STM815) (taxid: 391038)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|A4JF81|DNLJ_BURVG DNA ligase OS=Burkholderia vietnamiensis (strain G4 / LMG 22486) GN=ligA PE=3 SV=1

 Score =  664 bits (1714), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 316/679 (46%), Positives = 450/679 (66%), Gaps = 11/679 (1%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S+   R   L+ +L R N AYY+ D P + D +YD+L  EL+++E  +PEL+T DS TQ 
Sbjct: 11  SQPDARAAWLRDQLERANYAYYVLDQPDLPDAEYDRLFGELQQLEADHPELVTPDSPTQR 70

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELK--------LTKNIEYIAE 123
           VG         V H   M+SL+NGFSD+D++ F+KR+ + L         +T  +EY  E
Sbjct: 71  VGGAVASGFTPVVHDAPMLSLNNGFSDDDIVAFDKRVADALDKPTDLAGSVTDPVEYACE 130

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A++LRYE G   QASTRGDG  GE++T N+  I  IPL L   + P LL+VR E
Sbjct: 131 LKFDGLAISLRYERGVFVQASTRGDGTTGEDVTENVRTIRSIPLKLKGAHVPALLDVRGE 190

Query: 184 VLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243
           VL++K+DF +LN+ +     ++F NPRNAAAG LRQL+PKI   + L FF++G+G L GM
Sbjct: 191 VLMFKRDFARLNERQRAAEQREFANPRNAAAGSLRQLDPKITAQRPLSFFSYGIGVLDGM 250

Query: 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303
            MP +HS LL+WY+ +GL +  E +V+ G   L+EF++K+  +R +LPY+IDGVVYK+N 
Sbjct: 251 PMPDTHSALLDWYEALGLPVNRERAVVRGAQGLLEFFRKVGERRESLPYDIDGVVYKVNR 310

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
              Q +LGF SRAPRFALA+KF ++EALTK+ AI++Q+GRTG ITPVA L+PV + G T+
Sbjct: 311 RDEQDRLGFVSRAPRFALAHKFPAQEALTKLVAIDVQVGRTGAITPVARLEPVFVGGATV 370

Query: 364 TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNS 423
           T ATLHNE E+ RK+I+IGDTV+V R+G+VIP++  ++L  RP D+  F +P  CP+C S
Sbjct: 371 TNATLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVGALLERRPVDAAEFVMPTECPVCGS 430

Query: 424 KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV 483
           KI  +    IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  
Sbjct: 431 KIERLPDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVELNLVRTPA 489

Query: 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
           DL+ + F  L  LDR + K A N+L +++K+K TT +RFIY LGIRHVGE+TAK+LA +F
Sbjct: 490 DLFNLGFATLAELDRFAEKSAQNLLDSLEKAKHTTLARFIYGLGIRHVGESTAKDLAKHF 549

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-K 601
            +L+ +  A+ E+LL +  +G    ++  +F  +  +R +I QLR  G + W   P   K
Sbjct: 550 GSLDPIMDASIEELLEVNDVGPIVAESIHQFFAEEHNRTVIDQLRAPGKVTWPEGPPAPK 609

Query: 602 GNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKA 661
             +  L  K  V TG+L    R+ A  ++E  G KV   +SK T+Y+V G + G KL KA
Sbjct: 610 APQGVLAGKTVVLTGTLPTLTRDAAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKA 669

Query: 662 IKLNIKILDEKNFVKIVKG 680
            +L I +LDE    ++++G
Sbjct: 670 EELGIPVLDEDGLHQLLEG 688

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia vietnamiensis (strain G4 / LMG 22486) (taxid: 269482)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|Q13XB0|DNLJ_BURXL DNA ligase OS=Burkholderia xenovorans (strain LB400) GN=ligA PE=3 SV=1

 Score =  663 bits (1710), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/676 (47%), Positives = 452/676 (66%), Gaps = 8/676 (1%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S  + R   L+ EL R N AYY+ D P + D +YD+L  EL+ IE ++P+L+  DS TQ 
Sbjct: 12  SAPAERAAWLRAELERANYAYYVLDQPDLPDAEYDRLFKELESIETEHPDLIVPDSPTQR 71

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKN-----IEYIAELKF 126
           VG       + V H   M+SL+NGF+DED++ F+KR+ + L    +     +EY AELKF
Sbjct: 72  VGGEAASGFEPVVHEQPMLSLNNGFADEDIVAFDKRVGDALGKNASEPPVPVEYAAELKF 131

Query: 127 DGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI 186
           DG+A++LRY  G   QASTRGDG  GEN+T N+  I  IPL L  K  P +L+VR EVL+
Sbjct: 132 DGLAISLRYVDGVFVQASTRGDGTTGENVTENVRTIRSIPLRLKGKRVPHVLDVRGEVLM 191

Query: 187 YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246
           +K+DF +LN+ +     K+F NPRNAAAG LRQL+ KI   + L FF++G+G L GM+MP
Sbjct: 192 FKRDFERLNERQRAAEQKEFANPRNAAAGSLRQLDSKITAQRPLSFFSYGIGVLEGMDMP 251

Query: 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
           ++HSELL+WY+++GL + GE +V+ G   L+ F+  +  KR  LPY+IDGVVYK+N    
Sbjct: 252 ATHSELLDWYKELGLPVNGERAVVHGAEGLLGFFHAVGEKREKLPYDIDGVVYKVNRRDE 311

Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
           Q+ LGF SRAPRFALA+KF ++EALT++ AI++Q+GRTG +TPVA L+PV + G T+T A
Sbjct: 312 QEALGFVSRAPRFALAHKFPAQEALTRLVAIDVQVGRTGAVTPVARLEPVFVGGATVTNA 371

Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
           TLHNE E+ RK+I+IGDTV+V R+G+VIP++ S++L  RP+D++ F +P  CP+C S I 
Sbjct: 372 TLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVSALLDRRPDDAREFVMPTHCPVCGSNIE 431

Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
            +    IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  DL+
Sbjct: 432 RLPDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVEQNLVRTPADLF 490

Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
            + F  L  LDR + K A N+L +++K+K TT +RFIYALGIRHVGE+TAK+LA +F +L
Sbjct: 491 NLGFATLAELDRFAEKSAQNLLDSLEKAKHTTLARFIYALGIRHVGESTAKDLAKHFGSL 550

Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-KGNK 604
           + +  A+ E LL +  +G    ++  +F  +  +R +I QLR  G + W   P   K  +
Sbjct: 551 DPIMDASVEALLEVNDVGPVVAESIHQFFAEEHNRTVIEQLRAPGRVTWPEGPPAPKAPQ 610

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 664
             L  K  V TG+L +  R EA  ++E  G KV   +SK T+Y+V G + G KL KA +L
Sbjct: 611 GVLAGKTVVLTGTLPSLAREEAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKAEEL 670

Query: 665 NIKILDEKNFVKIVKG 680
            I +LDE    K+++G
Sbjct: 671 GIPVLDEDGMRKLLEG 686

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia xenovorans (strain LB400) (taxid: 266265)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|B2T5K0|DNLJ_BURPP DNA ligase OS=Burkholderia phytofirmans (strain DSM 17436 / PsJN) GN=ligA PE=3 SV=1

 Score =  663 bits (1710), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 320/676 (47%), Positives = 448/676 (66%), Gaps = 8/676 (1%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S  + R   L+ EL R N AYY+ D P + D +YD+L  EL+ IE ++P+L+  DS TQ 
Sbjct: 12  SAPAERAAWLRAELERANYAYYVLDQPDLPDAEYDKLFKELESIETEHPDLIVPDSPTQR 71

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKN-----IEYIAELKF 126
           VG       + V H   M+SL+NGF+DED++ F+KR+ + L    +     ++Y AELKF
Sbjct: 72  VGGEAASGFEPVVHDQPMLSLNNGFADEDIVAFDKRVGDALGKNASEPPVPVDYAAELKF 131

Query: 127 DGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI 186
           DG+A++LRY  G   QASTRGDG  GEN+T N+  I  IPL L  K  P +L+VR EVL+
Sbjct: 132 DGLAISLRYVDGAFVQASTRGDGTTGENVTENVRTIRSIPLKLKGKRVPHVLDVRGEVLM 191

Query: 187 YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246
           +K+DF +LN+ +     K+F NPRNAAAG LRQL+ KI   + L FFA+G+G L GM MP
Sbjct: 192 FKRDFERLNERQRAAEQKEFANPRNAAAGSLRQLDSKITAQRPLSFFAYGIGVLEGMEMP 251

Query: 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
           ++HSELL+WY+++GL +  E +V+ G   L+ F+  +  KR  LPY+IDGVVYK+N    
Sbjct: 252 ATHSELLDWYKELGLPVNSERAVVQGAEGLLGFFHGVGEKREKLPYDIDGVVYKVNRRDE 311

Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
           Q  LGF SRAPRFALA+KF ++EALTK+ AI++Q+GRTG ITPVA L+PV + G T+T A
Sbjct: 312 QDALGFVSRAPRFALAHKFPAQEALTKLVAIDVQVGRTGAITPVARLEPVFVGGATVTNA 371

Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
           TLHNE E+ RK+I+IGDTV+V R+G+VIP++ S++L  RP+D++ F +P  CP+C S I 
Sbjct: 372 TLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVSALLDRRPSDAREFVMPTQCPVCGSSIE 431

Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
            +    IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  DL+
Sbjct: 432 RLPDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVEQNLVRTPADLF 490

Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
            I F  L  LDR + K A N+L +++K+K TT +RFIYALGIRHVGE+TAK+LA +F +L
Sbjct: 491 NIGFATLAELDRFAEKSAQNLLDSLEKAKHTTLARFIYALGIRHVGESTAKDLAKHFGSL 550

Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-KGNK 604
           + +  A+ E LL +  +G    ++  +F  +  +R +I QLR  G + W   P   K  +
Sbjct: 551 DPIMDASVEALLEVNDVGPVVAESIHQFFAEEHNRTVIEQLRAPGKVTWPEGPPAPKAPQ 610

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 664
             L  K  V TG+L +  R EA  ++E  G KV   +SK T+YLV G   G KL KA +L
Sbjct: 611 GVLAGKTVVLTGTLPSLAREEAKEMLEAAGAKVAGSVSKKTDYLVAGADAGSKLAKAEEL 670

Query: 665 NIKILDEKNFVKIVKG 680
            + +LDE    K+++G
Sbjct: 671 GVPVLDEDGMRKLLEG 686

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia phytofirmans (strain DSM 17436 / PsJN) (taxid: 398527)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|A9AIK9|DNLJ_BURM1 DNA ligase OS=Burkholderia multivorans (strain ATCC 17616 / 249) GN=ligA PE=3 SV=1

 Score =  663 bits (1710), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 314/679 (46%), Positives = 450/679 (66%), Gaps = 11/679 (1%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S+   R   L+ +L R N AYY+ D P + D +YD+L  EL+++E  +P+L+T DS TQ 
Sbjct: 11  SQPDVRAAWLRDQLERANYAYYVLDQPDLPDAEYDRLFRELQQLESDHPDLVTPDSPTQR 70

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL--------KLTKNIEYIAE 123
           VG         V H   M+SL+NGF+D+D++ F+KR+ + L         +T  +EY  E
Sbjct: 71  VGGAVASGFTPVVHDAPMLSLNNGFADDDIVAFDKRVADALGKTTDLAGSVTDPVEYACE 130

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A++LRYE+G   QASTRGDG  GE++T N+  I  IPL L     P +L+VR E
Sbjct: 131 LKFDGLAISLRYEHGVFVQASTRGDGTTGEDVTENVRTIRSIPLKLKGDRVPAVLDVRGE 190

Query: 184 VLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243
           VL++K+DF +LN+ +     ++F NPRNAAAG LRQL+PKI   + L FFA+G+G L GM
Sbjct: 191 VLMFKRDFARLNERQRAAEQREFANPRNAAAGSLRQLDPKITAQRPLSFFAYGIGVLDGM 250

Query: 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303
            MP +HS LL+WY+ +GL +  E +V+ G   L++F++K+  KR +LPY+IDGVVYK+N 
Sbjct: 251 PMPDTHSALLDWYEALGLPVNRERAVVYGAQGLLDFFRKVGEKRESLPYDIDGVVYKVNR 310

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
              Q +LGF SRAPRFALA+KF ++EALTK+ AI +Q+GRTG ITPVA L+PV + G T+
Sbjct: 311 RDEQDRLGFVSRAPRFALAHKFPAQEALTKLVAIGVQVGRTGAITPVARLEPVFVGGATV 370

Query: 364 TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNS 423
           T ATLHNE E+ RK+I+IGDTV+V R+G+VIP++  ++L  RP D+  F +P  CP+C S
Sbjct: 371 TNATLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVGAVLDRRPADAAEFVMPTECPVCGS 430

Query: 424 KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV 483
           KI  +    IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  
Sbjct: 431 KIERLPDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVELNLVRTPA 489

Query: 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
           DL+ + F  L  LDR + K A N+L +++K+K TT +RFIYALGIRHVGE+TAK+LA +F
Sbjct: 490 DLFNLGFATLAELDRFAEKSAQNLLDSLEKAKHTTLARFIYALGIRHVGESTAKDLAKHF 549

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-K 601
            +L+ +  AT ++LL +  +G    ++  +F  +  +R +I QLR  G + W   P   K
Sbjct: 550 GSLDPIMNATIDELLEVNDVGPIVAESIHQFFAEEHNRTVIEQLRAPGKVTWPEGPPAPK 609

Query: 602 GNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKA 661
             +  L  K  V TG+L    R++A  ++E  G KV   +SK T+Y++ G + G KL KA
Sbjct: 610 APQGVLAGKTVVLTGTLPNLTRDDAKEMLEAAGAKVAGSVSKKTDYVIAGAEAGSKLAKA 669

Query: 662 IKLNIKILDEKNFVKIVKG 680
             L I +LDE    ++++G
Sbjct: 670 EALGIPVLDEDGLHQLLEG 688

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia multivorans (strain ATCC 17616 / 249) (taxid: 395019)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|Q2SX03|DNLJ_BURTA DNA ligase OS=Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) GN=ligA PE=3 SV=1

 Score =  660 bits (1702), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 312/676 (46%), Positives = 450/676 (66%), Gaps = 11/676 (1%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R   L+ EL R N AYY+ D P + D +YD+L  EL++IE ++P+L+T DS TQ VG   
Sbjct: 16  RAAWLRAELERANYAYYVLDQPDLPDAEYDRLFAELQQIEAEHPDLVTPDSPTQRVGGEV 75

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELK--------LTKNIEYIAELKFDG 128
                 V H   M+SL+NGFSD+DV+ F+KR+ + L         +T+ +EY  ELKFDG
Sbjct: 76  ASGFTPVVHDTPMLSLNNGFSDDDVVAFDKRVADGLDKPTDLAGTVTEPVEYACELKFDG 135

Query: 129 IAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK 188
           +A++LRYE G   QASTRGDG  GE++T NI  +  IPL L  K  P +L+VR EVL+++
Sbjct: 136 LAISLRYENGRFVQASTRGDGTTGEDVTENIRTVRSIPLTLKGKRVPRMLDVRGEVLMFR 195

Query: 189 KDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS 248
           +DF +LN+ +   G ++F NPRNAAAG LRQL+ KI  ++ L FFA+G+G L G+ MP +
Sbjct: 196 RDFARLNERQRAAGQREFANPRNAAAGSLRQLDSKITASRPLSFFAYGIGVLDGVEMPDT 255

Query: 249 HSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQK 308
           HS LL+WY+ +GL +  E +V+ G   L+EF+  +  +R +LPY+IDGVVYK+N    Q 
Sbjct: 256 HSSLLDWYETLGLPVNRERAVVRGAAGLLEFFHSVGARRESLPYDIDGVVYKVNRRDEQD 315

Query: 309 KLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATL 368
           +LGF SRAPRFALA+KF ++EALTK+ AI++Q+GRTG ITPVA L+PV + G T+T ATL
Sbjct: 316 RLGFVSRAPRFALAHKFPAQEALTKLVAIDVQVGRTGAITPVARLEPVFVGGATVTNATL 375

Query: 369 HNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYI 428
           HNE E+ RK+I+IGDTV+V R+G+VIP++ S++   RP D++ F +P  CP C S++  +
Sbjct: 376 HNEDEVRRKDIRIGDTVIVRRAGDVIPEVVSAVFDRRPADAREFVMPTECPECGSRVERL 435

Query: 429 ESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKI 488
               IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T  DL+ +
Sbjct: 436 PDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVEQNLVRTPADLFNL 494

Query: 489 NFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLEC 548
            F  L+ LDR + K A N++ +++K+K TT +RFIYALGIRHVGE+TAK+LA +F +L+ 
Sbjct: 495 GFSTLVELDRFAEKSAQNLIDSLEKAKHTTLARFIYALGIRHVGESTAKDLAKHFGSLDP 554

Query: 549 MFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT-KGNKNY 606
           +  A+ ++LL +  +G    ++  +F  +  +R +I QLR  G + W   P   +  +  
Sbjct: 555 IMDASIDELLEVNDVGPIVAESIHQFFAEAHNRTVIEQLRAKGKVTWPEGPPAPRAPQGV 614

Query: 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
           L  K  V TG+L    R  A  ++E  G KV   +SK T+Y+V G   G KL KA +L I
Sbjct: 615 LAGKTVVLTGTLPTLTREAAKEMLEAAGAKVAGSVSKKTDYVVAGADAGSKLAKAEELGI 674

Query: 667 KILDEKNFVKIVKGFS 682
            +LDE    K+++G +
Sbjct: 675 PVLDEAGMHKLLEGHA 690

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (taxid: 271848)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

>sp|Q0BE10|DNLJ_BURCM DNA ligase OS=Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) GN=ligA PE=3 SV=1

 Score =  659 bits (1701), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 316/680 (46%), Positives = 451/680 (66%), Gaps = 13/680 (1%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
           S+   R   L+ +L R N AYY+ D P + D +YD+L  EL+++E  +P+L+T DS TQ 
Sbjct: 11  SQPDARAAWLRDQLERANYAYYVLDQPDLPDAEYDRLFGELQQLETDHPDLVTPDSPTQR 70

Query: 72  VG-LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL--------KLTKNIEYIA 122
           VG  V G  +  VH    M+SL+NGF+DED+  F+KR+ + L         +T  +EY  
Sbjct: 71  VGGEVAGGFTPVVHDA-PMLSLNNGFADEDIAAFDKRVADALGKTTDLAGSVTDPVEYAC 129

Query: 123 ELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRC 182
           ELKFDG+A++LRYE+G   QASTRGDG  GE++T N+  I  IPL L   + P LL+VR 
Sbjct: 130 ELKFDGLAISLRYEHGVFVQASTRGDGTTGEDVTENVRTIRSIPLKLKGAHVPALLDVRG 189

Query: 183 EVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242
           EVL++K+DF +LN+ +     ++F NPRNAAAG LRQL+PKI   + L FFA+G+G L G
Sbjct: 190 EVLMFKRDFARLNERQRAAEQREFANPRNAAAGSLRQLDPKITAQRPLSFFAYGIGVLDG 249

Query: 243 MNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302
           M MP +HS LL+WY+  GL +  E +V+ G + L+ F++K+  KR +LPY+IDGVVYK+N
Sbjct: 250 MPMPDTHSALLDWYESFGLPVNRERAVVYGADGLLGFFRKVGEKRESLPYDIDGVVYKVN 309

Query: 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGIT 362
               Q +LGF SRAPRFALA+KF ++EALT++ AI++Q+GRTG ITPVA L+PV + G T
Sbjct: 310 RRDEQDRLGFVSRAPRFALAHKFPAQEALTRLVAIDVQVGRTGAITPVARLEPVFVGGAT 369

Query: 363 ITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICN 422
           +T ATLHNE E+ RK+I+IGDTV+V R+G+VIP++  ++L  RP+D+  F +P  CP+C 
Sbjct: 370 VTNATLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVGALLDRRPDDAAEFVMPTECPVCG 429

Query: 423 SKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTA 482
           SKI  +    IARC+G    C AQRK  L HF+ R+A++I GLG+K+I++LV  N+V T 
Sbjct: 430 SKIERLPDEAIARCTGGLF-CPAQRKQALWHFAQRRALDIDGLGEKIIDQLVELNLVRTP 488

Query: 483 VDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY 542
            DL+ + F  L  LDR + K A N+L +++K+K TT +RFIY LGIRHVGE+TAK+LA +
Sbjct: 489 ADLFNLGFATLAELDRFAEKSAQNLLDSLEKAKHTTLARFIYGLGIRHVGESTAKDLAKH 548

Query: 543 FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNPNT- 600
           F +L  +  A+ E+LL +  +G    ++  +F  +  +R +I QLR  G + W   P   
Sbjct: 549 FGSLTPIMDASIEELLEVNDVGPIVAESIHQFFAEEHNRTVIEQLRAPGKVTWAEGPPAP 608

Query: 601 KGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEK 660
           +  +  L  K  V TG+L    R+ A  ++E  G KV   +SK T+Y+V G   G KL K
Sbjct: 609 RAPQGVLAGKTVVLTGTLPNLTRDAAKEMLEAAGAKVAGSVSKKTDYVVAGADAGSKLAK 668

Query: 661 AIKLNIKILDEKNFVKIVKG 680
           A +L I +LDE    ++++G
Sbjct: 669 AEELGIPVLDEDGLHQLLEG 688

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) (taxid: 339670)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

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	687
399017276	705	DNA ligase, NAD-dependent [Herbaspirillu	0.976	0.951	0.517	0.0
340786485	694	DNA ligase [Collimonas fungivorans Ter33	0.965	0.955	0.517	0.0
152981161	692	DNA ligase [Janthinobacterium sp. Marsei	0.975	0.968	0.505	0.0
300311482	688	NAD-dependent DNA ligase [Herbaspirillum	0.957	0.956	0.509	0.0
134094553	696	DNA ligase [Herminiimonas arsenicoxydans	0.981	0.968	0.500	0.0
409405979	686	NAD-dependent DNA ligase [Herbaspirillum	0.966	0.967	0.5	0.0
398834963	682	DNA ligase, NAD-dependent [Herbaspirillu	0.966	0.973	0.490	0.0
237745525	685	DNA ligase [Oxalobacter formigenes HOxBL	0.963	0.966	0.501	0.0
329912476	679	DNA ligase [Oxalobacteraceae bacterium I	0.950	0.961	0.493	0.0
237747723	685	DNA ligase [Oxalobacter formigenes OXCC1	0.973	0.976	0.488	0.0

>gi|399017276|ref|ZP_10719473.1| DNA ligase, NAD-dependent [Herbaspirillum sp. CF444] gi|398104047|gb|EJL94204.1| DNA ligase, NAD-dependent [Herbaspirillum sp. CF444]

 Score =  754 bits (1947), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 348/672 (51%), Positives = 466/672 (69%), Gaps = 1/672 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R   LK  L RHN AYY+ D+P I D +YD+L  EL+ +E+++PEL T DS TQ VG   
Sbjct: 18  RAAWLKAALDRHNHAYYVLDDPSIPDAEYDKLFHELQALEQQHPELATADSPTQRVGGTP 77

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
               + V H   M+SL NGF DED+I F+KR+ + L    ++ Y AELKFDG+A++LRYE
Sbjct: 78  LPQFEQVRHAIPMLSLGNGFDDEDIIAFDKRVKDGLSSLTDVAYAAELKFDGLAISLRYE 137

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L  A+TRGDG  GEN+T NI  +  IPL L+   PP++LEVR EVL+YK DF KLN+
Sbjct: 138 NGVLVGAATRGDGTTGENVTANIRTVRAIPLRLHGDNPPQVLEVRGEVLMYKNDFAKLNQ 197

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +   GLK+F NPRNAAAG LRQL+ KI   + L FFA+G+G L GM+MP SHS LL+WY
Sbjct: 198 RQRDAGLKEFANPRNAAAGSLRQLDSKITAQRTLRFFAYGIGVLEGMDMPPSHSALLDWY 257

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
             +GL +C E +V+ G   L++FY  I  KR  LPYEIDGVVYK++ L  Q++LGF SRA
Sbjct: 258 ASLGLPVCKERAVVHGAEGLLKFYSGIGAKRGELPYEIDGVVYKVDRLDQQQQLGFVSRA 317

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PRFALA+K+ ++EALT ++ I +Q+GRTG ITPVA L PV + G+T+T ATLHNE E+ R
Sbjct: 318 PRFALAHKYPAQEALTVVQGIEVQVGRTGAITPVARLAPVFVGGVTVTNATLHNEDEVRR 377

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+IQIGDTV+V R+G+VIP++ + +   RP D++ F++P  CP+C S II +E   IARC
Sbjct: 378 KDIQIGDTVIVRRAGDVIPEVVAYVPESRPADAQPFEMPKECPVCGSPIIRLEEEAIARC 437

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           SG W++C AQRK GLQHF+SR+AM+I GLG ++IE+LV+ N++ TA DLY++   +L  L
Sbjct: 438 SGGWVKCSAQRKGGLQHFASRRAMDIEGLGDQLIEQLVDKNVITTAADLYRLGLTSLAEL 497

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           DR+++K A N+L A++KSK TT +RFIYALGIRHVGE TAKELA +F N++ +  ATEEQ
Sbjct: 498 DRMADKSAQNVLDALEKSKSTTLARFIYALGIRHVGEATAKELARHFGNMDAVLAATEEQ 557

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           LL +  IG    ++ I F    L+  L++QLR  GI+W            L  KIFV TG
Sbjct: 558 LLEVADIGPVVARSLISFFADGLNVELVNQLRAAGIHWTEGAGIDIPAKTLAGKIFVLTG 617

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
           +L    R++A  +IE  GGKV   +SK T+Y+V G + G KL KA +L I ILDE+  V 
Sbjct: 618 TLPTMSRDDAAQMIEAAGGKVSGSVSKKTSYVVAGAEAGSKLAKAEELGIAILDEEALVA 677

Query: 677 IVK-GFSTETKI 687
           +V+ G   +T +
Sbjct: 678 LVQNGPQEDTDV 689

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|340786485|ref|YP_004751950.1| DNA ligase [Collimonas fungivorans Ter331] gi|340551752|gb|AEK61127.1| DNA ligase [Collimonas fungivorans Ter331]

 Score =  737 bits (1902), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 344/665 (51%), Positives = 465/665 (69%), Gaps = 2/665 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R   L  EL+RHN +YY+ DNP I D +YDQL  EL+ +E+ +PEL T DS TQ VG   
Sbjct: 23  RAAWLAAELNRHNHSYYVLDNPSIPDAEYDQLFRELQALEQAHPELNTPDSPTQRVGAAP 82

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL--KLTKNIEYIAELKFDGIAVNLR 134
               + V H+  M+SL NGF D D+I F++R+ + L  +   +IEY AELKFDG+A+NLR
Sbjct: 83  LPLFEQVTHSIPMLSLGNGFEDNDIIEFDRRVRDGLDTQADSDIEYAAELKFDGLAINLR 142

Query: 135 YEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKL 194
           YE G L QA+TRGDG  GEN+T+NI  +  IPL L+ ++PP++L+VR EVL++K DF KL
Sbjct: 143 YEDGVLVQAATRGDGTTGENVTSNIRTVRAIPLRLHTEHPPKVLDVRGEVLMFKDDFAKL 202

Query: 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN 254
           N  +    +K+F NPRNAAAG LRQL+ +I   + L FFA+G+G L G +MP SHS LL+
Sbjct: 203 NARQREAEMKEFANPRNAAAGSLRQLDSRITAQRTLRFFAYGIGMLEGADMPPSHSALLD 262

Query: 255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTS 314
           WY ++GL +C E  V+ G + L++F++ I  KR  LPYEIDGVVYK+N L  Q+ LGF S
Sbjct: 263 WYSQLGLPVCKERGVVKGASGLLDFFRDIGGKRPQLPYEIDGVVYKVNRLLQQQTLGFVS 322

Query: 315 RAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEI 374
           RAPRFALA+KF ++EA T++  I +QIGRTG +TPVA L PV + G+T+T ATLHNE E+
Sbjct: 323 RAPRFALAHKFPAEEATTQVLGIEVQIGRTGAVTPVARLAPVFVGGVTVTNATLHNEDEV 382

Query: 375 YRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIA 434
            RK+I IGDTV+V R+G+VIP++ S +  LRP D++ F +P+ CPIC S I+ +E   IA
Sbjct: 383 RRKDIHIGDTVIVRRAGDVIPEVVSFVPELRPADAQSFVMPSECPICGSAIVKLEDEAIA 442

Query: 435 RCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL 494
           RCSG W++C AQRK GLQHF+SR+AM+I GLG ++IE+LV+ +++ TA DLYK+    L 
Sbjct: 443 RCSGGWVKCAAQRKGGLQHFASRRAMDIEGLGDQLIEQLVDRDLIHTAADLYKLGLVKLA 502

Query: 495 RLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATE 554
            LDR+++K A N++ A++KSK TT  RFIYALGIRHVGE TAKELA +F N++ + +A+E
Sbjct: 503 ALDRMADKSAQNVMSALEKSKSTTLGRFIYALGIRHVGEATAKELAAHFGNIDGLLQASE 562

Query: 555 EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVF 614
           EQLL +  IG    ++ + F   PL+R L+ QLR  GI+W  N    G   +L  K FV 
Sbjct: 563 EQLLEVADIGPVVARSLLAFFADPLNRELVEQLRAAGIHWPENLPAAGGSKFLLGKTFVL 622

Query: 615 TGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 674
           TGSL    R+ A  +IE  GGKV   +SK T+Y+V G + G KL KA +LNI ILDE   
Sbjct: 623 TGSLPTLTRDAAAAMIEAAGGKVTGSVSKKTSYVVAGAEAGSKLTKAEELNIPILDEDGL 682

Query: 675 VKIVK 679
             +++
Sbjct: 683 RTLLE 687

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|152981161|ref|YP_001353755.1| DNA ligase [Janthinobacterium sp. Marseille] gi|166215814|sp|A6SZQ8.1|DNLJ_JANMA RecName: Full=DNA ligase; AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] gi|151281238|gb|ABR89648.1| DNA ligase (Polydeoxyribonucleotide synthase) [Janthinobacterium sp. Marseille]

 Score =  736 bits (1899), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/672 (50%), Positives = 468/672 (69%), Gaps = 2/672 (0%)

Query: 7   KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKD 66
           ++ + S  + R   L+ EL+RHN +Y++ DNP I D +YD+L  EL+ +E  +PELL  D
Sbjct: 19  EEPDASNPAARAAWLRDELNRHNYSYHVLDNPSIPDAEYDKLFRELQALETSHPELLVFD 78

Query: 67  SLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKF 126
           S TQ VG +       V H+  M+SL NGF DED+I F+KR+++ L  T+ IEY  ELKF
Sbjct: 79  SPTQRVGALALSAFPQVTHSVPMLSLGNGFEDEDIIAFDKRVSDGLNSTE-IEYATELKF 137

Query: 127 DGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI 186
           DG+A+NLRYE G L +A+TRGDG  GEN+TTNI  +  IPL L+   PP++L+VR EV++
Sbjct: 138 DGLAINLRYEDGILVEAATRGDGATGENVTTNIRTVRAIPLRLHTATPPKVLDVRGEVMM 197

Query: 187 YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246
           YK D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FFA+G+G L G  MP
Sbjct: 198 YKADLAKLNARQRDAGGKEFANPRNAAAGSLRQLDSRITAQRTLRFFAYGIGMLEGAEMP 257

Query: 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
            SHS LL+WY ++GL +C E +V+ G   L+EFYK +  KR  LPYEIDGVVYK+N +  
Sbjct: 258 PSHSALLDWYAELGLPVCAERAVVKGAAGLLEFYKAVGQKRPTLPYEIDGVVYKVNRVEQ 317

Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
           Q++LGF SRAPR+A+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+T A
Sbjct: 318 QQQLGFVSRAPRYAIAHKFPAEEALTTVQGIEVQVGRTGAITPVARLAPVLVGGVTVTNA 377

Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
           TLHNE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP D++ F +P  CP+CNS I+
Sbjct: 378 TLHNEDEVRRKDIQIGDTVIVRRAGDVIPEVVAYVPEKRPVDAQPFVMPTNCPVCNSPIV 437

Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
            +E   IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA DLY
Sbjct: 438 KLEDEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAADLY 497

Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
           K+ F+ L  LDR+++K A N++ A++KSK TT +RFIYALGIRHVGE TAKELA +F NL
Sbjct: 498 KLGFRALAELDRMADKSAQNVMAALEKSKSTTLARFIYALGIRHVGEATAKELARHFGNL 557

Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNY 606
           E + +A+EEQLL +  IG    ++   F++ PL+  LI QL+  G+ W  +      K +
Sbjct: 558 EALLQASEEQLLEVADIGPVVAQSIRSFLSDPLNMELIEQLQAAGVRWPEHVVENKPKPF 617

Query: 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
              K FV TG+L    R++A   IE  GGKV   +SK T+Y+V G   G KL KA +L I
Sbjct: 618 AG-KTFVLTGTLPTLSRDQAAEKIEAAGGKVAGSVSKKTSYVVAGADAGSKLAKAEELGI 676

Query: 667 KILDEKNFVKIV 678
            ILDE   ++++
Sbjct: 677 TILDESALLQLL 688

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|300311482|ref|YP_003775574.1| NAD-dependent DNA ligase [Herbaspirillum seropedicae SmR1] gi|300074267|gb|ADJ63666.1| NAD-dependent DNA ligase (contains BRCT domain type II) protein [Herbaspirillum seropedicae SmR1]

 Score =  733 bits (1891), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/658 (50%), Positives = 455/658 (69%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R   L+ +L+RHN +YY+ D P I D +YD+L  EL+ +E  +PELLT DS TQ VG   
Sbjct: 21  RAFALRADLNRHNYSYYVLDQPSIPDAEYDRLFQELQALETAHPELLTPDSPTQRVGAGP 80

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
               + V H   M+SL NGFSD+D+  F+KR+ + L+  + + Y  ELKFDG+A++LRYE
Sbjct: 81  LPQFEPVRHDIPMLSLGNGFSDDDIEAFDKRVRDGLETLQEVRYATELKFDGLAISLRYE 140

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L QA+TRGDG  GEN+T NI  +  IPL L+ +  P+LL+VR EVL+YK DF +LN+
Sbjct: 141 NGVLVQAATRGDGTTGENVTANIRTVRAIPLRLHGEAIPQLLDVRGEVLMYKDDFARLNQ 200

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +   G K+F NPRNAAAG LRQL+ +I   + L FFA+G+G L G +MPSSHS LL+WY
Sbjct: 201 RQRDAGQKEFANPRNAAAGSLRQLDSRITAQRTLRFFAYGIGVLEGADMPSSHSALLDWY 260

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           Q++GL +C E +V++G   L+EF++ I  KR +LPYEIDGVVYK++ L  QK+LGF SRA
Sbjct: 261 QQLGLPVCKERAVVTGATGLLEFFRGIGAKRESLPYEIDGVVYKVDRLDQQKQLGFVSRA 320

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PRFALA+KF ++EALT ++ I +Q+GRTG ITPVA L PV + G+T+T ATLHNE E+ R
Sbjct: 321 PRFALAHKFPAQEALTVVQDIEVQVGRTGAITPVARLNPVFVGGVTVTNATLHNEDEVRR 380

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+IQIGDTV+V R+G+VIP++ + +   RP D++ F +P  CP+C S I+  E   +ARC
Sbjct: 381 KDIQIGDTVIVRRAGDVIPEVVAYVPEKRPADARAFVMPAACPVCGSPIVRAEDEAVARC 440

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           SG W++C AQRK GLQHF+SR+AM+I GLG++++E+LV+  +V T  DLY++    L  L
Sbjct: 441 SGGWLKCSAQRKGGLQHFASRRAMDIEGLGEQLVEQLVDRKVVNTPADLYRLGLSALAEL 500

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           DR++ K A N+L A+QKSK TT +RFIYALGIRHVGE TAKELA +F  L+ +  A+E Q
Sbjct: 501 DRMAEKSAQNVLDALQKSKSTTLARFIYALGIRHVGEATAKELARHFGGLDKILAASEAQ 560

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           LL +  +G     +   F +  L+  L+ QLR VG++W  +   +    +L  K FV TG
Sbjct: 561 LLEVADVGPVVATSIRSFFDDALNVELVEQLRAVGVHWPESAGVEAAAKHLAGKTFVLTG 620

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 674
           +L    R+EA  LIE  GGKV   +SK T Y+V G + G KL KA +L I ILDE   
Sbjct: 621 TLPNLSRDEASQLIEAAGGKVTGSVSKKTTYVVAGAEAGSKLAKAEELGIAILDEDGL 678

Source: Herbaspirillum seropedicae SmR1

Species: Herbaspirillum seropedicae

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|134094553|ref|YP_001099628.1| DNA ligase [Herminiimonas arsenicoxydans] gi|166215813|sp|A4G4R4.1|DNLJ_HERAR RecName: Full=DNA ligase; AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] gi|133738456|emb|CAL61501.1| DNA ligase (Polydeoxyribonucleotide synthase [NAD+]) [Herminiimonas arsenicoxydans]

 Score =  732 bits (1890), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 338/675 (50%), Positives = 462/675 (68%), Gaps = 1/675 (0%)

Query: 4   HAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELL 63
             K+  + S  S R   L+ EL+RHN AYY+ DNPI+ D +YDQL  EL+ +E  +PELL
Sbjct: 17  QPKEIPDASDPSARAAWLRSELNRHNYAYYVLDNPIVPDAEYDQLFRELQALEASHPELL 76

Query: 64  TKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAE 123
             DS TQ VG +       V H+  M+SL NGF DEDV+ F+KR++  L   + +EY  E
Sbjct: 77  VFDSPTQRVGALALTAFPPVTHSVPMLSLGNGFEDEDVLAFDKRVSEGLNSREEVEYATE 136

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A+NLRYE G L QA+TRGDG  GEN+T NI  +  IPL L+   PP++L+VR E
Sbjct: 137 LKFDGLAINLRYEDGVLVQAATRGDGATGENVTANIRTVRAIPLRLHTNNPPKVLDVRGE 196

Query: 184 VLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243
           V++YK D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FF++G+G L G 
Sbjct: 197 VMMYKADLAKLNARQRDAGAKEFANPRNAAAGSLRQLDSRITAQRSLRFFSYGIGLLEGA 256

Query: 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303
           +MP+SHS LL+WY ++G+ +C E +V+ GV  L+EFYK  + KR  LPYEIDGVVYK+N 
Sbjct: 257 DMPASHSALLDWYAELGIPVCSERAVVRGVQGLLEFYKATSEKRPQLPYEIDGVVYKVNR 316

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
           +  Q +LGF SRAPRFA+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+
Sbjct: 317 VDQQLQLGFVSRAPRFAIAHKFPAEEALTTVQDIEVQVGRTGAITPVARLAPVLVGGVTV 376

Query: 364 TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNS 423
           T ATLHNE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP  ++ F +P+ CP+C S
Sbjct: 377 TNATLHNEDEVRRKDIQIGDTVIVRRAGDVIPEVVAFVPERRPASARPFIMPSSCPVCGS 436

Query: 424 KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV 483
            I+ +E   IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA 
Sbjct: 437 PIVRLEDEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAA 496

Query: 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
           DLYK+ F+ L  LDR+++K A N+L A++KSK TT +RFIYALGIRHVGE TAKELA +F
Sbjct: 497 DLYKLGFRALAELDRMADKSAQNVLDALEKSKRTTLARFIYALGIRHVGEATAKELARHF 556

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGN 603
            NL+ + +A+ EQLL +  IG     +   F    ++  LI QLR  G+ W  +   +  
Sbjct: 557 GNLDALLQASPEQLLEVADIGPVVAASITAFFTDAMNIELIEQLRAAGVTWPEH-VVENR 615

Query: 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIK 663
              L  K FV TG+L    R+ A   IE  GGKV   +SK T+Y+V G + G KL KA +
Sbjct: 616 PRPLAGKTFVLTGTLPTLSRDAAAEKIEAAGGKVAGSVSKKTSYVVAGAEAGSKLAKAEE 675

Query: 664 LNIKILDEKNFVKIV 678
           L + ILDE   ++++
Sbjct: 676 LGVTILDETGLLQLL 690

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|409405979|ref|ZP_11254441.1| NAD-dependent DNA ligase [Herbaspirillum sp. GW103] gi|386434528|gb|EIJ47353.1| NAD-dependent DNA ligase [Herbaspirillum sp. GW103]

 Score =  728 bits (1880), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 332/664 (50%), Positives = 456/664 (68%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R   L+ EL+RHN +YY+ D P I D +YD+L  EL+ +E  +PELLT DS TQ VG   
Sbjct: 17  RARTLRDELNRHNHSYYVLDQPSIPDAEYDRLFQELQALETAHPELLTPDSPTQRVGAGP 76

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
               + V H   M+SL NGF+DED+  F+KR+ + L+  + + Y  ELKFDG+A++LRYE
Sbjct: 77  LPQFEPVRHDIPMLSLGNGFADEDIEAFDKRVRDGLETLQEVRYATELKFDGLAISLRYE 136

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L QA+TRGDG  GEN+T NI  +  IPL L+    P++++VR EVL+YK+DF +LN+
Sbjct: 137 NGVLVQAATRGDGTTGENVTANIRTVRAIPLRLHGDNLPQVIDVRGEVLMYKEDFARLNQ 196

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +   G K+F NPRNAAAG LRQL+ +I   + L FFA+G+G L G  MP SHS LL+WY
Sbjct: 197 RQRDAGQKEFANPRNAAAGSLRQLDSRITAQRTLRFFAYGIGVLEGAEMPPSHSALLDWY 256

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           Q++GL +C E +V+SG   L++F++ I  KR +LPYEIDGVVYK++ L  QK LGF SRA
Sbjct: 257 QELGLPVCKERAVVSGAAGLLDFFRSIGAKRESLPYEIDGVVYKVDRLDQQKHLGFVSRA 316

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PRFALA+KF ++EALT ++ I +Q+GRTG ITPVA L PV + G+T+T ATLHNE E+ R
Sbjct: 317 PRFALAHKFPAQEALTVVQDIEVQVGRTGAITPVARLNPVFVGGVTVTNATLHNEDEVRR 376

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+I+IGDTV+V R+G+VIP++ + +   RP D++ F +P  CP+C S I+  E   +ARC
Sbjct: 377 KDIRIGDTVIVRRAGDVIPEVVAFVPEKRPEDARAFVMPVACPVCGSPIVRAEEEAVARC 436

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           SG W++C AQRK GLQHF+SR+AM+I GLG++++E+LV+  +V T  DLY++    L  L
Sbjct: 437 SGGWLKCSAQRKGGLQHFASRRAMDIEGLGEQLVEQLVDRQVVNTPADLYRLGLSALAEL 496

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           DR++ K A N+L A+QKSK TT +RFIYALGIRHVGE TAKELA +F  ++ +  A+EEQ
Sbjct: 497 DRMAEKSAQNVLDALQKSKTTTLARFIYALGIRHVGEATAKELARHFGGIDKLLAASEEQ 556

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           LL +  IG     +   F N P++  L+ QLR VG++W  +        +L  K FV TG
Sbjct: 557 LLEVADIGPVVASSIRAFFNDPINVELVEQLRAVGVHWPESEGVDAGAKHLAGKTFVLTG 616

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
           +L    R++A  +IE  GGKV   +SK T+Y+V G + G KL KA +L + ILDE     
Sbjct: 617 TLPNLSRDDASQMIEAAGGKVSGSVSKKTSYVVAGAEAGSKLAKAEELGVAILDEDALKA 676

Query: 677 IVKG 680
           +  G
Sbjct: 677 LCAG 680

Source: Herbaspirillum sp. GW103

Species: Herbaspirillum sp. GW103

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|398834963|ref|ZP_10592357.1| DNA ligase, NAD-dependent [Herbaspirillum sp. YR522] gi|398219400|gb|EJN05881.1| DNA ligase, NAD-dependent [Herbaspirillum sp. YR522]

 Score =  712 bits (1837), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 326/664 (49%), Positives = 450/664 (67%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  +L+ EL+ HN AYY+ D P I D +YD+L  EL+ +E  +PEL++ DS TQ VG   
Sbjct: 17  RARQLRAELNGHNHAYYVLDQPSIPDAEYDRLFQELQALETAHPELVSPDSPTQRVGGAP 76

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                 V H   M+SL NGF+D+D++ F+KR+ + L+  + + Y  ELKFDG+A++LRY 
Sbjct: 77  LPQFDPVRHDVPMLSLGNGFADDDIVAFDKRVQDGLESLQQVRYATELKFDGLAISLRYV 136

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L QA+TRGDG  GEN+T NI  +  IPL L+    P +L+VR EVL+YK DF +LN 
Sbjct: 137 DGVLVQAATRGDGTTGENVTANIRTVRAIPLRLHGDKVPAVLDVRGEVLMYKHDFARLNS 196

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +   G K+F NPRNAAAG LRQL+ +I   + L FF++G+G L G  MP SHS LL+WY
Sbjct: 197 RQRDAGQKEFANPRNAAAGSLRQLDSRITAQRTLRFFSYGIGVLEGAEMPPSHSALLDWY 256

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
            ++GL +C E  V+SG   L+ FY+ I  KR  LPYEIDGVVYK++ L  QK+LGF SRA
Sbjct: 257 VQLGLPVCREREVVSGAEGLLAFYRGIGAKREGLPYEIDGVVYKVDRLDQQKQLGFVSRA 316

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PRFALA+KF ++EALT++  I +Q+GRTG ITPVA L PV + G+T+T ATLHNE E+ R
Sbjct: 317 PRFALAHKFPAQEALTQVLDIEVQVGRTGAITPVARLNPVFVGGVTVTNATLHNEDEVRR 376

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+++IGDTV+V R+G+VIP++ + +   RP D++ F +P  CP+C+S I+ +E   IARC
Sbjct: 377 KDVRIGDTVIVRRAGDVIPEVVAHVPDRRPEDARQFVMPTRCPVCDSPIVRLEDEAIARC 436

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           SG W++C AQRK GLQHF+SR+AM+I GLG++++E+LV+ ++V T VDLY++    L  L
Sbjct: 437 SGGWLKCSAQRKGGLQHFASRRAMDIEGLGEQLVEQLVDRHVVNTPVDLYRLGLSALSEL 496

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           DR+++K A N+L A+QKSK TT  RFIYALGIRHVGE TAKELA +F +L+ +  A E Q
Sbjct: 497 DRMADKSARNVLDALQKSKQTTLPRFIYALGIRHVGEATAKELARHFGSLDRLLAADEAQ 556

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           LL +  IG     +   F +   +  L+ QLR VG+ W  +  +     +L  K FV TG
Sbjct: 557 LLEVADIGPVVAASIRAFFDDAQNVELVEQLRAVGLEWSEDAGSDSQPKHLAGKTFVLTG 616

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
           +L    R++A  +IE  GGKV   +SK T+Y+V G + G KL +A +L + ILDE     
Sbjct: 617 TLPNLSRDQASQMIEAAGGKVAGSVSKKTSYVVAGAEAGSKLARAEELGLAILDEDALKA 676

Query: 677 IVKG 680
           +  G
Sbjct: 677 LCSG 680

Source: Herbaspirillum sp. YR522

Species: Herbaspirillum sp. YR522

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237745525|ref|ZP_04576005.1| DNA ligase [Oxalobacter formigenes HOxBLS] gi|229376876|gb|EEO26967.1| DNA ligase [Oxalobacter formigenes HOxBLS]

 Score =  707 bits (1824), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 333/664 (50%), Positives = 468/664 (70%), Gaps = 2/664 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  +L+ E+ R+N AYY+ D P++ D +YD++  EL+++E  YPEL+   S TQ VG   
Sbjct: 18  RAAKLRSEIERYNYAYYVLDAPVVPDAEYDRVFRELQELEAAYPELVVPGSPTQRVGGAP 77

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                 V H   M+SL NG +DE+V  F++R+  EL + + +EY AELKFDG+AV+LRYE
Sbjct: 78  LAQFDKVEHRLPMLSLQNGLTDEEVEAFDRRLGEELGIAQ-VEYEAELKFDGLAVSLRYE 136

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L QA+TRGDG  GENIT NI  I  +PL L+   PPE+LEVR EVL++KKDF  LN+
Sbjct: 137 KGVLVQAATRGDGMSGENITANIRTIRSVPLHLSELAPPEVLEVRGEVLMFKKDFQDLNR 196

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +   G K+F NPRNAAAG LRQL+ +I  ++ L FFA+G+GEL G  +P + + LLNW+
Sbjct: 197 RQRESGQKEFVNPRNAAAGSLRQLDSQITASRQLKFFAYGIGELDGAPLPETQNRLLNWF 256

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
            ++G+ +C E  V+ G   L+ F++ I  +R  LPYEIDGVVYK+N LS Q+KLGF SRA
Sbjct: 257 VQLGIPVCEERKVVRGFKGLMGFFQAIEARRDALPYEIDGVVYKVNRLSEQQKLGFISRA 316

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PRFALA+KF ++E LT++  IN+Q+GRTG ITPVA LKPV + G+T+T ATLHNE E+ R
Sbjct: 317 PRFALAHKFPAQEVLTEVTDINVQVGRTGAITPVARLKPVFVGGVTVTNATLHNEDEVRR 376

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+++IGDTV+V R+G+VIP++ +S+   RP D++ F +P +CP+C S I+  E   IARC
Sbjct: 377 KDVRIGDTVIVRRAGDVIPEVIASVPEKRPADAREFVMPALCPVCGSPIVRPEDEAIARC 436

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           SG WI+C AQ+K GLQ F+SRKAMNI GLG+++I++LV+  I+  A DLY+++ + L  L
Sbjct: 437 SGGWIKCAAQKKGGLQLFASRKAMNIEGLGEQLIDQLVDRQIINDAADLYRLDLETLSGL 496

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           DR+++K A+N+L  + +S+ TT SRF+YALGIRHVGETTA+ LA +F NL+ +  ATEEQ
Sbjct: 497 DRMADKSASNLLDELGRSRETTLSRFLYALGIRHVGETTARSLAEHFGNLQDLMNATEEQ 556

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNP-NTKGNKNYLKEKIFVFT 615
           LL +  IG     +  +F +   +R LI +L++ G++W       K     L+++ FV T
Sbjct: 557 LLEVDDIGPVVALSIRQFFDDVRNRELIGKLQNDGVHWPERAMKEKPPALPLQDRKFVLT 616

Query: 616 GSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFV 675
           G+L +  R  A  +I NLGGKV N +SK T+Y++ G +PG KL KA +L I+ILDE+ FV
Sbjct: 617 GTLSSLTREAAAEIIRNLGGKVSNSVSKKTDYVLAGSEPGSKLAKAQELGIRILDEEAFV 676

Query: 676 KIVK 679
           ++VK
Sbjct: 677 QLVK 680

Source: Oxalobacter formigenes HOxBLS

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|329912476|ref|ZP_08275756.1| DNA ligase [Oxalobacteraceae bacterium IMCC9480] gi|327545605|gb|EGF30768.1| DNA ligase [Oxalobacteraceae bacterium IMCC9480]

 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/653 (49%), Positives = 446/653 (68%)

Query: 27  RHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHT 86
           RH  AYY+ DNP+I D  YD L  EL+ +E  +PEL+T DS T+ VG         V H+
Sbjct: 22  RHAHAYYVLDNPVIPDADYDLLFRELEALEASHPELVTADSPTRRVGAPPLPEFVQVRHS 81

Query: 87  FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTR 146
             M+SL NGF+DEDVI F++R+ + L++   + Y  ELK+DG+A+NLRYE G L +A+TR
Sbjct: 82  VPMLSLSNGFADEDVIGFDRRVRDGLQIAGEVAYATELKYDGLAINLRYENGVLVEAATR 141

Query: 147 GDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKF 206
           GDG+ GEN+T NI  I  IPL L+   PP +++VR EVL+YK DF  LN  +   GLK+F
Sbjct: 142 GDGSTGENVTVNIRTIRGIPLRLHTDTPPAIIDVRGEVLLYKADFASLNARQRAAGLKEF 201

Query: 207 TNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGE 266
            NPRNAAAG LRQL+ +I   + L FFA+G+G L G+ MP SHS LL+WY+ +G+ +C E
Sbjct: 202 ANPRNAAAGSLRQLDSRITAQRALRFFAYGIGTLEGVAMPDSHSGLLDWYRALGIPVCDE 261

Query: 267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL 326
             V+ G   L++FY++I  KR +LPYEIDGVVYK++    Q++LGF +RAPR+ALA+KF 
Sbjct: 262 RKVVHGAAGLLDFYREIGAKRASLPYEIDGVVYKVDDAVQQQQLGFVARAPRYALAHKFP 321

Query: 327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVV 386
           ++EA T ++ I++Q+GRTG ITPVA L PV + G+ +T ATLHNE E+ RK+I+IGDTV+
Sbjct: 322 AEEASTVVQGIDVQVGRTGAITPVARLAPVAVGGVIVTNATLHNEDEVRRKDIRIGDTVI 381

Query: 387 VHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQ 446
           V R+G+VIP++ + I  LR  D + F +P+ CP+C S I+ +E   IARCSG WI+C AQ
Sbjct: 382 VRRAGDVIPEVVAFIADLRGPDVQEFVMPSACPVCGSAIVRLEDEAIARCSGGWIKCAAQ 441

Query: 447 RKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANN 506
           RK GL HF SR+AM+I GLG++++ +LV+  ++ T  DLYK+    L  L R+++K A N
Sbjct: 442 RKGGLLHFVSRRAMDIEGLGEQLVVQLVDREVIRTPADLYKLGLVGLSELARMADKSARN 501

Query: 507 ILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST 566
           +L A++KSK TT +RFIYALGIRHVGE TAKELA +F  L+ +  ATEEQLL +  +G  
Sbjct: 502 VLAALEKSKSTTLARFIYALGIRHVGEATAKELAAHFGQLDIVLAATEEQLLEVADVGPV 561

Query: 567 TVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEA 626
              + ++F   PL+  L+ QLR  G++W  +   +        K FV TG+L    R+EA
Sbjct: 562 VACSILEFFADPLNVELVEQLRAAGVHWTEHAGRQVVSLPQSGKTFVLTGTLPTLGRDEA 621

Query: 627 IILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK 679
             LIE  GGKV   +SK T+Y+V G   G KL KA +L + ILDE   ++++K
Sbjct: 622 AALIEAAGGKVAGSVSKKTSYVVAGSDAGSKLAKAQELGLAILDEAGLLQLLK 674

Source: Oxalobacteraceae bacterium IMCC9480

Species: Oxalobacteraceae bacterium IMCC9480

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237747723|ref|ZP_04578203.1| DNA ligase [Oxalobacter formigenes OXCC13] gi|229379085|gb|EEO29176.1| DNA ligase [Oxalobacter formigenes OXCC13]

 Score =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/671 (48%), Positives = 473/671 (70%), Gaps = 2/671 (0%)

Query: 10  NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLT 69
           N   L+ +   L+ E+ R+NIAYY+ D PI+ D++YD+L  +L+++E+ +PEL+  DS T
Sbjct: 11  NSVSLAEQAARLRSEIERYNIAYYVLDAPIVPDSEYDRLFRQLQELEKAHPELVVPDSPT 70

Query: 70  QHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGI 129
           Q VG +     + V H   M+SL NG S+E+V  F+KRI++EL   +N+EY AELKFDG+
Sbjct: 71  QRVGGLPLAQFEKVEHKIPMLSLQNGLSEEEVAAFDKRISDELD-GENVEYEAELKFDGL 129

Query: 130 AVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK 189
           AVNLRYE G L QA+TRGDG  GENIT NI  +  IPL L+   PPE+LEVR EVL++KK
Sbjct: 130 AVNLRYENGLLVQAATRGDGTSGENITNNIKTVRTIPLRLSDLAPPEVLEVRGEVLMFKK 189

Query: 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
           DF  LN+ +     K+F NPRNAAAG LRQL+ +I   + L FFA+G+GEL+G  +P S 
Sbjct: 190 DFHDLNRRQRENEQKEFVNPRNAAAGSLRQLDSQITATRQLRFFAYGLGELKGSPLPRSQ 249

Query: 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
           S LL+W+ ++G+ +C E  V+ G   L+ F+ +I  KR +LPYEIDGVVYK+N ++ Q+K
Sbjct: 250 SALLDWFVQLGIPVCDERKVVKGFKGLMGFFNRIEEKRESLPYEIDGVVYKVNSIAEQQK 309

Query: 310 LGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLH 369
           LGF SRAPRFA+A+KF ++E LT++  I++Q+GRTG ITPVA LKPV + G+T+T ATLH
Sbjct: 310 LGFISRAPRFAIAHKFPAQEVLTEVLDIDVQVGRTGAITPVARLKPVFVGGVTVTNATLH 369

Query: 370 NESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIE 429
           NE E+ RK+++IGDTV+V R+G+VIP++ + +   R  D++ F +P +CP+C S II  E
Sbjct: 370 NEDEVRRKDVRIGDTVIVRRAGDVIPEVLAVVPERRQADAREFVMPTVCPVCGSPIIRPE 429

Query: 430 SNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489
              IARCSG WI+C AQ+K GL  F SRKA+ I GLG+++I++LV+ N++  A DLY ++
Sbjct: 430 DEAIARCSGGWIKCPAQKKGGLLLFVSRKALGIEGLGEQLIDQLVDKNVINDAADLYTLD 489

Query: 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM 549
            + L +LDR++ K A+N+L  ++KSK TTF+RF+YALGIRHVGE TA+ LA YF NL  +
Sbjct: 490 LETLSQLDRMAEKSASNLLGELEKSKKTTFARFLYALGIRHVGEATARALAGYFGNLANL 549

Query: 550 FKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNP-NTKGNKNYLK 608
            +A+EEQLL +  IG     +  +F +   +  L+ +L  VG++W  +    K  +   +
Sbjct: 550 RQASEEQLLEVADIGPIVAASIKQFFSDERNLALVDKLLGVGLHWPEHEMKEKPEELPFQ 609

Query: 609 EKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKI 668
            K FV TG+L +  R+ A  +I NLGGKV + +S+NT+Y++ G +PG KL KA +L +++
Sbjct: 610 NKKFVLTGTLPSLTRDAAAEIIRNLGGKVSSSVSRNTDYVLAGSEPGSKLAKAEELGVRV 669

Query: 669 LDEKNFVKIVK 679
           +DE  F+++VK
Sbjct: 670 IDENEFLQLVK 680

Source: Oxalobacter formigenes OXCC13

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

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	687
TIGR_CMR|CBU_0542	673	CBU_0542 "DNA ligase, NAD-depe	0.966	0.986	0.417	3.2e-145
UNIPROTKB|P15042	671	ligA [Escherichia coli K-12 (t	0.960	0.983	0.404	1.5e-131
UNIPROTKB|Q9KTD1	669	ligA "DNA ligase" [Vibrio chol	0.970	0.997	0.409	1e-130
TIGR_CMR|VC_0971	669	VC_0971 "DNA ligase" [Vibrio c	0.970	0.997	0.409	1e-130
TIGR_CMR|SO_2896	689	SO_2896 "DNA ligase, NAD-depen	0.950	0.947	0.394	5.9e-128
TIGR_CMR|CHY_1100	664	CHY_1100 "DNA ligase, NAD-depe	0.951	0.984	0.401	2e-127
TIGR_CMR|GSU_0890	670	GSU_0890 "DNA ligase, NAD-depe	0.957	0.982	0.4	1.1e-124
TIGR_CMR|BA_0306	669	BA_0306 "DNA ligase, NAD-depen	0.949	0.974	0.366	2.5e-113
TIGR_CMR|DET_0596	677	DET_0596 "DNA ligase, NAD-depe	0.954	0.968	0.357	8.1e-108
UNIPROTKB|P63973	691	ligA "DNA ligase" [Mycobacteri	0.946	0.940	0.361	2.3e-101

TIGR_CMR|CBU_0542 CBU_0542 "DNA ligase, NAD-dependent" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 1419 (504.6 bits), Expect = 3.2e-145, P = 3.2e-145
 Identities = 279/669 (41%), Positives = 425/669 (63%)

Query:    12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
             +K+  R+  L++E++ HN  YY+   P I D+ YD+L  EL+K+E+KYPE +T  S TQ 
Sbjct:     8 AKIQKRIERLRQEINDHNYRYYVLSQPTIPDSVYDELFHELEKLEKKYPETITPSSPTQR 67

Query:    72 VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAV 131
             VG    +  + VHH   M+SLDN F ++ +  F+KRI   LKL K  EY+ E K DG+A+
Sbjct:    68 VGAEPLKVFEPVHHEIPMLSLDNVFDEKGLRAFDKRIRQRLKLDKPFEYVCEPKMDGVAL 127

Query:   132 NLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDF 191
             +L YE G L +A+TRGD                 PL L     PEL+E+R EVL+ ++ F
Sbjct:   128 SLLYENGELIRAATRGDGYTGENVTQNTRTIASVPLQLRGNDYPELVEIRGEVLMPREGF 187

Query:   192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251
              K N+     G K F NPRNAA+G LRQL+P+I   + L F+ + +G L+G + P +H +
Sbjct:   188 AKFNREAEKRGDKTFANPRNAASGSLRQLDPRITAKRPLIFYGYLIGLLKGKDFPKNHCD 247

Query:   252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
             +L W++  G+ +  E  V+ G+   +++Y+ +   R  +P++IDG+V K+N L  Q +LG
Sbjct:   248 VLKWFKDWGIPVISEIKVVGGIEGCLDYYEHLVKTREKMPFDIDGIVIKVNSLQVQAELG 307

Query:   312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
             F SRAPR+A+AYKF ++E +T +KAI  Q+GRTG +TPVA L+PV + G+T++ ATLHN 
Sbjct:   308 FVSRAPRWAIAYKFPAQEKMTVVKAIEFQVGRTGAVTPVARLEPVSVSGVTVSNATLHNF 367

Query:   372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
              E+YRK++++GDTV+V R+G+VIP++   IL+ RP  +K+ KIP+ CP+C++++I  E  
Sbjct:   368 DELYRKDVRVGDTVIVRRAGDVIPEVVGPILAKRPKKAKLIKIPSRCPVCHAEVIKPEGE 427

Query:   432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
              +ARC G  + C AQ +  ++HF+SR+A++I GLG K++E  +   ++     +Y++   
Sbjct:   428 AVARCVGG-LYCRAQLRESIKHFASRRALDIEGLGDKLVELFIQEKLIKDITGIYQLKKS 486

Query:   492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
              +  L R+  K A N+L AI+KSK TT  RF+YALGIR VG+TTA+ LA +F  L+ + K
Sbjct:   487 AITALPRMGEKSAENLLTAIEKSKKTTLPRFLYALGIRGVGDTTARTLARHFHELDLLMK 546

Query:   552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGN-KNYLKEK 610
             A+ E L  I  IG    +    F +Q  +  LI++L  +G++W   P  K   K+ +  K
Sbjct:   547 ASIETLQEIRDIGPVAAENIHAFFHQKNNAELINKLIHLGVHW---PQEKAVVKSEIAGK 603

Query:   611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 670
              FV TG+L +  R EA   IE  GGK  + +SKNT+Y++ G+ PG K EKA  L I ++D
Sbjct:   604 TFVLTGALKSLTREEAEEKIERSGGKATSSVSKNTDYVIVGENPGSKYEKAKALGISLID 663

Query:   671 EKNFVKIVK 679
             E+ F+K++K
Sbjct:   664 EEAFLKLLK 672

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

UNIPROTKB|P15042 ligA [Escherichia coli K-12 (taxid:83333)]

 Score = 1290 (459.2 bits), Expect = 1.5e-131, P = 1.5e-131
 Identities = 269/665 (40%), Positives = 402/665 (60%)

Query:    17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
             ++TEL+  L  H   Y++ D P I D +YD+L+ EL+++E K+PEL+T DS TQ VG   
Sbjct:     7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAP 66

Query:    77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                   + H   M+SLDN F +E  + FNKR+ + LK  + + +  ELK DG+AV++ YE
Sbjct:    67 LAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYE 126

Query:   137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
              G L  A+TRGD                 PL L+ +  P  LEVR EV + +  F K+N+
Sbjct:   127 NGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINE 186

Query:   197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                  G K F NPRNAAAG LRQL+P+I   + L FF +GVG L G  +P +H   L  +
Sbjct:   187 DARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQF 246

Query:   257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
             +K GL +    ++     +++ FY K+   R  L ++IDGVV K+N L+ Q++LGF +RA
Sbjct:   247 KKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARA 306

Query:   317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
             PR+A+A+KF ++E +T ++ +  Q+GRTG ITPVA L+PV + G+ ++ ATLHN  EI R
Sbjct:   307 PRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIER 366

Query:   377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
               ++IGD VV+ R+G+VIP++ + +LS RP D++    P  CP+C S +  +E   +ARC
Sbjct:   367 LGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARC 426

Query:   437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
             +G  I C AQRK  L+HF SR+AM++ G+G K+I++LV    V T  DL+K+    L  L
Sbjct:   427 TGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGL 485

Query:   497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
             +R+  K A N++ A++K+K TTF+RF+YALGIR VGE TA  LA YF  LE +  A+ E+
Sbjct:   486 ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEE 545

Query:   557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNP---NTKGNKNYLKEKIFV 613
             L  +P +G         F  +  +R +IS+L   G++W   P   N +   +    K  V
Sbjct:   546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHW-PAPIVINAEEIDSPFAGKTVV 604

Query:   614 FTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKN 673
              TGSL    R++A   +  LG KV   +SK T+ ++ G+  G KL KA +L I+++DE  
Sbjct:   605 LTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAE 664

Query:   674 FVKIV 678
              ++++
Sbjct:   665 MLRLL 669

GO:0003911 "DNA ligase (NAD+) activity" evidence=IEA;IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

UNIPROTKB|Q9KTD1 ligA "DNA ligase" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 1282 (456.3 bits), Expect = 1.0e-130, P = 1.0e-130
 Identities = 274/669 (40%), Positives = 403/669 (60%)

Query:    12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
             S ++ R+TEL+K LH H + YY+ D P I D +YD+L+ EL ++E  +PEL++ DS +  
Sbjct:     2 SDVAQRLTELRKTLHEHGVRYYVEDAPSIPDAEYDRLMRELLELEAAHPELMSSDSPSLR 61

Query:    72 VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAV 131
             VG    +  + V H   M+SLDN F D ++  F +R+T+ +   ++  +  E K DG+AV
Sbjct:    62 VGGRPLDAFESVVHEIPMLSLDNAFDDGELESFYRRMTDRIPAVQHSAFCCEPKLDGLAV 121

Query:   132 NLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDF 191
             +L YE G L +A+TRGD                 PL L     P  LEVR EV + K  F
Sbjct:   122 SLLYENGVLTRAATRGDGTTGENITENVRTIKSIPLRLQGADFPTRLEVRGEVFMPKAGF 181

Query:   192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251
               LN      G K+F NPRNAAAG LRQL+ KI   + L F+A+ VG + G  + +SH +
Sbjct:   182 EALNARALKKGEKQFVNPRNAAAGSLRQLDSKITAQRPLAFYAYSVGVIEGGELATSHYQ 241

Query:   252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
                  +  GL IC E  +++ + ++  FY+ I  +R +L YEIDGVV K++ +  Q++LG
Sbjct:   242 RFLQLKGWGLPICPETKLVTSLAEVKAFYQDILQRRQSLAYEIDGVVIKVDDIQLQERLG 301

Query:   312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
             F +RAPR+A+AYKF ++E LT +  +  Q+GRTG ITPVA L+PV + G+T++ ATLHN 
Sbjct:   302 FVARAPRWAIAYKFPAQEELTLLNDVEFQVGRTGAITPVAKLEPVFVGGVTVSNATLHNA 361

Query:   372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
              EI R  + +GDTVV+ R+G+VIP+I S +L  RP ++K    P  CP+C S +  +E  
Sbjct:   362 DEIERLGVMVGDTVVIRRAGDVIPQIVSVVLERRPENAKSIVFPTRCPVCQSDVERVEGE 421

Query:   432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
              +ARCSG  I C AQRK  L+HF SRKAM++ GLG K+IE+LV+  +V T  DL+++   
Sbjct:   422 AVARCSGGLI-CQAQRKEALKHFVSRKAMDVEGLGDKVIEQLVDREMVSTPADLFRLRAG 480

Query:   492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
              L  L+R+  K A N++ A+ K+K TT  +F+YALGIR VGE TA  LA +F +LE + +
Sbjct:   481 ELTILERMGPKSAQNVIDALNKAKQTTLPKFLYALGIREVGEATALNLAQHFLSLEAIQQ 540

Query:   552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW-LNNPNTKGNKNYLKEK 610
             A+ EQ + +P +G         F  Q  ++ +I++L + GI W           + L  K
Sbjct:   541 ASLEQFIEVPDVGVVVASHLQAFFAQDRNQQVINELLEQGITWPALTAAPVAVDSALAGK 600

Query:   611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 670
             I V TGS     RN+A   ++ LG KV   +SKNT+ +  G+  G KL KA +L I++ D
Sbjct:   601 IVVLTGSFTQLSRNDAKAALQALGAKVTGSVSKNTDMVFAGEAAGSKLAKATELGIQVFD 660

Query:   671 EKNFVKIVK 679
             E+  ++ +K
Sbjct:   661 EQALIEFLK 669

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006266 "DNA ligation" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|VC_0971 VC_0971 "DNA ligase" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 1282 (456.3 bits), Expect = 1.0e-130, P = 1.0e-130
 Identities = 274/669 (40%), Positives = 403/669 (60%)

Query:    12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
             S ++ R+TEL+K LH H + YY+ D P I D +YD+L+ EL ++E  +PEL++ DS +  
Sbjct:     2 SDVAQRLTELRKTLHEHGVRYYVEDAPSIPDAEYDRLMRELLELEAAHPELMSSDSPSLR 61

Query:    72 VGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAV 131
             VG    +  + V H   M+SLDN F D ++  F +R+T+ +   ++  +  E K DG+AV
Sbjct:    62 VGGRPLDAFESVVHEIPMLSLDNAFDDGELESFYRRMTDRIPAVQHSAFCCEPKLDGLAV 121

Query:   132 NLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDF 191
             +L YE G L +A+TRGD                 PL L     P  LEVR EV + K  F
Sbjct:   122 SLLYENGVLTRAATRGDGTTGENITENVRTIKSIPLRLQGADFPTRLEVRGEVFMPKAGF 181

Query:   192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251
               LN      G K+F NPRNAAAG LRQL+ KI   + L F+A+ VG + G  + +SH +
Sbjct:   182 EALNARALKKGEKQFVNPRNAAAGSLRQLDSKITAQRPLAFYAYSVGVIEGGELATSHYQ 241

Query:   252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
                  +  GL IC E  +++ + ++  FY+ I  +R +L YEIDGVV K++ +  Q++LG
Sbjct:   242 RFLQLKGWGLPICPETKLVTSLAEVKAFYQDILQRRQSLAYEIDGVVIKVDDIQLQERLG 301

Query:   312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
             F +RAPR+A+AYKF ++E LT +  +  Q+GRTG ITPVA L+PV + G+T++ ATLHN 
Sbjct:   302 FVARAPRWAIAYKFPAQEELTLLNDVEFQVGRTGAITPVAKLEPVFVGGVTVSNATLHNA 361

Query:   372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
              EI R  + +GDTVV+ R+G+VIP+I S +L  RP ++K    P  CP+C S +  +E  
Sbjct:   362 DEIERLGVMVGDTVVIRRAGDVIPQIVSVVLERRPENAKSIVFPTRCPVCQSDVERVEGE 421

Query:   432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
              +ARCSG  I C AQRK  L+HF SRKAM++ GLG K+IE+LV+  +V T  DL+++   
Sbjct:   422 AVARCSGGLI-CQAQRKEALKHFVSRKAMDVEGLGDKVIEQLVDREMVSTPADLFRLRAG 480

Query:   492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
              L  L+R+  K A N++ A+ K+K TT  +F+YALGIR VGE TA  LA +F +LE + +
Sbjct:   481 ELTILERMGPKSAQNVIDALNKAKQTTLPKFLYALGIREVGEATALNLAQHFLSLEAIQQ 540

Query:   552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW-LNNPNTKGNKNYLKEK 610
             A+ EQ + +P +G         F  Q  ++ +I++L + GI W           + L  K
Sbjct:   541 ASLEQFIEVPDVGVVVASHLQAFFAQDRNQQVINELLEQGITWPALTAAPVAVDSALAGK 600

Query:   611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 670
             I V TGS     RN+A   ++ LG KV   +SKNT+ +  G+  G KL KA +L I++ D
Sbjct:   601 IVVLTGSFTQLSRNDAKAALQALGAKVTGSVSKNTDMVFAGEAAGSKLAKATELGIQVFD 660

Query:   671 EKNFVKIVK 679
             E+  ++ +K
Sbjct:   661 EQALIEFLK 669

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006266 "DNA ligation" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|SO_2896 SO_2896 "DNA ligase, NAD-dependent" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 1256 (447.2 bits), Expect = 5.9e-128, P = 5.9e-128
 Identities = 261/661 (39%), Positives = 399/661 (60%)

Query:    21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENS 80
             L + L+ HNI YY+ D P I+D++YD+L+ +LKK+E +YP+ +  DS TQ VG +     
Sbjct:    30 LSQSLNEHNIRYYVDDAPSITDSEYDRLMQQLKKLEAEYPQFVLADSPTQRVGGLALAKF 89

Query:    81 KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYL 140
             + + H   M+SLDN F + D   F+KR+++ +     + +  E K DG+AV++ Y  G L
Sbjct:    90 EQITHLKPMLSLDNAFDEADFTAFHKRVSDRVG---QVSFCCEPKLDGLAVSILYRNGVL 146

Query:   141 KQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYH 200
             ++A+TRGD                 PL L     PEL+EVR E  + K  F  LN+    
Sbjct:   147 ERAATRGDGTVGEDITENVKTIKSIPLRLRGNNYPELVEVRGEAFMPKAAFEALNERARL 206

Query:   201 LGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVG--ELRGMNMPSSHSELLNWYQK 258
                K+F NPRNAAAG LRQL+ KI  ++ L F+A+ +G  E     +  +H E L   + 
Sbjct:   207 KDDKQFVNPRNAAAGSLRQLDSKITASRALSFYAYALGVVEPSSHELAKTHYEQLQQLKS 266

Query:   259 IGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPR 318
              GL +  E  V   +N++  +YK I  +R +LP+EIDGVV K+N ++ Q+ LGF +++PR
Sbjct:   267 WGLPVSSEIKVCDELNQVFAYYKDILTRRSDLPFEIDGVVMKVNDIAQQQTLGFVAKSPR 326

Query:   319 FALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKN 378
             +A+AYKF ++E +T ++ ++ Q+GRTG +TPVA LKPV + G+T++ ATLHN  EI R  
Sbjct:   327 WAIAYKFPAQEEMTLLEGVDFQVGRTGAVTPVARLKPVFVGGVTVSNATLHNADEIERLG 386

Query:   379 IQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSG 438
             + +GDTV++ R+G+VIP+I + +   R  D++    P  CP+C S +  +E   +ARCSG
Sbjct:   387 VMVGDTVIIRRAGDVIPQIVAIVPERRSEDAQAIVFPQHCPVCGSLVERLEGEAVARCSG 446

Query:   439 SWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDR 498
               + C AQRK  ++HF+SRKA++I G+G K++E+L++  +V +  DL+K+    +  LDR
Sbjct:   447 G-LFCEAQRKEAIKHFASRKALDIDGMGDKIVEQLIDKELVQSPADLFKLTASMMTMLDR 505

Query:   499 VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLL 558
             +  K A N+ LAI+ +K TT  RF+YALGIR VGE TA  LA +F +L+ +  AT EQL+
Sbjct:   506 MGMKSATNLALAIEAAKTTTLPRFLYALGIREVGEATAANLAAHFGSLDALRIATIEQLI 565

Query:   559 NIPKIGSTTVKAFIKFINQPLHRL-LISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGS 617
              +  IG    +    F  QP H L +I  L   G+ W        ++  LK + +V TG+
Sbjct:   566 EVEDIGEVVAQHVAHFFAQP-HNLEVIDALIAAGVNWPAIEAPSADEQPLKGQTWVLTGT 624

Query:   618 LYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKI 677
             L    RN+A   ++ LG KV   +SKNT+ LV G+  G KL KA +L +K++ E   + +
Sbjct:   625 LNQLNRNDAKAQLQVLGAKVAGSVSKNTDCLVAGEAAGSKLAKAQELGVKVIGEDELLAL 684

Query:   678 V 678
             +
Sbjct:   685 L 685

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|CHY_1100 CHY_1100 "DNA ligase, NAD-dependent" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 1251 (445.4 bits), Expect = 2.0e-127, P = 2.0e-127
 Identities = 266/662 (40%), Positives = 401/662 (60%)

Query:    17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
             R+ EL+  LH HN  YY+ D P ISD +YD++L EL  +E++YPE +T DS +Q VG   
Sbjct:     9 RIEELRALLHYHNYRYYVLDQPEISDAEYDRMLRELISLEQQYPEFITPDSPSQRVGGEV 68

Query:    77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
              +  + V H   M SLDN F  ED+  F++R+ + L   + +EY  ELK DG+A++L YE
Sbjct:    69 AKEFREVAHLKPMYSLDNAFGPEDLKEFDRRVRSLLP-GQEVEYEVELKIDGLAISLVYE 127

Query:   137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
              G L + +TRG+                 PL L  + P  LLEVR E  + K+ F +LN+
Sbjct:   128 NGVLVRGATRGNGTTGEDITANVKTIKAIPLKL--RNPIPLLEVRGEAYMPKESFARLNE 185

Query:   197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
              R   G   F NPRNAAAG LRQL+PK+   + L  F + +GE++G   P + +EL+ W 
Sbjct:   186 QREERGEPLFANPRNAAAGSLRQLDPKVTAERDLSAFMYAIGEVQGYE-PKTQAELMEWL 244

Query:   257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
              ++G  +     V + ++ +I + +  + KRF+LPY IDG+V K+N L+ Q+ LGFT+++
Sbjct:   245 SELGFKVNPYREVFNNIDDVINYCQSWHEKRFSLPYVIDGLVIKVNSLAQQEALGFTAKS 304

Query:   317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
             PR+A+AYKF ++ A T++K I +++GRTG++TP A+ +PV + G T+TRA+LHNE  I  
Sbjct:   305 PRWAIAYKFPAEIAETRLKDIIVRVGRTGVLTPTAIFEPVSLAGTTVTRASLHNEDYIRE 364

Query:   377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
             K+I+IGD + V ++G +IP++   +   R    K F +P+ CP+C  K + +      RC
Sbjct:   365 KDIRIGDIIRVQKAGEIIPEVVEVVKEKRTGAEKEFVMPDTCPVCQGKAVRLPGEAAWRC 424

Query:   437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
             + +   C AQ K G+ HF+SR AMNI GLG  + E L+ A ++    DLY ++ + + RL
Sbjct:   425 TNA--SCPAQLKEGIVHFASRGAMNIEGLGPAVAELLLEAGLIHNYADLYYLSAEEVARL 482

Query:   497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
              R+  K A N++ AI+KSK  +  R IY LGIR VGE  A++LA +FK L+ +  A EE+
Sbjct:   483 PRMGKKSAENLINAIEKSKQNSLERLIYGLGIRLVGEKAARDLAVHFKELDKLIAAGEEE 542

Query:   557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
             ++ IP +G     +   F  Q  +  LI +L+  G+        + N+  L+   FV TG
Sbjct:   543 IMAIPSVGPKMAASIKAFFAQKENLELIEKLKAAGVNTKYLAEVRDNR--LEGLTFVLTG 600

Query:   617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
             +L +F R EA  LI +LGGKV + +SK T+Y+V G+ PG KL KA +L I IL E+ F +
Sbjct:   601 TLSSFTRKEAEQLILSLGGKVSSSVSKKTSYVVVGEDPGSKLTKAKELGIPILTEEEFRQ 660

Query:   677 IV 678
             +V
Sbjct:   661 MV 662

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|GSU_0890 GSU_0890 "DNA ligase, NAD-dependent" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 1225 (436.3 bits), Expect = 1.1e-124, P = 1.1e-124
 Identities = 266/665 (40%), Positives = 395/665 (59%)

Query:    17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
             RV  L+ EL RHN  YY  D P I+D +YD L  EL  +E ++P+L   DS TQ VG   
Sbjct:     9 RVAALRTELERHNRLYYAEDRPEITDAEYDLLFRELVDLETRFPDLAAPDSPTQRVGGAP 68

Query:    77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIE--YIAELKFDGIAVNLR 134
              +  + V H   M+SL+N F+D ++  F+ R+   L L  ++E  Y+ E K DG+AV L 
Sbjct:    69 LDKFEQVTHRIPMLSLENAFTDVEIADFDDRVKRFLGLHGDVEIDYVCEPKMDGLAVELV 128

Query:   135 YEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKL 194
             YE G L   STRGD                 PL L  + PPELLEVR EV +    F +L
Sbjct:   129 YERGILTVGSTRGDGVVGENVTHNLKTVRGIPLRLRCEQPPELLEVRGEVYLPLAAFQRL 188

Query:   195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN 254
             N  R   G   F NPRNAAAG +RQL+ +I   + L  F +  GE+RG +  ++ +E L+
Sbjct:   189 NAQREEEGEPPFANPRNAAAGSIRQLDSRITARRPLAIFCYAPGEVRGASF-AAQTEFLD 247

Query:   255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTS 314
                + GL +      + GV +++ +Y+++  +R +LPYEIDGVV K++  + Q++LG  S
Sbjct:   248 RIGEWGLPVNPLIRPVKGVAEILAYYREMTERRDSLPYEIDGVVVKVDSFALQRELGEKS 307

Query:   315 RAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEI 374
             R+PR+A+A KF  ++A+T ++ I   +GRTG+ITP A L+PV + G+T++RATLHN  E+
Sbjct:   308 RSPRWAVAVKFPPRQAVTVVEDIVPSVGRTGVITPTANLRPVEVSGVTVSRATLHNWEEM 367

Query:   375 YRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIA 434
              RK+I+IGDTVV+ R+G+VIP +   +   R    +   IP +CP C S+++ I   +  
Sbjct:   368 ERKDIRIGDTVVIERAGDVIPAVVKVLTEKRSGSERPLPIPAVCPECGSEVVKIPDEVAV 427

Query:   435 RCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL 494
             RC G  + C AQ +  + HF+SR AM++ GLG+K IE+L+   +V    DLY +     +
Sbjct:   428 RCMG--LSCPAQIRESIIHFASRDAMDMEGLGEKYIEQLLRLGLVKNVADLYTLTKDQFM 485

Query:   495 RLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATE 554
             + DR+ +KLA N+L AI+ SK    SRFI+ALGIRHVGE TAK LA  F ++E + +ATE
Sbjct:   486 QFDRMGDKLAENLLNAIEASKQRELSRFIFALGIRHVGEHTAKLLAGAFGSIENLERATE 545

Query:   555 EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVF 614
             E+LL+I ++G    ++ I F     +R  I ++   G+         G +     K FVF
Sbjct:   546 EELLSIREVGPQVARSIITFFRNEGNRETIRRMFKAGVRPTAEEKKVGGR--FTGKTFVF 603

Query:   615 TGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 674
             TG+L  F R EA  ++E  GG     +SK T+Y+V G + G KL+KA +L +++L E  F
Sbjct:   604 TGALTRFSRPEAQKMVEKEGGHAAGSVSKKTDYVVAGAEAGSKLDKARQLGVRVLTEDEF 663

Query:   675 VKIVK 679
             + +++
Sbjct:   664 LAMLE 668

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|BA_0306 BA_0306 "DNA ligase, NAD-dependent" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 1118 (398.6 bits), Expect = 2.5e-113, P = 2.5e-113
 Identities = 244/665 (36%), Positives = 392/665 (58%)

Query:    17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
             R+ EL+  L+  N  Y++ DNP +SD +YD+ + EL K+E + PE +++DS +  VG   
Sbjct:     9 RIEELRDLLNTFNYQYHVLDNPSVSDAEYDRNMQELIKLEAENPEFMSEDSPSIRVGGTV 68

Query:    77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
              +  + V H   M+SL N F++ D+  F++R+   +    N+ YI ELK DG+AV+L YE
Sbjct:    69 LDIFEKVTHKSPMLSLGNAFNEGDLRDFDRRVRQGID-DANVRYICELKIDGLAVSLHYE 127

Query:   137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
              G   Q +TRGD                 PL LN +     LE R E  + K+ F+KLN+
Sbjct:   128 KGRFIQGATRGDGVTGEDITQNLKTIKAIPLRLNEEVT---LEARGEAYMPKRSFVKLNE 184

Query:   197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
              +   G   F NPRNAAAG +RQL+PKI   + L  F +G+  +    +PS HSE L++ 
Sbjct:   185 EKEQNGEDVFANPRNAAAGSIRQLDPKIAAKRNLSMFVYGLANVEEKTIPS-HSESLDYL 243

Query:   257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
              ++G            + ++I + ++   KR +L YEIDG+V K++ ++ Q+ LG T+++
Sbjct:   244 GELGFKTNPNRRTCETIEEVIAYVEEWQEKRPHLDYEIDGIVIKVDDVALQESLGTTAKS 303

Query:   317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
             PR+A+AYKF ++E +T++  I + +GRTG++TP A L+PV + G  + RA+LHNE  I  
Sbjct:   304 PRWAIAYKFPAEEVVTRLTGIELSVGRTGVVTPTAELEPVRVAGTIVRRASLHNEDLIRE 363

Query:   377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
             K+I+IGD VVV ++G++IP++ + I   R    + + +P  CP C S+++ +E  +  RC
Sbjct:   364 KDIRIGDYVVVKKAGDIIPEVVNVIFDKRTGGEEEYHMPTHCPACESELVRLEEEVALRC 423

Query:   437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
                   C AQ + GL HF SR AMNI GLG+++I +L +A+ + T  DLY +  + LL+L
Sbjct:   424 INP--TCPAQIREGLIHFVSRNAMNIDGLGERVITQLFDADYIRTFADLYSLTKEQLLQL 481

Query:   497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
             +R   K A N++ AI+ SK  +  R ++ LGIRHVG   A+  A +F+ ++ + KATEE+
Sbjct:   482 ERFGEKSATNLVQAIENSKENSLERLLFGLGIRHVGAKAARTFAEHFETMDALVKATEEE 541

Query:   557 LLNIPKIGSTTVKAFIKFI-NQPLHRLLISQLRDVGI---Y-WLNNPNTKGNKNYLKEKI 611
             L  I +IG    ++ + +  N+ +  LL  Q ++ G+   Y  +   + +  ++Y   K 
Sbjct:   542 LKAINEIGEKMAQSVVAYFDNEDVLELL-QQFKEYGVNMTYKGIKIADLQNVESYFAGKT 600

Query:   612 FVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDE 671
              V TG L    R+EA   IE LGGKV   +SK+T+ +V G+  G KL +A K N+++ +E
Sbjct:   601 VVLTGKLEVMGRSEAKKKIEALGGKVTGSVSKSTDLVVAGEAAGSKLAQAEKHNVEVWNE 660

Query:   672 KNFVK 676
             + F++
Sbjct:   661 ERFLQ 665

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

TIGR_CMR|DET_0596 DET_0596 "DNA ligase, NAD-dependent" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 1066 (380.3 bits), Expect = 8.1e-108, P = 8.1e-108
 Identities = 241/674 (35%), Positives = 376/674 (55%)

Query:    18 VTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGG 77
             +  L++E++RHN  YY+ DNP ISD++YD LL  LK++EE +PEL+T DS TQ VG    
Sbjct:     8 IENLRREINRHNQLYYVQDNPEISDSEYDALLRRLKELEEAHPELVTADSPTQRVGAEPL 67

Query:    78 ENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYI--AELKFDGIAVNLRY 135
             +    V+H + ++SL N FSD ++  +  R+    KL  N  +    E K DG+AV L Y
Sbjct:    68 KAFGIVNHPYPLLSLANAFSDTELEAWYLRVK---KLLGNAAFQIDCEPKMDGLAVALTY 124

Query:   136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
               G     +TRGD                 PL      PP + E+R EV + K+ F KLN
Sbjct:   125 RNGKFTTGATRGDGFQGENITRNLRTIHSIPLNTEEDAPP-VFEIRGEVYLPKEGFAKLN 183

Query:   196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
             + R   GL  F NPRNAAAG LRQL+P +   + L  F + +G      +P SH ++L +
Sbjct:   184 RERADKGLSLFANPRNAAAGSLRQLDPSVTAERPLDIFIYALGYAEDSLLPDSHWQILEY 243

Query:   256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
             + ++G  I     +++ + +  E+Y+++   R +LPYE DGVV+K++ +S Q+KLG   R
Sbjct:   244 FSRLGFKINPRNRLVNTLEEAKEYYREMAENRDSLPYEADGVVFKVDSVSLQQKLGDAGR 303

Query:   316 APRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIY 375
              PR+A+AYKF +++  T ++ I I +GRTG + P A+L+PV + G+ + +A+LHNE +I 
Sbjct:   304 EPRWAIAYKFPAEQVTTLLRKIGISVGRTGTLNPYAILEPVNVGGVVVKQASLHNEDDIL 363

Query:   376 RKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKI------PNI----CPICNSKI 425
             RK+I+ GDTVV+ R+G VIP++ + +L+ R  +SK F +      P +    CP+C  +I
Sbjct:   364 RKDIREGDTVVIQRAGEVIPEVVAPVLAKRSPESKPFSMEETLFNPKLSRPACPVCGGEI 423

Query:   426 IYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDL 485
                    +  C+   + C AQ +  L+HF SR  M+I G+G+ +   L    +V    DL
Sbjct:   424 YRPAGEAMHYCAN--VSCPAQFERQLEHFVSRGTMDIRGIGESLSVILAQEGLVKNVSDL 481

Query:   486 YKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN 545
             Y +   +LL+L R+  K A+NI+ AI  SK     R I+ LGIRHVG  TA  L++ + +
Sbjct:   482 YYLTAADLLKLPRMGEKSADNIIKAIADSKSRPLDRVIFGLGIRHVGNETAALLSSRYGD 541

Query:   546 LECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKN 605
             +  +  A  ++L  IP IG+    +   + ++  +  +I +L   G+   ++        
Sbjct:   542 IWALAGAGLDELQTIPDIGAKIASSIKAYFSEEKNIAVIRRLETAGVKLASDQKPSYKPL 601

Query:   606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLN 665
              L    FV TG L +  R EA   I +LGG   + ++K T YLV G   G KL KA  + 
Sbjct:   602 PLSGVEFVVTGKLDSLSREEAQQKIRSLGGTAKDNVTKATRYLVVGADAGSKLAKARSMG 661

Query:   666 IKILDEKNFVKIVK 679
             +K L E+ F+ +++
Sbjct:   662 VKELSEQEFINMLE 675

GO:0003911 "DNA ligase (NAD+) activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006310 "DNA recombination" evidence=ISS

UNIPROTKB|P63973 ligA "DNA ligase" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 1005 (358.8 bits), Expect = 2.3e-101, P = 2.3e-101
 Identities = 243/672 (36%), Positives = 368/672 (54%)

Query:    21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GEN 79
             L +E+  H   YY+ D PIISD ++D+LL  L+ +EE++PEL T DS TQ VG  G   +
Sbjct:    20 LAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATD 79

Query:    80 SKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGY 139
              + V H  +M+SLDN F+ +++  +  RI  E+    +  Y+ ELK DG+A++L Y  G 
Sbjct:    80 FEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGR 137

Query:   140 LKQASTRGDXXXXXXXXXXXXXXXXXP--LVLNIKYP-PELLEVRCEVLIYKKDFIKLNK 196
             L +ASTRGD                 P  L     YP PE+LEVR EV     DF  LN 
Sbjct:   138 LTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNA 197

Query:   197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                  G   F NPRN+AAG LRQ +P +   + L    HG+G + G    + H   L   
Sbjct:   198 SLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLA-L 256

Query:   257 QKIGLSICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
             +  GL +    ++   L+GV + I+++ +    R  + +EIDGVV K++ ++ Q++LG T
Sbjct:   257 RAWGLPVSEHTTLATDLAGVRERIDYWGE---HRHEVDHEIDGVVVKVDEVALQRRLGST 313

Query:   314 SRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESE 373
             SRAPR+A+AYK+  +EA TK+  I + +GRTG ITP A + PV + G T+ +ATLHN SE
Sbjct:   314 SRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASE 373

Query:   374 IYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII-YIESNL 432
             I RK + IGDTVV+ ++G+VIP++   ++ LR    + F +P  CP C S +    E + 
Sbjct:   374 IKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDA 433

Query:   433 IARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKN 492
               RC  +   C  Q +  + H +SR  ++I  LG +    L+ A ++    +L+ +  ++
Sbjct:   434 DIRCPNAR-GCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERD 492

Query:   493 LLRLDRVSNKL----ANN--ILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
             LLR D    K     AN   +L+ + K+K     R + AL IRHVG T A+ LA  F +L
Sbjct:   493 LLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSL 552

Query:   547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNY 606
             + +  A+ +QL  +  +G T   A  ++     HR ++ + R  G+  ++  +    +  
Sbjct:   553 DAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDERDESVPRT- 611

Query:   607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
             L     V TGSL  F R++A   I   GGK    +SK TNY+V G  PG K +KA++L +
Sbjct:   612 LAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGV 671

Query:   667 KILDEKNFVKIV 678
              ILDE  F +++
Sbjct:   672 PILDEDGFRRLL 683

GO:0000287 "magnesium ion binding" evidence=IDA

GO:0003911 "DNA ligase (NAD+) activity" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0006266 "DNA ligation" evidence=IDA;IMP

GO:0040007 "growth" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B3R2C2	DNLJ_CUPTR	6, ., 5, ., 1, ., 2	0.4590	0.9548	0.9252	yes	N/A
B6J878	DNLJ_COXB1	6, ., 5, ., 1, ., 2	0.4275	0.9665	0.9866	yes	N/A
B1XTU0	DNLJ_POLNS	6, ., 5, ., 1, ., 2	0.4618	0.9665	0.9895	yes	N/A
B1YSH2	DNLJ_BURA4	6, ., 5, ., 1, ., 2	0.4661	0.9708	0.9652	yes	N/A
Q63T07	DNLJ_BURPS	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
B4ECN6	DNLJ_BURCJ	6, ., 5, ., 1, ., 2	0.4624	0.9723	0.9667	yes	N/A
B2T5K0	DNLJ_BURPP	6, ., 5, ., 1, ., 2	0.4733	0.9723	0.9709	yes	N/A
Q2YBB7	DNLJ_NITMU	6, ., 5, ., 1, ., 2	0.4287	0.9708	0.9434	yes	N/A
Q604U8	DNLJ_METCA	6, ., 5, ., 1, ., 2	0.4415	0.9548	0.9747	yes	N/A
Q1LNG5	DNLJ_RALME	6, ., 5, ., 1, ., 2	0.4503	0.9606	0.9153	yes	N/A
B8GTL0	DNLJ_THISH	6, ., 5, ., 1, ., 2	0.4221	0.9679	0.9851	yes	N/A
B2JID1	DNLJ_BURP8	6, ., 5, ., 1, ., 2	0.4762	0.9752	0.9809	yes	N/A
Q62JB9	DNLJ_BURMA	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
A1K713	DNLJ_AZOSB	6, ., 5, ., 1, ., 2	0.4330	0.9505	0.9422	yes	N/A
Q470D2	DNLJ_CUPPJ	6, ., 5, ., 1, ., 2	0.4659	0.9621	0.9296	yes	N/A
Q2SX03	DNLJ_BURTA	6, ., 5, ., 1, ., 2	0.4615	0.9679	0.9623	yes	N/A
Q13XB0	DNLJ_BURXL	6, ., 5, ., 1, ., 2	0.4704	0.9723	0.9709	yes	N/A
A0K8E8	DNLJ_BURCH	6, ., 5, ., 1, ., 2	0.4624	0.9723	0.9667	yes	N/A
A9II69	DNLJ_BORPD	6, ., 5, ., 1, ., 2	0.4130	0.9592	0.9454	yes	N/A
A9NC33	DNLJ_COXBR	6, ., 5, ., 1, ., 2	0.4289	0.9665	0.9910	yes	N/A
B6J1C6	DNLJ_COXB2	6, ., 5, ., 1, ., 2	0.4275	0.9665	0.9807	yes	N/A
Q1BHI7	DNLJ_BURCA	6, ., 5, ., 1, ., 2	0.4624	0.9723	0.9667	yes	N/A
C1D4R5	DNLJ_LARHH	6, ., 5, ., 1, ., 2	0.4254	0.9534	0.9465	yes	N/A
Q82TW6	DNLJ_NITEU	6, ., 5, ., 1, ., 2	0.4272	0.9650	0.9735	yes	N/A
A2SB66	DNLJ_BURM9	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
Q12AD4	DNLJ_POLSJ	6, ., 5, ., 1, ., 2	0.4381	0.9694	0.9433	yes	N/A
Q7WCJ7	DNLJ_BORBR	6, ., 5, ., 1, ., 2	0.4254	0.9490	0.9367	yes	N/A
A4SYV5	DNLJ_POLSQ	6, ., 5, ., 1, ., 2	0.4588	0.9665	0.9895	yes	N/A
A3NWN7	DNLJ_BURP0	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
A1V575	DNLJ_BURMS	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
Q83DZ6	DNLJ_COXBU	6, ., 5, ., 1, ., 2	0.4275	0.9665	0.9866	yes	N/A
Q7VRX7	DNLJ_BORPE	6, ., 5, ., 1, ., 2	0.4269	0.9490	0.9367	yes	N/A
Q7W0T4	DNLJ_BORPA	6, ., 5, ., 1, ., 2	0.4239	0.9490	0.9367	yes	N/A
B1JUF5	DNLJ_BURCC	6, ., 5, ., 1, ., 2	0.4624	0.9723	0.9667	yes	N/A
Q0KA11	DNLJ_CUPNH	6, ., 5, ., 1, ., 2	0.4634	0.9548	0.9252	yes	N/A
A4G4R4	DNLJ_HERAR	6, ., 5, ., 1, ., 2	0.5007	0.9810	0.9683	yes	N/A
A3NAV3	DNLJ_BURP6	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
Q0BE10	DNLJ_BURCM	6, ., 5, ., 1, ., 2	0.4647	0.9708	0.9652	yes	N/A
Q39F38	DNLJ_BURS3	6, ., 5, ., 1, ., 2	0.4653	0.9723	0.9667	yes	N/A
Q5NYU3	DNLJ_AROAE	6, ., 5, ., 1, ., 2	0.4232	0.9621	0.9706	yes	N/A
Q3SL40	DNLJ_THIDA	6, ., 5, ., 1, ., 2	0.4184	0.9475	0.9489	yes	N/A
A4JF81	DNLJ_BURVG	6, ., 5, ., 1, ., 2	0.4653	0.9723	0.9667	yes	N/A
A9AIK9	DNLJ_BURM1	6, ., 5, ., 1, ., 2	0.4624	0.9723	0.9667	yes	N/A
Q47FA0	DNLJ_DECAR	6, ., 5, ., 1, ., 2	0.4298	0.9621	0.9677	yes	N/A
Q1H1G6	DNLJ_METFK	6, ., 5, ., 1, ., 2	0.4300	0.9679	0.9595	yes	N/A
A9KCS0	DNLJ_COXBN	6, ., 5, ., 1, ., 2	0.4260	0.9665	0.9910	yes	N/A
Q21WC8	DNLJ_RHOFD	6, ., 5, ., 1, ., 2	0.4258	0.9650	0.9608	yes	N/A
Q3JR23	DNLJ_BURP1	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
A3MKU9	DNLJ_BURM7	6, ., 5, ., 1, ., 2	0.4640	0.9752	0.9696	yes	N/A
A6SZQ8	DNLJ_JANMA	6, ., 5, ., 1, ., 2	0.5059	0.9752	0.9682	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	6.5.1.2	0.914
3rd Layer	6.5.1	0.921

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	687
PRK07956	665	PRK07956, ligA, NAD-dependent DNA ligase LigA; Val	0.0
COG0272	667	COG0272, Lig, NAD-dependent DNA ligase (contains B	0.0
TIGR00575	652	TIGR00575, dnlj, DNA ligase, NAD-dependent	0.0
smart00532	441	smart00532, LIGANc, Ligase N family	1e-173
PRK14351	689	PRK14351, ligA, NAD-dependent DNA ligase LigA; Pro	1e-167
cd00114	307	cd00114, LIGANc, NAD+ dependent DNA ligase adenyla	1e-118
pfam01653	314	pfam01653, DNA_ligase_aden, NAD-dependent DNA liga	1e-105
PRK14350	669	PRK14350, ligA, NAD-dependent DNA ligase LigA; Pro	5e-92
pfam03120	82	pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase	1e-33
PRK08097	562	PRK08097, ligB, NAD-dependent DNA ligase LigB; Rev	5e-21
pfam12826	64	pfam12826, HHH_2, Helix-hairpin-helix motif	2e-18
COG5275	276	COG5275, COG5275, BRCT domain type II [General fun	7e-13
PRK06195	309	PRK06195, PRK06195, DNA polymerase III subunit eps	6e-11
pfam00533	77	pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain	4e-09
cd00027	72	cd00027, BRCT, Breast Cancer Suppressor Protein (B	8e-09
smart00292	78	smart00292, BRCT, breast cancer carboxy-terminal d	3e-06
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	0.002

>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated

 Score =  807 bits (2087), Expect = 0.0
 Identities = 299/664 (45%), Positives = 432/664 (65%), Gaps = 7/664 (1%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R+ EL++EL+ H  AYY+ D P ISD +YD+L  EL  +E ++PEL+T DS TQ VG   
Sbjct: 8   RIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAP 67

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            +  + V H   M+SLDN FS+E++  F+KR+   L     + Y+ ELK DG+AV+L YE
Sbjct: 68  LDGFEKVRHLVPMLSLDNAFSEEELRAFDKRVRKRLP-DPPLTYLCELKIDGLAVSLLYE 126

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L +A+TRGDG  GE+IT N+  I  IPL L+   P E LEVR EV + K DF  LN+
Sbjct: 127 NGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGNEP-ERLEVRGEVFMPKADFEALNE 185

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G K F NPRNAAAG LRQL+PKI   + L FFA+GVGE+ G  +P S SE L + 
Sbjct: 186 ERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGGELPDSQSEALEFL 245

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +  G  +     + + + +++ FY++I  +R +LPY+IDGVV K++ L+ Q++LGFT++A
Sbjct: 246 KAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKA 305

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+AYKF ++EA TK+  I +Q+GRTG +TPVA L+PV + G+T++RATLHN  EI R
Sbjct: 306 PRWAIAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIER 365

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+I+IGDTVVV R+G+VIP++   +L  RP D +   +P  CP+C S+++ +E   + RC
Sbjct: 366 KDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVMPTHCPVCGSELVRVEGEAVLRC 425

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           +   + C AQ K  L HF SR AM+I GLG+K+IE+L    ++    DL+K+  ++LL L
Sbjct: 426 TNG-LSCPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGL 484

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           +    K A N+L AI+KSK T+ +RF+YALGIRHVGE  AK LA +F +LE +  A+EE+
Sbjct: 485 EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEE 544

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           L  +  +G    ++ ++F     +R LI +L + G+    N   KG +  L  K  V TG
Sbjct: 545 LAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAGV----NMEYKGEEVDLAGKTVVLTG 600

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
           +L    R+EA   +E LG KV   +SK T+ +V G+  G KL KA +L I++LDE+ F++
Sbjct: 601 TLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLR 660

Query: 677 IVKG 680
           ++  
Sbjct: 661 LLGE 664

Length = 665

>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

 Score =  747 bits (1930), Expect = 0.0
 Identities = 296/663 (44%), Positives = 425/663 (64%), Gaps = 5/663 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
            + EL++ L++H+  YY+ D P +SD +YDQL  EL+++EEK+PEL+T DS TQ VG   
Sbjct: 10  EIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDSPTQRVGAAP 69

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
               K V H   M+SLDN F +E++  F++RI   L    ++EY+ E K DG+A++L YE
Sbjct: 70  LNAFKKVRHPVPMLSLDNAFDEEELRAFDRRIRKFLGD--SVEYVVEPKIDGLAISLVYE 127

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L +A+TRGDG  GE+IT N+  I  IPL   +   P +LEVR EV + K+DF  LN+
Sbjct: 128 NGKLVRAATRGDGTTGEDITANVRTIRSIPL--KLPGAPAVLEVRGEVFMPKEDFEALNE 185

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G K F NPRNAAAG LRQL+PKI   + L FF + VG+     +  + SE L + 
Sbjct: 186 EREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGLLADTQSERLAFL 245

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +  G  +     +    ++++ FY++   KR +LPY+IDGVV K+N L+ Q++LGFTS+A
Sbjct: 246 KAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKA 305

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+AYKF ++EA+TK+  I +Q+GRTG ITPVA L+PV + G+T++RATLHN  EI R
Sbjct: 306 PRWAIAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKR 365

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+I+IGDTVVV ++G+VIP++   +L  RP + K    P  CP+C S+++  E  ++ RC
Sbjct: 366 KDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPIPFPTHCPVCGSELVREEGEVVIRC 425

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           +   + C AQ K  L HF SR A++I GLG+K+IE+L    ++    DLY +  ++LL L
Sbjct: 426 TNG-LNCPAQLKERLIHFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSL 484

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           +    K A N+L AI+KSK    +RF+YALGIRHVGETTAK LA +F  LE +  A+EE+
Sbjct: 485 EGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEE 544

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTG 616
           L +IP IG    ++ I+F     +R LI +L   G+ W          + L  K FV TG
Sbjct: 545 LASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTG 604

Query: 617 SLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 676
           +L    R+EA  L+E LG KV   +SK T+Y+V G+  G KL KA +L +KI+DE+ F+ 
Sbjct: 605 TLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLA 664

Query: 677 IVK 679
           ++ 
Sbjct: 665 LLG 667

Length = 667

>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent

 Score =  695 bits (1796), Expect = 0.0
 Identities = 293/657 (44%), Positives = 421/657 (64%), Gaps = 8/657 (1%)

Query: 21  LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENS 80
           L+K +  H+  YY+ D P ISD +YD+L  EL+++EEK+PEL+T DS TQ VG       
Sbjct: 1   LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRF 60

Query: 81  KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYL 140
             V H+  M+SLDN F ++++  F KRI  +L L   +EY+ E K DG++V+L YE G L
Sbjct: 61  PKVRHSTPMLSLDNAFDEDELAAFIKRIRRQLGLK--VEYVVEPKIDGLSVSLTYENGVL 118

Query: 141 KQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYH 200
            +A TRGDG +GE++T N+  I  IPL L    PPE LEVR EV + K+DF  LN+ R  
Sbjct: 119 VRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALNEERRE 178

Query: 201 LGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG 260
            G K F NPRNAAAG LRQL+P+I   + L FFA+G+GE   +   +   E L W +K G
Sbjct: 179 QGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELPDAT-QYEALAWLKKWG 237

Query: 261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFA 320
             +     +   + +++E+Y++I  KR +LPYEIDGVV K++ L+ Q +LGFTS+APR+A
Sbjct: 238 FPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWA 297

Query: 321 LAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQ 380
           +AYKF ++EA TK+  + +Q+GRTG ITPVA L+PV + G T++RATLHNE EI   +I+
Sbjct: 298 IAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIR 357

Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSW 440
           IGDTVVV ++G+VIPK+   +L  R    +  + P  CP C S ++ IE   + RC    
Sbjct: 358 IGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGSPLVKIEEEAVIRCPNL- 416

Query: 441 IECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS 500
             C AQR   ++HF+SR AM+I GLG K+IE+L    +V +  DLY +  ++LL L+   
Sbjct: 417 -NCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFG 475

Query: 501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI 560
            K A N+L AI+KSK    +R ++ALGIRHVGE TAK LA +F  L+ +  A+ E+LL++
Sbjct: 476 EKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSV 535

Query: 561 PKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNP---NTKGNKNYLKEKIFVFTGS 617
             +G    ++ + F + P +R LI +L ++G+   + P   N +   + L  K FV TG+
Sbjct: 536 EGVGPKVAESIVNFFHDPNNRQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGT 595

Query: 618 LYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 674
           L    R+EA  L+ENLGGKV + +SK T+Y++ G+K G KL KA +L I I++E+  
Sbjct: 596 LSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEEEL 652

All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed [DNA metabolism, DNA replication, recombination, and repair]. Length = 652

>gnl|CDD|214709 smart00532, LIGANc, Ligase N family

 Score =  501 bits (1293), Expect = e-173
 Identities = 205/443 (46%), Positives = 291/443 (65%), Gaps = 5/443 (1%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
            ++EL+K L++H+  YY+ D PIISD +YD+L+ ELK++EEK+PEL T DS TQ VG   
Sbjct: 4   EISELRKLLNQHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKP 63

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            E    V H   M+SLDN F ++++  F++RI   L       Y+ E K DG++V+L YE
Sbjct: 64  LEGFNKVRHPVPMLSLDNAFDEDELRAFDERIEKALGS--PFAYVVEPKIDGLSVSLLYE 121

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L QA+TRGDG +GE++T N+  I  IPL L+   P E LEVR EV + K+DF+ LN+
Sbjct: 122 NGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVP-ERLEVRGEVFMPKEDFLALNE 180

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G K F NPRNAAAG LRQL+P+I   + L  F +G+G    + +P + SE L W 
Sbjct: 181 ELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQSEALKWL 240

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +++G  +     +    +++IE+Y++   KR  LPYEIDGVV K++ L+ Q++LGFTS+A
Sbjct: 241 KELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKA 300

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+AYKF ++EA TK+  I +Q+GRTG ITPVA L+PV + G T++RATLHNE EI  
Sbjct: 301 PRWAIAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEE 360

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
           K+I+IGDTVVV ++G+VIPK+   +   RP D +  ++P  CP C S+++  E  +  RC
Sbjct: 361 KDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHCPSCGSELVREEGEVDIRC 420

Query: 437 SGSWIECIAQRKAGLQHFSSRKA 459
                 C AQ    + HF+SRKA
Sbjct: 421 PN--PLCPAQLIERIIHFASRKA 441

Length = 441

>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional

 Score =  494 bits (1273), Expect = e-167
 Identities = 235/660 (35%), Positives = 376/660 (56%), Gaps = 18/660 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           +  +L++ +  H+  YY+  +P+I+D  YD L   L+ +E+ + +L T++S T+ VG   
Sbjct: 35  QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTENSPTRRVGGEP 93

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            +  + V H   M+S+D     +DV  F++R+  E+     +EY+ E KFDG++V + YE
Sbjct: 94  LDELETVEHVAPMLSIDQSGEADDVREFDERVRREVG---AVEYVCEPKFDGLSVEVVYE 150

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G  ++A+TRGDG  G+++T N+  I  +P  L   YP + L VR EV + K  F   N+
Sbjct: 151 DGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRGDYP-DFLAVRGEVYMPKDAFQAYNR 209

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G + F NPRNAAAG LRQL+P +   + L  F   V  L    +  SH E L  +
Sbjct: 210 ERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDV--LDASELFDSHWEELERF 267

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
            + GL +      +  ++  I +  ++   R +L YEIDGVV K++    +++LG T+RA
Sbjct: 268 PEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARA 327

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A AYKF ++   T I+ I +Q+GRTG +TPVALL PV + G+T++RA+LHN +EI  
Sbjct: 328 PRWAFAYKFPARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGVTVSRASLHNPAEIEE 387

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN-LIAR 435
             + +GD V V R+G+VIP +   ++      +  F+ P+ CP+C+S    +E +  +A 
Sbjct: 388 LGVNVGDRVRVKRAGDVIPYV-EEVVEKDSEGT--FEFPDTCPVCDSA---VERDGPLAF 441

Query: 436 CSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLR 495
           C+G  + C AQ +  ++H++SR A++I GLG++ +++LV+A +V +  DLY +   +L  
Sbjct: 442 CTGG-LACPAQLERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAE 500

Query: 496 LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEE 555
           L+      A N+L  ++ S+    + F+ ALGI  VG TTA+ LA  F   E +  A EE
Sbjct: 501 LEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEE 560

Query: 556 QLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFT 615
            L  +  +G T  +   +F +   +R +I  L D G+      +  G+   L    FVFT
Sbjct: 561 ALRAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDA--LDGLTFVFT 618

Query: 616 GSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEKNF 674
           GSL  + R+EA  L+E  GG     +S NT+YLV G+ PG+ K + A   ++  LDE+ F
Sbjct: 619 GSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEF 678

Length = 689

>gnl|CDD|238062 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain

 Score =  355 bits (913), Expect = e-118
 Identities = 144/310 (46%), Positives = 201/310 (64%), Gaps = 7/310 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVG-LV 75
           R+ EL++ L++H+  YY+ D P +SD +YD+L  EL+ +EE++PEL T DS TQ VG   
Sbjct: 2   RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTP 61

Query: 76  GGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
                K V H   M+SLDN F +E++  F++RI   L   +   Y+ E K DG++++LRY
Sbjct: 62  LSGFKK-VRHPVPMLSLDNAFDEEELRAFDERIKRFLG--EEPAYVVEPKIDGLSISLRY 118

Query: 136 EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
           E G L QA+TRGDG  GE++T N+  I  IPL   +   PE LEVR EV + K DF  LN
Sbjct: 119 ENGVLVQAATRGDGTTGEDVTENVRTIRSIPL--TLAGAPETLEVRGEVFMPKADFEALN 176

Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
           K R   G K F NPRNAAAG LRQL+PKI   + L FF +G+GE  G+  P + SE L +
Sbjct: 177 KEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG-PKTQSEALAF 235

Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
            ++ G  +  E  +   + +++ FY +I  KR +LPYEIDGVV K++ L+ Q++LGFTS+
Sbjct: 236 LKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSK 295

Query: 316 APRFALAYKF 325
           APR+A+AYKF
Sbjct: 296 APRWAIAYKF 305

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only. Length = 307

>gnl|CDD|216629 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation domain

 Score =  323 bits (829), Expect = e-105
 Identities = 131/310 (42%), Positives = 193/310 (62%), Gaps = 4/310 (1%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
            +  L++ + +++  YY+ DNP + D +YD+L   L+ +EEK+PEL+T DS TQ VG   
Sbjct: 6   EIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELITPDSPTQRVGAPL 65

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
             + K V H   M+SLDN F ++++  + +RI   L       Y+ E K DG+AV+L YE
Sbjct: 66  LGDFKKVRHPAPMLSLDNAFDEDELAAWIRRIRRRLGN-SEKAYVVEPKIDGVAVSLTYE 124

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L +A+TRGDG  GE++T N+  I  IPL   +   P  LEVR EV + K+DF  LN+
Sbjct: 125 DGVLVRAATRGDGTTGEDVTQNVKTIRAIPL--TLPGDPARLEVRGEVFMPKEDFEALNE 182

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNW 255
            R   G K F NPRNAAAG LRQL+P+I   + L FF +G+G   G+ + P + SE L  
Sbjct: 183 EREEEGEKPFANPRNAAAGSLRQLDPEITAKRKLRFFVYGLGLPEGLELGPQTQSEALKQ 242

Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
            + +G  +     +   +++++++Y +   KR  LP+EIDGVV K+N L  Q++LGFTS+
Sbjct: 243 LKSLGFPVSPHTRLCKNIDEVLDYYAEWEKKRDELPFEIDGVVVKVNELPLQRELGFTSK 302

Query: 316 APRFALAYKF 325
           APR+A+AYKF
Sbjct: 303 APRWAIAYKF 312

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism. Length = 314

>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional

 Score =  299 bits (767), Expect = 5e-92
 Identities = 210/682 (30%), Positives = 352/682 (51%), Gaps = 33/682 (4%)

Query: 12  SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
             +   + +LKK + + +  YY+  +P + D  YD+ L  L+++E KYPE  T DS T  
Sbjct: 3   KDIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLK 62

Query: 72  VGLVGGENSKYVHHTFKMMSLDNGFS-DEDVIIFNKRITNELKLTKNIEYIAELKFDGIA 130
            G     + K V H+F ++SLD  +      +   K       L  +     E K DG +
Sbjct: 63  FGSDLLNDFKEVEHSFPILSLDKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCS 122

Query: 131 VNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKD 190
           + L Y+ G L++A TRGDG  G ++T N+  I  +PL ++ K     L +R E+ I K++
Sbjct: 123 IVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDEKVE---LVLRGEIYITKEN 179

Query: 191 FIKLNKYRYHLGLKK-FTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
           F+K+NK      L+K +TN RN A+GILR+++ +   N  L  F + +     + + ++H
Sbjct: 180 FLKINKT-----LEKPYTNARNLASGILRRIDSREVANFPLDIFVYDILY-SSLELKTNH 233

Query: 250 SELLNWYQKIGLSI---CGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
            +  +  +K G  +   C  +   + + +++ + K I  KR +  YEIDGVV K++  + 
Sbjct: 234 -DAFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFAL 292

Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
           ++ LG+TS  P++++AYKF S    +K+  I +Q+GR+G ITPVA ++ V + G  IT A
Sbjct: 293 REILGYTSHHPKWSMAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNA 352

Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
           +LHN+  I    + +GD V + R G+VIP +   I  L       FKIP+ CP C + +I
Sbjct: 353 SLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKL---SVGFFKIPDNCPSCKTALI 409

Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
              ++L   C  +    +   +  +++F S+K MNI+GL  K IE L     + + +DLY
Sbjct: 410 KEGAHLF--CVNNHCPSVIVER--IKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLY 465

Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKEL----ANY 542
             NF  L+ L    +K  NN+  +I+ SK   FS+ + ++GI+ +GE T   L     N 
Sbjct: 466 TFNFDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNS 525

Query: 543 FKNLECMFKATE---EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL-NNP 598
           F  +  + +  E    +LL I  IG       I+  N  +     +  +++G     ++ 
Sbjct: 526 FDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSI 585

Query: 599 NTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKL 658
           N     ++L  K F  TGS   + R+  I  +   G      ++K  ++L+ G+K G KL
Sbjct: 586 NIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKL 645

Query: 659 EKAIKLNIKIL---DEKNFVKI 677
           +KA  L IKI+   D K++V +
Sbjct: 646 KKANNLGIKIMSLFDIKSYVDL 667

Length = 669

>gnl|CDD|145978 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain

 Score =  123 bits (310), Expect = 1e-33
 Identities = 47/81 (58%), Positives = 65/81 (80%)

Query: 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHR 389
           A+TK+  I +Q+GRTG+ITPVA+L+PV + G T++RATLHNE EI  K+I+IGDTVVV +
Sbjct: 1   AVTKLLDIEVQVGRTGVITPVAILEPVELAGTTVSRATLHNEDEIEEKDIRIGDTVVVRK 60

Query: 390 SGNVIPKITSSILSLRPNDSK 410
           +G+VIPKI   +L  RP D++
Sbjct: 61  AGDVIPKIVGVVLEKRPGDTR 81

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding. Length = 82

>gnl|CDD|236150 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed

 Score = 97.3 bits (243), Expect = 5e-21
 Identities = 106/492 (21%), Positives = 192/492 (39%), Gaps = 83/492 (16%)

Query: 125 KFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEV 184
           K DG+AV L Y  G L QA +RG+G  GE+ T    +I  IP    +      L ++ E+
Sbjct: 125 KVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQ--QLPGALANLVLQGEL 182

Query: 185 LIYKKDFIKLNKYR-YHLGLKKFTNPRNAAAGILR--QLNPKINKNKILHFFA----HGV 237
                 F++   +    +G     N R   AG++     +P +N+   +  F      G 
Sbjct: 183 ------FLRREGHIQQQMGGI---NARAKVAGLMMRKDPSPTLNQ---IGVFVWAWPDG- 229

Query: 238 GELRGMNMPSSHSELLNWYQKIGLSICGEYSV----LSGVNKLIEFYKKINIKRFNLPYE 293
                   P+S  E L      G  +   Y+        V +  E +      R  LP+ 
Sbjct: 230 --------PASMPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY-----RAPLPFV 276

Query: 294 IDGVVYKINCLSTQKKLG--FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA 351
            DGVV +      ++  G  +      +A+A+K+   + + +++A+   +GRTG IT V 
Sbjct: 277 TDGVVVR----QAKEPPGRYWQPGQGEWAVAWKYPPVQQVAEVRAVQFAVGRTGKITVVL 332

Query: 352 LLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKI 411
            L+PV++D   ++R  + +     + +I  GD V+V  +G  IP++   +   R  +   
Sbjct: 333 ELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVV--WRGAERTK 390

Query: 412 FKIPNI-------C----PICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAM 460
              P+        C    P C       +   +AR    W+             S ++ +
Sbjct: 391 PTPPDADRFHSLSCFRASPGC-------QEQFLARL--VWL-------------SGKQGL 428

Query: 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS 520
            + G+G+     L    +         +  + L     +    A  +      ++   FS
Sbjct: 429 GLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFS 488

Query: 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580
           R++ ALGI  + +     L +   + + +   +E+Q   +P IG    +  I F+  P  
Sbjct: 489 RWLKALGIP-LPQAALNALDDR--SWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEV 545

Query: 581 RLLISQLRDVGI 592
           + L   L   GI
Sbjct: 546 KALADWLAAQGI 557

Length = 562

>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif

 Score = 79.4 bits (197), Expect = 2e-18
 Identities = 29/64 (45%), Positives = 42/64 (65%)

Query: 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580
           R ++ALGIRHVGE TAK LA +F +L+ +  A+ E+LL I  IG    ++ ++F   P +
Sbjct: 1   RLLFALGIRHVGEKTAKLLAKHFGSLDALANASVEELLEIDDIGPIVAQSIVEFFANPAN 60

Query: 581 RLLI 584
           R LI
Sbjct: 61  RELI 64

The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. Length = 64

>gnl|CDD|227600 COG5275, COG5275, BRCT domain type II [General function prediction only]

 Score = 69.4 bits (169), Expect = 7e-13
 Identities = 32/84 (38%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 602 GNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEK 660
           G +  LK K+FVFTG L    R++A  L++  GG+V    S  T +LV G   G  K+EK
Sbjct: 152 GERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEK 211

Query: 661 AIKLNIKILDEKNFVKIVKGFSTE 684
             +L IK +DE+ F  ++K     
Sbjct: 212 IKQLKIKAIDEEGFDSLIKDTPAA 235

Length = 276

>gnl|CDD|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated

 Score = 63.6 bits (155), Expect = 6e-11
 Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 14/92 (15%)

Query: 603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKL---E 659
                KE++ VFTG L +  R+EA+IL+  LGG V + ++K T YLV   K  + L   E
Sbjct: 217 GFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREE 276

Query: 660 KAIKL-----------NIKILDEKNFVKIVKG 680
            + KL           NIK L+E+ F++  K 
Sbjct: 277 MSNKLKKAIDLKKKGQNIKFLNEEEFLQKCKE 308

Length = 309

>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain

 Score = 53.1 bits (128), Expect = 4e-09
 Identities = 31/68 (45%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIK 663
              K K FV TG L + +R E   LIE LGGKV + +SK T +++ G+  G  KL KAI 
Sbjct: 4   KLFKGKTFVITG-LDSLEREELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIA 62

Query: 664 LNIKILDE 671
           L I I+ E
Sbjct: 63  LGIPIVTE 70

The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants. Length = 77

>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain

 Score = 52.3 bits (126), Expect = 8e-09
 Identities = 30/63 (47%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 610 KIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKI 668
             FV TG L + +R+E   LIE LGGKV + +SK T +++ G   G KKL KAIKL I I
Sbjct: 2   LTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPI 61

Query: 669 LDE 671
           +  
Sbjct: 62  VTP 64

The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks. Length = 72

>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 28/70 (40%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG---KKLEKA 661
              K K F  TGS    +R+E   LIE LGGKV + +S  T   V    P     +L KA
Sbjct: 2   KLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKA 61

Query: 662 IKLNIKILDE 671
           I L I I+ E
Sbjct: 62  IALGIPIVKE 71

Length = 78

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 512 QKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA 570
           +K  +T   +  Y +  +  VG   A+ L  +F ++E +  A+EE+L+ +  IG  T K 
Sbjct: 703 EKKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKR 762

Query: 571 FIKFINQP 578
             + +   
Sbjct: 763 IREVVTSE 770

Length = 773

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	687
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	100.0
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	100.0
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	100.0
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	100.0
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	100.0
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	100.0
smart00532	441	LIGANc Ligase N family.	100.0
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	100.0
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	100.0
PF03120	82	DNA_ligase_OB: NAD-dependent DNA ligase OB-fold do	99.97
PRK06195	309	DNA polymerase III subunit epsilon; Validated	99.64
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	99.64
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	99.58
COG5275	276	BRCT domain type II [General function prediction o	99.5
cd07894	342	Adenylation_RNA_ligase Adenylation domain of RNA c	99.17
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	99.12
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	98.76
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	98.74
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	98.73
cd07896	174	Adenylation_kDNA_ligase_like Adenylation domain of	98.72
PRK09125	282	DNA ligase; Provisional	98.62
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	98.6
cd07898	201	Adenylation_DNA_ligase Adenylation domain of ATP-d	98.52
smart00292	80	BRCT breast cancer carboxy-terminal domain.	98.5
cd07901	207	Adenylation_DNA_ligase_Arch_LigB Adenylation domai	98.41
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	98.39
PRK03180	508	ligB ATP-dependent DNA ligase; Reviewed	98.37
TIGR02779	298	NHEJ_ligase_lig DNA polymerase LigD, ligase domain	98.32
cd07906	190	Adenylation_DNA_ligase_LigD_LigC Adenylation domai	98.26
PRK07636	275	ligB ATP-dependent DNA ligase; Reviewed	98.22
cd07900	219	Adenylation_DNA_ligase_I_Euk Adenylation domain of	98.21
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	98.2
PRK05601	377	DNA polymerase III subunit epsilon; Validated	98.19
PF01068	202	DNA_ligase_A_M: ATP dependent DNA ligase domain; I	98.18
TIGR00574	514	dnl1 DNA ligase I, ATP-dependent (dnl1). All prote	98.15
PRK08224	350	ligC ATP-dependent DNA ligase; Reviewed	98.15
cd06846	182	Adenylation_DNA_ligase_like Adenylation domain of	98.11
cd07897	207	Adenylation_DNA_ligase_Bac1 Adenylation domain of	98.1
cd07903	225	Adenylation_DNA_ligase_IV Adenylation domain of DN	98.04
COG1793	444	CDC9 ATP-dependent DNA ligase [DNA replication, re	98.03
PRK01109	590	ATP-dependent DNA ligase; Provisional	97.94
cd07905	194	Adenylation_DNA_ligase_LigC Adenylation domain of	97.93
PHA00454	315	ATP-dependent DNA ligase	97.91
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	97.89
cd07902	213	Adenylation_DNA_ligase_III Adenylation domain of D	97.88
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	97.87
cd08039	235	Adenylation_DNA_ligase_Fungal Adenylation domain o	97.87
PRK09633	610	ligD ATP-dependent DNA ligase; Reviewed	97.87
PHA02587	488	30 DNA ligase; Provisional	97.82
PRK09247	539	ATP-dependent DNA ligase; Validated	97.8
PRK09632	764	ATP-dependent DNA ligase; Reviewed	97.76
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	97.7
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	97.67
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	97.64
KOG2841|consensus	254		97.6
PRK08609	570	hypothetical protein; Provisional	97.58
PRK12766	232	50S ribosomal protein L32e; Provisional	97.58
PRK05972	860	ligD ATP-dependent DNA ligase; Reviewed	97.53
PLN03113	744	DNA ligase 1; Provisional	97.51
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	97.43
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.41
cd07895	215	Adenylation_mRNA_capping Adenylation domain of GTP	97.41
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	97.31
PRK14973	936	DNA topoisomerase I; Provisional	97.3
PRK12766	232	50S ribosomal protein L32e; Provisional	97.21
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	97.14
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	97.08
PRK13482	352	DNA integrity scanning protein DisA; Provisional	96.96
TIGR01209	374	RNA ligase, Pab1020 family. Members of this family	96.96
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	96.92
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	96.91
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	96.9
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	96.87
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	96.84
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	96.68
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	96.56
PRK14973	936	DNA topoisomerase I; Provisional	96.51
PF03118	66	RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha	96.47
PRK08609	570	hypothetical protein; Provisional	96.44
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	96.4
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	96.33
COG1423	382	ATP-dependent DNA ligase, homolog of eukaryotic li	96.33
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	96.28
KOG1968|consensus	871		96.27
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	96.25
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	96.0
PRK13766	773	Hef nuclease; Provisional	95.93
PRK07758	95	hypothetical protein; Provisional	95.87
PRK00254	720	ski2-like helicase; Provisional	95.78
COG2003	224	RadC DNA repair proteins [DNA replication, recombi	95.77
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	95.75
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	95.67
PRK00254	720	ski2-like helicase; Provisional	95.66
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	95.64
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	95.55
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	95.55
TIGR01259	120	comE comEA protein. This model describes the ComEA	95.45
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	95.41
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.41
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	95.4
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	95.36
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	95.27
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	95.27
TIGR01259	120	comE comEA protein. This model describes the ComEA	95.16
PRK02362	737	ski2-like helicase; Provisional	95.14
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	95.07
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	95.02
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	94.99
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	94.85
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	94.8
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	94.61
PRK02515	132	psbU photosystem II complex extrinsic protein prec	94.6
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.55
PRK01172	674	ski2-like helicase; Provisional	94.46
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	94.43
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	94.21
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	94.19
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	94.09
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	94.07
TIGR02307	325	RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of t	94.07
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	93.97
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	93.92
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	93.91
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	93.88
PHA02142	366	putative RNA ligase	93.87
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	93.82
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	93.76
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	93.73
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	93.64
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.64
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	93.53
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	93.27
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	93.06
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	92.93
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	92.86
KOG2534|consensus	353		92.69
COG1623	349	Predicted nucleic-acid-binding protein (contains t	92.63
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	92.61
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	92.39
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	92.25
PRK02515	132	psbU photosystem II complex extrinsic protein prec	92.05
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	92.02
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	91.97
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	91.65
PRK00024	224	hypothetical protein; Reviewed	91.34
TIGR00608	218	radc DNA repair protein radc. This family is based	91.3
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	91.16
PF09414	186	RNA_ligase: RNA ligase; InterPro: IPR021122 This e	90.71
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	90.38
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	90.38
PRK10702	211	endonuclease III; Provisional	90.25
KOG1929|consensus	811		89.56
PRK13482	352	DNA integrity scanning protein DisA; Provisional	89.09
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	88.74
TIGR02236	310	recomb_radA DNA repair and recombination protein R	88.67
KOG0967|consensus	714		87.89
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	87.67
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	87.54
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	87.38
PTZ00035	337	Rad51 protein; Provisional	86.83
PRK01172	674	ski2-like helicase; Provisional	86.76
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	86.66
PRK00420	112	hypothetical protein; Validated	86.05
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	86.02
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	85.53
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	85.3
PRK10736	374	hypothetical protein; Provisional	85.3
KOG3226|consensus	508		85.07
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	84.77
PRK04301	317	radA DNA repair and recombination protein RadA; Va	84.71
COG2231	215	Uncharacterized protein related to Endonuclease II	84.42
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	84.34
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	84.13
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	84.06
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	83.93
PRK13766	773	Hef nuclease; Provisional	83.31
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	83.24
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	83.17
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	83.11
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	82.56
KOG2841|consensus	254		82.42
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	82.05
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	81.93
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	81.92
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	81.72
PRK09482	256	flap endonuclease-like protein; Provisional	81.65
PF01331	192	mRNA_cap_enzyme: mRNA capping enzyme, catalytic do	80.96
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	80.78
TIGR01083	191	nth endonuclease III. This equivalog model identif	80.46
TIGR03491	457	RecB family nuclease, putative, TM0106 family. Mem	80.42
COG1623	349	Predicted nucleic-acid-binding protein (contains t	80.41

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=100.00  E-value=2.7e-202  Score=1669.97  Aligned_cols=665  Identities=45%  Similarity=0.724  Sum_probs=643.3

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccc
Q psy11422         10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKM   89 (687)
Q Consensus        10 ~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pM   89 (687)
                      ++.+++++|.+|+++|++|+++||++|+|.|||++||+|+++|++||.+||++.++|||||+||+.+..+|.||+|.+||
T Consensus         3 ~~~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~lE~~~Pel~~~dSPtqrVG~~~~~~F~kv~H~~pM   82 (667)
T COG0272           3 SMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDSPTQRVGAAPLNAFKKVRHPVPM   82 (667)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHHHHHHhCCCcCCCCCCccccCccchhccccccCCCcc
Confidence            46777899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccc
Q psy11422         90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL  169 (687)
Q Consensus        90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l  169 (687)
                      |||+|+||.+||.+|++|+.+.++.  +..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|
T Consensus        83 lSL~naf~~~el~~f~~ri~~~~~~--~~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~IP~~l  160 (667)
T COG0272          83 LSLDNAFDEEELRAFDRRIRKFLGD--SVEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSIPLKL  160 (667)
T ss_pred             cchhhcCCHHHHHHHHHHHHHhcCC--CcceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhhhhhc
Confidence            9999999999999999999998873  67899999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCH
Q psy11422        170 NIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH  249 (687)
Q Consensus       170 ~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~  249 (687)
                      ++  +|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|.||+|+|+...+...+.||
T Consensus       161 ~~--~p~~lEVRGEvfm~k~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~~~~~t~  238 (667)
T COG0272         161 PG--APAVLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGLLADTQ  238 (667)
T ss_pred             cC--CCceEEEEeEEEEeHHHHHHHHHHHHHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCCCCccCH
Confidence            85  6899999999999999999999999999999999999999999999999999999999999999876542336899


Q ss_pred             HHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11422        250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (687)
Q Consensus       250 ~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (687)
                      ++.|++|++|||+|+++.+.|.|.+|+.+||++|.+.|+.|||+|||+||||||+++|+.||+|+|+||||||||||+++
T Consensus       239 ~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~e  318 (667)
T COG0272         239 SERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAEE  318 (667)
T ss_pred             HHHHHHHHHcCCCCCcHhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11422        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (687)
Q Consensus       330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (687)
                      +.|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+|+||+|||+|.|.|||||||+|++|+.+.|+++.
T Consensus       319 ~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~d~I~rkdIrIGDtV~V~kAGdVIP~V~~Vv~e~R~~~~  398 (667)
T COG0272         319 AVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKRKDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNE  398 (667)
T ss_pred             eeeEEEEEEEecCCceeeeeeEEEEeEEECCEEEEEeecCCHHHHHhcCCCCCCEEEEEecCCCCcceeeeecccCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11422        410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN  489 (687)
Q Consensus       410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  489 (687)
                      .+|.+|++||+|||+|++.++++.+||+|+.. ||+|.+++|.||+||+||||+|||+|+|++|+++++|++++|||+|+
T Consensus       399 ~~~~~P~~CP~C~s~l~r~~~e~~~rC~n~~~-C~aq~~e~l~hfvSr~AmdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt  477 (667)
T COG0272         399 KPIPFPTHCPVCGSELVREEGEVVIRCTNGLN-CPAQLKERLIHFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLT  477 (667)
T ss_pred             CCCCCCCCCCCCCCeeEeccCceeEecCCCCC-ChHHHhhheeeEecCCccCCCCcCHHHHHHHHHcCccCCHHHHHhCC
Confidence            99999999999999999988999999999767 99999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK  569 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~  569 (687)
                      .++|+.++|||+|+++||+++|++||+.+|+|||+||||||||+++|+.|+.+|+|+++|..|+.++|..++|||+++|.
T Consensus       478 ~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~  557 (667)
T COG0272         478 EEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVAR  557 (667)
T ss_pred             HHHHhhccchhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEE
Q psy11422        570 AFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLV  649 (687)
Q Consensus       570 sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV  649 (687)
                      +|.+||+++.|++++++|.+.|+.+..........++|.||+|||||+|+.|+|++++++++++||+|++||||||||||
T Consensus       558 si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vv  637 (667)
T COG0272         558 SIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVV  637 (667)
T ss_pred             HHHHHHcCHHHHHHHHHHHHcCCCccccccccccccccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEE
Confidence            99999999999999999999998876543222222789999999999999999999999999999999999999999999


Q ss_pred             EcCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        650 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       650 ~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      +|+++|||++||++|||+||+|++|+++|+
T Consensus       638 aG~~aGSKl~kA~eLgv~i~~E~~~~~ll~  667 (667)
T COG0272         638 AGENAGSKLAKAQELGVKIIDEEEFLALLG  667 (667)
T ss_pred             EcCCCChHHHHHHHcCCeEecHHHHHHhhC
Confidence            999999999999999999999999999874

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=100.00  E-value=6.7e-187  Score=1595.94  Aligned_cols=662  Identities=45%  Similarity=0.721  Sum_probs=633.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11422         11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM   90 (687)
Q Consensus        11 ~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl   90 (687)
                      ++.++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+...|.||+|++|||
T Consensus         2 ~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMl   81 (665)
T PRK07956          2 MEEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAPLDGFEKVRHLVPML   81 (665)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCccccCccccccCcceeCCCcCc
Confidence            45667899999999999999999999999999999999999999999999999999999999999888999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11422         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (687)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (687)
                      ||+|+|+.+||.+|++|+.+.++. .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+
T Consensus        82 SL~k~~~~~el~~w~~r~~~~~~~-~~~~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~  160 (665)
T PRK07956         82 SLDNAFSEEELRAFDKRVRKRLPD-PPLTYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLH  160 (665)
T ss_pred             CccccCCHHHHHHHHHHHHHhcCC-CCcceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhc
Confidence            999999999999999999887752 2357999999999999999999999999999999999999999999999999996


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEeccccc-CCCCCCCH
Q psy11422        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELR-GMNMPSSH  249 (687)
Q Consensus       171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~-~~~~~~~~  249 (687)
                      . ..|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..+ +.. +.+|
T Consensus       161 ~-~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~~~~-~~t~  238 (665)
T PRK07956        161 G-NEPERLEVRGEVFMPKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGGEL-PDSQ  238 (665)
T ss_pred             c-cCCCeEEEEEEEEEEHHHHHHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccCCCC-CCCH
Confidence            3 258899999999999999999999999999999999999999999999999999999999999997433 222 4799


Q ss_pred             HHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11422        250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (687)
Q Consensus       250 ~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (687)
                      ++.|++|++|||+++++.+.+.+.+++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++
T Consensus       239 ~e~l~~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrWaiA~Kf~~~~  318 (665)
T PRK07956        239 SEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAEE  318 (665)
T ss_pred             HHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHHhcCccCCCCCceeEecCCCce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11422        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (687)
Q Consensus       330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (687)
                      ++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.
T Consensus       319 ~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~  398 (665)
T PRK07956        319 ATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDE  398 (665)
T ss_pred             eEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11422        410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN  489 (687)
Q Consensus       410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  489 (687)
                      .+|.+|++||+||++|++.++++.+||+|... ||+|++++|.||+||+||||+||||++|++||++|+|++++|||+|+
T Consensus       399 ~~~~~P~~CP~Cgs~l~~~~~~~~~~C~n~~~-C~aq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  477 (665)
T PRK07956        399 REIVMPTHCPVCGSELVRVEGEAVLRCTNGLS-CPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLT  477 (665)
T ss_pred             ccCcCCCCCCCCCCEeEecCCCeEEECCCCCC-CHHHHHHHHHHhhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHhcC
Confidence            89999999999999999888899999999756 99999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK  569 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~  569 (687)
                      .++|..++|||+|+++||+++|+.+|+.+|+|||+|||||+||+++|++|+++|++++++..|+.++|.+++|||+++|+
T Consensus       478 ~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~  557 (665)
T PRK07956        478 AEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQ  557 (665)
T ss_pred             HHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEE
Q psy11422        570 AFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLV  649 (687)
Q Consensus       570 sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV  649 (687)
                      +|++||+++.|++++++|.+.|+++....    .+.+|+|++|||||+|+.|+|++++++|+++||+|++|||++|||||
T Consensus       558 sI~~ff~~~~~~~~i~~L~~~gv~~~~~~----~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv  633 (665)
T PRK07956        558 SIVEFFAVEENRELIDELLEAGVNMEYKG----EEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVV  633 (665)
T ss_pred             HHHHHHhhhhHHHHHHHHHHcCCCccccc----cCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEE
Confidence            99999999999999999999998875421    23469999999999999899999999999999999999999999999


Q ss_pred             EcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        650 KGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       650 ~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      +|+++|+|++||+++||+||+|++|++||++
T Consensus       634 ~G~~~gsK~~kA~~lgI~ii~E~~f~~~l~~  664 (665)
T PRK07956        634 AGEAAGSKLAKAQELGIEVLDEEEFLRLLGE  664 (665)
T ss_pred             ECCCCChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence            9999999999999999999999999999964

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=100.00  E-value=9.2e-186  Score=1578.99  Aligned_cols=651  Identities=31%  Similarity=0.496  Sum_probs=613.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11422         14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD   93 (687)
Q Consensus        14 ~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~   93 (687)
                      ++++|++|+++|++||++||++++|+|||++||+|+++|++||++||++.+++|||++||+.+...|.||+|++|||||+
T Consensus         5 ~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~lE~~~p~~~~~~Spt~~Vg~~~~~~f~kv~H~~pMlSL~   84 (669)
T PRK14350          5 IQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLKFGSDLLNDFKEVEHSFPILSLD   84 (669)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCccCCccccccCCceecCCcccccc
Confidence            46789999999999999999999999999999999999999999999999999999999999888999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHhhcc-CCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccC
Q psy11422         94 NGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (687)
Q Consensus        94 k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (687)
                      |+|+.+||.+|++|+.+.+.. ..+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+. 
T Consensus        85 k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~~-  163 (669)
T PRK14350         85 KVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDE-  163 (669)
T ss_pred             ccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcCC-
Confidence            999999999999999742211 112579999999999999999999999999999999999999999999999999963 


Q ss_pred             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHH
Q psy11422        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL  252 (687)
Q Consensus       173 ~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~  252 (687)
                        |..+|||||+||++++|+++|+++    .++|+||||+|||+|||+||.+++.|+|+||+|+|+..+. . ..+|++.
T Consensus       164 --~~~levRGEv~m~~~~F~~lN~~~----~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~-~-~~t~~e~  235 (669)
T PRK14350        164 --KVELVLRGEIYITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL-E-LKTNHDA  235 (669)
T ss_pred             --CceEEEEEEEEeeHHHHHHHHHhh----hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC-C-CCCHHHH
Confidence              578999999999999999999876    3689999999999999999999999999999999964332 2 3699999


Q ss_pred             HHHHHhcCCCCCCCceEeCC---HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11422        253 LNWYQKIGLSICGEYSVLSG---VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (687)
Q Consensus       253 l~~L~~~Gf~~~~~~~~~~~---~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (687)
                      |++|++|||+++++...+.+   .+++++|+++|.+.|+.+||+|||+|||+|++.+|+.||+|+|+||||||||||+++
T Consensus       236 l~~L~~~GF~v~~~~~~~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~~  315 (669)
T PRK14350        236 FDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESLS  315 (669)
T ss_pred             HHHHHHCCCCCCcceEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCce
Confidence            99999999999998888876   999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11422        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (687)
Q Consensus       330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (687)
                      ++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++. 
T Consensus       316 ~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~-  394 (669)
T PRK14350        316 GFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF-  394 (669)
T ss_pred             eEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC-
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999888754 


Q ss_pred             ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11422        410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN  489 (687)
Q Consensus       410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  489 (687)
                        |.+|++||+||++|++  +++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|+
T Consensus       395 --~~~P~~CP~C~s~l~~--~~~~~~C~n~-~-C~aq~~~~i~hf~sr~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L~  468 (669)
T PRK14350        395 --FKIPDNCPSCKTALIK--EGAHLFCVNN-H-CPSVIVERIKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTFN  468 (669)
T ss_pred             --CCCCCCCCCCCCEeee--CCEEEEECCC-C-CHHHHHhhhheeccCCcccccCcCHHHHHHHHHcCCcCCHHHHhhCC
Confidence              8899999999999986  4699999996 6 99999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHH-hhcCChHHHHh------cCHHHHhcCCC
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA-NYFKNLECMFK------ATEEQLLNIPK  562 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La-~~f~sld~l~~------As~eeL~~I~G  562 (687)
                      .++|++++|||+|+|+||+++|++||+.||+|||+|||||+||+.+|+.|+ ++|++++++.+      ++.++|.+++|
T Consensus       469 ~~~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~g  548 (669)
T PRK14350        469 FDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKG  548 (669)
T ss_pred             HHHHhhccCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCC
Confidence            999999999999999999999999999999999999999999999999999 89999999986      68899999999


Q ss_pred             CCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCC-CCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccc
Q psy11422        563 IGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN-TKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFI  641 (687)
Q Consensus       563 IG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~-~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sV  641 (687)
                      ||+++|++|.+||+++.|.++|++|.+.|+++...+. ....+++|+||+|||||+|+.++|++++++|+++||+|++||
T Consensus       549 iG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssV  628 (669)
T PRK14350        549 IGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCV  628 (669)
T ss_pred             ccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccc
Confidence            9999999999999999999999999999987653211 112346899999999999999999999999999999999999


Q ss_pred             cccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        642 SKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       642 sk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      |++|||||+|+++|+|++||++|||+||+|++|++||+.
T Consensus       629 Skktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l~~  667 (669)
T PRK14350        629 TKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYVDL  667 (669)
T ss_pred             cCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHhcC
Confidence            999999999999999999999999999999999999975

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=100.00  E-value=1.1e-184  Score=1576.63  Aligned_cols=649  Identities=45%  Similarity=0.738  Sum_probs=620.3

Q ss_pred             HHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHH
Q psy11422         21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDED  100 (687)
Q Consensus        21 L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~e  100 (687)
                      |+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.+.|.||+|++|||||+|+|+.+|
T Consensus         1 L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMlSL~k~~~~~e   80 (652)
T TIGR00575         1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRFPKVRHSTPMLSLDNAFDEDE   80 (652)
T ss_pred             CHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCccccCCCCCccccCcccccccCccccCCcCcCccccCCHHH
Confidence            67899999999999999999999999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEE
Q psy11422        101 VIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEV  180 (687)
Q Consensus       101 l~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~ev  180 (687)
                      |.+|++|+.+.++  .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++.+.|..+||
T Consensus        81 l~~~~~r~~~~~~--~~~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDvT~nv~~I~~iP~~i~~~~~p~~lev  158 (652)
T TIGR00575        81 LAAFIKRIRRQLG--LKVEYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEV  158 (652)
T ss_pred             HHHHHHHHHHhcC--CCceEEEEEeccceEEEEEEECCEEEEEEecCCCccchhHhhhhhhhcccchhhcCCCCCceEEE
Confidence            9999999988765  13579999999999999999999999999999999999999999999999999974235889999


Q ss_pred             EEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcC
Q psy11422        181 RCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG  260 (687)
Q Consensus       181 RGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~G  260 (687)
                      |||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+|++.|++|++||
T Consensus       159 RGEv~m~~~~F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~~~~~-~~t~~e~l~~L~~~G  237 (652)
T TIGR00575       159 RGEVFMPKEDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELP-DATQYEALAWLKKWG  237 (652)
T ss_pred             EEEEEEEHHHHHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccccCCCC-CCCHHHHHHHHHHCC
Confidence            9999999999999999999999999999999999999999999999999999999996433322 379999999999999


Q ss_pred             CCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEe
Q psy11422        261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ  340 (687)
Q Consensus       261 f~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q  340 (687)
                      |+++++...+.+++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|++|+||
T Consensus       238 F~v~~~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~~~~T~l~~I~~q  317 (652)
T TIGR00575       238 FPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEEAQTKLLDVVVQ  317 (652)
T ss_pred             CCCCCCeEeeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCceeeEEEEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCCCCCCC
Q psy11422        341 IGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPI  420 (687)
Q Consensus       341 vGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~  420 (687)
                      |||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++..+|.+|++||+
T Consensus       318 VGRTG~iTPvA~lePV~l~G~~VsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~P~~CP~  397 (652)
T TIGR00575       318 VGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPS  397 (652)
T ss_pred             cCCCceeeeEEEEeeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCcCceeeeeccccCCCCCCCCCCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999989888889999999999


Q ss_pred             CCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCcc
Q psy11422        421 CNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS  500 (687)
Q Consensus       421 C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG  500 (687)
                      ||++|++.++++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++||++|+|++++|||+|+.++|.+|+|||
T Consensus       398 C~s~l~~~~~~~~~~C~n~-~-C~aq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG  475 (652)
T TIGR00575       398 CGSPLVKIEEEAVIRCPNL-N-CPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFG  475 (652)
T ss_pred             CCCEeEecCCcEEEEECCC-C-CHHHHHHHhHHhhcCCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCcc
Confidence            9999999888899999995 6 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhH
Q psy11422        501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (687)
Q Consensus       501 ~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n  580 (687)
                      +|+|+||+++|+.+|+.+|.|||++|||||||+++|+.|+++|+++++|..|+.++|.+++|||+++|++|.+||+++.|
T Consensus       476 ~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~  555 (652)
T TIGR00575       476 EKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNN  555 (652)
T ss_pred             HHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCcccccCCC-C--CCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc
Q psy11422        581 RLLISQLRDVGIYWLNNPN-T--KGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK  657 (687)
Q Consensus       581 ~~~i~~L~~~Gv~~~~~~~-~--~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K  657 (687)
                      +++|++|.+.|+++..... .  ...+++|+|++|||||+|..++|++++++|+++||+|++|||++|||||+|+++|+|
T Consensus       556 ~~~i~~L~~~gv~~~~~~~~~~~~~~~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK  635 (652)
T TIGR00575       556 RQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSK  635 (652)
T ss_pred             HHHHHHHHHcCCCcccccccccccccCCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChH
Confidence            9999999999988653211 1  112468999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeEEeHHHH
Q psy11422        658 LEKAIKLNIKILDEKNF  674 (687)
Q Consensus       658 l~kA~~lgI~Ii~E~~f  674 (687)
                      ++||++|||+||+|++|
T Consensus       636 l~kA~~lgi~ii~E~~~  652 (652)
T TIGR00575       636 LAKAQELGIPIINEEEL  652 (652)
T ss_pred             HHHHHHcCCcEechhhC
Confidence            99999999999999987

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=100.00  E-value=1.9e-183  Score=1566.28  Aligned_cols=659  Identities=35%  Similarity=0.593  Sum_probs=627.3

Q ss_pred             cCCChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecc
Q psy11422          7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHT   86 (687)
Q Consensus         7 ~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~   86 (687)
                      ...+.+.++++|++|+++|++||++||++++|+|||++||+|+++|++||++| ++.+++|||++||+.+..+|.||+|+
T Consensus        25 ~~~~~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~-~~~~~~spt~~Vg~~~~~~f~kv~H~  103 (689)
T PRK14351         25 EELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTENSPTRRVGGEPLDELETVEHV  103 (689)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhc-CCCCCCCCCccCCccccccCCceecC
Confidence            34455666789999999999999999999999999999999999999999999 89999999999999999999999999


Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC
Q psy11422         87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP  166 (687)
Q Consensus        87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP  166 (687)
                      +|||||+|+|+.+|+.+|++|+.+.++   ...|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||
T Consensus       104 ~pMlSL~k~~~~~el~~f~~r~~~~~~---~~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I~~IP  180 (689)
T PRK14351        104 APMLSIDQSGEADDVREFDERVRREVG---AVEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVP  180 (689)
T ss_pred             CcccccCccCCHHHHHHHHHHHHHhcC---CceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhhcccc
Confidence            999999999999999999999988776   36799999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC
Q psy11422        167 LVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP  246 (687)
Q Consensus       167 ~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~  246 (687)
                      ++|+. .+|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++ . +
T Consensus       181 ~~l~~-~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~-~-~  257 (689)
T PRK14351        181 QKLRG-DYPDFLAVRGEVYMPKDAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASE-L-F  257 (689)
T ss_pred             hhhcc-cCCCeEEEEEEEEEEHHHHHHHHHHHHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCC-C-C
Confidence            99974 2588999999999999999999999999999999999999999999999999999999999999965433 2 4


Q ss_pred             CCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11422        247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (687)
Q Consensus       247 ~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (687)
                      .+|++.|++|++|||+++++.+.+.+++++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||
T Consensus       258 ~t~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~  337 (689)
T PRK14351        258 DSHWEELERFPEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFP  337 (689)
T ss_pred             CCHHHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCC
Confidence            79999999999999999998888999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCC
Q psy11422        327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP  406 (687)
Q Consensus       327 ~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~  406 (687)
                      +++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.+.++
T Consensus       338 ~~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~G~tVsratLhN~~~i~~~di~iGD~V~V~raGdVIPkI~~vv~~~~~  417 (689)
T PRK14351        338 ARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGVTVSRASLHNPAEIEELGVNVGDRVRVKRAGDVIPYVEEVVEKDSE  417 (689)
T ss_pred             CceeEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCccceeeeeecccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999987554


Q ss_pred             CCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh
Q psy11422        407 NDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY  486 (687)
Q Consensus       407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~  486 (687)
                      .+   |.+|++||+||++|++  +++.++|+|... ||+|++++|.||+||++|||+|||+++|++|+++|+|++++|||
T Consensus       418 ~~---~~~P~~CP~C~~~l~~--~~~~~~C~n~~~-Cpaq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~  491 (689)
T PRK14351        418 GT---FEFPDTCPVCDSAVER--DGPLAFCTGGLA-CPAQLERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLY  491 (689)
T ss_pred             CC---CcCCCCCCCCCCEeee--CCceEEcCCCCC-CHHHHHHHHHHHhcccccCCCCcCHHHHHHHHHcCCCCCHHHHH
Confidence            33   7899999999999986  467889999656 99999999999999999999999999999999999999999999


Q ss_pred             cCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHH
Q psy11422        487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST  566 (687)
Q Consensus       487 ~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~  566 (687)
                      +|+.++|..++|||+|+|+||+++|++||+++|+|||+||||||||+++|++|+++|+++++|..|+.++|.+++|||++
T Consensus       492 ~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k  571 (689)
T PRK14351        492 DLTVADLAELEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPT  571 (689)
T ss_pred             HcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccccc
Q psy11422        567 TVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTN  646 (687)
Q Consensus       567 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~  646 (687)
                      +|++|++||+++.|+++++.|.+.|+++....  ...+++|+|++|||||+|..|+|++++++|+++||+|++|||++||
T Consensus       572 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~--~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~  649 (689)
T PRK14351        572 VAEEIREFFDSERNRAVIDDLLDHGVDPQPAE--SEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTD  649 (689)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHhccccccccc--ccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCcc
Confidence            99999999999999999999999998765421  2235689999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        647 YLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       647 ~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      |||+|+++| +|++||+++||+||+|++|++||++
T Consensus       650 ~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~  684 (689)
T PRK14351        650 YLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAE  684 (689)
T ss_pred             EEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHHh
Confidence            999999999 9999999999999999999999986

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=100.00  E-value=3.9e-153  Score=1280.92  Aligned_cols=532  Identities=21%  Similarity=0.318  Sum_probs=501.2

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccc
Q psy11422          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFK   88 (687)
Q Consensus         9 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~p   88 (687)
                      .+...++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+       ||+|++|
T Consensus        25 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~p~~~~~~spt~~vg~-------kv~H~~P   97 (562)
T PRK08097         25 WSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVPLPPLNG-------KVLHPVA   97 (562)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcCcCCCCCCCCCCCC-------ceECCCC
Confidence            455677889999999999999999999999999999999999999999999999999999999986       9999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcc
Q psy11422         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (687)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (687)
                      ||||+|+||.+||.+|++++.         .|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++
T Consensus        98 MlSL~k~~s~eel~~w~~~~~---------~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~  168 (562)
T PRK08097         98 HTGVKKLADKQALARWMAGRS---------DLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQ  168 (562)
T ss_pred             cccccccCCHHHHHHHHhhcc---------ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchh
Confidence            999999999999999998852         59999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCC
Q psy11422        169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS  248 (687)
Q Consensus       169 l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~  248 (687)
                      |+.  .|..+|||||+||++++|++.+     .|   |+||||+|||+|||+||+++ .|+|+||+|++..  +   +.+
T Consensus       169 l~~--~~~~levRGEv~m~~~~F~~~~-----~g---~aNPRN~AAGsLr~~d~~~~-~r~L~~f~y~~~~--~---~~t  232 (562)
T PRK08097        169 LPG--ALANLVLQGELFLRREGHIQQQ-----MG---GINARAKVAGLMMRKDPSPT-LNQIGVFVWAWPD--G---PAS  232 (562)
T ss_pred             hcC--CCCeEEEEEEEEEeHHHHHHHh-----cC---cCCchHHHhHHHhhcCcHhh-hccceEEEEECCC--C---CCC
Confidence            974  3778999999999999999632     22   89999999999999999998 8999999999842  2   479


Q ss_pred             HHHHHHHHHhcCCCCCC-CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11422        249 HSELLNWYQKIGLSICG-EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (687)
Q Consensus       249 ~~e~l~~L~~~Gf~~~~-~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (687)
                      |++.|++|++|||++++ +.+.+.+.+++++|+++|.  |..+||+|||+|||+||+.+|+  |+|+|+||||||||||+
T Consensus       233 ~~e~l~~L~~~GF~v~~~~~~~~~~~~~i~~~~~~~~--r~~l~y~iDGiViKvn~~~~~~--~~ts~~PrWAiAyKf~~  308 (562)
T PRK08097        233 MPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY--RAPLPFVTDGVVVRQAKEPPGR--YWQPGQGEWAVAWKYPP  308 (562)
T ss_pred             HHHHHHHHHHCCCCcCccceEeeCCHHHHHHHHHHHh--hccCCCCCCcEEEEecCHHHHh--hccCCCCCceEEEcCCC
Confidence            99999999999999996 7778999999999999886  9999999999999999999998  78999999999999999


Q ss_pred             ceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCC
Q psy11422        328 KEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPN  407 (687)
Q Consensus       328 ~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~  407 (687)
                      ++++|+|++|+|||||||++||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.  |++
T Consensus       309 ~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~GttVsrATLhN~~~i~~~~I~iGD~V~V~raGdVIP~I~~vv~--~~~  386 (562)
T PRK08097        309 VQQVAEVRAVQFAVGRTGKITVVLELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVVW--RGA  386 (562)
T ss_pred             cEEEEEEEEEEEecCCCceeeEEEEEEEEEeCCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCCCcceeeeec--ccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999997  455


Q ss_pred             CCccccCCCCCCCCCCcceeecCceeEEecC-CCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh
Q psy11422        408 DSKIFKIPNICPICNSKIIYIESNLIARCSG-SWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY  486 (687)
Q Consensus       408 ~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n-~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~  486 (687)
                      ...++.+|+.           ++++.+||+| ... ||+|++++|.|||||+||||+|||+++|++|+++|+|++++|||
T Consensus       387 ~~~~~~~P~~-----------~~~~~~~C~n~~~~-Cpaq~~~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Diy  454 (562)
T PRK08097        387 ERTKPTPPDA-----------DRFHSLSCFRASPG-CQEQFLARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWL  454 (562)
T ss_pred             cCCCCcCCCC-----------CCceEEEeCCCCCC-CHHHHHHHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHHh
Confidence            5556777764           2357899998 555 99999999999999999999999999999999999999999999


Q ss_pred             cCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHH
Q psy11422        487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST  566 (687)
Q Consensus       487 ~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~  566 (687)
                      +|+.++|++++|||+|+++||+++|++||+++|+|||+|||||+||+.+|+.   +|+++++|..++.++|.+++|||++
T Consensus       455 ~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~~  531 (562)
T PRK08097        455 ALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGEG  531 (562)
T ss_pred             cCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchHH
Confidence            9999999999999999999999999999999999999999999999988876   8999999999999999999999999


Q ss_pred             HHHHHHHHHcchhHHHHHHHHHhcCcc
Q psy11422        567 TVKAFIKFINQPLHRLLISQLRDVGIY  593 (687)
Q Consensus       567 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~  593 (687)
                      +|++|++||+++.|++++++|.++|++
T Consensus       532 ~a~si~~~f~~~~~~~~i~~L~~~gv~  558 (562)
T PRK08097        532 RARQLIAFLQHPEVKALADWLAAQGIT  558 (562)
T ss_pred             HHHHHHHHHcCHHHHHHHHHHHHcCCC
Confidence            999999999999999999999998875

>smart00532 LIGANc Ligase N family

Probab=100.00  E-value=9e-138  Score=1137.31  Aligned_cols=440  Identities=47%  Similarity=0.758  Sum_probs=419.8

Q ss_pred             HHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCC
Q psy11422         15 SFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDN   94 (687)
Q Consensus        15 ~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k   94 (687)
                      +++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+.++|.||+|++|||||+|
T Consensus         2 ~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~le~~~p~~~~~~spt~~VG~~~~~~f~kv~H~~pMlSL~k   81 (441)
T smart00532        2 QKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKPLEGFNKVRHPVPMLSLDN   81 (441)
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHHHhCccccCCCCCccccCcccccCCcceecCCcccCccc
Confidence            46899999999999999999999999999999999999999999999999999999999998889999999999999999


Q ss_pred             CCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCC
Q psy11422         95 GFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYP  174 (687)
Q Consensus        95 ~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~  174 (687)
                      +|+.+||.+|++++.+.++  .+..|+|||||||+||+|+|++|+|++|+|||||.+|||||+|+++|++||++|+. +.
T Consensus        82 ~~~~~el~~f~~~~~~~~~--~~~~~~~epKiDGlsisL~Ye~G~l~~a~TRGDG~~GeDVT~nv~~i~~iP~~i~~-~~  158 (441)
T smart00532       82 AFDEDELRAFDERIEKALG--SPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSG-DV  158 (441)
T ss_pred             cCCHHHHHHHHHHHHHhcC--CCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceehhhhhhhhcCcChhhcc-cC
Confidence            9999999999999987765  23679999999999999999999999999999999999999999999999999974 25


Q ss_pred             CceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHH
Q psy11422        175 PELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN  254 (687)
Q Consensus       175 ~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~  254 (687)
                      |..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+++..++.....+|++.|+
T Consensus       159 p~~leiRGEv~~~~~~F~~ln~~~~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~~~~t~~e~l~  238 (441)
T smart00532      159 PERLEVRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQSEALK  238 (441)
T ss_pred             CCeEEEEceEEEEHHHHHHHHHHHHhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCCCccCHHHHHH
Confidence            88999999999999999999999999999999999999999999999999999999999999975433211268999999


Q ss_pred             HHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEE
Q psy11422        255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI  334 (687)
Q Consensus       255 ~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v  334 (687)
                      +|++|||+++++...+.+.+++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|
T Consensus       239 ~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~l  318 (441)
T smart00532      239 WLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEEAETKL  318 (441)
T ss_pred             HHHHCCCCCCCCeEeeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCceeEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccC
Q psy11422        335 KAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKI  414 (687)
Q Consensus       335 ~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~  414 (687)
                      ++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++++.+|.+
T Consensus       319 ~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLhN~~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~~~r~~~~~~~~~  398 (441)
T smart00532      319 LDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEM  398 (441)
T ss_pred             EEEEEecCCCceeeEEEEEEeEEECCEEEEecccCCHHHHHHcCCCCCCEEEEEECCCcCcceeecccccCCCCCccCcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988888889999


Q ss_pred             CCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccc
Q psy11422        415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKA  459 (687)
Q Consensus       415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~  459 (687)
                      |++||+||++|++.++++.+||+|. . ||+|++++|.||+||+|
T Consensus       399 P~~CP~C~s~l~~~~~~~~~~C~n~-~-C~aq~~~~l~hf~sr~a  441 (441)
T smart00532      399 PTHCPSCGSELVREEGEVDIRCPNP-L-CPAQLIERIIHFASRKA  441 (441)
T ss_pred             CCCCCCCCCEeEecCCceEEEeCCC-C-CHHHHHHHHHhhhcCCC
Confidence            9999999999998888899999996 6 99999999999999975

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=100.00  E-value=9.5e-95  Score=765.07  Aligned_cols=306  Identities=47%  Similarity=0.768  Sum_probs=292.6

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCC
Q psy11422         17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGF   96 (687)
Q Consensus        17 ~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~   96 (687)
                      +|++|+++|++||++||++++|+|||++||+|+++|++||++||++..++|||++||+.+.+.|.||+|++|||||+|+|
T Consensus         2 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMlSL~k~~   81 (307)
T cd00114           2 RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTPLSGFKKVRHPVPMLSLDNAF   81 (307)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCcccCccccccCCccCCCCcCccccccC
Confidence            68999999999999999999999999999999999999999999999999999999999888999999999999999999


Q ss_pred             ChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCc
Q psy11422         97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPE  176 (687)
Q Consensus        97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~  176 (687)
                      +.+||.+|++|+.+.++  .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.  .|.
T Consensus        82 ~~~el~~~~~r~~~~~~--~~~~~~vepKiDGlsisL~Y~~G~L~~a~TRGdG~~GeDVT~nv~~I~~IP~~i~~--~~~  157 (307)
T cd00114          82 DEEELRAFDERIKRFLG--EEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLAG--APE  157 (307)
T ss_pred             CHHHHHHHHHHHHHhcC--CCCcEEEEEeccceEEEEEEECCEEEEEEecCCCcchhhHHhhHhhhcccChhhcC--CCC
Confidence            99999999999987775  24689999999999999999999999999999999999999999999999999974  488


Q ss_pred             eEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHH
Q psy11422        177 LLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY  256 (687)
Q Consensus       177 ~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L  256 (687)
                      .+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..++.+ +.+|++.|++|
T Consensus       158 ~levRGEv~m~~~~F~~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~~-~~t~~e~l~~L  236 (307)
T cd00114         158 TLEVRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG-PKTQSEALAFL  236 (307)
T ss_pred             eEEEEEEEEEEHHHHHHHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCCC-CCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999997544323 47999999999


Q ss_pred             HhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11422        257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (687)
Q Consensus       257 ~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (687)
                      ++|||+|+++...+.+++++++|+++|.+.|..+||+|||||||||++.+|+.||.|+|+||||||||||+
T Consensus       237 ~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrWaiA~Kf~~  307 (307)
T cd00114         237 KEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA  307 (307)
T ss_pred             HHCCCCCCCCeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCceEEeCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999996

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.

>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=100.00  E-value=3.1e-94  Score=764.33  Aligned_cols=313  Identities=44%  Similarity=0.689  Sum_probs=270.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcc-cCCCCcceeccccccC
Q psy11422         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTFKMMS   91 (687)
Q Consensus        13 ~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~pMlS   91 (687)
                      +++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++.+++|||++||+. +...|.+|+|++||||
T Consensus         2 ~~~~~i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~~le~~~pe~~~~~spt~~Vg~~~~~~~f~kv~H~~pMlS   81 (315)
T PF01653_consen    2 EAKERIEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELKALEAEYPELITPDSPTQRVGGSPPSSKFKKVRHPVPMLS   81 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHHHHHHHSGGG--TTSGGGGGSSSS-SSSSEEEEESS----
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCcccccccccccccCceeeecccccC
Confidence            457899999999999999999999999999999999999999999999999999999999954 5566999999999999


Q ss_pred             CCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccccc
Q psy11422         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (687)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (687)
                      |+|+|+.+||.+|++++.+.++.. ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus        82 L~k~~s~eel~~w~~r~~~~~~~~-~~~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~iP~~i~~  160 (315)
T PF01653_consen   82 LDKAYSEEELRKWLKRVEKALGEE-EEEFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKSIPLRIPE  160 (315)
T ss_dssp             -EEESSHHHHHHHHHHHHHHCSS--SSEEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTTS-SB-SS
T ss_pred             ccccCCHHHHHHHHHHHHHHhccc-ccceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhcCchhhcc
Confidence            999999999999999999988742 1269999999999999999999999999999999999999999999999999985


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHH
Q psy11422        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (687)
Q Consensus       172 ~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e  251 (687)
                      .  |+.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|..+++...+.+|++
T Consensus       161 ~--p~~~eVRGEv~m~~~~F~~ln~~~~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~t~~e  238 (315)
T PF01653_consen  161 K--PGRLEVRGEVYMSKSDFEKLNEEREEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPEGDLGFNTQSE  238 (315)
T ss_dssp             S--SSEEEEEEEEE--HHHHHHHHHHHHHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEETTSTT-SBHHH
T ss_pred             C--CcceEEEEEEEEehhhHHHHHHHHHHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEecccccccChHHHHH
Confidence            3  79999999999999999999999999999999999999999999999999999999999999997655223589999


Q ss_pred             HHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCc
Q psy11422        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (687)
Q Consensus       252 ~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (687)
                      .|++|++|||+|+++...+.+.+++++++++|.+.|..+||+|||||||+||+.+|+.||+|+|+|||||||||||+
T Consensus       239 ~l~~L~~~GF~v~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~~~LG~t~~~PrwAiAyKfpae  315 (315)
T PF01653_consen  239 RLQFLKEWGFPVNPYIRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLALQERLGYTSKHPRWAIAYKFPAE  315 (315)
T ss_dssp             HHHHHHHTT--B-TTEEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHHHHHH-BESSSBSSEEEEE---G
T ss_pred             HHHHHHHcCCCCCcceEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHHHHhcCCcCCCCCeEEEECcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999986

It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....

>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []

Probab=99.97  E-value=1.6e-31  Score=227.67  Aligned_cols=82  Identities=51%  Similarity=0.764  Sum_probs=70.5

Q ss_pred             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11422        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (687)
Q Consensus       330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (687)
                      ++|+|++|+|||||||++||||+|+||.|+|++|+||||||+++|+++||++||+|.|+|||||||+|++|+++.|++++
T Consensus         1 ~~T~v~~I~~~vGRtG~itPva~lePV~l~G~~VsratLhN~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r~~~~   80 (82)
T PF03120_consen    1 QETKVRDIEWQVGRTGKITPVAVLEPVELDGTTVSRATLHNYDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKRTGDE   80 (82)
T ss_dssp             EEEEEEEEEEEE-TTSBEEEEEEEEEEECTTCEEEEEE--SHHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG--SS-
T ss_pred             CeEEEEEEEEecCCCeEEEEEEEEEEEEECCeEEEEEEecCHHHHHHcCCCCCCEEEEEECCCccceEeEeehhcCCCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             cc
Q psy11422        410 KI  411 (687)
Q Consensus       410 ~~  411 (687)
                      +|
T Consensus        81 ~p   82 (82)
T PF03120_consen   81 QP   82 (82)
T ss_dssp             BB
T ss_pred             CC
Confidence            53

This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=99.64  E-value=2.7e-16  Score=168.24  Aligned_cols=77  Identities=44%  Similarity=0.691  Sum_probs=72.4

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcC---------CCCccHHHHHHc-----CCeEE
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQ---------KPGKKLEKAIKL-----NIKIL  669 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~---------~~g~Kl~kA~~l-----gI~Ii  669 (687)
                      ..+|+|++|||||+|..|+|++++++++++||+|++|||++|||||+|+         ++|+|++||++|     ||+||
T Consensus       218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~ii  297 (309)
T PRK06195        218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFL  297 (309)
T ss_pred             CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEEe
Confidence            4579999999999999899999999999999999999999999999995         467999999999     99999


Q ss_pred             eHHHHHHHHhc
Q psy11422        670 DEKNFVKIVKG  680 (687)
Q Consensus       670 ~E~~f~~~l~~  680 (687)
                      +|++|++||..
T Consensus       298 ~E~~f~~l~~~  308 (309)
T PRK06195        298 NEEEFLQKCKE  308 (309)
T ss_pred             cHHHHHHHHhh
Confidence            99999999863

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=99.64  E-value=4e-16  Score=167.01  Aligned_cols=74  Identities=16%  Similarity=0.239  Sum_probs=71.0

Q ss_pred             cCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC--ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11422        607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       607 l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g--~Kl~kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      ++|++|||||+|+ ++|++++++++++||+|++|||++|||||+|+++|  +|++||+++||+||+|++|++||+.-
T Consensus       233 ~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll~~~  308 (313)
T PRK06063        233 VQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLRAV  308 (313)
T ss_pred             cCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHHHhh
Confidence            5899999999997 89999999999999999999999999999999988  89999999999999999999999754

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B

Probab=99.58  E-value=2.6e-15  Score=123.61  Aligned_cols=64  Identities=45%  Similarity=0.719  Sum_probs=55.2

Q ss_pred             HHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHH
Q psy11422        521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI  584 (687)
Q Consensus       521 r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i  584 (687)
                      |||+||||||||+.+|+.|+++|+++++|..|+.++|.+++|||+++|++|++||++++|+++|
T Consensus         1 R~l~aLGI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~~i   64 (64)
T PF12826_consen    1 RFLFALGIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENRELI   64 (64)
T ss_dssp             HHHHHCTSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHHHH
T ss_pred             CeeeeCCCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhhhC
Confidence            7999999999999999999999999999999999999999999999999999999999998764

>COG5275 BRCT domain type II [General function prediction only]

Probab=99.50  E-value=4.2e-14  Score=138.43  Aligned_cols=81  Identities=38%  Similarity=0.657  Sum_probs=76.8

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      ..++|.|+.|||||.|..++|++++.++..+||+|..+.|.+|+|||.|+++| +|++|+++|+|+.|+|+.|..++...
T Consensus       153 ~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~  232 (276)
T COG5275         153 ERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDT  232 (276)
T ss_pred             CcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHHHHhcC
Confidence            45699999999999999999999999999999999999999999999999999 99999999999999999999999765


Q ss_pred             cC
Q psy11422        682 ST  683 (687)
Q Consensus       682 s~  683 (687)
                      ++
T Consensus       233 pa  234 (276)
T COG5275         233 PA  234 (276)
T ss_pred             cc
Confidence            43

>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins

Probab=99.17  E-value=3.9e-10  Score=121.99  Aligned_cols=144  Identities=22%  Similarity=0.200  Sum_probs=109.0

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~  198 (687)
                      .|+||+|+||.++++.|.+|+ +.|.||| |.+++++|++++.+  +|..+.. ..| .+.+.||++++...|..     
T Consensus        49 ~~~vEEKlDG~nvri~~~~G~-v~a~TR~-G~i~e~~T~~~~ei--v~~~~~~-~~p-~~iLdGElvg~~~p~v~-----  117 (342)
T cd07894          49 PVAVEEKMNGYNVRIVRIGGK-VLAFTRG-GFICPFTTDRLRDL--IDPEFFD-DHP-DLVLCGEVVGPENPYVP-----  117 (342)
T ss_pred             CEEEEEeECCcEEEEEEECCE-EEEEeCC-CccCccchhhHhhh--chHHhhc-cCC-CEEEEEEEEecCCcccc-----
Confidence            799999999999999999998 7999999 99999999999987  5777643 134 48999999998755421     


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCCCCCc--eEeCCHHHH
Q psy11422        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEY--SVLSGVNKL  276 (687)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~~~~~--~~~~~~~ei  276 (687)
                          .   .             .|.   .+++.||+|++...++.. ..++.+..++|.++||+.++..  ..+.+.+++
T Consensus       118 ----~---~-------------~~~---~~~v~F~vFDI~~~~~~~-~lp~~eR~~lLe~lg~~~v~~~~~~~~~d~~~l  173 (342)
T cd07894         118 ----G---S-------------YPE---VEDVGFFVFDIRKKNTGR-PLPVEERRELLEKYGLPTVRLFGEFTADEIEEL  173 (342)
T ss_pred             ----c---c-------------Ccc---ccccEEEEEeeEEcCCCC-CCCHHHHHHHHHhcCCCCcceEEEEecCCHHHH
Confidence                0   0             111   268999999998654322 3678999999999999877643  234567788


Q ss_pred             HHHHHHHHHhhcCCCCccceEEEEECC
Q psy11422        277 IEFYKKINIKRFNLPYEIDGVVYKINC  303 (687)
Q Consensus       277 ~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (687)
                      .++++.+.+.-      --|||+|--+
T Consensus       174 ~~~l~~~~~~G------~EGVVlK~~~  194 (342)
T cd07894         174 KEIIRELDKEG------REGVVLKDPD  194 (342)
T ss_pred             HHHHHHHHHCC------CceEEEeccc
Confidence            88877764322      4799998755

RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=99.12  E-value=1.1e-10  Score=137.41  Aligned_cols=78  Identities=21%  Similarity=0.249  Sum_probs=71.8

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC---CC-ccHHHHHHcCCeEEeHHHHHHHH
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK---PG-KKLEKAIKLNIKILDEKNFVKIV  678 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~---~g-~Kl~kA~~lgI~Ii~E~~f~~~l  678 (687)
                      ...+|.|++|||||+|+. +|++++++|+.+||+|++|||++|++|++|.+   +| +|+++|+++||+||+|++|++++
T Consensus       186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~i  264 (815)
T PLN03122        186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDSI  264 (815)
T ss_pred             cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEccccccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHHH
Confidence            345899999999999986 99999999999999999999999999999976   55 89999999999999999999999


Q ss_pred             hcc
Q psy11422        679 KGF  681 (687)
Q Consensus       679 ~~~  681 (687)
                      ...
T Consensus       265 ~~~  267 (815)
T PLN03122        265 EKQ  267 (815)
T ss_pred             hcC
Confidence            753

>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1

Probab=98.76  E-value=3.6e-08  Score=82.91  Aligned_cols=74  Identities=26%  Similarity=0.302  Sum_probs=67.0

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC--CCccHHHHHHcCCeEEeHHHHHHHH
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK--PGKKLEKAIKLNIKILDEKNFVKIV  678 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~--~g~Kl~kA~~lgI~Ii~E~~f~~~l  678 (687)
                      ...|.|.+|+| +.+....|++++.+|+.+||++..+++++|++||++..  ...|...|...+|+|++++++.+.|
T Consensus         3 ~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci   78 (78)
T PF00533_consen    3 PKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI   78 (78)
T ss_dssp             TTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred             CCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence            45799999999 55556899999999999999999999999999999987  5689999999999999999998764

The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=98.74  E-value=8.6e-09  Score=83.75  Aligned_cols=57  Identities=28%  Similarity=0.362  Sum_probs=52.6

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       456 sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .++.++|+|+|++++.+|++.| +.|+.||++++.++|..++|||+++|++|++++++
T Consensus         4 ~~~L~~I~Gig~~~a~~L~~~G-~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~   60 (60)
T PF14520_consen    4 FDDLLSIPGIGPKRAEKLYEAG-IKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE   60 (60)
T ss_dssp             HHHHHTSTTCHHHHHHHHHHTT-CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred             HHhhccCCCCCHHHHHHHHhcC-CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence            4567899999999999999999 69999999999999999999999999999998753

...

>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A

Probab=98.73  E-value=1.6e-08  Score=82.74  Aligned_cols=62  Identities=31%  Similarity=0.386  Sum_probs=53.3

Q ss_pred             EEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHH
Q psy11422        611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKN  673 (687)
Q Consensus       611 ~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~  673 (687)
                      +|||||..+ -.|.++..+++.+||++...++++|++||+....|.|+++|.++||+|++.++
T Consensus         2 ~i~~sg~~~-~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W   63 (63)
T PF12738_consen    2 VICFSGFSG-KERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW   63 (63)
T ss_dssp             EEEEEEB-T-TTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred             EEEECCCCH-HHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence            699999775 47999999999999999999999999999988888999999999999999764

>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins

Probab=98.72  E-value=8.2e-08  Score=94.42  Aligned_cols=139  Identities=16%  Similarity=0.246  Sum_probs=94.6

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~  198 (687)
                      .|++|+|+||+.+.+   +|.  ++.||+    |+|+|........         +|. +.+.||+++....|+.+    
T Consensus        17 ~~~~e~K~DG~R~~~---~~~--~~~SR~----g~~~t~~~~~~~~---------l~~-~ilDGElv~~~~~f~~l----   73 (174)
T cd07896          17 GYLVSEKLDGVRAYW---DGK--QLLSRS----GKPIAAPAWFTAG---------LPP-FPLDGELWIGRGQFEQT----   73 (174)
T ss_pred             HeeechhhceEEEEE---ecc--EEEecC----CcCCCCCHHHHhh---------CCC-CccCceEEcCCCCHHHH----
Confidence            689999999999854   454  889996    9999976222222         333 78999999987777665    


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhc-------CCCCCCCceEeC
Q psy11422        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLSICGEYSVLS  271 (687)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------Gf~~~~~~~~~~  271 (687)
                                     +|.++++++......++.|++|++...     ..+..+..+.|.++       .|.+++ ...+.
T Consensus        74 ---------------~~~~~~~~~~~~~~~~~~f~vFDil~~-----~~p~~eR~~~L~~~i~~~~~~~~~~~~-~~~~~  132 (174)
T cd07896          74 ---------------SSIVRSKKPDDEDWRKVKFMVFDLPSA-----KGPFEERLERLKNLLEKIPNPHIKIVP-QIPVK  132 (174)
T ss_pred             ---------------HHHHhcCCCChhhcccceEEEEeCCCC-----CCCHHHHHHHHHHHHHhCCCCcEEEEe-eeeeC
Confidence                           344444444333446799999999862     14566666665432       233333 23467


Q ss_pred             CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11422        272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (687)
Q Consensus       272 ~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (687)
                      +.+++.++++.+.+.      ..+|+|+|-.|..++
T Consensus       133 ~~~~i~~~~~~~~~~------g~EGlv~K~~ds~Y~  162 (174)
T cd07896         133 SNEALDQYLDEVVAA------GGEGLMLRRPDAPYE  162 (174)
T ss_pred             CHHHHHHHHHHHHhc------CCCeEEEecCCCccc
Confidence            888999988876433      569999998887664

The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me

>PRK09125 DNA ligase; Provisional

Probab=98.62  E-value=3.3e-06  Score=89.56  Aligned_cols=198  Identities=17%  Similarity=0.185  Sum_probs=124.4

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~  198 (687)
                      .|++|+|+||+-+.   .+|  +++.||    .|+|+|+--....         .+| .+.+-||+++...+|+.+... 
T Consensus        44 ~~~~E~K~DG~R~~---~~~--v~l~SR----~g~~it~p~~~~~---------~~~-~~vLDGElv~~~~~F~~l~~r-  103 (282)
T PRK09125         44 GYLVSEKLDGVRAY---WDG--KQLLTR----QGNPIAAPAWFTA---------GFP-PFPLDGELWAGRGQFEAISSI-  103 (282)
T ss_pred             hEEEEeeeeeEeEE---ECC--eEEEcC----CCCcCCCchhHHh---------cCC-CccEeEEEEeCCCCHHHHHHH-
Confidence            69999999999994   366  589999    7888887211111         134 578999999988999877543 


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCC-CCC-----ceEeCC
Q psy11422        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSI-CGE-----YSVLSG  272 (687)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~-~~~-----~~~~~~  272 (687)
                                        ++++++......++.|++|++...+     .+..+..+.|+++==+. .+.     ...+.+
T Consensus       104 ------------------~~~k~~~~~~~~~v~~~vFDll~~~-----gpl~eRr~~L~~li~~~~~~~i~~~~~~~~~~  160 (282)
T PRK09125        104 ------------------VRDKTPDDAAWRKVRFMVFDLPDAP-----GDFEERLAVLKKLLAKLPSPYIKIIEQIRVRS  160 (282)
T ss_pred             ------------------HccCCcchhhhcccEEEEEEcCCCC-----CCHHHHHHHHHHHHhhCCCCcEEEEeEEEcCC
Confidence                              2222222122347999999997653     25667777776541111 111     223568


Q ss_pred             HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-cceeeeEE
Q psy11422        273 VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPVA  351 (687)
Q Consensus       273 ~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~iTPvA  351 (687)
                      .+++.++++.+.+      --..|+|+|--|..+.  -|   +...| +-+| +...++..|.++.|-.|| +|.+.-..
T Consensus       161 ~~~~~~~~~~~~~------~G~EGiV~K~~ds~Y~--~G---Rs~~w-lKiK-~~~~~d~vIvG~~~g~Gk~~g~~gsll  227 (282)
T PRK09125        161 EAALQQFLDQIVA------AGGEGLMLHRPDAPYE--AG---RSDDL-LKLK-PYYDAEATVIGHLPGKGKFAGMLGALL  227 (282)
T ss_pred             HHHHHHHHHHHHH------cCCCEEEEeCCCCCCc--CC---CCCCc-EEEE-ecCCCcEEEEEEEcCCCcccCceeeEE
Confidence            8899998887643      2358999997765554  23   44567 4444 335678999999998874 45443221


Q ss_pred             EEEEEEECCEEEEEecCCCHHHHH
Q psy11422        352 LLKPVLIDGITITRATLHNESEIY  375 (687)
Q Consensus       352 ~lePV~l~G~tVsraTLhN~~~i~  375 (687)
                      .-   .-+|.+++=+|....+.-+
T Consensus       228 v~---~~~g~~~~VgsG~t~~~r~  248 (282)
T PRK09125        228 VE---TPDGREFKIGSGFSDAERE  248 (282)
T ss_pred             EE---eCCCCEEEeCCCCCHHHhc
Confidence            11   1256555445666665543

>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain

Probab=98.60  E-value=2.7e-07  Score=74.81  Aligned_cols=70  Identities=41%  Similarity=0.550  Sum_probs=63.5

Q ss_pred             CeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc-HHHHHHcCCeEEeHHHHHHHH
Q psy11422        609 EKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK-LEKAIKLNIKILDEKNFVKIV  678 (687)
Q Consensus       609 g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K-l~kA~~lgI~Ii~E~~f~~~l  678 (687)
                      |..|+|+|.+...+|.+++++++.+||++..+++..+++||+++....+ +..|...+++|++++++.+.+
T Consensus         1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~   71 (72)
T cd00027           1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL   71 (72)
T ss_pred             CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHh
Confidence            6789999998557999999999999999999999999999999877644 899999999999999998765

The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.

>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases

Probab=98.52  E-value=3.1e-06  Score=85.30  Aligned_cols=165  Identities=16%  Similarity=0.162  Sum_probs=104.9

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~----~F~~  193 (687)
                      ..|++|+|+||.-+.+.+..|. +++.||    -|.|+|+....+...   +.  ..|..+.+-||++....    .|..
T Consensus        21 ~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~i~~~---~~--~~~~~~vLDGElv~~~~~~~~~f~~   90 (201)
T cd07898          21 AAAWVEDKYDGIRAQVHKDGGR-VEIFSR----SLEDITDQFPELAAA---AK--ALPHEFILDGEILAWDDNRGLPFSE   90 (201)
T ss_pred             CeEEEEEeeceEEEEEEEeCCE-EEEEcC----CChhchhhhhhHHHH---HH--hCCCCEEEEEEEEEEeCCCCCcHHH
Confidence            4799999999999998776555 699999    467898755433321   11  13557899999986432    3665


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce----
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS----  268 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~----  268 (687)
                      +.....   .      |+..      ..  .....++.|++|++...++.++ ..+..|..+.|+++.-+......    
T Consensus        91 ~~~~~~---~------~~~~------~~--~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~~  153 (201)
T cd07898          91 LFKRLG---R------KFRD------KF--LDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPA  153 (201)
T ss_pred             HHHHhc---c------cccc------hh--hhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEeee
Confidence            433211   0      0000      00  1123469999999987555332 24788999999998655433322    


Q ss_pred             -EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11422        269 -VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (687)
Q Consensus       269 -~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (687)
                       .+++.+++.++++.+.+      -..+|+|+|--+..++  .|  .+...|
T Consensus       154 ~~~~~~~~~~~~~~~~~~------~g~EGim~K~~~s~Y~--~g--~Rs~~w  195 (201)
T cd07898         154 LPVESAEELEAAFARARA------RGNEGLMLKDPDSPYE--PG--RRGLAW  195 (201)
T ss_pred             EEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCcC--CC--CcCCCc
Confidence             34678888888776653      3459999999775543  12  235667

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=98.50  E-value=6.5e-07  Score=74.24  Aligned_cols=75  Identities=37%  Similarity=0.515  Sum_probs=66.8

Q ss_pred             ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc-cccEEEEcCCCCc--cHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK-NTNYLVKGQKPGK--KLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk-~t~~LV~G~~~g~--Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      +|+|.+|+|+|.+....|+++.+++..+||++...++. +++++|+++....  ++..|...+++|++++++.+.+..
T Consensus         2 ~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~   79 (80)
T smart00292        2 LFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA   79 (80)
T ss_pred             ccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHC
Confidence            68999999999777789999999999999999999998 9999999886553  368888999999999999988753

>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases

Probab=98.41  E-value=3.9e-06  Score=85.05  Aligned_cols=155  Identities=19%  Similarity=0.133  Sum_probs=103.4

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh-----hHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFI  192 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~-----~F~  192 (687)
                      ..|++|+|+||.-+.+.+.+| =+++.||+    |.|+|+.+..+...-..+..   ...+.+-||+++...     +|+
T Consensus        25 ~~~~~E~K~DG~R~~~~~~~~-~v~~~SR~----~~~~t~~~pel~~~~~~~~~---~~~~iLDGElv~~~~~g~~~~F~   96 (207)
T cd07901          25 GEAAVEYKYDGIRVQIHKDGD-EVRIFSRR----LEDITNALPEVVEAVRELVK---AEDAILDGEAVAYDPDGRPLPFQ   96 (207)
T ss_pred             CcEEEEEeEcceeEEEEEeCC-EEEEEeCC----CccccchhhHHHHHHHhcCC---CCCEEEeCEEEEECCCCCccCHH
Confidence            479999999999999877655 47999996    89999987665432111210   146899999998762     576


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc--
Q psy11422        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY--  267 (687)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~--  267 (687)
                      .+-.+.                   ++...  ......++.|++|++...++.++ .....+..+.|.++.-+. +..  
T Consensus        97 ~l~~r~-------------------~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~  156 (207)
T cd07901          97 ETLRRF-------------------RRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILL  156 (207)
T ss_pred             HHHHHh-------------------ccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEE
Confidence            553321                   11110  01123579999999987655332 247889999998876543 221  


Q ss_pred             ---eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        268 ---SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       268 ---~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                         ..+.+.+++.++++.+.+.      -..|||+|--+..+
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y  192 (207)
T cd07901         157 APRIVTDDPEEAEEFFEEALEA------GHEGVMVKSLDSPY  192 (207)
T ss_pred             EEEEecCCHHHHHHHHHHHHHc------CCceEEEeCCCCCc
Confidence               2356788999988877543      35899999877544

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.39  E-value=1.5e-07  Score=64.56  Aligned_cols=28  Identities=36%  Similarity=0.816  Sum_probs=19.1

Q ss_pred             CCCCCCCcceeecCceeEEecCCCCCCHH
Q psy11422        417 ICPICNSKIIYIESNLIARCSGSWIECIA  445 (687)
Q Consensus       417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~  445 (687)
                      +||+||++|++.++++++||+|+.. |||
T Consensus         1 ~CP~C~s~l~~~~~ev~~~C~N~l~-CpA   28 (28)
T PF03119_consen    1 TCPVCGSKLVREEGEVDIRCPNPLS-CPA   28 (28)
T ss_dssp             B-TTT--BEEE-CCTTCEEE--CGC--HH
T ss_pred             CcCCCCCEeEcCCCCEeEECCCCCc-CCC
Confidence            5999999999999999999999767 997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>PRK03180 ligB ATP-dependent DNA ligase; Reviewed

Probab=98.37  E-value=1.7e-05  Score=90.66  Aligned_cols=216  Identities=17%  Similarity=0.107  Sum_probs=137.3

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh-----hHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~-----~F~~  193 (687)
                      .|++|+|+||.-+.+...+|. ++..||+    |+|+|+....+......++    ...+.+-||++.-..     .|+.
T Consensus       205 ~~~~E~K~DG~R~qih~~~~~-v~l~SR~----~~d~T~~fPei~~~~~~~~----~~~~ILDGElv~~d~~g~~~~F~~  275 (508)
T PRK03180        205 PAAVEAKLDGARVQVHRDGDD-VRVYTRT----LDDITARLPEVVEAVRALP----VRSLVLDGEAIALRPDGRPRPFQV  275 (508)
T ss_pred             CeEEEEEEceeEEEEEEECCE-EEEEeCC----CCcchhhhHHHHHHHHhCC----CcceeecceEEEECCCCCcCCHHH
Confidence            699999999999999887665 7999996    8899988765543222221    246889999997643     5655


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcc--cccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCC-CCceE
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC-GEYSV  269 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~--~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~-~~~~~  269 (687)
                      +-.+                   ++++.+.  .....++.|++|++...+|.++ ..+..+..+.|.++--+.. .....
T Consensus       276 l~~R-------------------~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~~~~~~~~  336 (508)
T PRK03180        276 TASR-------------------FGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHRVPRLV  336 (508)
T ss_pred             HHHH-------------------hccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccccccccee
Confidence            4321                   1111111  1123579999999987666443 2468888888887632111 11234


Q ss_pred             eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeec-Ccceee
Q psy11422        270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIG-RTGIIT  348 (687)
Q Consensus       270 ~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvG-RTG~iT  348 (687)
                      +.+.+++.++++...+.      ..-|||+|--+..++  -|.  +...| +-+|- .......|.+..|--| |+|.++
T Consensus       337 ~~~~~~~~~~~~~a~~~------g~EGlm~K~~ds~Y~--~Gr--R~~~W-lK~K~-~~t~D~VviG~~~G~Gkr~g~~~  404 (508)
T PRK03180        337 TADPAAAAAFLAAALAA------GHEGVMVKSLDAPYA--AGR--RGAGW-LKVKP-VHTLDLVVLAAEWGSGRRTGKLS  404 (508)
T ss_pred             cCCHHHHHHHHHHHHHc------CCceEEEeCCCCCcC--CCC--CCCCc-EEEcC-CCceEEEEEeeecCCCCCCCCcc
Confidence            56788999988776432      458999998775443  122  23456 56664 5778889999988888 566654


Q ss_pred             e--EEEEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11422        349 P--VALLKPVLIDGI--TITRA-TLHNESEIYR  376 (687)
Q Consensus       349 P--vA~lePV~l~G~--tVsra-TLhN~~~i~~  376 (687)
                      .  +|..+|=  +|.  +|-++ |.++-+++++
T Consensus       405 ~~llg~~d~~--~~~l~~vgkv~sG~td~~l~~  435 (508)
T PRK03180        405 NLHLGARDPA--TGGFVMLGKTFKGMTDAMLAW  435 (508)
T ss_pred             ceEEEEEeCC--CCeEEEecCccCCCCHHHHHH
Confidence            3  2333331  244  44444 6666655544

>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain

Probab=98.32  E-value=3e-05  Score=83.00  Aligned_cols=209  Identities=19%  Similarity=0.187  Sum_probs=131.7

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~  193 (687)
                      ..|++|+|+||.-+.+...+| -++..||    .|+|+|+....+...-..++    ...+.+-||+++-    ..+|+.
T Consensus        12 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~~p~l~~~~~~~~----~~~~iLDGElv~~d~~g~~~F~~   82 (298)
T TIGR02779        12 DDWRYEVKYDGYRCLARIEGG-KVRLISR----NGHDWTEKFPILAAALAALP----ILPAVLDGEIVVLDESGRSDFSA   82 (298)
T ss_pred             CCEEEEEEEceEEEEEEEeCC-EEEEEeC----CCCchHhHhHHHHHHHHhCC----CCcEEEEeEEEEECCCCCCCHHH
Confidence            469999999999998866555 4799999    78999987644443311121    2368999999983    456766


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC-c-e--
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-Y-S--  268 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~-~-~--  268 (687)
                      +-..                   ++...     ..++.|++|++...++.++ .....+..+.|+++-=+.... . .  
T Consensus        83 l~~r-------------------~~~~~-----~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~~  138 (298)
T TIGR02779        83 LQNR-------------------LRAGR-----DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRY  138 (298)
T ss_pred             HHhh-------------------hhcCC-----CCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEec
Confidence            5321                   11111     1579999999987665432 246778888887762111111 1 1  


Q ss_pred             EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceee
Q psy11422        269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIIT  348 (687)
Q Consensus       269 ~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iT  348 (687)
                      ...+.+++.++++...+.      -..|||+|--|..++.  |   +.+.| +-+| +....+..|.+....-||.|.+.
T Consensus       139 ~~~~~~~~~~~~~~~~~~------g~EGiv~K~~ds~Y~~--G---rs~~W-lK~K-~~~~~d~vV~G~~~g~g~~~~~g  205 (298)
T TIGR02779       139 SVHFEGDGQALLEAACRL------GLEGVVAKRRDSPYRS--G---RSADW-LKLK-CRRRQEFVIGGYTPPNGSRSGFG  205 (298)
T ss_pred             ccCchhHHHHHHHHHHHc------CCceEEEeCCCCCCCC--C---CCCCc-EEEc-cCCCCEEEEEEEECCCCCCCccc
Confidence            235677888887766432      3589999998866542  2   36778 4555 33456778888888877665544


Q ss_pred             eEE--EEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11422        349 PVA--LLKPVLIDGI--TITRA-TLHNESEIYR  376 (687)
Q Consensus       349 PvA--~lePV~l~G~--tVsra-TLhN~~~i~~  376 (687)
                      ...  ..++    |.  .|-++ |..+.+..++
T Consensus       206 slll~~~~~----~~l~~vg~vgsG~s~~~~~~  234 (298)
T TIGR02779       206 ALLLGVYEG----GGLRYVGRVGTGFSEAELAT  234 (298)
T ss_pred             eEEEEEECC----CeEEEEeEecCCCCHHHHHH
Confidence            332  1222    33  34444 6777766665

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.

>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases

Probab=98.26  E-value=1.3e-05  Score=80.12  Aligned_cols=162  Identities=17%  Similarity=0.198  Sum_probs=101.1

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh----hhHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIKL  194 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~----~~F~~~  194 (687)
                      .|++|+|+||.-+.+.+.+| -+++.||    .|+++|+....|...=..+    .+..+.+-||+++-.    ..|..+
T Consensus        17 ~~~~e~K~DG~R~~i~~~~~-~v~~~SR----~g~~~t~~~p~l~~~~~~~----~~~~~iLDGElv~~~~~~~~~F~~l   87 (190)
T cd07906          17 DWLYEIKWDGYRALARVDGG-RVRLYSR----NGLDWTARFPELAEALAAL----PVRDAVLDGEIVVLDEGGRPDFQAL   87 (190)
T ss_pred             CeEEEEeEceEEEEEEEECC-EEEEEcC----CCCcchhhhHHHHHHHHhc----CCCCEEEEeEEEEECCCCCCCHHHH
Confidence            69999999999999988766 5799999    5788887554433210011    134688999999843    356543


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceEeCCH
Q psy11422        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSGV  273 (687)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~~~~~  273 (687)
                      -.                   ..++.+ .......+.|++|++...++... ..+..+..+.|..+.-+..+...++...
T Consensus        88 ~~-------------------~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~~  147 (190)
T cd07906          88 QN-------------------RLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF  147 (190)
T ss_pred             HH-------------------hhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECceE
Confidence            21                   111111 12234579999999976554332 2578999999999876653434433322


Q ss_pred             -HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11422        274 -NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (687)
Q Consensus       274 -~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (687)
                       .+..++++++.+      -..+|+|+|--+..+.  .|.  +.+.|
T Consensus       148 ~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~--~g~--rs~~w  184 (190)
T cd07906         148 EGGGAALFAAACE------LGLEGIVAKRADSPYR--SGR--RSRDW  184 (190)
T ss_pred             cCCHHHHHHHHHH------cCCcEEEEecCCCCcC--CCC--CCCcc
Confidence             222455554432      3469999999885554  233  24667

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor

>PRK07636 ligB ATP-dependent DNA ligase; Reviewed

Probab=98.22  E-value=0.00018  Score=76.12  Aligned_cols=205  Identities=17%  Similarity=0.206  Sum_probs=127.5

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~----~~F~~  193 (687)
                      ..|++|+|+||.-+.+.-.+| -+++.||    .|.|+|+....+...       ..|..+.+-||++...    .+|+.
T Consensus        18 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~fPe~~~~-------~~~~~~vLDGElv~~d~~g~~~F~~   85 (275)
T PRK07636         18 ENYITEPKFDGIRLIASKNNG-LIRLYTR----HNNEVTAKFPELLNL-------DIPDGTVLDGELIVLGSTGAPDFEA   85 (275)
T ss_pred             CcEEEEEEEceeEEEEEEeCC-EEEEEeC----CCCCchhhhhhHHhh-------hcCCCEEEEeEEEEECCCCCCCHHH
Confidence            369999999999997654455 4799999    688999876554321       1244588999999843    46766


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceEeCC
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG  272 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~~~~  272 (687)
                      +-...                   ++..+  ....++.|++|++...++.++ .....+..+.|+++.-+. +....+..
T Consensus        86 l~~r~-------------------~~~~~--~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~-~~~~~~~~  143 (275)
T PRK07636         86 VMERF-------------------QSKKS--TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH-PNVKIIEG  143 (275)
T ss_pred             HHHHh-------------------ccccc--cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC-CCEEEccc
Confidence            53211                   11111  124679999999987665433 247889999999986543 33333332


Q ss_pred             -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeEE
Q psy11422        273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA  351 (687)
Q Consensus       273 -~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA  351 (687)
                       .++..++++...+      -...|||+|--|..++.    ..+...| +-.| ..+..+..|.+.  ..|..|.+  ++
T Consensus       144 ~~~~~~~~~~~~~~------~g~EGiV~K~~ds~Y~~----g~Rs~~W-lKiK-~~~~~e~vV~G~--~~~~~g~l--lg  207 (275)
T PRK07636        144 IEGHGTAYFELVEE------RELEGIVIKKANSPYEI----NKRSDNW-LKVI-NYQYTDVLITGY--RKEEFGLL--LS  207 (275)
T ss_pred             ccccHHHHHHHHHH------cCCcEEEEeCCCCCCCC----CCCCCCe-EEEe-cCCeEEEEEEEE--ecCCCcEE--EE
Confidence             2345566655532      23579999998866531    2345678 6666 346667777666  34445533  43


Q ss_pred             EEEEEEECCEEEEEecCCCHHHHHhc
Q psy11422        352 LLKPVLIDGITITRATLHNESEIYRK  377 (687)
Q Consensus       352 ~lePV~l~G~tVsraTLhN~~~i~~~  377 (687)
                      .     .+|..|-++.-...+..+++
T Consensus       208 ~-----~~g~~~G~vgt~~~~~~~~l  228 (275)
T PRK07636        208 Y-----LDGRSAGIMEFMPYDARKKF  228 (275)
T ss_pred             e-----cCCeEEEEECCCCHHHHHHH
Confidence            2     25666666633555554443

>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I

Probab=98.21  E-value=3.7e-05  Score=78.72  Aligned_cols=179  Identities=17%  Similarity=0.175  Sum_probs=112.5

Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccC-
Q psy11422         87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI-  165 (687)
Q Consensus        87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-  165 (687)
                      .|||.- -+.+.+++.+   .+    +   ...|++|+|+||.-+.+.|.+|.-++..||.    |+|+|+....+... 
T Consensus        11 ~PMLA~-~~~~~~~~~~---~~----~---~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~----g~~~t~~~pel~~~~   75 (219)
T cd07900          11 KPMLAK-PTKGVSEVLD---RF----E---DKEFTCEYKYDGERAQIHLLEDGKVKIFSRN----LENNTEKYPDIVAVL   75 (219)
T ss_pred             ccccCC-ccCCHHHHHH---Hh----C---CCeEEEEEeecceEEEEEEcCCCeEEEECCC----CccccchhhHHHHHH
Confidence            488863 3345555422   22    1   2479999999999999999763347999994    89999887654432 


Q ss_pred             CcccccCCCCceEEEEEEEEeehh------hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEeccc
Q psy11422        166 PLVLNIKYPPELLEVRCEVLIYKK------DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGE  239 (687)
Q Consensus       166 P~~l~~~~~~~~~evRGEi~~~~~------~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~  239 (687)
                      ...+..  -+..+.+-||+++-..      .|+.+-..                   .+...+......++.|++|++..
T Consensus        76 ~~~~~~--~~~~~iLDGElv~~~~~~g~~~~F~~l~~r-------------------~~~~~~~~~~~~~~~~~vFDiL~  134 (219)
T cd07900          76 PKSLKP--SVKSFILDSEIVAYDRETGKILPFQVLSTR-------------------KRKDVDANDIKVQVCVFAFDLLY  134 (219)
T ss_pred             HHHhcc--cCccEEEeeEEEEEEcCCCCCcChHHHhhh-------------------cccccccccCcccEEEEEEEEEE
Confidence            222211  1456899999987543      45543221                   01111111234679999999988


Q ss_pred             ccCCCC-CCCHHHHHHHHHhcCCCCCCCc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC--hhhh
Q psy11422        240 LRGMNM-PSSHSELLNWYQKIGLSICGEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC--LSTQ  307 (687)
Q Consensus       240 ~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~--~~~~  307 (687)
                      .++..+ ..+..+..+.|.++-=+.....     ..+.+.+++.++++.+.+.      ..-|||+|--+  ..++
T Consensus       135 l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~~~s~Y~  204 (219)
T cd07900         135 LNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTEEIQEFLEEAVKN------NCEGLMVKTLDSDATYE  204 (219)
T ss_pred             ECCchhhcCCHHHHHHHHHHhcCCCCCeEEEEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCccC
Confidence            766442 2467888888887632222111     2346788999988877543      45899999877  5443

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=98.20  E-value=3.2e-06  Score=68.67  Aligned_cols=55  Identities=33%  Similarity=0.421  Sum_probs=50.2

Q ss_pred             HHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       522 ~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      +..-+.|||||+++++.|.+. |.++++|..++.++|.+++|||+++|++|...++
T Consensus         4 ~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~   59 (60)
T PF14520_consen    4 FDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR   59 (60)
T ss_dssp             HHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred             HHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence            445568999999999999988 9999999999999999999999999999998764

...

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=98.19  E-value=2.8e-06  Score=92.01  Aligned_cols=74  Identities=18%  Similarity=0.173  Sum_probs=69.2

Q ss_pred             ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC--ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g--~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      -.+||.|||||... ++|+++.+.+..+|..++.+||..|.+|||.+...  .|...|..+|||+++|++|+++|..
T Consensus       294 lv~Gm~v~~~~e~~-~~~d~li~~~~~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~~gipl~~d~~fl~~~~~  369 (377)
T PRK05601        294 LVAGMEVVVAPEIT-MDPDIIIQAIVRAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQRKGIPLLSDVAFLAAVER  369 (377)
T ss_pred             cccCcEEEEeCCcc-CCHHHHHHHHHHccchhhhccccceeEEEeCCCCCccchhhhhhhcCCCccCHHHHHHHHHH
Confidence            46899999999986 79999999999999999999999999999998654  9999999999999999999999964

>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=98.18  E-value=3.5e-05  Score=77.13  Aligned_cols=157  Identities=17%  Similarity=0.189  Sum_probs=101.3

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc-cCCcccccCCCCceEEEEEEEEe------ehhh
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH-KIPLVLNIKYPPELLEVRCEVLI------YKKD  190 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~-~iP~~l~~~~~~~~~evRGEi~~------~~~~  190 (687)
                      ..|++|+|+||+-+.+.+.+|. +++.||    .|.++|+....+. .+...+..  -+..+.+-||++.      ....
T Consensus        19 ~~~~~e~K~DG~R~~i~~~~~~-v~~~SR----~g~~~~~~~~~l~~~l~~~~~~--~~~~~vLDGElv~~d~~~~~~~~   91 (202)
T PF01068_consen   19 GPWYVEPKYDGVRCQIHKDGGG-VRLFSR----NGKDITSQFPELAEALRELLFP--DGPDFVLDGELVVLDPNTGSPLP   91 (202)
T ss_dssp             SCEEEEEEESSEEEEEEEETTE-EEEEET----TSSB-GGGHHHHHHHHHHHBCT--SCTEEEEEEEEEEBETTTSSBCC
T ss_pred             CCeEEEEeEeeEEeeeeecccc-ceeecc----cccchhhHHHHHHHHHHHHhcC--CCCceEEEEEEEEEecCCCcchh
Confidence            4799999999999999887776 689999    6888998544331 12222211  1236999999999      3344


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC--
Q psy11422        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE--  266 (687)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~-~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~--  266 (687)
                      |.                   ..++.+++.+... ....++.|++|++...++..+ ..+..+..+.|.++--+....  
T Consensus        92 f~-------------------~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~  152 (202)
T PF01068_consen   92 FQ-------------------ELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIR  152 (202)
T ss_dssp             HH-------------------HHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEE
T ss_pred             HH-------------------HHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCcee
Confidence            44                   4444443322211 114579999999986554321 247888899988775122222  


Q ss_pred             ---ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        267 ---YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       267 ---~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                         ...+.+.+++.++++.+.+..      -.|+|+|--+..+
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~g------~EG~v~K~~~~~Y  189 (202)
T PF01068_consen  153 IVESYVVNSKEELEELFEEAIDQG------FEGLVLKDPDSPY  189 (202)
T ss_dssp             EEEEEEESSHHHHHHHHHHHHHTT------SSEEEEEETTSSC
T ss_pred             EeeeecCCCHHHHHHHHHHHHHcC------CceEEEECCCCcc
Confidence               234678999999988775433      4899999866444

It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....

>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1)

Probab=98.15  E-value=9.2e-05  Score=85.09  Aligned_cols=220  Identities=19%  Similarity=0.178  Sum_probs=134.7

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh-cc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII-HK-IPLVLNIKYPPELLEVRCEVLIYKK------D  190 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i-~~-iP~~l~~~~~~~~~evRGEi~~~~~------~  190 (687)
                      .|++|+|+||.-+.+.+.+|. ++..||    -|+|+|+....+ .. +...++.   ...+.+-||++.-..      .
T Consensus       188 ~~~~E~K~DG~R~qih~~~~~-v~l~SR----~g~~~t~~~pei~~~~~~~~~~~---~~~~ILDGElv~~d~~~g~~~~  259 (514)
T TIGR00574       188 KFYVEYKYDGERVQIHKDGDK-FKIFSR----RLENYTYAYPEIFTEFIKEAFPG---IKSCILDGEMVAIDPETGKILP  259 (514)
T ss_pred             ceEEEEeecceEEEEEEcCCE-EEEEcC----CCcccccccchhHHHHHHHhcCc---cceeeecceEEEEEcCCCCCcC
Confidence            799999999999999875555 799999    578999765443 21 1111211   125789999997643      4


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcC-cccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce
Q psy11422        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLN-PKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS  268 (687)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~-~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~  268 (687)
                      |+.+-...                   ++.+ .......++.||+|++...++.++ ..+..+..+.|.++-=+.+....
T Consensus       260 F~~l~~r~-------------------~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~  320 (514)
T TIGR00574       260 FQTLLRRK-------------------RRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESILKPIPNRIE  320 (514)
T ss_pred             cHhHHhhh-------------------hhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhccCCCCcEE
Confidence            65442211                   1101 011123578999999987665432 25788999999886433332222


Q ss_pred             -----EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC-----CceeeEEEEEEE
Q psy11422        269 -----VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL-----SKEALTKIKAIN  338 (687)
Q Consensus       269 -----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~-----~~~~~T~v~~I~  338 (687)
                           .+.+.+++.++++...+.      -..|+|+|--+..++  .|  .+.+.| +=+|-.     .+.....|.+..
T Consensus       321 ~~~~~~~~~~e~~~~~~~~~~~~------g~EGlv~K~~ds~Y~--~G--~Rs~~W-lK~K~~y~~~~~~~~D~vvig~~  389 (514)
T TIGR00574       321 IAEMKITSNVEELEKFLNEAISE------GCEGLMLKDLKSIYE--PG--KRGWLW-LKFKPEYLEGMGDTLDLVVIGAY  389 (514)
T ss_pred             EEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCccc--CC--CCCCcc-eeCchhhcccccCceeEEEEeeE
Confidence                 245788999988766543      359999998775554  23  345667 344421     356778888988


Q ss_pred             EeecC-cceeeeEEE--EEEEEECCE--EEEEe-cCCCHHHHHhcC
Q psy11422        339 IQIGR-TGIITPVAL--LKPVLIDGI--TITRA-TLHNESEIYRKN  378 (687)
Q Consensus       339 ~qvGR-TG~iTPvA~--lePV~l~G~--tVsra-TLhN~~~i~~~~  378 (687)
                      +.-|| .|.++....  .++-  .|.  +|.++ |.+..+.++++.
T Consensus       390 ~g~gk~~g~~~~~l~g~~d~~--~~~~~~v~kvgsG~sd~~l~~l~  433 (514)
T TIGR00574       390 YGKGKRTGMYGSFLLACYDPE--SEEFKTITKVGTGFTDADLQELG  433 (514)
T ss_pred             ecCCccCCceeEEEEEEEcCC--CCeEEEEEEECCCCCHHHHHHHH
Confidence            88774 455444322  2210  022  44444 777777777653

All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08224 ligC ATP-dependent DNA ligase; Reviewed

Probab=98.15  E-value=8.8e-05  Score=81.10  Aligned_cols=214  Identities=14%  Similarity=0.136  Sum_probs=130.8

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh---hhHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK---KDFIKLN  195 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~---~~F~~~n  195 (687)
                      .|.+|+|+||.-+.+.+.+|. ++..||    -|.|+|+....|...-..+    .|..+.+-||++.-.   .+|+.+.
T Consensus        25 ~w~~E~K~DG~R~~~~~~~~~-v~l~SR----ng~d~t~~fPel~~~~~~~----~~~~~vLDGEiVv~~~~~~~F~~Lq   95 (350)
T PRK08224         25 GWSYEPKWDGFRCLVFRDGDE-VELGSR----NGKPLTRYFPELVAALRAE----LPERCVLDGEIVVARDGGLDFEALQ   95 (350)
T ss_pred             cEEEEEeECeeEEEEEEECCE-EEEEeC----CCCCchhhhHHHHHHHHhh----CCCCEEEeeEEEEeCCCCCCHHHHH
Confidence            699999999999988776665 799999    7899998876654322222    245789999999865   3788775


Q ss_pred             HHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceE---eC
Q psy11422        196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSV---LS  271 (687)
Q Consensus       196 ~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~---~~  271 (687)
                      ....   .    ++.+     .+++    ....++.|++|++...++.++ .....+..+.|+++ |+..+...+   ..
T Consensus        96 ~r~~---~----~~~~-----~~~~----~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l-~~~~~~i~~~~~~~  158 (350)
T PRK08224         96 QRIH---P----AASR-----VRKL----AEETPASFVAFDLLALGDRDLTGRPFAERRAALEAA-AAGSGPVHLTPATT  158 (350)
T ss_pred             hhhh---c----cccc-----hhhh----hhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHh-cCCCCcEEEecccC
Confidence            3211   0    0101     1111    123469999999988666443 24677888888877 333222233   23


Q ss_pred             CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeE-
Q psy11422        272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV-  350 (687)
Q Consensus       272 ~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPv-  350 (687)
                      +.++..++++...      .--..|||+|--|..++  -|..+    | +-+|. ....+..|.+..+.-|+ |.+.-. 
T Consensus       159 ~~~~~~~~~~~a~------~~G~EGIV~Kr~dS~Y~--~Grr~----W-lKiK~-~~~~d~vI~G~~~g~~~-~~~gsll  223 (350)
T PRK08224        159 DPATARRWFEEFE------GAGLDGVIAKPLDGPYQ--PGKRA----M-FKVKH-ERTADCVVAGYRYHKSG-PVVGSLL  223 (350)
T ss_pred             CHHHHHHHHHHHH------hCCCcEEEEeCCCCCcC--CCCcC----E-EEEcc-CCcEEEEEEEEEcCCCC-CccccEE
Confidence            4567777776553      23468999999886554  23322    7 55553 45667788887776655 332221 


Q ss_pred             -EEEEEEEECCE--EEEEecCCCHHHHHh
Q psy11422        351 -ALLKPVLIDGI--TITRATLHNESEIYR  376 (687)
Q Consensus       351 -A~lePV~l~G~--tVsraTLhN~~~i~~  376 (687)
                       +..++   +|.  .|-+++..+.+..++
T Consensus       224 lg~~d~---~g~l~~vG~v~Gf~~~~~~~  249 (350)
T PRK08224        224 LGLYDD---DGQLHHVGVTSAFPMARRRE  249 (350)
T ss_pred             EEEECC---CCcEEEEEEECCCCHHHHHH
Confidence             11111   242  455566666665554

>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases

Probab=98.11  E-value=3e-05  Score=76.76  Aligned_cols=150  Identities=17%  Similarity=0.160  Sum_probs=96.4

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~  197 (687)
                      ..|.+|+|+||.-+.+.+.+|. +.++||    .|+++|.-...+..  ..+.  ..+..+.+-||++.....+      
T Consensus        19 ~~~~~e~K~DG~R~~~~~~~~~-v~~~sR----~g~~~~~~~~~~~~--~~~~--~~~~~~ilDGElv~~~~~~------   83 (182)
T cd06846          19 DEYYVQEKYDGKRALIVALNGG-VFAISR----TGLEVPLPSILIPG--RELL--TLKPGFILDGELVVENREV------   83 (182)
T ss_pred             CcEEEEEccCceEEEEEEcCCe-EEEEeC----CCCEEecccccccc--hHHh--ccCCCeeEEEEEEeccCCC------
Confidence            4799999999999999887665 789999    57777765433321  0111  1244689999999864433      


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCC--CceE-----
Q psy11422        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--EYSV-----  269 (687)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~--~~~~-----  269 (687)
                                                  ....+.|++|++...++.+. .....++++.|+++-=....  ...+     
T Consensus        84 ----------------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~~  135 (182)
T cd06846          84 ----------------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLEN  135 (182)
T ss_pred             ----------------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEeec
Confidence                                        12368999999987665332 24678888888776422211  1111     


Q ss_pred             eC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11422        270 LS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (687)
Q Consensus       270 ~~-~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (687)
                      +. ..+++.++++++      .+...||+|+|--+..+.   |...+.+.|
T Consensus       136 ~~~~~~~~~~~~~~~------~~~g~EGvi~K~~~s~Y~---~~~gr~~~w  177 (182)
T cd06846         136 APSYDETLDDLLEKL------KKKGKEGLVFKHPDAPYK---GRPGSSGNQ  177 (182)
T ss_pred             ccccchHHHHHHHHh------hhcCCceEEEEcCCCCcc---ccCCCCCce
Confidence            11 222356665544      346789999999886663   445566766

ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq

>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases

Probab=98.10  E-value=6e-05  Score=76.45  Aligned_cols=157  Identities=17%  Similarity=0.114  Sum_probs=100.8

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~----~F~~  193 (687)
                      ..|++|+|+||.-+.+...+| =++..||    .|+|+|+....+...-..     .|..+.+-||+++-..    +|+.
T Consensus        24 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~~p~l~~~~~~-----l~~~~iLDGElv~~~~~~~~~F~~   93 (207)
T cd07897          24 SDWQAEWKWDGIRGQLIRRGG-EVFLWSR----GEELITGSFPELLAAAEA-----LPDGTVLDGELLVWRDGRPLPFND   93 (207)
T ss_pred             ccEEEEEeEceEEEEEEEcCC-EEEEEeC----CCCcccccchHHHHHHHh-----CCCCeEEEeEEEEecCCCccCHHH
Confidence            379999999999998765444 5799999    467898765544332111     3556899999998654    7877


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC-CC-----
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GE-----  266 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~-~~-----  266 (687)
                      +..+..   .      ++ +...       .....++.|++|++...++..+. ....+..+.|.++--+.. ..     
T Consensus        94 l~~r~~---~------~~-~~~~-------~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~~~~  156 (207)
T cd07897          94 LQQRLG---R------KT-VGKK-------LLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLDLSP  156 (207)
T ss_pred             HHHHhc---c------cc-cchh-------hHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCceeecc
Confidence            643311   0      00 0011       11235789999999876653321 357788888877622221 11     


Q ss_pred             ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11422        267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (687)
Q Consensus       267 ~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (687)
                      ...+.+.+++.++++...+.      ...|||+|--+..++
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~  191 (207)
T cd07897         157 LIAFADWEELAALRAQSRER------GAEGLMLKRRDSPYL  191 (207)
T ss_pred             eEecCCHHHHHHHHHHHHHc------CCeEEEEeCCCCCcC
Confidence            12356788999988876543      358999999886554

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.

>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV

Probab=98.04  E-value=0.00023  Score=72.89  Aligned_cols=167  Identities=19%  Similarity=0.164  Sum_probs=103.4

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC---ccccc--CCCCceEEEEEEEEeehh---
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP---LVLNI--KYPPELLEVRCEVLIYKK---  189 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP---~~l~~--~~~~~~~evRGEi~~~~~---  189 (687)
                      ..|++|+|+||.-+.+.+.+|. +++.||    .|.|+|+....+...-   ..|..  ...+..+.+-||+++...   
T Consensus        33 ~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~~  107 (225)
T cd07903          33 KPFYIETKLDGERIQLHKDGNE-FKYFSR----NGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKETK  107 (225)
T ss_pred             CeEEEEEeeCceEEEEEecCCE-EEEEeC----CCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCcC
Confidence            5799999999999999887665 799999    6888887654332210   01100  012457899999997432   


Q ss_pred             ---hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCC
Q psy11422        190 ---DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG  265 (687)
Q Consensus       190 ---~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~  265 (687)
                         .|..+               ++.++  ++..   ......+.|++|++...++.+. .....+..+.|.++--+...
T Consensus       108 ~~~~f~~l---------------~~~~~--~~~~---~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~~~  167 (225)
T cd07903         108 RFLPFGTL---------------KDVAK--LREV---EDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPG  167 (225)
T ss_pred             eeccchHH---------------HHHHh--hccc---ccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCCCC
Confidence               34332               11111  1100   1123568999999987655432 24688888889887433222


Q ss_pred             Cc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11422        266 EY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (687)
Q Consensus       266 ~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (687)
                      ..     ..+.+.+++.++++.+.+..      ..|+|+|--+..+..  |  .+...|
T Consensus       168 ~i~~~~~~~~~~~~~~~~~~~~~~~~g------~EGlv~K~~~s~Y~~--g--~Rs~~w  216 (225)
T cd07903         168 RLEVVKRTEASTKEEIEEALNEAIDNR------EEGIVVKDLDSKYKP--G--KRGGGW  216 (225)
T ss_pred             eEEEEEEEeCCCHHHHHHHHHHHHHcC------CceEEEecCCCCCcc--C--CcCCCc
Confidence            22     22456788999888775433      699999998755441  2  245667

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di

>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]

Probab=98.03  E-value=0.00044  Score=77.91  Aligned_cols=215  Identities=19%  Similarity=0.211  Sum_probs=138.9

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhh-hhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIH-IIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~-~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~  193 (687)
                      .|.+|+|+||.-+.+...+|. ++.+||    .|+|||+... .+..+=..++    +..+.+-||+++-    ..+|+.
T Consensus       134 ~w~~E~K~DG~R~q~h~~~~~-vrl~SR----~g~d~T~~fP~~~~~~~~~l~----~~~~iiDGE~V~~~~~~~~~F~~  204 (444)
T COG1793         134 DWAYEEKFDGYRVQIHIDGGK-VRLYSR----NGEDWTGRFPDILEAAAEALP----ADDFILDGEIVVLDEEGRLDFQA  204 (444)
T ss_pred             CEEEEEeeceEEEEEEEcCCE-EEEEeC----CCccchhhChHHHHHHHhcCC----CCceEEeeeEEEECCCCCCCHHH
Confidence            599999999999999998885 799999    6999998876 3433322232    3468999999995    568887


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhc--C---CCCCC
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI--G---LSICG  265 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~--G---f~~~~  265 (687)
                      +.+..                   +++.+  ......++.||+|++...++.++. ....+..+.|.++  +   +...+
T Consensus       205 Lq~r~-------------------~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~~~~  265 (444)
T COG1793         205 LQQRL-------------------RRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIEIAE  265 (444)
T ss_pred             HHHHh-------------------hhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhcccccccccc
Confidence            65432                   22211  111334789999999987776542 2556666666553  1   23333


Q ss_pred             CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcc
Q psy11422        266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTG  345 (687)
Q Consensus       266 ~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG  345 (687)
                      ... +.+.+++..+++...      ..-+.|||+|--|..++.    ..+.-.| +-+| +.++..-.|.+..++-|+-+
T Consensus       266 ~i~-~~~~~~~~~~~~~a~------~~g~EGvv~K~~ds~Y~~----g~R~~~W-~K~K-~~~~~d~vv~G~~~g~Gkr~  332 (444)
T COG1793         266 RIP-FSDAEEGEAFLEAAI------ELGLEGVVAKRPDSPYRA----GGRSNKW-LKVK-RDETLDLVVVGAEYGKGKRS  332 (444)
T ss_pred             cee-ccChhhHHHHHHHHH------hcCceEEEEeCCCCCcCC----CCCCCcc-eEec-cCCcccEEEEEEEecCCccc
Confidence            332 367788888776543      346899999955544441    1122334 3444 33788999999999998865


Q ss_pred             eeeeEEEEEEEEECCE-----EEEEecCCCHHHHHh
Q psy11422        346 IITPVALLKPVLIDGI-----TITRATLHNESEIYR  376 (687)
Q Consensus       346 ~iTPvA~lePV~l~G~-----tVsraTLhN~~~i~~  376 (687)
                        +-=+-+-.+.-++.     .++=.|...-++.++
T Consensus       333 --~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~  366 (444)
T COG1793         333 --LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEE  366 (444)
T ss_pred             --ccceEEEEEEcCCCceEEEEecccCCCCHHHHHH
Confidence              44455566666664     333345565444433

>PRK01109 ATP-dependent DNA ligase; Provisional

Probab=97.94  E-value=0.00028  Score=82.41  Aligned_cols=216  Identities=17%  Similarity=0.151  Sum_probs=134.5

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC-cccccCCCCceEEEEEEEEeehh------hH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP-LVLNIKYPPELLEVRCEVLIYKK------DF  191 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP-~~l~~~~~~~~~evRGEi~~~~~------~F  191 (687)
                      .|++|.|+||.-+.+.+.+|. ++..||+    |+|+|+....|...- ..+.    +..+.+-||++.-..      .|
T Consensus       249 ~~~~E~K~DG~R~qih~~~~~-v~l~SR~----~~d~T~~~pel~~~~~~~~~----~~~~ILDGElv~~d~~~g~~~~F  319 (590)
T PRK01109        249 EALVEYKYDGERAQIHKKGDK-VKIFSRR----LENITHQYPDVVEYAKEAIK----AEEAIVEGEIVAVDPETGEMRPF  319 (590)
T ss_pred             CeEEEecCCceEEEEEEcCCE-EEEEeCC----chhhccccchHHHHHHHhcC----ccceEEeeeEEEEECCCCcccCh
Confidence            589999999999999886665 7999994    999998876654321 1232    346889999987541      46


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc---
Q psy11422        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY---  267 (687)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~---  267 (687)
                      +.+-.+    .       |......       .....++.|++|++...+|..+ ..+..++.+.|.++- ...+..   
T Consensus       320 ~~l~~R----~-------r~~~~~~-------~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~-~~~~~~~~~  380 (590)
T PRK01109        320 QELMHR----K-------RKYDIEE-------AIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIV-KENDKVKLA  380 (590)
T ss_pred             HHHhhc----c-------cccchhh-------hcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhc-CCCCceEEe
Confidence            654321    0       1100000       1124579999999988766443 246888888888763 222222   


Q ss_pred             --eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCC-------CceeeEEEEE
Q psy11422        268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA  336 (687)
Q Consensus       268 --~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~  336 (687)
                        ....+.+++.++++...+.      -.-|||+|--  |..++  -|  .+...|   +|+-       .+.....|.+
T Consensus       381 ~~~~~~~~~~~~~~~~~a~~~------g~EGiv~K~~~~ds~Y~--~g--~Rs~~W---lK~K~dy~~~~~~~~DlvviG  447 (590)
T PRK01109        381 ERIITDDVEELEKFFHRAIEE------GCEGLMAKSLGKDSIYQ--AG--ARGWLW---IKYKRDYQSEMADTVDLVVVG  447 (590)
T ss_pred             eeEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCCcC--CC--CCCccH---HHhhHHhhcccCCceeEEEEE
Confidence              2345778999988766543      3589999987  54443  12  345677   5554       3456778888


Q ss_pred             EEEeecC-cceeeeE--EEEEEEEECCE--EEEEe-cCCCHHHHHhc
Q psy11422        337 INIQIGR-TGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYRK  377 (687)
Q Consensus       337 I~~qvGR-TG~iTPv--A~lePV~l~G~--tVsra-TLhN~~~i~~~  377 (687)
                      ..|--|| +|.+...  |..+|  =+|.  +|-++ |..+.+.++++
T Consensus       448 ~~~g~Gkr~~~~g~~ll~~~d~--~~~~~~~v~kvgtG~sd~~~~~l  492 (590)
T PRK01109        448 AFYGRGRRGGKYGSLLMAAYDP--KTDTFETVCKVGSGFTDEDLDEL  492 (590)
T ss_pred             eEeCCCccCCccccEEEEEEcC--CCCeEEEEEEECCCCCHHHHHHH
Confidence            8777665 5555432  22222  1232  34444 77777777654

>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases

Probab=97.93  E-value=0.00012  Score=73.47  Aligned_cols=158  Identities=15%  Similarity=0.115  Sum_probs=98.3

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee---hhhHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY---KKDFIKL  194 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~---~~~F~~~  194 (687)
                      ..|++|+|+||.-+.+.+.+|. ++..||    .|+|+|+....+...-..+    .|..+.+-||+++-   ..+|+.+
T Consensus        16 ~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~----~~~~~iLDGElv~~~~~~~~F~~l   86 (194)
T cd07905          16 GGWQYEPKWDGFRCLAFRDGDE-VRLQSR----SGKPLTRYFPELVAAARAL----LPPGCVLDGELVVWRGGRLDFDAL   86 (194)
T ss_pred             CceEEEeeeceEEEEEEEeCCE-EEEEeC----CCCchhhhhHHHHHHHHhh----CCCCEEEEeEEEEEcCCCCCHHHH
Confidence            3699999999999998876664 799999    7889997654433211111    24568999999984   3467665


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCCCCce---Ee
Q psy11422        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYS---VL  270 (687)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~~~~~---~~  270 (687)
                      -..-   .      +|..   ..    +......++.|++|++...++.++. ....+..+.|.++-=+..+...   .+
T Consensus        87 ~~r~---~------~~~~---~~----~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~  150 (194)
T cd07905          87 QQRI---H------PAAS---RV----RRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPAT  150 (194)
T ss_pred             HHHh---c------cccc---ch----hhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECCcc
Confidence            4321   1      1100   00    1112346799999999876554322 4677888888766211112122   23


Q ss_pred             CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       271 ~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                      .+.+++.++++...+      -..-|||+|--+..+
T Consensus       151 ~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y  180 (194)
T cd07905         151 TDRAEAREWLEEFEG------AGLEGVVAKRLDGPY  180 (194)
T ss_pred             CCHHHHHHHHHHHHH------CCCceEEEeCCCCCc
Confidence            466777777776543      235899999877554

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is

>PHA00454 ATP-dependent DNA ligase

Probab=97.91  E-value=0.0027  Score=68.63  Aligned_cols=217  Identities=19%  Similarity=0.130  Sum_probs=122.9

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh---ccCCccccc--CCCCceEEEEEEEEeehhhHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII---HKIPLVLNI--KYPPELLEVRCEVLIYKKDFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i---~~iP~~l~~--~~~~~~~evRGEi~~~~~~F~~  193 (687)
                      .|.+|+|+||.-+.+...+|.=+++.||.-    .+++.-+...   ..++..+..  ...|..+.+-||++....+|+.
T Consensus        28 ~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g----~~~p~l~~~~~~~~~~~~~~~~~~~~l~~~~vLDGElv~~~~~f~~  103 (315)
T PHA00454         28 YLIADVKYDGVRGNIVVDNTADHGWLSREG----KTIPALEHLNGFDRRWAKLLNDDRCIFPDGFMLDGELMVKGVDFNT  103 (315)
T ss_pred             cEEEEEccceEEEEEEEcCCCeEEEEeCCC----CcccchhhhhhhhhhhhhhhhhhhhcCCCCeEEEEEEEecCCCHHH
Confidence            699999999999998776664479999953    3454322111   112222221  0124578999999997666765


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcC--cccccccccEEEEEecccccCC----CC----CCCHHHHHHHHHhcC---
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLN--PKINKNKILHFFAHGVGELRGM----NM----PSSHSELLNWYQKIG---  260 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~--~~~~~~r~l~f~~y~~~~~~~~----~~----~~~~~e~l~~L~~~G---  260 (687)
                      +.                   |.|+++.  +......++.|++|++...++.    .+    .....+.-+.|.++-   
T Consensus       104 ~~-------------------~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~~~  164 (315)
T PHA00454        104 GS-------------------GLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPLLMEYF  164 (315)
T ss_pred             HH-------------------HHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHHHHhhC
Confidence            43                   3343332  1222346899999999875522    11    123444445554331   


Q ss_pred             ----CCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEE
Q psy11422        261 ----LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKA  336 (687)
Q Consensus       261 ----f~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~  336 (687)
                          +..++ ...+.+.+++.++++...+      -...|||+|--|..++.  |..   ..|- -+| +...++..|.+
T Consensus       165 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~ds~Y~~--Grr---~~~~-K~K-~~~~~d~vIvG  230 (315)
T PHA00454        165 PEIDWFLSE-SYEVYDMESLQELYEKKRA------EGHEGLVVKDPSLIYRR--GKK---SGWW-KMK-PECEADGTIVG  230 (315)
T ss_pred             CCcceEeec-eEEcCCHHHHHHHHHHHHh------CCCceEEEeCCCCCCCC--CCc---cCcE-EEc-ccCceeEEEEE
Confidence                12222 2234578899998876642      34689999987765542  332   2362 444 33467888888


Q ss_pred             EEEeecC-c--ceeeeEEEEEEEEECCEEEEEecCCCHHHHHh
Q psy11422        337 INIQIGR-T--GIITPVALLKPVLIDGITITRATLHNESEIYR  376 (687)
Q Consensus       337 I~~qvGR-T--G~iTPvA~lePV~l~G~tVsraTLhN~~~i~~  376 (687)
                      ..+--|+ .  |.+--  -+--. =+|. ...+|..+.+..++
T Consensus       231 ~~~g~g~~~~~g~~~~--~~~~~-~~g~-l~~gtGfs~~~~~~  269 (315)
T PHA00454        231 VVWGTPGLANEGKVIG--FRVLL-EDGR-VVNATGISRALMEE  269 (315)
T ss_pred             EEECCCCccCCceEEE--EEEEe-CCCc-EEEccCCCHHHHHH
Confidence            8887742 3  33322  11000 1343 33477777766654

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=97.89  E-value=2.1e-05  Score=95.20  Aligned_cols=76  Identities=26%  Similarity=0.298  Sum_probs=68.4

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcC---CCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQ---KPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~---~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..||.|+.|++.|+|+ .++.+++.+|+.+||+++.+|++.|++||+..   +.++|+++|+++||+|++|+++.+.+..
T Consensus       391 ~~~l~~~~i~i~G~~~-~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~~~  469 (981)
T PLN03123        391 SEFLGDLKVSIVGASK-EKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCFKK  469 (981)
T ss_pred             CCCcCCeEEEEecCCC-CcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHHhc
Confidence            3689999999999996 47899999999999999999999999998886   3569999999999999999999877643

>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III

Probab=97.88  E-value=0.00027  Score=72.00  Aligned_cols=152  Identities=15%  Similarity=0.154  Sum_probs=95.9

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhh-hhhhcc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIHK-IPLVLNIKYPPELLEVRCEVLIYKK------D  190 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~------~  190 (687)
                      .|++|+|+||.-+.+.+.+|. +++.||+    |.|+|.. +..+.. ++..+..   ...+.+-||+++-..      .
T Consensus        35 ~~~~E~K~DG~R~~i~~~~~~-v~l~SR~----g~~~t~~~~~~~~~~~~~~~~~---~~~~iLDGEiv~~d~~~g~~~~  106 (213)
T cd07902          35 GMYAEIKYDGERVQVHKQGDN-FKFFSRS----LKPVLPHKVAHFKDYIPKAFPH---GHSMILDSEVLLVDTKTGKPLP  106 (213)
T ss_pred             ceEEEeccCCEEEEEEEcCCE-EEEEcCC----CcccccchhHHHHHHHHHhccc---ccceeeeeEEEEEECCCCcccc
Confidence            599999999999988776555 7999995    7888853 222221 2322321   346899999998432      2


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC---
Q psy11422        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---  266 (687)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~---  266 (687)
                      |..+..                   ..+.  .  ....++.|++|++...++.++ .....+..+.|.++--+....   
T Consensus       107 F~~l~~-------------------~~~~--~--~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~~~~  163 (213)
T cd07902         107 FGTLGI-------------------HKKS--A--FKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIML  163 (213)
T ss_pred             cchhhh-------------------hhcc--c--cccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCeEEE
Confidence            332210                   0010  0  123469999999887655432 146788888888763222221   


Q ss_pred             --ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11422        267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (687)
Q Consensus       267 --~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (687)
                        ...+.+.+++.++++.+.+.      -..|||+|--+..++
T Consensus       164 ~~~~~~~~~~~l~~~~~~~~~~------g~EGvV~K~~~s~Y~  200 (213)
T cd07902         164 SEMKFVKKADDLSAMIARVIKE------GLEGLVLKDLKSVYE  200 (213)
T ss_pred             EEEEEcCCHHHHHHHHHHHHHC------CCCeEEEeCCCCCcc
Confidence              12346788998888877543      358999999875554

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B

Probab=97.87  E-value=1.6e-05  Score=65.60  Aligned_cols=58  Identities=21%  Similarity=0.250  Sum_probs=45.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCC
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTT  518 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~  518 (687)
                      +|+|+|+|+++.+.|.+.=  .|++.|...+.++|..+||+|++.|++|++.++..+++.
T Consensus         5 aLGI~~VG~~~ak~L~~~f--~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~   62 (64)
T PF12826_consen    5 ALGIPGVGEKTAKLLAKHF--GSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENRE   62 (64)
T ss_dssp             HCTSTT--HHHHHHHHHCC--SCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHH
T ss_pred             eCCCCCccHHHHHHHHHHc--CCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhh
Confidence            6999999999999998764  599999999999999999999999999999998876543

>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins

Probab=97.87  E-value=0.00031  Score=72.72  Aligned_cols=170  Identities=16%  Similarity=0.149  Sum_probs=102.8

Q ss_pred             CeeEEEEEccceeEEEEEEe---CCEEEEEEecCCCCccchhhhhhhhhccC-Ccccc----cCCCCceEEEEEEEEeeh
Q psy11422        117 NIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLN----IKYPPELLEVRCEVLIYK  188 (687)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~----~~~~~~~~evRGEi~~~~  188 (687)
                      ...|++|+|.||.-+.+.+.   +|.-++..||    -|+|+|+....+..+ ...+.    ....+..+.+-||+++-.
T Consensus        21 ~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR----~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDGEiVv~d   96 (235)
T cd08039          21 SRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSK----SGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEGEMVVWS   96 (235)
T ss_pred             CCcEEEEEeecceEEEEEEecccCCCEEEEEeC----CCCcccccchhHHHHHHHHhhccccccCCCccEEEEeEEEEEE
Confidence            34799999999999999875   2445899999    789999865433211 11110    000135799999996532


Q ss_pred             ------hhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCC
Q psy11422        189 ------KDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL  261 (687)
Q Consensus       189 ------~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf  261 (687)
                            ..|+.+... .        ..++....  ...++......++.|++|++...+|..+ ..+..+..+.|.++--
T Consensus        97 ~~~g~~~~F~~L~~~-~--------~~~~~~~~--~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~  165 (235)
T cd08039          97 DRQGKIDPFHKIRKH-V--------ERSGSFIG--TDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVH  165 (235)
T ss_pred             CCCCccCCHHHHHhh-c--------ccccchhc--cccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcc
Confidence                  378876321 1        11111000  0111122234679999999987655432 2578889999988743


Q ss_pred             CCCCCceE-----e-----CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11422        262 SICGEYSV-----L-----SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (687)
Q Consensus       262 ~~~~~~~~-----~-----~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (687)
                      +++....+     +     .+.+++.++++...+.      -.-|||+|--+..+.
T Consensus       166 ~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~------g~EGIv~K~~~S~Y~  215 (235)
T cd08039         166 VIPGYAGLSERFPIDFSRSSGYERLRQIFARAIAE------RWEGLVLKGDEEPYF  215 (235)
T ss_pred             cCCCcEEEEEEEeecccCCCCHHHHHHHHHHHHHc------CCceEEEecCCCCcc
Confidence            33322111     1     2577888887765432      348999999886554

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res

>PRK09633 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.87  E-value=0.00054  Score=79.91  Aligned_cols=187  Identities=16%  Similarity=0.160  Sum_probs=116.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccC----CcccccCCCCceEEEEEEEEee----hh
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI----PLVLNIKYPPELLEVRCEVLIY----KK  189 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i----P~~l~~~~~~~~~evRGEi~~~----~~  189 (687)
                      ..|++|.|+||.-+.+.+.+|. ++..||    -|+|+|+....|...    +..++.   ...+.+-||++.-    ..
T Consensus        16 ~~w~~E~K~DG~R~~~h~~~~~-V~L~SR----ng~d~T~~fPel~~~~~~~~~~~~~---~~~~ILDGEiVvld~~g~~   87 (610)
T PRK09633         16 DEWRYEVKYDGFRCLLIIDETG-ITLISR----NGRELTNTFPEIIEFCESNFEHLKE---ELPLTLDGELVCLVNPYRS   87 (610)
T ss_pred             CcEEEEEeEcceEEEEEEECCE-EEEEeC----CCCcchhhhhHHHHHHHhhhhcccc---CCceeeeeEEEEecCCCCC
Confidence            3699999999999998887665 799999    689999876654332    222211   1247899999984    46


Q ss_pred             hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC----
Q psy11422        190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC----  264 (687)
Q Consensus       190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~----  264 (687)
                      +|+.+......      .++.+     +.+    .....++.|++|++...+|.++. .+..+..+.|+++-=+..    
T Consensus        88 ~F~~Lq~R~~~------~~~~~-----i~~----~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~  152 (610)
T PRK09633         88 DFEHVQQRGRL------KNTEV-----IAK----SANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPAS  152 (610)
T ss_pred             CHHHHHhhhhc------cccch-----hhh----hhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccc
Confidence            78876543110      11111     111    11346799999999887665432 467777777776511110    


Q ss_pred             ------CCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEE
Q psy11422        265 ------GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAIN  338 (687)
Q Consensus       265 ------~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~  338 (687)
                            +....+.+.+++.++++...+      ...-|||+|--+..++.    ..+...| +-+|. .......|.+..
T Consensus       153 ~~~~~~~~i~~~~~~~~~~~l~~~a~~------~g~EGIV~Kr~dS~Y~~----G~Rs~~W-lKiK~-~~~~d~vI~G~~  220 (610)
T PRK09633        153 PDPYAKARIQYIPSTTDFDALWEAVKR------YDGEGIVAKKKTSKWLE----NKRSKDW-LKIKN-WRYVHVIVTGYD  220 (610)
T ss_pred             cccccccceEEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCCCC----CCCCCCe-EEEec-cCCceeEEEEEe
Confidence                  133455677788887776543      23599999988755421    2244556 45553 355566777764


Q ss_pred             E
Q psy11422        339 I  339 (687)
Q Consensus       339 ~  339 (687)
                      +
T Consensus       221 ~  221 (610)
T PRK09633        221 P  221 (610)
T ss_pred             c
Confidence            4

>PHA02587 30 DNA ligase; Provisional

Probab=97.82  E-value=0.0017  Score=74.26  Aligned_cols=222  Identities=13%  Similarity=0.123  Sum_probs=130.4

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh----ccCCcccccCCCCceEEEEEEEEeehh-----
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII----HKIPLVLNIKYPPELLEVRCEVLIYKK-----  189 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i----~~iP~~l~~~~~~~~~evRGEi~~~~~-----  189 (687)
                      .|.+|+|.||.-+.+...+|. ++..||    -|+|+|. ...|    ..+...+..  .|..+.+-||++.-..     
T Consensus       153 ~~~~E~K~DG~R~q~h~~~~~-v~l~SR----~g~~~~~-~p~i~~~l~~~~~~~~~--~~~~~VLDGElv~~~~~~~~~  224 (488)
T PHA02587        153 PAYAQLKADGARCFADIDADG-IEIRSR----NGNEYLG-LDLLKEELKKMTAEARQ--RPGGVVIDGELVYVEVETKKP  224 (488)
T ss_pred             cEEEEEccCceEEEEEEeCCE-EEEEec----CCccccC-ChhHHHHHHHHhhhhcc--cCCcEEEEeEEEEEecccCCC
Confidence            699999999999999887765 799999    4777753 2221    112222211  2456899999997622     


Q ss_pred             -------------hH-HHHHHHHHHcCCCCCCChhhhHHhHhh---hcCcccccccccEEEEEecccc----cCCCCCCC
Q psy11422        190 -------------DF-IKLNKYRYHLGLKKFTNPRNAAAGILR---QLNPKINKNKILHFFAHGVGEL----RGMNMPSS  248 (687)
Q Consensus       190 -------------~F-~~~n~~~~~~g~~~f~NpRN~aaG~lr---~~~~~~~~~r~l~f~~y~~~~~----~~~~~~~~  248 (687)
                                   +| +.+-             .|..-.|..+   +.........++.|++|++...    .+......
T Consensus       225 ~~~~f~~~~~~~~~f~q~l~-------------~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~p  291 (488)
T PHA02587        225 NGLSFLFDDSKAKEFVGVVA-------------DRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMP  291 (488)
T ss_pred             ccchhhcccccccchhhhhh-------------hhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCC
Confidence                         11 1111             1221112211   1111123456799999998632    11111246


Q ss_pred             HHHHHHHHHhcCCCC--CCCc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceE
Q psy11422        249 HSELLNWYQKIGLSI--CGEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFAL  321 (687)
Q Consensus       249 ~~e~l~~L~~~Gf~~--~~~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prwai  321 (687)
                      ..+..+.|.++ |..  .+..     ..+.+.+++.+++++..+      --..|||+|--+..++  -|   +...| +
T Consensus       292 l~eRr~~L~~l-~~~~~~~~i~l~~~~~~~~~ee~~~~~~~a~~------~G~EGimlK~~ds~Y~--~G---Rs~~W-l  358 (488)
T PHA02587        292 YDDRFSKLAQM-FEDCGYDRVELIENQVVNNLEEAKEIYKRYVD------QGLEGIILKNTDGLWE--DG---RSKDQ-I  358 (488)
T ss_pred             HHHHHHHHHHH-HhhcCCCcEEEEeeEEcCCHHHHHHHHHHHHh------CCCCeEEEECCCCCCC--CC---CCCCc-E
Confidence            77888887765 210  1111     235788999998876643      3468999998775553  24   22235 5


Q ss_pred             eecCCCceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEE-ecCCCHHHHHhcC
Q psy11422        322 AYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITR-ATLHNESEIYRKN  378 (687)
Q Consensus       322 A~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsr-aTLhN~~~i~~~~  378 (687)
                      =+| +.......|.++.++-+|.|++.-...-   .-+|.++-+ .|...-+.+++++
T Consensus       359 KiK-~~~~~dlvVvG~~~~~k~~~~~gs~ll~---~~~g~~~~~vgsGftd~~~~~l~  412 (488)
T PHA02587        359 KFK-EVIDIDLEIVGVYEHKKDPNKVGGFTLE---SACGKITVNTGSGLTDTTHRKKD  412 (488)
T ss_pred             Eec-CCCceEEEEEeEEeCCCCCCceeEEEEE---ecCCcEEEEECCCCChHHhhhhc
Confidence            566 4456888999999987777765433211   114544433 4788888776653

>PRK09247 ATP-dependent DNA ligase; Validated

Probab=97.80  E-value=0.00064  Score=78.56  Aligned_cols=219  Identities=16%  Similarity=0.138  Sum_probs=137.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh------hhH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KDF  191 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~------~~F  191 (687)
                      ..|++|+|+||.-+.+.+.+|. ++..||    -|+|+|+....|...-..     .|..+.+-||++.-.      ..|
T Consensus       225 ~~~~~E~K~DG~R~qih~~~~~-v~lfSR----~g~d~t~~fPei~~~~~~-----l~~~~ILDGElv~~~~~~~~~~~F  294 (539)
T PRK09247        225 ADWQAEWKWDGIRVQLVRRGGE-VRLWSR----GEELITERFPELAEAAEA-----LPDGTVLDGELLVWRPEDGRPQPF  294 (539)
T ss_pred             CcEEEEEeEcceEEEEEEeCCE-EEEEeC----CCccchhhhHHHHHHHHh-----CCCCEEEEeEEEEEECCCCCcCCH
Confidence            3799999999999998776665 799999    577999877665543222     344689999998754      466


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCC-C-C
Q psy11422        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC-G-E  266 (687)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~-~-~  266 (687)
                      +.+..+                   ++++..  ......++.|++|++...+|.++ .....++.+.|.++ |... . .
T Consensus       295 ~~l~~R-------------------~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~-~~~~~~~~  354 (539)
T PRK09247        295 ADLQQR-------------------IGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEAL-IARLPDPR  354 (539)
T ss_pred             HHHHHH-------------------hcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHH-hcccCCCe
Confidence            665432                   111111  11123579999999988766443 24677888888765 2211 1 1


Q ss_pred             -----ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEee
Q psy11422        267 -----YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQI  341 (687)
Q Consensus       267 -----~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qv  341 (687)
                           ...+.+.+++.+++++..+      -...|+|+|--+..++  -|..  ...| +=+|-........|.+..|--
T Consensus       355 i~~~~~~~~~~~~e~~~~~~~a~~------~g~EGlm~K~~~s~Y~--~Grr--~~~W-lK~K~~~~t~DlVvig~~~G~  423 (539)
T PRK09247        355 LDLSPLVPFSDWDELAALRAAARE------RGVEGLMLKRRDSPYL--VGRK--KGPW-WKWKRDPLTIDAVLMYAQRGH  423 (539)
T ss_pred             EEecCceecCCHHHHHHHHHHHHH------CCCceEEEecCCCCcC--CCCC--cchh-hcccCCCCcEEEEEEEeecCC
Confidence                 2234678899988876643      3469999997774443  2221  2234 234433346777888777766


Q ss_pred             cC-cceeee--EEEEEEEEECC--EEEEEe-cCCCHHHHHhc
Q psy11422        342 GR-TGIITP--VALLKPVLIDG--ITITRA-TLHNESEIYRK  377 (687)
Q Consensus       342 GR-TG~iTP--vA~lePV~l~G--~tVsra-TLhN~~~i~~~  377 (687)
                      || +|.++.  +|..+|=.=.+  ++|-++ |.++-++++++
T Consensus       424 Gkr~g~~~~~lla~~~~~~~~~~~~~v~kvgsGftd~~l~~l  465 (539)
T PRK09247        424 GRRASLYTDYTFGVWDGPEGGRQLVPFAKAYSGLTDEEIKQL  465 (539)
T ss_pred             CCcCCccccEEEEEEcCCCCceeEEEEEEECCCCCHHHHHHH
Confidence            65 465654  46554421001  255565 88888888766

>PRK09632 ATP-dependent DNA ligase; Reviewed

Probab=97.76  E-value=0.0014  Score=78.05  Aligned_cols=209  Identities=17%  Similarity=0.142  Sum_probs=127.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~  193 (687)
                      ..|++|.|+||.-+.+.+.+|. ++..||    -|.|+|+....|..+...+.    ...+.+-||+++-    ..+|+.
T Consensus       477 ~~w~~E~K~DG~R~~~~~~~g~-vrL~SR----nG~d~T~~fPel~~~~~~l~----~~~~ILDGEiVvld~~G~~~F~~  547 (764)
T PRK09632        477 SQWAFEGKWDGYRLLAEADHGA-LRLRSR----SGRDVTAEYPELAALAEDLA----DHHVVLDGEIVALDDSGVPSFGL  547 (764)
T ss_pred             CCEEEEEEECceeEEEEEeCCE-EEEEeC----CCCCccccchhHHHHHhhCC----CcceeeeeEEEEeCCCCCCCHHH
Confidence            3699999999999988887776 799999    78999998766554444442    2368899999984    346765


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCCCCceEeCC
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYSVLSG  272 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~~~~~~~~~  272 (687)
                      +...                           ....++.|++|++...+|.++. ....+..+.|+++- ...+...+...
T Consensus       548 Lq~r---------------------------~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~-~~~~~i~~s~~  599 (764)
T PRK09632        548 LQNR---------------------------GRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALA-PSGGSLTVPPL  599 (764)
T ss_pred             Hhhh---------------------------hhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhh-CCCCcEEecce
Confidence            4321                           0124699999999887765432 46778888887763 21221222111


Q ss_pred             -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-cceeeeE
Q psy11422        273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPV  350 (687)
Q Consensus       273 -~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~iTPv  350 (687)
                       ..++.++++...+      --.-|||+|--|..++  -|  .+...| +-+|. ....+..|.+..+.-|| .|.+.-.
T Consensus       600 ~~~~~~~~l~~a~~------~GlEGIVaKr~dS~Y~--pG--rRs~~W-lKiK~-~~~~e~VI~G~~~g~G~r~g~~gsL  667 (764)
T PRK09632        600 LPGDGAEALAYSRE------LGWEGVVAKRRDSTYQ--PG--RRSSSW-IKDKH-WRTQEVVIGGWRPGEGGRSSGIGSL  667 (764)
T ss_pred             ecccHHHHHHHHHH------cCCcEEEEeCCCCCCC--CC--CcCCCe-EEEec-CCceEEEEEEEEcCCCCcCCceeeE
Confidence             1134445544432      3468999999885553  12  124456 45553 34456777777776663 4444333


Q ss_pred             EEEEEEEECC--EEEEEe-cCCCHHHHHhc
Q psy11422        351 ALLKPVLIDG--ITITRA-TLHNESEIYRK  377 (687)
Q Consensus       351 A~lePV~l~G--~tVsra-TLhN~~~i~~~  377 (687)
                      ..=  |.=+|  ..|-++ |..+.+..+++
T Consensus       668 LlG--v~d~~~L~yvGkVGTGftd~~l~~L  695 (764)
T PRK09632        668 LLG--IPDPGGLRYVGRVGTGFTERELASL  695 (764)
T ss_pred             EEE--EEcCCeeEEEEEEeCCCCHHHHHHH
Confidence            211  11122  344455 77887777663

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=97.70  E-value=0.00012  Score=73.43  Aligned_cols=53  Identities=15%  Similarity=0.295  Sum_probs=47.5

Q ss_pred             cCCCCCCHHHHHHHHhhcCC---hHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~s---ld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      +.|||||+++|..|+++|+.   .+.+.+++.++|.+++|||+++|+.|...++..
T Consensus        76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~  131 (192)
T PRK00116         76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK  131 (192)
T ss_pred             hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            57999999999999999987   667788899999999999999999999888654

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=97.67  E-value=2.5e-05  Score=82.49  Aligned_cols=59  Identities=20%  Similarity=0.205  Sum_probs=54.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL  516 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~  516 (687)
                      ..|.++|+|||++..||+++.|.++++|-. +....+..++|||+|++++|+.++.....
T Consensus        94 ~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~  153 (326)
T COG1796          94 PLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEE  153 (326)
T ss_pred             HHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhh
Confidence            478999999999999999999999999998 67889999999999999999999987544

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=97.64  E-value=6.8e-05  Score=86.51  Aligned_cols=53  Identities=21%  Similarity=0.313  Sum_probs=50.4

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      .+|||||+++.+.|+++|||++++..||.+||.+++||+.++|+.|.++|+..
T Consensus       517 ~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~~  569 (574)
T PRK14670        517 TKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEKQ  569 (574)
T ss_pred             ccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            38999999999999999999999999999999999999999999999999653

>KOG2841|consensus

Probab=97.60  E-value=4.9e-05  Score=76.73  Aligned_cols=60  Identities=32%  Similarity=0.450  Sum_probs=54.2

Q ss_pred             HHHHHHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchh
Q psy11422        520 SRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (687)
Q Consensus       520 ~r~L~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~  579 (687)
                      .+++..| .||+|++.-|..|+.+||++..+.+|+.++|.+++|+|+..|+.|++||+.|.
T Consensus       191 s~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~pf  251 (254)
T KOG2841|consen  191 SSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQPF  251 (254)
T ss_pred             HHHHHHHHhCCCCCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhccc
Confidence            3455544 79999999999999999999999999999999999999999999999998763

>PRK08609 hypothetical protein; Provisional

Probab=97.58  E-value=2.4e-05  Score=90.78  Aligned_cols=58  Identities=26%  Similarity=0.253  Sum_probs=52.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL  516 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~  516 (687)
                      .+.|+|+||+++.+||+...|+|++||.. +...+|..++|||+|++++|+.+|+..+.
T Consensus        90 l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~  148 (570)
T PRK08609         90 LLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGK  148 (570)
T ss_pred             HhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhc
Confidence            56899999999999999888999999998 56778999999999999999999987543

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=97.58  E-value=0.00011  Score=74.88  Aligned_cols=52  Identities=21%  Similarity=0.279  Sum_probs=49.3

Q ss_pred             cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      ..|||||+++++.|+++ |+|++.|..|+.++|.+++|||.++|+.|.++|+.
T Consensus         6 ~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~   58 (232)
T PRK12766          6 EDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG   58 (232)
T ss_pred             ccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence            37899999999999999 99999999999999999999999999999999953

>PRK05972 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.53  E-value=0.0031  Score=75.84  Aligned_cols=179  Identities=18%  Similarity=0.147  Sum_probs=113.0

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIKL  194 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~~  194 (687)
                      .|++|.|+||.-+.+.+.+|. ++..||    -|+|+|+....|...-..+.    .....+-|||++-    ..+|+.+
T Consensus       250 ~W~~E~K~DG~R~~a~~~gg~-vrL~SR----nG~d~T~~fPel~~~~~~l~----~~~~ILDGEIVvld~~G~~~F~~L  320 (860)
T PRK05972        250 GWIYEIKFDGYRILARIEGGE-VRLFTR----NGLDWTAKLPALAKAAAALG----LPDAWLDGEIVVLDEDGVPDFQAL  320 (860)
T ss_pred             ceEEEeeeCcEEEEEEEECCE-EEEEeC----CCCccccccHHHHHHHHhcC----CCceeEeEEEEEECCCCCCCHHHH
Confidence            699999999999999887776 699999    68899988665543322221    2357899999984    4577766


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCC-CCCceEeCC
Q psy11422        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYSVLSG  272 (687)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~-~~~~~~~~~  272 (687)
                      ....                   +..     ...++.|++|++...+|.++. ....+..+.|+++-=+. .+...++..
T Consensus       321 q~r~-------------------~~~-----~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s~~  376 (860)
T PRK05972        321 QNAF-------------------DEG-----RTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFSEH  376 (860)
T ss_pred             HHHh-------------------hcc-----CCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEece
Confidence            4321                   000     023689999999887765432 46788888888763111 122333332


Q ss_pred             H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC
Q psy11422        273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR  343 (687)
Q Consensus       273 ~-~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR  343 (687)
                      + .+..++++...      .--..|||+|--|..++.  |   +...| +=+|.- ...+..|-+....-|+
T Consensus       377 ~~~~g~~ll~~a~------~~GlEGIVaKr~dS~Y~~--G---Rs~~W-lKiK~~-~~~E~VIgGy~~~~Gk  435 (860)
T PRK05972        377 FDAGGDAVLASAC------RLGLEGVIGKRADSPYVS--G---RSEDW-IKLKCR-ARQEFVIGGYTDPKGS  435 (860)
T ss_pred             ecchHHHHHHHHH------HcCCceEEEeCCCCCCCC--C---CCCCc-EEEecC-CCceEEEEEEeCCCCc
Confidence            2 23444554442      234689999998866641  3   45567 445532 3346677676665554

>PLN03113 DNA ligase 1; Provisional

Probab=97.51  E-value=0.0028  Score=75.44  Aligned_cols=221  Identities=17%  Similarity=0.142  Sum_probs=130.9

Q ss_pred             eeEEEEEccceeEEEEEEe-CCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh------hh
Q psy11422        118 IEYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KD  190 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~------~~  190 (687)
                      ..|++|.|.||.-+.+.|. +|. ++..||    -|+|+|+....+...-..+... ....+.+-||++.-.      -.
T Consensus       391 ~~~~~E~KyDGeR~QiH~~~~g~-v~lfSR----n~ed~T~~fPel~~~~~~~~~~-~~~~~ILDGEiVa~d~~~~~~lp  464 (744)
T PLN03113        391 MEFTCEYKYDGERAQIHFLEDGS-VEIYSR----NAERNTGKYPDVVVAISRLKKP-SVKSFILDCELVAYDREKKKILP  464 (744)
T ss_pred             CCEEEEEeeccceEEEEEecCCE-EEEEeC----CCCcccccchhHHHHHHHhccc-cCCCEEEEeEEEEEECCCCCcCC
Confidence            4799999999999999984 665 799999    6899998876543321122100 124689999999753      35


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC-CCce
Q psy11422        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GEYS  268 (687)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~-~~~~  268 (687)
                      |+.+-.+ .          |.-+.  +      .....++.||+|++...+|..+. .+..++.+.|.++ |... ....
T Consensus       465 Fq~Lq~R-~----------rk~~~--~------~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~-~~~~~~~i~  524 (744)
T PLN03113        465 FQILSTR-A----------RKNVV--M------SDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYES-FEEDPGFFQ  524 (744)
T ss_pred             HHHHHhh-h----------ccccc--h------hccccceEEEEEeccccCccChhcCCHHHHHHHHHHH-hccCCCcEE
Confidence            7665432 1          11000  0      01125799999999887765432 4677888888775 4322 2222


Q ss_pred             E-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC-ChhhhhhhCCCCCCCCceEeecCCC-----ceeeEEEEEE
Q psy11422        269 V-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN-CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKAI  337 (687)
Q Consensus       269 ~-----~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~-~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~I  337 (687)
                      +     ..+.+++.+|++...+      .-.-|||+|-- ..+.++   ...+...| +=+|-..     +.....|.+-
T Consensus       525 ~~~~~~~~~~ee~~~~~~~ai~------~g~EGlmvK~l~~dS~Y~---pGkRs~~W-lKlK~dy~~~~~dtlDlVvIGa  594 (744)
T PLN03113        525 FATAITSNDLEEIQKFLDAAVD------ASCEGLIIKTLNKDATYE---PSKRSNNW-LKLKKDYMESIGDSLDLVPIAA  594 (744)
T ss_pred             EeeeeccCCHHHHHHHHHHHHH------cCCceEEEeccCCCCCcc---CCCCCCCe-EEEechhhccccccccEEEEEE
Confidence            2     3468889998876643      35689999972 111221   12245567 3444221     2445566666


Q ss_pred             EEeec-CcceeeeE--EEEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11422        338 NIQIG-RTGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYR  376 (687)
Q Consensus       338 ~~qvG-RTG~iTPv--A~lePV~l~G~--tVsra-TLhN~~~i~~  376 (687)
                      .|--| |+|.++..  |..+|-  +|.  +|-++ |.+.-+++++
T Consensus       595 ~~G~GkR~g~~g~fLla~yd~~--~~~~~~v~KvgTGfsd~~l~~  637 (744)
T PLN03113        595 FHGRGKRTGVYGAFLLACYDSN--KEEFQSICKIGTGFSEAVLEE  637 (744)
T ss_pred             EeCCCCcCCccceEEEEEEcCC--CCEEEEeeEECCCCCHHHHHH
Confidence            66555 56665543  344432  122  34454 7777776665

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=97.43  E-value=0.00018  Score=83.02  Aligned_cols=50  Identities=24%  Similarity=0.373  Sum_probs=48.1

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+|||||+++.+.|+++|||++++..||.++|.++ |||+++|+.|+++|+
T Consensus       517 d~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~  566 (567)
T PRK14667        517 DKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS  566 (567)
T ss_pred             ccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence            38999999999999999999999999999999999 999999999999884

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.41  E-value=0.00048  Score=82.26  Aligned_cols=122  Identities=16%  Similarity=0.191  Sum_probs=90.0

Q ss_pred             hhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc-cCCHHHHHHHcC
Q psy11422        449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK-LTTFSRFIYALG  527 (687)
Q Consensus       449 ~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk-~~~l~r~L~aLG  527 (687)
                      ..|..|.|- . .|+|+|+++++++++.-....+.-|.+ ..+.|..++|+|+|.++.|.+++++.+ ...+..||..+|
T Consensus        78 ~~i~~yL~s-~-~~~GIG~~~A~~iv~~fg~~~~~~i~~-~~~~L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~g  154 (720)
T TIGR01448        78 EGIVAYLSS-R-SIKGVGKKLAQRIVKTFGEAAFDVLDD-DPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLG  154 (720)
T ss_pred             HHHHHHHhc-C-CCCCcCHHHHHHHHHHhCHhHHHHHHh-CHHHHhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcC
Confidence            344455542 2 599999999999999877555554443 467899999999999999999998755 345556777777


Q ss_pred             CCCCCHHHHHHHHhhcCCh-HHHHhcCHHHHh-cCCCCCHHHHHHHHHHHc
Q psy11422        528 IRHVGETTAKELANYFKNL-ECMFKATEEQLL-NIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       528 Ip~vG~~~Ak~La~~f~sl-d~l~~As~eeL~-~I~GIG~~~A~sI~~ff~  576 (687)
                      |+   ...|.+|.++|+.- -+....++=.|. .++|||-++|..|...+.
T Consensus       155 i~---~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g  202 (720)
T TIGR01448       155 IG---IKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALG  202 (720)
T ss_pred             CC---HHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcC
Confidence            76   67899999999742 223333444555 599999999999877663

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes

Probab=97.41  E-value=0.0016  Score=66.33  Aligned_cols=156  Identities=20%  Similarity=0.176  Sum_probs=96.8

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~  197 (687)
                      ..|++|+|.||+-+.+...+..-+.++||+    |++++.....+..+. ...  ..+....+-||++.....       
T Consensus        41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~----~~~~~~~~~~~~~~~-~~~--~~~~~~ilDGElv~~~~~-------  106 (215)
T cd07895          41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRK----NDVFKVPGLFFPRRK-NLE--PHHQGTLLDGELVIDKVP-------  106 (215)
T ss_pred             CCeEEEEeEcCeEEEEEEecCCcEEEEeCC----CCeEEeccccCCCcc-ccc--ccccCeeeEEEEEEEcCC-------
Confidence            479999999999998866541457999996    456666544432110 011  123467899999965311       


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC----------
Q psy11422        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE----------  266 (687)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~----------  266 (687)
                          +                        ...+.|++|++....|... .....++++.|.++-......          
T Consensus       107 ----~------------------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~  158 (215)
T cd07895         107 ----G------------------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKA  158 (215)
T ss_pred             ----C------------------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcC
Confidence                0                        2368999999987665432 246788888888764332110          


Q ss_pred             ----ceEeC---CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11422        267 ----YSVLS---GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK  324 (687)
Q Consensus       267 ----~~~~~---~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K  324 (687)
                          .....   ..+++....+.+   +..++...||+|+|-.+..++-  |   +.+.| +=||
T Consensus       159 ~~~~~i~~k~~~~~~~~~~~~~~~---~~~~~~~~EGlIfk~~~~~Y~~--G---r~~~~-lKwK  214 (215)
T cd07895         159 KEPFSVRLKDFFPLYKIEKLFEKI---IPKLPHENDGLIFTPNDEPYVP--G---TDKNL-LKWK  214 (215)
T ss_pred             CCCeEEEecceEeHHhHHHHHHhc---cccCCCCCCCEEEccCCCCccC--c---cCCcc-eeeC
Confidence                01111   233444444433   3467899999999999876542  2   56677 5555

RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=97.31  E-value=0.0003  Score=82.01  Aligned_cols=52  Identities=23%  Similarity=0.360  Sum_probs=50.1

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      .+|||||+++++.|+++|+|++++..|+.++|.+++|||+++|++|.+||++
T Consensus       546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~  597 (598)
T PRK00558        546 DDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK  597 (598)
T ss_pred             hhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence            4999999999999999999999999999999999999999999999999964

>PRK14973 DNA topoisomerase I; Provisional

Probab=97.30  E-value=0.0012  Score=80.49  Aligned_cols=127  Identities=15%  Similarity=0.133  Sum_probs=101.1

Q ss_pred             hhhhhcc----cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCH-HHHH
Q psy11422        449 AGLQHFS----SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTF-SRFI  523 (687)
Q Consensus       449 ~~i~~F~----sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l-~r~L  523 (687)
                      +++.-|+    -...|.++|+-+.++++||++|+ +++.|+-.+..+.|+.++|+.+-.+.++..........+- .++.
T Consensus       790 ~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~-~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  868 (936)
T PRK14973        790 ASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGF-DTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGRPVPEKIS  868 (936)
T ss_pred             HHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcC-CCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhh
Confidence            3555555    33489999999999999999996 9999999999999999999999999888666552211110 0111


Q ss_pred             ---------HHcCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        524 ---------YALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       524 ---------~aLGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                               ..+.|+|+|+.+...|.. .+.+.+.|.+++.++|....||+.+.+..++.+..
T Consensus       869 ~~~~~~~~~el~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~  931 (936)
T PRK14973        869 KAAFERGRAELLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK  931 (936)
T ss_pred             hhhhcccchhhhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence                     136789999999987764 47789999999999999999999999999888764

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=97.21  E-value=0.00051  Score=69.96  Aligned_cols=54  Identities=24%  Similarity=0.316  Sum_probs=50.6

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ...+|+|+|++++.+|+++|+ .|+.+|-..+.++|.+++|||++.|++|++.+.
T Consensus         4 ~L~~IpGIG~krakkLl~~GF-~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~   57 (232)
T PRK12766          4 ELEDISGVGPSKAEALREAGF-ESVEDVRAADQSELAEVDGIGNALAARIKADVG   57 (232)
T ss_pred             ccccCCCcCHHHHHHHHHcCC-CCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence            356899999999999999995 999999999999999999999999999999875

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=97.14  E-value=0.0011  Score=66.47  Aligned_cols=57  Identities=16%  Similarity=0.261  Sum_probs=45.3

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCCh-HHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      ..++|+|+|||++.++++.-....+ ..+..-+.+.|.++||+|+|+|++|+..+...
T Consensus        74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~  131 (192)
T PRK00116         74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK  131 (192)
T ss_pred             HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            3678999999999999986533332 23445677899999999999999999998754

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=97.08  E-value=0.0011  Score=68.81  Aligned_cols=53  Identities=25%  Similarity=0.464  Sum_probs=51.0

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      ..|||||...|..|+.+|+|+.++..|+.++|..+.|||++.|..|+.||..+
T Consensus       185 ~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~  237 (254)
T COG1948         185 ESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTE  237 (254)
T ss_pred             HcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhch
Confidence            58999999999999999999999999999999999999999999999999765

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=96.96  E-value=0.0015  Score=70.81  Aligned_cols=52  Identities=19%  Similarity=0.285  Sum_probs=48.3

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      -.||++++..|+.|.++||++..+.+|+.++|.+++|||++.|..|++.+..
T Consensus       290 s~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R  341 (352)
T PRK13482        290 SKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR  341 (352)
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999998877654

>TIGR01209 RNA ligase, Pab1020 family

Probab=96.96  E-value=0.015  Score=63.76  Aligned_cols=165  Identities=23%  Similarity=0.213  Sum_probs=97.8

Q ss_pred             eccccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc
Q psy11422         84 HHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH  163 (687)
Q Consensus        84 ~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~  163 (687)
                      +|-.+++.|+.+            +.+.+.   ...+++|.|+||--+.+...+|++ .|.||| |.+=-==|+.++..-
T Consensus        60 P~I~R~~~L~~g------------i~~~f~---~~~v~vEEKlDG~Nvri~~~~g~l-~a~tRG-gyicp~tt~r~~~~~  122 (374)
T TIGR01209        60 PHIKRILLLRPG------------IKRHFK---DPEVVVEEKMNGYNVRIVKYGGNV-YALTRG-GFICPFTTERLPDLI  122 (374)
T ss_pred             CCcceeeccchh------------hHHhcC---CCcEEEEEeecCceEEEEeECCEE-EEEccC-cccCCCcHHHHHHHh
Confidence            566688888875            222221   235999999999999998889985 899999 332110112333332


Q ss_pred             cCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCC
Q psy11422        164 KIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM  243 (687)
Q Consensus       164 ~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~  243 (687)
                      +  ..+..+ . .++.+-||++=+..-               |+           +.+... ...+..||+|++-..+..
T Consensus       123 ~--~~~~~d-~-p~l~LcGE~iGpenp---------------Y~-----------~hs~~y-~~l~~~FfvFDI~d~~t~  171 (374)
T TIGR01209       123 D--LEFFDD-N-PDLVLCGEMAGPENP---------------YT-----------PEYYPE-VKEDLGFFLFDIREGKTN  171 (374)
T ss_pred             h--HHhhcc-C-CCeEEEEEEcCCCCC---------------Cc-----------ccCccc-cCCCceEEEEEEEECCCC
Confidence            2  233321 2 358889998733111               10           000101 122689999998543222


Q ss_pred             CCCCCHHHHHHHHHhcCCCCCCCceEeCCHHHHH-H---HHHHHHHhhcCCCCccceEEEEECCh
Q psy11422        244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLI-E---FYKKINIKRFNLPYEIDGVVYKINCL  304 (687)
Q Consensus       244 ~~~~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~-~---~~~~~~~~r~~l~y~iDGiVikv~~~  304 (687)
                      . +-+..+..++++.+|++.++..... +.+++. +   .++.+.+..      =-|||+|-.+.
T Consensus       172 ~-~L~~~er~~l~e~yglp~Vpvlg~~-~~~~~~~~~~eii~~L~~~g------REGVVlK~~~~  228 (374)
T TIGR01209       172 R-SLPVEERLELAEKYGLPHVEILGVY-TADEAVEEIYEIIERLNKEG------REGVVMKDPEM  228 (374)
T ss_pred             c-cCCHHHHHHHHHHCCCCccceeeEE-cHHHHHHHHHHHHHHhhhcC------cceEEEcCccc
Confidence            2 3688899999999999988754443 344444 3   333333221      37999997653

Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity.

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=96.92  E-value=0.0014  Score=76.52  Aligned_cols=50  Identities=32%  Similarity=0.426  Sum_probs=47.8

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      +|||||++++++|+++|+|++++..||.++|.++  ||.++|+.|+++|+.+
T Consensus       556 ~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~  605 (624)
T PRK14669        556 EIPGVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAHFTTE  605 (624)
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCc
Confidence            9999999999999999999999999999999998  9999999999999654

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=96.91  E-value=0.0014  Score=45.85  Aligned_cols=30  Identities=33%  Similarity=0.667  Sum_probs=25.9

Q ss_pred             ChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11422        545 NLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       545 sld~l~~As~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      +++.+..++.++|.++||||+++|..|.+|
T Consensus         1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    1 SLDGLIPASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence            357788899999999999999999999876

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=96.90  E-value=0.0015  Score=76.60  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=47.3

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+|||||+++++.|+.+|+|+++|..|+.++|.++  ||+++|++|.+||+
T Consensus       572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~v--ig~k~A~~I~~~~~  620 (621)
T PRK14671        572 TDIAGIGEKTAEKLLEHFGSVEKVAKASLEELAAV--AGPKTAETIYRYYH  620 (621)
T ss_pred             hcCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhC
Confidence            59999999999999999999999999999999999  99999999999985

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=96.87  E-value=0.0013  Score=76.55  Aligned_cols=51  Identities=20%  Similarity=0.295  Sum_probs=47.9

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      .|||||+++.+.|+++|||++++..||.++|.+++||+.++|+.|...-..
T Consensus       612 ~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~  662 (691)
T PRK14672        612 RLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR  662 (691)
T ss_pred             cCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence            899999999999999999999999999999999999999999999875543

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=96.84  E-value=0.0015  Score=76.39  Aligned_cols=51  Identities=29%  Similarity=0.431  Sum_probs=48.7

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      ..|||||+++++.|.++|||++++..|+.++|.+++|||++.|+.|.++|+
T Consensus       640 ~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~  690 (694)
T PRK14666        640 QRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK  690 (694)
T ss_pred             hhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence            389999999999999999999999999999999999999999999999874

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=96.68  E-value=0.002  Score=74.50  Aligned_cols=49  Identities=20%  Similarity=0.269  Sum_probs=46.7

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .+|||||+++.+.|++||+|+..+..|+.+||.++ ||+.++|+.|++++
T Consensus       533 d~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~  581 (581)
T COG0322         533 DDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL  581 (581)
T ss_pred             ccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence            48999999999999999999999999999999999 99999999998764

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=96.56  E-value=0.0032  Score=74.23  Aligned_cols=80  Identities=24%  Similarity=0.383  Sum_probs=52.1

Q ss_pred             cccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11422        458 KAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v  531 (687)
                      +.+.++|+|+|++++|++.-   .-..+..++     ..+.+||+|++.|..|++.+   ++-++.+...+   ..|+|+
T Consensus       467 ~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L-----~aLgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI  538 (652)
T TIGR00575       467 DLLELEGFGEKSAQNLLNAIEKSKEKPLARLL-----FALGIRHVGEVTAKNLAKHFGTLDKLKAASLEEL---LSVEGV  538 (652)
T ss_pred             HHhhccCccHHHHHHHHHHHHHhccCcHHHHH-----hhccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH---hcCCCc
Confidence            46678999999998887631   111222222     24567899999998888765   23333333322   368889


Q ss_pred             CHHHHHHHHhhcCC
Q psy11422        532 GETTAKELANYFKN  545 (687)
Q Consensus       532 G~~~Ak~La~~f~s  545 (687)
                      |+.+|..|.+.|.+
T Consensus       539 G~~~A~~I~~ff~~  552 (652)
T TIGR00575       539 GPKVAESIVNFFHD  552 (652)
T ss_pred             CHHHHHHHHHHHhh
Confidence            99999888887754

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>PRK14973 DNA topoisomerase I; Provisional

Probab=96.51  E-value=0.023  Score=69.58  Aligned_cols=149  Identities=13%  Similarity=0.246  Sum_probs=106.2

Q ss_pred             CCCCCCCCCcceee--cC--ceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCCh
Q psy11422        415 PNICPICNSKIIYI--ES--NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF  490 (687)
Q Consensus       415 P~~CP~C~~~l~~~--~~--~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~  490 (687)
                      ...||.||.+++..  .|  +-++-|  + . |.....      ..+++-+++|+|+++.++|-.++ +.++.++-..+.
T Consensus       635 ~~~Cp~CG~p~~~~~r~Gr~g~fl~C--P-~-C~~~~~------~~~~~~~~~~~~~~~~~k~~~~~-~~~~~~~~~~~~  703 (936)
T PRK14973        635 DEVCPIHHLNHVRLIRKGARPWDIGC--P-L-CSHIES------NTESLLLMPSMTEELLQKLNAVH-IYTVSELASREP  703 (936)
T ss_pred             CCCCCCCCCCceEEeecCCCcccccC--c-c-ccchhh------cccchhhccccchhhhhhhhhcc-CCchhhhccCCH
Confidence            46899999864432  22  235557  3 3 743221      33467789999999999999888 588899988888


Q ss_pred             hhhhcccCccHHHHHHHHHHHHH-----cccCCHHHHHHHcCCCCCCHHHHHHHHh----hcCChHHHHhcCHHHHhcCC
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELAN----YFKNLECMFKATEEQLLNIP  561 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~-----sk~~~l~r~L~aLGIp~vG~~~Ak~La~----~f~sld~l~~As~eeL~~I~  561 (687)
                      +.+...-+.+.+.+.++...-+.     .+...+.+|+...=.|.=|...|+.+..    ...++..|..|++.+|.. .
T Consensus       704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  782 (936)
T PRK14973        704 EALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKFVRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKK-A  782 (936)
T ss_pred             hHhhhhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccHHHHHHHHHhcCcchHHHHhhCCHHHHHH-c
Confidence            88887667777777777665322     1234677888888888778777765543    346788899999887765 4


Q ss_pred             CCCHHHHHHHHHHH
Q psy11422        562 KIGSTTVKAFIKFI  575 (687)
Q Consensus       562 GIG~~~A~sI~~ff  575 (687)
                      |+++.-+.++.++-
T Consensus       783 ~~sE~~~~~~~~~a  796 (936)
T PRK14973        783 GLSEAEAASLLAEA  796 (936)
T ss_pred             CCCHHHHHHHHHHH
Confidence            89988888877765

>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals

Probab=96.47  E-value=0.0052  Score=51.04  Aligned_cols=52  Identities=23%  Similarity=0.299  Sum_probs=43.9

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      +-=||+..+...|-.+| |.++.||..++.++|..++|||+|+.+.|.+.+++
T Consensus        15 ~~L~LS~Ra~n~L~~~~-I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~e   66 (66)
T PF03118_consen   15 EDLGLSVRAYNCLKRAG-IHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLKE   66 (66)
T ss_dssp             GGSTSBHHHHHHHHCTT---BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHhC-CcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHcC
Confidence            44579999999998887 69999999999999999999999999999887753

The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....

>PRK08609 hypothetical protein; Provisional

Probab=96.44  E-value=0.0059  Score=71.16  Aligned_cols=85  Identities=13%  Similarity=0.195  Sum_probs=66.4

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHH--------HHHHHcCCCCCCHHHHHHHHhh--cCChHHHHhcCH-HHHhc
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS--------RFIYALGIRHVGETTAKELANY--FKNLECMFKATE-EQLLN  559 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~--------r~L~aLGIp~vG~~~Ak~La~~--f~sld~l~~As~-eeL~~  559 (687)
                      .+|.++||+|++.|++|.+-++.-+-..|.        .++.-+.|||||+++|+++-+.  +.|+++|..|.. ..+..
T Consensus        48 ~~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~  127 (570)
T PRK08609         48 DDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQA  127 (570)
T ss_pred             hhhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhh
Confidence            378999999999999998877643222222        3555569999999999999864  569999998754 35889


Q ss_pred             CCCCCHHHHHHHHHHH
Q psy11422        560 IPKIGSTTVKAFIKFI  575 (687)
Q Consensus       560 I~GIG~~~A~sI~~ff  575 (687)
                      ++|||+++.+.|...+
T Consensus       128 ~~gfg~k~~~~il~~i  143 (570)
T PRK08609        128 LAGFGKKTEEKILEAV  143 (570)
T ss_pred             ccCcchhHHHHHHHHH
Confidence            9999999999986655

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=96.40  E-value=0.0044  Score=71.98  Aligned_cols=49  Identities=27%  Similarity=0.415  Sum_probs=46.9

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .|||||+++++.|+++|+|++++..|+.++|.+++|+|+++|+.|.+++
T Consensus       529 ~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~~~  577 (577)
T PRK14668        529 DVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRERL  577 (577)
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHhC
Confidence            8999999999999999999999999999999999999999999998763

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=96.33  E-value=0.0038  Score=62.66  Aligned_cols=52  Identities=21%  Similarity=0.443  Sum_probs=43.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc-CC---hhhhhcccCccHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ..++|+|+|||++..+..   +-++.+|.. +.   ...|.++||||+|+|++|+-.+.
T Consensus        73 ~L~~V~GIGpK~Al~iL~---~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk  128 (191)
T TIGR00084        73 ELIKVNGVGPKLALAILS---NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELK  128 (191)
T ss_pred             HHhCCCCCCHHHHHHHHh---cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence            478999999999999965   347888887 33   37799999999999999995554

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.

>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]

Probab=96.33  E-value=0.078  Score=56.97  Aligned_cols=168  Identities=20%  Similarity=0.171  Sum_probs=111.5

Q ss_pred             eeccccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh
Q psy11422         83 VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII  162 (687)
Q Consensus        83 v~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i  162 (687)
                      .+|..+|+-|+.+     +.+|..          ...++||.|+||-.+.+.--+|+ +-|+||| |-+====|+.++.+
T Consensus        68 fPkI~R~llL~p~-----ik~~F~----------~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~l  130 (382)
T COG1423          68 FPKIRRALLLEPT-----IKKHFG----------RGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRDL  130 (382)
T ss_pred             Cchhheeeccchh-----hHhhcC----------CCcEEEEEeccCceEEEEEECCE-EEEEecC-ceecCchhHHHHhh
Confidence            4677788888865     444432          13799999999999999877887 5899999 76555556666654


Q ss_pred             ccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC
Q psy11422        163 HKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG  242 (687)
Q Consensus       163 ~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~  242 (687)
                        ||+.+..+ +| .+.+-||.+=+.               .||-      .     .++ . ...++.||.|++..-..
T Consensus       131 --~~~eff~d-~p-~lvlcgEmvG~e---------------nPYv------~-----~~~-y-~~e~v~fFvFDire~~t  178 (382)
T COG1423         131 --IDLEFFDD-YP-DLVLCGEMVGPE---------------NPYV------P-----GPY-Y-EKEDVGFFVFDIREKNT  178 (382)
T ss_pred             --cchhhHhh-CC-CcEEEEEeccCC---------------CCCC------C-----CCC-C-ccCCceEEEEEEEecCC
Confidence              56666543 45 578899987331               2221      1     111 1 23579999999976322


Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCceEeC--CH-HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        243 MNMPSSHSELLNWYQKIGLSICGEYSVLS--GV-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       243 ~~~~~~~~e~l~~L~~~Gf~~~~~~~~~~--~~-~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                      . -+-++.+.++.+.+.||+.+.......  .. ++|...++++.+...      -|||+|-.|..+
T Consensus       179 g-r~Lp~eer~~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~keGR------EGVV~Kdpdm~~  238 (382)
T COG1423         179 G-RPLPVEERLELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNKEGR------EGVVMKDPDMRV  238 (382)
T ss_pred             C-CCCCHHHHHHHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhhcCC------cceEecCccccc
Confidence            1 246899999999999999775333221  12 445555666654332      699999888544

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=96.28  E-value=0.0053  Score=72.57  Aligned_cols=80  Identities=18%  Similarity=0.339  Sum_probs=48.6

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhh---hcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v  531 (687)
                      +.+.++|+|+|+.++|+++     +..--...-+++   +.++|+|++.|..|++.+   +.-++.+...+   ..|+||
T Consensus       480 ~L~~l~gfG~Ksa~~ll~~-----Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI  551 (665)
T PRK07956        480 DLLGLEGFGEKSAQNLLDA-----IEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEEL---AAVEGV  551 (665)
T ss_pred             HHhcCcCcchHHHHHHHHH-----HHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHH---hccCCc
Confidence            4567888888888888763     111111121222   356888888888777644   33333343332   367888


Q ss_pred             CHHHHHHHHhhcCC
Q psy11422        532 GETTAKELANYFKN  545 (687)
Q Consensus       532 G~~~Ak~La~~f~s  545 (687)
                      |+.+|..|.+.|.+
T Consensus       552 G~~~A~sI~~ff~~  565 (665)
T PRK07956        552 GEVVAQSIVEFFAV  565 (665)
T ss_pred             CHHHHHHHHHHHhh
Confidence            88888888777754

>KOG1968|consensus

Probab=96.27  E-value=0.0032  Score=75.88  Aligned_cols=70  Identities=27%  Similarity=0.227  Sum_probs=67.3

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHH
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEK  672 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~  672 (687)
                      ...++.|.+|++||.++.+.+..++..++.+|+.+..+++.+|+++++|++++ .|+++++++.+++++|+
T Consensus       170 ~~~~~s~~~~~~tg~ld~~~~~s~~~~~k~~~~~~~~~ls~kt~~s~~~~e~~~~kle~~~~~~~~~~~e~  240 (871)
T KOG1968|consen  170 WSKPLSGIKFTPTGVLDDIGTGSAEPSLKEFGASKTESLSDKTVESCLGDEAIAKKLEKIKELEIPVLLEE  240 (871)
T ss_pred             ccCCCcCceeeecCcccccccccchhhhhhccccccccCCCCcceeecCccccchhhcccccccccccchh
Confidence            35689999999999999999999999999999999999999999999999998 99999999999999999

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=96.25  E-value=0.0056  Score=72.48  Aligned_cols=17  Identities=18%  Similarity=0.063  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHh
Q psy11422         16 FRVTELKKELHRHNIAY   32 (687)
Q Consensus        16 ~~i~~L~~~l~~~~~~Y   32 (687)
                      .+|+.|.++|+.+...|
T Consensus        61 ~eYD~L~~eL~~LE~~~   77 (689)
T PRK14351         61 RAYDALFARLQALEDAF   77 (689)
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            58899999999888876

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.00  E-value=0.025  Score=57.03  Aligned_cols=72  Identities=15%  Similarity=0.223  Sum_probs=50.7

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHH----HHhcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLEC----MFKATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~----l~~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.              ..-++++|||+++|..++..|+ .+.    +..-+.+.|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF--------------~~Li~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vpGIGk  118 (194)
T PRK14605         54 REDALSLFGFATTEELSLF--------------ETLIDVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIPGIGK  118 (194)
T ss_pred             ecCCceeeCCCCHHHHHHH--------------HHHhCCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence            4566666677766544333              2225889999999998888875 444    34557888999999999


Q ss_pred             HHHHHHHHHHc
Q psy11422        566 TTVKAFIKFIN  576 (687)
Q Consensus       566 ~~A~sI~~ff~  576 (687)
                      ++|+.|.--++
T Consensus       119 KtAerIilELk  129 (194)
T PRK14605        119 KTASRIVLELK  129 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999665443

>PRK13766 Hef nuclease; Provisional

Probab=95.93  E-value=0.011  Score=71.42  Aligned_cols=53  Identities=26%  Similarity=0.459  Sum_probs=50.5

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      .+|||||+..|+.|.++|++++++..++.++|.+++|+|++.|+.|.+||+.+
T Consensus       718 ~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~  770 (773)
T PRK13766        718 ESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSE  770 (773)
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhh
Confidence            48999999999999999999999999999999999999999999999999765

>PRK07758 hypothetical protein; Provisional

Probab=95.87  E-value=0.019  Score=50.72  Aligned_cols=51  Identities=18%  Similarity=0.177  Sum_probs=46.5

Q ss_pred             cCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .++|+-.....|..+| |.++.||..+++++|+++.|||+|+.+.|.+.+.+
T Consensus        39 ~~~LSvRA~N~Lk~AG-I~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E   89 (95)
T PRK07758         39 LSLLSAPARRALEHHG-IHTVEELSKYSEKEILKLHGMGPASLPKLRKALEE   89 (95)
T ss_pred             CccccHHHHHHHHHcC-CCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence            4578888999999998 59999999999999999999999999999988765

>PRK00254 ski2-like helicase; Provisional

Probab=95.78  E-value=0.028  Score=67.52  Aligned_cols=52  Identities=25%  Similarity=0.484  Sum_probs=49.4

Q ss_pred             cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      ..|||+|+.++++|.++ |++++++..|+.++|.+++|||+++|++|.++++.
T Consensus       648 ~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~  700 (720)
T PRK00254        648 MRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGV  700 (720)
T ss_pred             hcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhcc
Confidence            48999999999999999 99999999999999999999999999999999863

>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]

Probab=95.77  E-value=0.081  Score=54.00  Aligned_cols=115  Identities=18%  Similarity=0.188  Sum_probs=74.0

Q ss_pred             CCHHHHHHHcCCCCCCH-HHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccc
Q psy11422        517 TTFSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL  595 (687)
Q Consensus       517 ~~l~r~L~aLGIp~vG~-~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~  595 (687)
                      ..|-.++..-|+|+-.. ..|+.|+++|+++..+..|+.++|+.++|+|...|-++..-+.-.  +.....-...+..+.
T Consensus        27 ~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~--~R~~~~~~~~~~~i~  104 (224)
T COG2003          27 AELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIELG--KRILAERLREGVVIT  104 (224)
T ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHHHH--HHHHHHHhccCCccC
Confidence            34555666678886433 567899999999999999999999999999998888776644211  011111111111111


Q ss_pred             cCC--------------C------CCCCCCccCCeEEEEEcCCCc---CCHHHHHHHHHhc
Q psy11422        596 NNP--------------N------TKGNKNYLKEKIFVFTGSLYA---FKRNEAIILIENL  633 (687)
Q Consensus       596 ~~~--------------~------~~~~~~~l~g~~vv~TG~l~~---~~R~e~~~~i~~~  633 (687)
                      +++              .      --+..+.+=....+|+|+++.   ++|+-++..+..+
T Consensus       105 sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~V~PREI~k~Al~~n  165 (224)
T COG2003         105 SPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYN  165 (224)
T ss_pred             CHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceecceeEEeeecccceecHHHHHHHHHHhc
Confidence            110              0      012334556778999999875   5888888777654

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.75  E-value=0.037  Score=55.72  Aligned_cols=71  Identities=13%  Similarity=0.170  Sum_probs=44.9

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.            +  .-+++.|||+++|-.++..+ +.+++.    +-+...|.++||||+
T Consensus        53 rED~~~LYGF~t~~Er~lF------------~--~LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpGIGk  117 (196)
T PRK13901         53 REDELKLFGFLNSSEREVF------------E--ELIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKGIGN  117 (196)
T ss_pred             ecCCceeeCCCCHHHHHHH------------H--HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence            3555566677655443332            1  22577888888887777665 344444    346778888888888


Q ss_pred             HHHHHHHHHH
Q psy11422        566 TTVKAFIKFI  575 (687)
Q Consensus       566 ~~A~sI~~ff  575 (687)
                      ++|+.|.--+
T Consensus       118 KtAeRIIlEL  127 (196)
T PRK13901        118 KMAGKIFLKL  127 (196)
T ss_pred             HHHHHHHHHH
Confidence            8888876444

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.67  E-value=0.039  Score=55.32  Aligned_cols=73  Identities=16%  Similarity=0.229  Sum_probs=48.7

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.            +.|  +++.|||+++|-.++..+ +.+++.    +-+...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF------------~~L--i~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpGIGk  118 (188)
T PRK14606         54 SQDGITLYGFSNERKKELF------------LSL--TKVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPGISK  118 (188)
T ss_pred             ecCCceeeCCCCHHHHHHH------------HHH--hccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence            4556666677655443322            222  578888888888888665 355444    447788999999999


Q ss_pred             HHHHHHHHHHcc
Q psy11422        566 TTVKAFIKFINQ  577 (687)
Q Consensus       566 ~~A~sI~~ff~~  577 (687)
                      ++|+.|.--+++
T Consensus       119 KtAerIilELkd  130 (188)
T PRK14606        119 KTAERIVMELKD  130 (188)
T ss_pred             HHHHHHHHHHHH
Confidence            999988754433

>PRK00254 ski2-like helicase; Provisional

Probab=95.66  E-value=0.014  Score=69.99  Aligned_cols=54  Identities=20%  Similarity=0.326  Sum_probs=50.1

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+.|+|+|++++.+|+++|+ .|+.||..++.++|.+++|+|+|.|++|.+.+..
T Consensus       647 L~~ipgig~~~~~~l~~~g~-~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~  700 (720)
T PRK00254        647 LMRLPMIGRKRARALYNAGF-RSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGV  700 (720)
T ss_pred             hhcCCCCCHHHHHHHHHccC-CCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhcc
Confidence            34799999999999999995 9999999999999999999999999999998763

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.64  E-value=0.033  Score=56.10  Aligned_cols=53  Identities=23%  Similarity=0.312  Sum_probs=42.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc----CChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.|+|+|||++..+.+..   ++.+|..    =+.+.|.++||+|+|+|++|+-.+..
T Consensus        74 ~Li~V~GIGpK~Al~ILs~~---~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~  130 (194)
T PRK14605         74 TLIDVSGIGPKLGLAMLSAM---NAEALASAIISGNAELLSTIPGIGKKTASRIVLELKD  130 (194)
T ss_pred             HHhCCCCCCHHHHHHHHHhC---CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999999965   4555544    24577999999999999998766643

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=95.55  E-value=0.012  Score=67.95  Aligned_cols=19  Identities=32%  Similarity=0.422  Sum_probs=15.6

Q ss_pred             cccccCCCCHHHHHHHHHC
Q psy11422        458 KAMNIIGLGKKMIEKLVNA  476 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~  476 (687)
                      +.+.++|+|+|.+++|+++
T Consensus       460 ~l~~l~gfgeks~~nll~a  478 (562)
T PRK08097        460 QLANTPGIGKARAEQLWHQ  478 (562)
T ss_pred             HHhcCcCccHHHHHHHHHH
Confidence            5777899999999998763

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=95.55  E-value=0.024  Score=57.01  Aligned_cols=69  Identities=17%  Similarity=0.206  Sum_probs=48.3

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhc----CHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~A----s~eeL~~I~GIG~  565 (687)
                      .+|-..|=||..+....+              |..-++++|||+++|..|+..+ +.+++..|    +...|.++||||+
T Consensus        53 red~~~LyGF~~~~Er~l--------------F~~L~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ipGiGk  117 (191)
T TIGR00084        53 REDAELLFGFNTLEEREL--------------FKELIKVNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIPGVGK  117 (191)
T ss_pred             ecCCceeeCCCCHHHHHH--------------HHHHhCCCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCCCCCH
Confidence            455556667775544333              2333688999999998888765 35555443    5678999999999


Q ss_pred             HHHHHHHH
Q psy11422        566 TTVKAFIK  573 (687)
Q Consensus       566 ~~A~sI~~  573 (687)
                      ++|+.|.-
T Consensus       118 KtAerIil  125 (191)
T TIGR00084       118 KTAERLLL  125 (191)
T ss_pred             HHHHHHHH
Confidence            99999873

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.

>TIGR01259 comE comEA protein

Probab=95.45  E-value=0.014  Score=54.29  Aligned_cols=61  Identities=16%  Similarity=0.303  Sum_probs=45.2

Q ss_pred             ChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcC
Q psy11422        481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI  560 (687)
Q Consensus       481 ~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I  560 (687)
                      .+-||-+++.++|..+||+|++.|++|++..+.  +.+                        |        ++.++|.++
T Consensus        58 ~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~------------------------f--------~s~eeL~~V  103 (120)
T TIGR01259        58 AAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGA------------------------F--------KSVDDLTKV  103 (120)
T ss_pred             CCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCC------------------------c--------CCHHHHHcC
Confidence            345777788888888888888888888887654  111                        2        356778888


Q ss_pred             CCCCHHHHHHHHHHH
Q psy11422        561 PKIGSTTVKAFIKFI  575 (687)
Q Consensus       561 ~GIG~~~A~sI~~ff  575 (687)
                      +|||+++++.|..|+
T Consensus       104 ~GIg~k~~~~i~~~l  118 (120)
T TIGR01259       104 SGIGEKSLEKLKDYA  118 (120)
T ss_pred             CCCCHHHHHHHHhce
Confidence            888888888887765

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=95.41  E-value=0.037  Score=46.06  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=17.5

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        553 TEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       553 s~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.++|.+++|||+++++.|..|+
T Consensus        45 s~~dL~~v~gi~~~~~~~i~~~~   67 (69)
T TIGR00426        45 TVEDLKQVPGIGNSLVEKNLAVI   67 (69)
T ss_pred             CHHHHHcCCCCCHHHHHHHHhhc
Confidence            56777778888888888877764

Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.41  E-value=0.022  Score=68.64  Aligned_cols=51  Identities=20%  Similarity=0.353  Sum_probs=48.1

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCC-HHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIG-STTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG-~~~A~sI~~ff~~~  578 (687)
                      +.|||||+..|+.|+.+|+|+.+|.+|+.++|..+  +| ++.|+.|++||+.+
T Consensus       760 ~~lPgI~~~~a~~ll~~f~si~~l~~as~eeL~~~--iG~~~~A~~i~~fl~~~  811 (814)
T TIGR00596       760 LKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNEL--IGDEEAAKRLYDFLRTE  811 (814)
T ss_pred             HHCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCCHHHHHHHHHHhccc
Confidence            49999999999999999999999999999999996  88 99999999999865

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.40  E-value=0.058  Score=53.82  Aligned_cols=72  Identities=19%  Similarity=0.329  Sum_probs=48.0

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHh----cCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK----ATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~----As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+.-..+.              ..-+++.|||+++|-.++..+ +.+++..    -+...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF--------------~~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpGIGk  118 (183)
T PRK14601         54 KEDSNKLYGFLDKDEQKMF--------------EMLLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPGIGP  118 (183)
T ss_pred             ecCCceeeCCCCHHHHHHH--------------HHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence            4556666677755433222              222578888888888777665 3555544    36788999999999


Q ss_pred             HHHHHHHHHHc
Q psy11422        566 TTVKAFIKFIN  576 (687)
Q Consensus       566 ~~A~sI~~ff~  576 (687)
                      ++|+.|.--++
T Consensus       119 KtAeRIilELk  129 (183)
T PRK14601        119 KSAKRIIAELS  129 (183)
T ss_pred             HHHHHHHHHHH
Confidence            99998765443

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.36  E-value=0.058  Score=54.41  Aligned_cols=73  Identities=18%  Similarity=0.240  Sum_probs=48.2

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.            +  .-+++.|||+++|-.++..+ +.++|.    +-+...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF------------~--~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpGIGk  118 (195)
T PRK14604         54 REDALTLYGFSTPAQRQLF------------E--LLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPGIGK  118 (195)
T ss_pred             ecCCceeeCCCCHHHHHHH------------H--HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence            4555566677755443332            2  22578888888888877665 355444    346788889999999


Q ss_pred             HHHHHHHHHHcc
Q psy11422        566 TTVKAFIKFINQ  577 (687)
Q Consensus       566 ~~A~sI~~ff~~  577 (687)
                      ++|+.|.--+++
T Consensus       119 KtAerIilELk~  130 (195)
T PRK14604        119 KTAERIVLELKG  130 (195)
T ss_pred             HHHHHHHHHHHH
Confidence            999888755543

>smart00483 POLXc DNA polymerase X family

Probab=95.27  E-value=0.042  Score=59.97  Aligned_cols=64  Identities=23%  Similarity=0.244  Sum_probs=46.4

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccC--------CHH-HHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCH
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLT--------TFS-RFIYALGIRHVGETTAKELANY-FKNLECMFKATE  554 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~--------~l~-r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~  554 (687)
                      ++|.++||+|++.|++|.+-++.-+-.        +.. -++.=+.|||||+++|+.+.+. +.|+++|..+-.
T Consensus        48 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~  121 (334)
T smart00483       48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKE  121 (334)
T ss_pred             HHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhccc
Confidence            478899999999999999887642211        111 2444469999999999988872 458888876643

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=95.27  E-value=0.047  Score=65.51  Aligned_cols=75  Identities=15%  Similarity=0.138  Sum_probs=40.5

Q ss_pred             ccCccHHHHHHHHHHHHH-----cccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHH
Q psy11422        496 LDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA  570 (687)
Q Consensus       496 l~gfG~Ksa~~Ll~~Ie~-----sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~s  570 (687)
                      ++|+|+|+|++|++.+-.     -.+.+ .+   -..|||+|++.++.|.+.+.......  ..-.+..-.|++...|..
T Consensus        89 ~~GIG~~~A~~iv~~fg~~~~~~i~~~~-~~---L~~v~gi~~~~~~~i~~~~~~~~~~~--~~~~~L~~~gi~~~~a~k  162 (720)
T TIGR01448        89 IKGVGKKLAQRIVKTFGEAAFDVLDDDP-EK---LLEVPGISKANLEKFVSQWSQQGDER--RLLAGLQGLGIGIKLAQR  162 (720)
T ss_pred             CCCcCHHHHHHHHHHhCHhHHHHHHhCH-HH---HhcCCCCCHHHHHHHHHHHHHhHHHH--HHHHHHHHcCCCHHHHHH
Confidence            567777777777665421     11111 11   12567777777776666553222211  122344555777777777


Q ss_pred             HHHHHc
Q psy11422        571 FIKFIN  576 (687)
Q Consensus       571 I~~ff~  576 (687)
                      |+++|.
T Consensus       163 i~~~yg  168 (720)
T TIGR01448       163 IYKFYQ  168 (720)
T ss_pred             HHHHHh
Confidence            777663

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR01259 comE comEA protein

Probab=95.16  E-value=0.029  Score=52.17  Aligned_cols=47  Identities=9%  Similarity=0.183  Sum_probs=37.5

Q ss_pred             ccccccCCCCHHHHHHHHHC----CCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        457 RKAMNIIGLGKKMIEKLVNA----NIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       457 r~~l~I~GLG~k~i~~L~~~----g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      ...+.++|+|+++++++++.    |...        +.++|..++|+|+|.+++|.+.|
T Consensus        68 ~eL~~lpGIG~~~A~~Ii~~R~~~g~f~--------s~eeL~~V~GIg~k~~~~i~~~l  118 (120)
T TIGR01259        68 EELQALPGIGPAKAKAIIEYREENGAFK--------SVDDLTKVSGIGEKSLEKLKDYA  118 (120)
T ss_pred             HHHhcCCCCCHHHHHHHHHHHHhcCCcC--------CHHHHHcCCCCCHHHHHHHHhce
Confidence            35678999999999999984    4443        34677889999999999987654

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>PRK02362 ski2-like helicase; Provisional

Probab=95.14  E-value=0.021  Score=68.71  Aligned_cols=63  Identities=21%  Similarity=0.281  Sum_probs=52.9

Q ss_pred             HHhhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        447 RKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       447 ~~~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      +.++|.|=+..   ..+.|||+|++++.+|+++| |+|+.||..++.++|.++  ||+|.|++|++++.
T Consensus       639 l~~~l~~gv~~~~~~L~~ip~i~~~~a~~l~~~g-i~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~  704 (737)
T PRK02362        639 LEKRVEYGVREELLDLVGLRGVGRVRARRLYNAG-IESRADLRAADKSVVLAI--LGEKIAENILEQAG  704 (737)
T ss_pred             HHHHHHhCCCHHHHHHhCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence            34444443332   46789999999999999977 699999999999999999  99999999999976

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.07  E-value=0.049  Score=55.29  Aligned_cols=73  Identities=18%  Similarity=0.209  Sum_probs=52.8

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHH----HhcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l----~~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.              ..-+++.|||+++|-.++..+. .++|    .+-+...|.++||||+
T Consensus        55 rEd~~~LyGF~~~~Er~lF--------------~~Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~ipGIGk  119 (203)
T PRK14602         55 REDALELFGFATWDERQTF--------------IVLISISKVGAKTALAILSQFR-PDDLRRLVAEEDVAALTRVSGIGK  119 (203)
T ss_pred             ecCcceeeCCCCHHHHHHH--------------HHHhCCCCcCHHHHHHHHhhCC-HHHHHHHHHhCCHHHHhcCCCcCH
Confidence            4666677788766443332              2226889999999998888764 5544    4558899999999999


Q ss_pred             HHHHHHHHHHcc
Q psy11422        566 TTVKAFIKFINQ  577 (687)
Q Consensus       566 ~~A~sI~~ff~~  577 (687)
                      ++|+.|.--+++
T Consensus       120 KtAerIilELkd  131 (203)
T PRK14602        120 KTAQHIFLELKY  131 (203)
T ss_pred             HHHHHHHHHHHH
Confidence            999998755443

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.02  E-value=0.069  Score=53.43  Aligned_cols=48  Identities=19%  Similarity=0.302  Sum_probs=31.3

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +++.|||+++|-.++..+ +.+++.    +-|...| ++||||+++|+.|.--+
T Consensus        76 isV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilEL  127 (186)
T PRK14600         76 VKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITEL  127 (186)
T ss_pred             hCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHH
Confidence            467777777777776655 344443    3356667 78888888887776444

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=94.99  E-value=0.027  Score=66.64  Aligned_cols=81  Identities=17%  Similarity=0.252  Sum_probs=52.4

Q ss_pred             cccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHH-HHH---HHccc------CCHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNIL-LAI---QKSKL------TTFSRFIY  524 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll-~~I---e~sk~------~~l~r~L~  524 (687)
                      +.+.++|+|+|.+++|+++-   .=..+.-++.     =+.+|++|++.|+.|. ..+   ++-.+      .++.++  
T Consensus       471 ~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~-----ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l--  543 (669)
T PRK14350        471 RLINLKGFKDKRINNLKRSIEASKKRPFSKLLL-----SMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKL--  543 (669)
T ss_pred             HHhhccCccHHHHHHHHHHHHHHhCCCHHHHHH-----HcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHH--
Confidence            56678999999999998741   1123344333     2457889998888877 332   22111      222232  


Q ss_pred             HcCCCCCCHHHHHHHHhhcCCh
Q psy11422        525 ALGIRHVGETTAKELANYFKNL  546 (687)
Q Consensus       525 aLGIp~vG~~~Ak~La~~f~sl  546 (687)
                       +.|+|||+.+|..|.+.|.+-
T Consensus       544 -~~i~giG~~~a~si~~ff~~~  564 (669)
T PRK14350        544 -LKIKGIGEKIALNIIEAFNDK  564 (669)
T ss_pred             -hhCCCccHHHHHHHHHHHcCH
Confidence             368999999999998888653

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=94.85  E-value=0.039  Score=64.09  Aligned_cols=57  Identities=21%  Similarity=0.253  Sum_probs=51.1

Q ss_pred             cccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       454 F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      +-| ...+|+|+||++..+|++.-  .|+.+|..++.++|.++||++++.|++|++.+.+
T Consensus       512 ~~s-~L~~I~GiG~kr~~~LL~~F--gs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~  568 (574)
T PRK14670        512 IKL-NYTKIKGIGEKKAKKILKSL--GTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK  568 (574)
T ss_pred             ccc-ccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            345 36699999999999999975  5999999999999999999999999999999865

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=94.80  E-value=0.2  Score=46.70  Aligned_cols=83  Identities=22%  Similarity=0.215  Sum_probs=60.9

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHhcCCh-----hhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHH
Q psy11422        463 IGLGKKMIEKLVNANIVVTAVDLYKINF-----KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAK  537 (687)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~-----~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak  537 (687)
                      ||+|++...+|-+.| |.|..||+....     ..|..--|+..+...++...         .++   .-|||||+.-|.
T Consensus         1 pgi~~~~~~~L~~~G-I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~---------AdL---~ri~gi~~~~a~   67 (122)
T PF14229_consen    1 PGIGPKEAAKLKAAG-IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQ---------ADL---MRIPGIGPQYAE   67 (122)
T ss_pred             CCCCHHHHHHHHHcC-CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhH---------HHh---hhcCCCCHHHHH
Confidence            799999999997777 699999999653     23655556666555444321         122   268999999998


Q ss_pred             HHHh-hcCChHHHHhcCHHHHh
Q psy11422        538 ELAN-YFKNLECMFKATEEQLL  558 (687)
Q Consensus       538 ~La~-~f~sld~l~~As~eeL~  558 (687)
                      .|.. .+.|+++|..+++++|.
T Consensus        68 LL~~AGv~Tv~~LA~~~p~~L~   89 (122)
T PF14229_consen   68 LLEHAGVDTVEELAQRNPQNLH   89 (122)
T ss_pred             HHHHhCcCcHHHHHhCCHHHHH
Confidence            8774 48899999998887764

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.61  E-value=0.066  Score=54.06  Aligned_cols=73  Identities=14%  Similarity=0.189  Sum_probs=50.5

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHH----HhcCHHHHhcCCCCCH
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS  565 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l----~~As~eeL~~I~GIG~  565 (687)
                      .||-..|=||..+....+.            +.  -+++.|||+++|-.++..+ +.+++    .+-|...|.++||||+
T Consensus        53 rEd~~~LyGF~~~~Er~lF------------~~--L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGk  117 (197)
T PRK14603         53 REDALSLYGFPDEDSLELF------------EL--LLGVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGK  117 (197)
T ss_pred             ccCCceeeCcCCHHHHHHH------------HH--HhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence            4555666677755443322            22  2578899999988888765 35444    4457889999999999


Q ss_pred             HHHHHHHHHHcc
Q psy11422        566 TTVKAFIKFINQ  577 (687)
Q Consensus       566 ~~A~sI~~ff~~  577 (687)
                      ++|+.|.--+++
T Consensus       118 KtAerIilELkd  129 (197)
T PRK14603        118 KLAERIALELKG  129 (197)
T ss_pred             HHHHHHHHHHHH
Confidence            999998755543

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=94.60  E-value=0.039  Score=51.55  Aligned_cols=26  Identities=19%  Similarity=0.344  Sum_probs=16.9

Q ss_pred             HHHhcCChhhhhcccCccHHHHHHHH
Q psy11422        483 VDLYKINFKNLLRLDRVSNKLANNIL  508 (687)
Q Consensus       483 ~DL~~L~~~~L~~l~gfG~Ksa~~Ll  508 (687)
                      -||-+.+..+|.++||+|++.|++|+
T Consensus        53 IdiN~A~~~el~~lpGigP~~A~~IV   78 (132)
T PRK02515         53 IDLNNSSVRAFRQFPGMYPTLAGKIV   78 (132)
T ss_pred             ccCCccCHHHHHHCCCCCHHHHHHHH
Confidence            35556666666666777766666666

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.55  E-value=0.06  Score=58.14  Aligned_cols=55  Identities=22%  Similarity=0.215  Sum_probs=50.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ....++|+|++++++|.+.|+ .|+.||+.++.++|..+.|++++.+.+|++....
T Consensus         7 ~l~~l~gIg~~~a~~L~~~Gi-~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~   61 (317)
T PRK04301          7 DLEDLPGVGPATAEKLREAGY-DTVEAIAVASPKELSEAAGIGESTAAKIIEAARE   61 (317)
T ss_pred             cHhhcCCCCHHHHHHHHHcCC-CCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            456799999999999999995 8999999999999999999999999999988754

>PRK01172 ski2-like helicase; Provisional

Probab=94.46  E-value=0.067  Score=63.70  Aligned_cols=63  Identities=17%  Similarity=0.173  Sum_probs=54.0

Q ss_pred             hhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        449 AGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       449 ~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      .||.|=+..   ..|.|||+|..++.+|+++| ++|+.||-.++.+++..+.|+|++.+++|+++..
T Consensus       601 ~rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g-~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~  666 (674)
T PRK01172        601 IRIKEGIREDLIDLVLIPKVGRVRARRLYDAG-FKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM  666 (674)
T ss_pred             HHHHcCCCHHHHhhcCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence            345555443   35679999999999999999 5999999999999999999999999999999843

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.43  E-value=0.12  Score=51.70  Aligned_cols=53  Identities=15%  Similarity=0.269  Sum_probs=43.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.+.|+|||++-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.+..
T Consensus        74 ~Li~VsGIGpK~Al~ILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkd  130 (183)
T PRK14601         74 MLLKVNGIGANTAMAVCSSL---DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSD  130 (183)
T ss_pred             HHhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999998754   77788773    3467889999999999999988764

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=94.21  E-value=0.058  Score=37.75  Aligned_cols=28  Identities=29%  Similarity=0.358  Sum_probs=22.3

Q ss_pred             hHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11422        482 AVDLYKINFKNLLRLDRVSNKLANNILL  509 (687)
Q Consensus       482 i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~  509 (687)
                      ...+...+.++|.++||+|+++|+.|+.
T Consensus         2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen    2 LDGLIPASIEELMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred             CCCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence            3456667889999999999999998875

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=94.19  E-value=0.044  Score=63.79  Aligned_cols=81  Identities=19%  Similarity=0.284  Sum_probs=39.4

Q ss_pred             cccccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH---cccCCHHHHHHHcCCC
Q psy11422        456 SRKAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK---SKLTTFSRFIYALGIR  529 (687)
Q Consensus       456 sr~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~---sk~~~l~r~L~aLGIp  529 (687)
                      ..+.+.++|+|++.+++|+++-   .=.+..-|+.     =+.++.+|++.|..|...+..   -...++..+   ..||
T Consensus       478 ~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~-----aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l---~~i~  549 (667)
T COG0272         478 EEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLY-----ALGIRHVGETTAKSLARHFGTLEALLAASEEEL---ASIP  549 (667)
T ss_pred             HHHHhhccchhhhHHHHHHHHHHHhccCCHHHHHH-----HcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHH---hhcc
Confidence            3556667777777777666521   0011111111     134556666666666554432   111222111   2466


Q ss_pred             CCCHHHHHHHHhhcC
Q psy11422        530 HVGETTAKELANYFK  544 (687)
Q Consensus       530 ~vG~~~Ak~La~~f~  544 (687)
                      +||..+|..|.+.|.
T Consensus       550 giG~~vA~si~~ff~  564 (667)
T COG0272         550 GIGEVVARSIIEFFA  564 (667)
T ss_pred             chhHHHHHHHHHHHc
Confidence            666666666665554

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.09  E-value=0.12  Score=52.00  Aligned_cols=53  Identities=13%  Similarity=0.347  Sum_probs=44.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.|.|+|||++-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.+..
T Consensus        73 ~LisVsGIGPK~ALaILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkd  129 (196)
T PRK13901         73 ELIGVDGIGPRAALRVLSGI---KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRG  129 (196)
T ss_pred             HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999998754   67777762    3567899999999999999988764

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=94.07  E-value=0.078  Score=62.47  Aligned_cols=54  Identities=9%  Similarity=0.056  Sum_probs=49.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..++|+|+|++++.+|++.-  .|+.+|...+.++|.+++|+|++.|++|++.++.
T Consensus       638 ~L~~IPGIGpkr~k~LL~~F--GSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~  691 (694)
T PRK14666        638 ELQRVEGIGPATARLLWERF--GSLQAMAAAGEEGLAAVPGIGPARAAALHEHLKT  691 (694)
T ss_pred             HHhhCCCCCHHHHHHHHHHh--CCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHH
Confidence            46789999999999999974  4999999999999999999999999999998864

>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family

Probab=94.07  E-value=0.25  Score=53.43  Aligned_cols=128  Identities=16%  Similarity=0.134  Sum_probs=79.2

Q ss_pred             CeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhh--------h-hhhhhccCCcccccCC--CCceEEEEEEEE
Q psy11422        117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENIT--------T-NIHIIHKIPLVLNIKY--PPELLEVRCEVL  185 (687)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT--------~-n~~~i~~iP~~l~~~~--~~~~~evRGEi~  185 (687)
                      ...|+++.|+||.-.+++|.+|.-++...| +|..++|-.        + +...|..+...|....  -...+.|-||++
T Consensus        24 ~~ewvatEKlhGaNfsi~~~~~~~i~~akR-~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl~  102 (325)
T TIGR02307        24 LTEWVAREKIHGTNFSIIIERDFKVTCAKR-TGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGELA  102 (325)
T ss_pred             CceEEEEEEecCcceEEEEeCCceEEEeec-ccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEee
Confidence            348999999999999999988833577777 566665422        1 1112333333332110  135799999998


Q ss_pred             eehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC--CCCCCCHHHHHHHHHhcC-CC
Q psy11422        186 IYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMPSSHSELLNWYQKIG-LS  262 (687)
Q Consensus       186 ~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~--~~~~~~~~e~l~~L~~~G-f~  262 (687)
                      =.                 .+.+|.+              -. .++|++|++..+..  ..+ -+.-+.++.+...| |+
T Consensus       103 G~-----------------~~q~~~~--------------Y~-~~~fyaFdI~~~~~~~~~~-L~~d~~~e~~~~~~~l~  149 (325)
T TIGR02307       103 GP-----------------GYQKPVV--------------YS-DKDFYAFDIKYTETSDDVT-LVDDYMMESFCNVPKLK  149 (325)
T ss_pred             cC-----------------cccCccc--------------cc-cccEEEEEEEEeccCcceE-ecHHHHHHHHHHcCCcc
Confidence            32                 2444544              11 47999999854421  112 35556777888886 88


Q ss_pred             CCCCceEeCCHHHHHHH
Q psy11422        263 ICGEYSVLSGVNKLIEF  279 (687)
Q Consensus       263 ~~~~~~~~~~~~ei~~~  279 (687)
                      .++. ....++++++++
T Consensus       150 ~ap~-L~rGt~~e~l~~  165 (325)
T TIGR02307       150 YAPL-LGRGTLDELLAF  165 (325)
T ss_pred             cchh-hcccCHHHHHhc
Confidence            7653 334678887775

Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.97  E-value=0.053  Score=54.67  Aligned_cols=53  Identities=23%  Similarity=0.365  Sum_probs=43.3

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.|.|+|||+.-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.++.
T Consensus        74 ~Li~V~GIGpK~Al~iLs~~---~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~  130 (195)
T PRK14604         74 LLIGVSGVGPKAALNLLSSG---TPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKG  130 (195)
T ss_pred             HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999998754   66777762    3567889999999999999988764

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.92  E-value=0.062  Score=54.54  Aligned_cols=52  Identities=21%  Similarity=0.352  Sum_probs=43.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+.+.|+|||++-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.+..
T Consensus        76 Li~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkd  131 (203)
T PRK14602         76 LISISKVGAKTALAILSQF---RPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKY  131 (203)
T ss_pred             HhCCCCcCHHHHHHHHhhC---CHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence            6789999999999999854   66777762    3567899999999999999988764

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.91  E-value=0.058  Score=54.06  Aligned_cols=53  Identities=23%  Similarity=0.384  Sum_probs=42.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.|.|+|||++-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.+..
T Consensus        74 ~Li~V~GIGpK~AL~iLs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkd  130 (188)
T PRK14606         74 SLTKVSRLGPKTALKIISNE---DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKD  130 (188)
T ss_pred             HHhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999998753   66777762    3466889999999999999988764

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=93.88  E-value=0.25  Score=50.71  Aligned_cols=83  Identities=24%  Similarity=0.341  Sum_probs=50.9

Q ss_pred             HHHHHHHHCCCC-----CChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHH
Q psy11422        468 KMIEKLVNANIV-----VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKEL  539 (687)
Q Consensus       468 k~i~~L~~~g~I-----~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~L  539 (687)
                      +.+..|.+.+..     .++.+|..++.++|.++   -||-..+|..|.+-.+                         .+
T Consensus        50 ~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~-------------------------~i  104 (218)
T PRK13913         50 KSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSE-------------------------NI  104 (218)
T ss_pred             HHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHH-------------------------HH
Confidence            444556665432     38999999988887765   4787777776665322                         22


Q ss_pred             HhhcCChHHHH-hcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        540 ANYFKNLECMF-KATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       540 a~~f~sld~l~-~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .+.|++++.+. ..+.++|.+++|||+++|..|.-|-
T Consensus       105 ~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya  141 (218)
T PRK13913        105 LKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV  141 (218)
T ss_pred             HHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH
Confidence            22333333222 1234678888888888888776654

>PHA02142 putative RNA ligase

Probab=93.87  E-value=0.57  Score=51.49  Aligned_cols=147  Identities=18%  Similarity=0.217  Sum_probs=80.0

Q ss_pred             CeeEEEEEccceeEEEEEEe--CCEEEE--------EEecCCCCccc---hh-----hhh-----hhhhccCCcccccCC
Q psy11422        117 NIEYIAELKFDGIAVNLRYE--YGYLKQ--------ASTRGDGNIGE---NI-----TTN-----IHIIHKIPLVLNIKY  173 (687)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~--~G~l~~--------a~TRGdG~~Ge---Dv-----T~n-----~~~i~~iP~~l~~~~  173 (687)
                      ...|.++.|+||.|+++.|.  .+.+..        |.+..+|..|-   +.     ..|     +.. .+||..|..  
T Consensus       168 ~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~-~~i~~~l~~--  244 (366)
T PHA02142        168 DVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVEN-YQIVDRLKE--  244 (366)
T ss_pred             CceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHH-cCcHHHHHh--
Confidence            46799999999999999754  111111        11222332221   11     111     112 236666653  


Q ss_pred             CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHH
Q psy11422        174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL  253 (687)
Q Consensus       174 ~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l  253 (687)
                      .+..+.|.||+|=+                           |.  |.+.--.  ..-+|++|++-..+...+ -++.+..
T Consensus       245 ~~~~iaIqGEl~Gp---------------------------~I--Q~N~~~~--~~~~F~vF~v~~i~~~~y-l~~~e~~  292 (366)
T PHA02142        245 LGMSVAIQGELMGP---------------------------GI--QKNRENF--DKYRIFAFRAWFIDEQRF-ATDEEFQ  292 (366)
T ss_pred             hCCcEEEEEEEecc---------------------------cc--cCccccC--CCCceEEEEEEEecccee-CCHHHHH
Confidence            35679999999931                           11  2221111  123799998732222223 5777888


Q ss_pred             HHHHhcCCCCCCCc------eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11422        254 NWYQKIGLSICGEY------SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN  302 (687)
Q Consensus       254 ~~L~~~Gf~~~~~~------~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~  302 (687)
                      ++++++|++.++..      ....+++|++++-. .   ..-.+-.--|+|+|--
T Consensus       293 ~~~~~~gl~~VPvL~~~~~~~~~~s~eE~L~~A~-~---p~~~~~~~EGiViKp~  343 (366)
T PHA02142        293 DLCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD-I---PSINHKIAEGVVYKSV  343 (366)
T ss_pred             HHHHHcCCceeeeecccccccccCCHHHHHhhcC-C---CcccccccceEEEeec
Confidence            89999999876532      11237888887642 0   1111112479999763

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=93.82  E-value=0.2  Score=38.60  Aligned_cols=47  Identities=17%  Similarity=0.325  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        465 LGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       465 LG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      +.+.++.+|+++| +.++.||-.+..++|..++|+++..+.+|+....
T Consensus         1 i~~~~~~~L~~~G-~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~   47 (50)
T TIGR01954         1 IDEEIAQLLVEEG-FTTVEDLAYVPIDELLSIEGFDEETAKELINRAR   47 (50)
T ss_pred             CCHHHHHHHHHcC-CCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHH
Confidence            4578999999999 5899999999999999999999999999987654

NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.76  E-value=0.061  Score=54.30  Aligned_cols=53  Identities=25%  Similarity=0.314  Sum_probs=43.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.+.|+|||++-.+....   ++.+|..+    +...|.++||+|+|+|++|+-.+..
T Consensus        73 ~L~~V~GIGpK~AL~iLs~~---~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkd  129 (197)
T PRK14603         73 LLLGVSGVGPKLALALLSAL---PPALLARALLEGDARLLTSASGVGKKLAERIALELKG  129 (197)
T ss_pred             HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            36789999999999998754   66777762    3567889999999999999987754

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=93.73  E-value=0.31  Score=48.30  Aligned_cols=84  Identities=15%  Similarity=0.277  Sum_probs=54.9

Q ss_pred             HHHHHHHCCCCCChHHHhcCChhhhhcc---c----CccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHh
Q psy11422        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---D----RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELAN  541 (687)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~----gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~  541 (687)
                      .+..|++.-...++.+|..+..++|..+   .    ||-..+|.+|.+.                         |+.|.+
T Consensus        39 A~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~-------------------------a~~iie   93 (177)
T TIGR03252        39 GPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQAL-------------------------AQYVVD   93 (177)
T ss_pred             HHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHH-------------------------HHHHHH
Confidence            3447765333368999998887666544   1    6777777766653                         333443


Q ss_pred             hc-CChHHHHhc----C---HHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        542 YF-KNLECMFKA----T---EEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       542 ~f-~sld~l~~A----s---~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      .| ++++.|..+    +   .++|.+++|||+++|.-+..+|..
T Consensus        94 ~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~  137 (177)
T TIGR03252        94 TYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK  137 (177)
T ss_pred             HhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            33 355556541    1   368999999999999998877643

This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.64  E-value=0.064  Score=53.68  Aligned_cols=52  Identities=19%  Similarity=0.333  Sum_probs=40.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.+.|+|||++-.+....   ++.+|..+    +...| ++||+|+|+|++|+-.+..
T Consensus        74 ~LisV~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~  129 (186)
T PRK14600         74 MLVKVSGVNYKTAMSILSKL---TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQY  129 (186)
T ss_pred             HHhCcCCcCHHHHHHHHccC---CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence            36789999999999998754   67777762    24557 9999999999999977754

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.64  E-value=0.12  Score=55.43  Aligned_cols=51  Identities=25%  Similarity=0.263  Sum_probs=47.7

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      .|+|+|++++++|.+.|+ .|+.||..++.++|..+.|++++.|+.|++...
T Consensus         3 ~i~gig~~~~~~L~~~Gi-~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~   53 (310)
T TIGR02236         3 DLPGVGPATAEKLREAGY-DTFEAIAVASPKELSEIAGISEGTAAKIIQAAR   53 (310)
T ss_pred             ccCCCCHHHHHHHHHcCC-CCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence            689999999999999995 899999999999999999999999999988775

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.

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=93.53  E-value=0.14  Score=51.87  Aligned_cols=50  Identities=18%  Similarity=0.311  Sum_probs=33.2

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      +.+.|||+++|-.++..+ +++.|.    ..+..-|.++||||+++|+.|.--+.
T Consensus        76 isVnGIGpK~ALaiLs~~-~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk  129 (201)
T COG0632          76 ISVNGIGPKLALAILSNL-DPEELAQAIANEDVKALSKIPGIGKKTAERIVLELK  129 (201)
T ss_pred             HccCCccHHHHHHHHcCC-CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHh
Confidence            345666666666555443 344443    34678899999999999999876543

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=93.27  E-value=0.24  Score=53.01  Aligned_cols=114  Identities=16%  Similarity=0.160  Sum_probs=73.0

Q ss_pred             ccccCCCCHHHHHHHHHC-C----CCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc---------cCCHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNA-N----IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK---------LTTFSRFIY  524 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~-g----~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk---------~~~l~r~L~  524 (687)
                      .|++.|=-+=.+....++ +    .=+++++++..  ..+..|+|+|+..|++|..-++.-.         ..|. -++.
T Consensus        18 ~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~--~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~-gl~~   94 (326)
T COG1796          18 YMELEGENPFKIRAYRKAAQSLENLTEDLEEIEER--GRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPE-GLEP   94 (326)
T ss_pred             HHHhcCCCccchHHHHHHHHhhhhcccchHHHHhh--cccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCc-chHH
Confidence            466666664233322221 1    11345555543  2578899999999988887765321         2232 2555


Q ss_pred             HcCCCCCCHHHHHHHHhhc--CChHHHHhcCH-HHHhcCCCCCHHHHHHHHHHH
Q psy11422        525 ALGIRHVGETTAKELANYF--KNLECMFKATE-EQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       525 aLGIp~vG~~~Ak~La~~f--~sld~l~~As~-eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      -|.+||+|++.-..|...+  .+++.|..|-. -.+..+.|+|++.+..|.++.
T Consensus        95 Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i  148 (326)
T COG1796          95 LLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENI  148 (326)
T ss_pred             HhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHH
Confidence            6789999997777777654  57777776543 357789999999988887754

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=93.06  E-value=0.19  Score=59.17  Aligned_cols=60  Identities=15%  Similarity=0.088  Sum_probs=54.1

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~  520 (687)
                      .-+|+|+|+++..+|++.-  .|+.+|..++.++|.+++|++++.|++|+.+-.+|-..|.+
T Consensus       610 L~~IpGiG~kr~~~LL~~F--gS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~  669 (691)
T PRK14672        610 FERLPHVGKVRAHRLLAHF--GSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVR  669 (691)
T ss_pred             cccCCCCCHHHHHHHHHHh--cCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchh
Confidence            5589999999999999975  59999999999999999999999999999998887777654

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=92.93  E-value=0.22  Score=53.77  Aligned_cols=62  Identities=26%  Similarity=0.364  Sum_probs=42.8

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHH--------HHHHHcCCCCCCHHHHHHHHh-hcCChHHHHhc
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS--------RFIYALGIRHVGETTAKELAN-YFKNLECMFKA  552 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~--------r~L~aLGIp~vG~~~Ak~La~-~f~sld~l~~A  552 (687)
                      +++.++||+|++.|++|.+-++.-+-..+.        -++.=++|||||+++|+.+.+ .+.|+++|..+
T Consensus        45 ~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~dL~~a  115 (307)
T cd00141          45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKA  115 (307)
T ss_pred             HHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHHHcCCCCHHHHHHH
Confidence            356888999999998888877652222222        233445899999999988883 25677777765

X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=92.86  E-value=0.19  Score=41.77  Aligned_cols=58  Identities=16%  Similarity=0.159  Sum_probs=39.3

Q ss_pred             HHHhcCChhhhhc-ccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhh
Q psy11422        483 VDLYKINFKNLLR-LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY  542 (687)
Q Consensus       483 ~DL~~L~~~~L~~-l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~  542 (687)
                      -||-++..+.|.. +||+|++.|++|++......  ++..+-.-..++|+|.+++++|...
T Consensus         8 invNta~~~~L~~~ipgig~~~a~~Il~~R~~~g--~~~s~~dL~~v~gi~~~~~~~i~~~   66 (69)
T TIGR00426         8 VNINTATAEELQRAMNGVGLKKAEAIVSYREEYG--PFKTVEDLKQVPGIGNSLVEKNLAV   66 (69)
T ss_pred             eECcCCCHHHHHhHCCCCCHHHHHHHHHHHHHcC--CcCCHHHHHcCCCCCHHHHHHHHhh
Confidence            4566677778888 88888888888888776432  2222222246788888888877644

Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.

>KOG2534|consensus

Probab=92.69  E-value=0.78  Score=49.01  Aligned_cols=136  Identities=16%  Similarity=0.199  Sum_probs=78.6

Q ss_pred             hhhhhcccCccHHHHHHHHHHHHHcccCCHHH--------HHH-HcCCCCCCHHHHHHHH-hhcCChHHHHhcCHHHHhc
Q psy11422        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSR--------FIY-ALGIRHVGETTAKELA-NYFKNLECMFKATEEQLLN  559 (687)
Q Consensus       490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r--------~L~-aLGIp~vG~~~Ak~La-~~f~sld~l~~As~eeL~~  559 (687)
                      .+++.+|||+|+|.|.+|.+-++.-.-..+.+        .|. =-+|-|||.++|++-- ..|.|++.+. -+.+.|..
T Consensus        55 ~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~R-k~~~kft~  133 (353)
T KOG2534|consen   55 GEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVR-KKPDKFTR  133 (353)
T ss_pred             HHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHH-hCHHHHHH
Confidence            57788899999999999988776533333322        222 2388999999987544 4688888888 45566654


Q ss_pred             CCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcc
Q psy11422        560 IPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVN  639 (687)
Q Consensus       560 I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~  639 (687)
                      -.-+|    -+-++=|-..-.++....+... |.       ......+.+..+.+||.+..              |   .
T Consensus       134 qqk~G----l~yy~Df~~~v~ReE~~~i~~~-V~-------~av~~~~p~~~vt~~GsfRR--------------G---k  184 (353)
T KOG2534|consen  134 QQKAG----LKYYEDFLKRVTREEATAIQQT-VQ-------EAVWAFDPEAFVTVTGSFRR--------------G---K  184 (353)
T ss_pred             HHHHh----HHHHHHHhhhccHHHHHHHHHH-HH-------HHHhhcCCCcEEEEeccccC--------------C---c
Confidence            43232    2222222111112211221110 00       00112456889999999742              2   3


Q ss_pred             cccccccEEEEcCCCC
Q psy11422        640 FISKNTNYLVKGQKPG  655 (687)
Q Consensus       640 sVsk~t~~LV~G~~~g  655 (687)
                      ++..++|+|+.-...+
T Consensus       185 ~~ggDvD~LithP~~~  200 (353)
T KOG2534|consen  185 KMGGDVDFLITHPGST  200 (353)
T ss_pred             ccCCCeeEEEeCCCCC
Confidence            4556899999865443

>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]

Probab=92.63  E-value=0.14  Score=53.70  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=45.3

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .||.+-......+...|++++.+..||.++|.+++|||+..|..|.+.++
T Consensus       297 kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~  346 (349)
T COG1623         297 KIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLS  346 (349)
T ss_pred             cCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence            67777777888999999999999999999999999999999999988764

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=92.61  E-value=0.18  Score=58.65  Aligned_cols=50  Identities=18%  Similarity=0.207  Sum_probs=46.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      ..+|+|+|+++..+|+++-  .|+.+|..++.++|.++ |++++.|++|++.+
T Consensus       516 Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l  565 (567)
T PRK14667        516 LDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKL-GIPPSVKQEVKKYL  565 (567)
T ss_pred             cccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence            5689999999999999975  59999999999999999 99999999998876

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=92.39  E-value=0.18  Score=48.67  Aligned_cols=58  Identities=21%  Similarity=0.342  Sum_probs=35.6

Q ss_pred             HHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCC
Q psy11422        484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKI  563 (687)
Q Consensus       484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GI  563 (687)
                      +|-+.+.++|..|||+|+++|+.|++.-++.  -+                        |.        +.+||.+++||
T Consensus        90 NiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~--G~------------------------f~--------sv~dL~~v~Gi  135 (149)
T COG1555          90 NINTASAEELQALPGIGPKKAQAIIDYREEN--GP------------------------FK--------SVDDLAKVKGI  135 (149)
T ss_pred             cccccCHHHHHHCCCCCHHHHHHHHHHHHHc--CC------------------------CC--------cHHHHHhccCC
Confidence            3444556777777777777777777654431  11                        33        34666667777


Q ss_pred             CHHHHHHHHHHH
Q psy11422        564 GSTTVKAFIKFI  575 (687)
Q Consensus       564 G~~~A~sI~~ff  575 (687)
                      |+++-+.+..++
T Consensus       136 G~~~~ekl~~~i  147 (149)
T COG1555         136 GPKTLEKLKDYI  147 (149)
T ss_pred             CHHHHHHHHhhc
Confidence            777776666543

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=92.25  E-value=0.073  Score=43.89  Aligned_cols=30  Identities=23%  Similarity=0.231  Sum_probs=22.0

Q ss_pred             HHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        484 DLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ||-+++.++|..+||+|++.|++|++..++
T Consensus         7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~   36 (65)
T PF12836_consen    7 DINTASAEELQALPGIGPKQAKAIVEYREK   36 (65)
T ss_dssp             ETTTS-HHHHHTSTT--HHHHHHHHHHHHH
T ss_pred             cCccCCHHHHHHcCCCCHHHHHHHHHHHHh
Confidence            566678889999999999999999886543

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=92.05  E-value=0.27  Score=46.08  Aligned_cols=41  Identities=15%  Similarity=0.242  Sum_probs=32.5

Q ss_pred             CCCCCCHHHHHHHHhh--cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        527 GIRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~--f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .+||||++.|++|.++  |.        +.|||.+++|||++..+.+..+.
T Consensus        65 ~lpGigP~~A~~IV~nGpf~--------sveDL~~V~GIgekqk~~l~k~~  107 (132)
T PRK02515         65 QFPGMYPTLAGKIVKNAPYD--------SVEDVLNLPGLSERQKELLEANL  107 (132)
T ss_pred             HCCCCCHHHHHHHHHCCCCC--------CHHHHHcCCCCCHHHHHHHHHhh
Confidence            4899999999999863  44        56889999999998777766654

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=92.02  E-value=0.14  Score=51.85  Aligned_cols=20  Identities=25%  Similarity=0.464  Sum_probs=9.4

Q ss_pred             hhhcccCccHHHHHHHHHHH
Q psy11422        492 NLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       492 ~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      -|.++||+|+|.|++|+-.+
T Consensus       109 ~L~k~PGIGkKtAerivleL  128 (201)
T COG0632         109 ALSKIPGIGKKTAERIVLEL  128 (201)
T ss_pred             hhhcCCCCCHHHHHHHHHHH
Confidence            34444455555554444443

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=91.97  E-value=0.12  Score=55.83  Aligned_cols=47  Identities=30%  Similarity=0.355  Sum_probs=35.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK  515 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk  515 (687)
                      ..++|+|+||+++.+|| +..|+|++||...-          |.|+.++++.+|+..+
T Consensus        86 ~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~----------g~k~~~~i~~gl~~~~  132 (307)
T cd00141          86 LLLRVPGVGPKTARKLY-ELGIRTLEDLRKAA----------GAKLEQNILIGLEYYE  132 (307)
T ss_pred             HHHcCCCCCHHHHHHHH-HcCCCCHHHHHHHh----------ccccHHHHHHHHHHHH
Confidence            34678888888888888 44468888888732          7788888888887543

X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=91.65  E-value=0.22  Score=58.44  Aligned_cols=52  Identities=23%  Similarity=0.297  Sum_probs=47.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ...|+|+|+++..+|++.-  .|+.+|+..+.++|.+++|+|++.|++|.+.+.
T Consensus       545 L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~  596 (598)
T PRK00558        545 LDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEALH  596 (598)
T ss_pred             HhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence            4589999999999999965  589999999999999999999999999998764

>PRK00024 hypothetical protein; Reviewed

Probab=91.34  E-value=0.56  Score=48.37  Aligned_cols=57  Identities=21%  Similarity=0.306  Sum_probs=45.8

Q ss_pred             HHHHHHHcCCCCCCH-HHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        519 FSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       519 l~r~L~aLGIp~vG~-~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      |-.+|...|+|+-.. ..|+.|.++|+++.++..++.++|.+++|||+..|..|..-+
T Consensus        29 LLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~   86 (224)
T PRK00024         29 LLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL   86 (224)
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence            334455668886443 478888899999999999999999999999999998776544

>TIGR00608 radc DNA repair protein radc

Probab=91.30  E-value=0.4  Score=49.25  Aligned_cols=57  Identities=21%  Similarity=0.325  Sum_probs=46.0

Q ss_pred             HHHHHHHcCCCCC-C-HHHHHHHHhhc---CChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        519 FSRFIYALGIRHV-G-ETTAKELANYF---KNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       519 l~r~L~aLGIp~v-G-~~~Ak~La~~f---~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      |-.+|...|.|+- . ...|+.|.++|   +++..+..++.++|.+++|||+..|..|..-+
T Consensus        19 LLailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~   80 (218)
T TIGR00608        19 LLAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV   80 (218)
T ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHH
Confidence            3445556788865 2 25788888899   99999999999999999999999888876654

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains

Probab=91.16  E-value=0.19  Score=39.82  Aligned_cols=27  Identities=37%  Similarity=0.386  Sum_probs=20.6

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (687)
                      ++|-|+|++|++++++.|+ +|++||-.
T Consensus         5 ~~I~GVG~~tA~~w~~~G~-rtl~Dl~~   31 (52)
T PF10391_consen    5 TGIWGVGPKTARKWYAKGI-RTLEDLRK   31 (52)
T ss_dssp             HTSTT--HHHHHHHHHTT---SHHHHHH
T ss_pred             hhcccccHHHHHHHHHhCC-CCHHHHhh
Confidence            4799999999999999885 99999953

There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....

>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain

Probab=90.71  E-value=0.3  Score=48.35  Aligned_cols=155  Identities=15%  Similarity=0.118  Sum_probs=74.7

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCC------ccchhhhh-----hhhhccCCcccc---cCCCCceEEEEEEE
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGN------IGENITTN-----IHIIHKIPLVLN---IKYPPELLEVRCEV  184 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~------~GeDvT~n-----~~~i~~iP~~l~---~~~~~~~~evRGEi  184 (687)
                      +|+++.|+||-++++.+.++.-++..+|..-.      .|-+...+     +..+. ....+.   ....+..+.|.||+
T Consensus         2 e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~~~~~f~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~i~GE~   80 (186)
T PF09414_consen    2 EVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILDPNEDFFGYQSGDNRYWAQARWLF-ELLKLAELASELLPENIIIYGEL   80 (186)
T ss_dssp             EEEEEEE-SSEEEEEEEEECTCEEEEETTEE--TT---TTCHHHHHHCHHHHHHHH-HHHHHHCCEC----SEEEEEEEE
T ss_pred             eEEEEEEeCCccEEEEEeCCCceeEeccccccCccccccccccchHHHHHHHHHHH-hhhhhhhhcccccceEEEEEEEe
Confidence            58999999999999988655434555654311      11111111     11111 111111   00136789999999


Q ss_pred             EeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCC---CCCCCHHHHHHHHHhcCC
Q psy11422        185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM---NMPSSHSELLNWYQKIGL  261 (687)
Q Consensus       185 ~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~---~~~~~~~e~l~~L~~~Gf  261 (687)
                      +=-+.              ..-.|.=        +      ...+..|++|++......   .+ -+..+...++..+||
T Consensus        81 ~G~~~--------------~Iq~~~~--------~------~~~~~~F~~Fdi~~~~~~~~~~~-l~~~~~~~~~~~~gl  131 (186)
T PF09414_consen   81 VGAKP--------------SIQKNRY--------Q------LDPPKDFYVFDIYDIDEQGEIRY-LSWDEVREFAEELGL  131 (186)
T ss_dssp             ECEEC--------------TTCSS------------------ECCCEEEEEEEEEEETCCGEEE--HHHHHHHHHCCCT-
T ss_pred             eeecc--------------ccccccc--------c------cCCCceEEEEEEEEcCCCCeeEE-CCHHHHHHHHHHCCC
Confidence            95220              0001100        0      012689999998765321   12 356677788889999


Q ss_pred             CCCCCceEeCCHHHHHHHHHHHHHh-hcCCCCccceEEEEECCh
Q psy11422        262 SICGEYSVLSGVNKLIEFYKKINIK-RFNLPYEIDGVVYKINCL  304 (687)
Q Consensus       262 ~~~~~~~~~~~~~ei~~~~~~~~~~-r~~l~y~iDGiVikv~~~  304 (687)
                      +++|.... ..+.+...+-.....- ...-+=.-=|+|+|..+.
T Consensus       132 ~~VPvl~~-g~~~~~~~~~~~~~~~~~~~~~~~~EGiVik~~~~  174 (186)
T PF09414_consen  132 KTVPVLYR-GTFTELDDLDDLFESGKPSGEGNIREGIVIKPEDE  174 (186)
T ss_dssp             EES-ECEE-ECHHHHCTS-CCGBBTTS-STT-B--EEEEEETTT
T ss_pred             CEeCEEEE-EccchhhhhhHHHhhcccCCCCCccCEEEEEEeEe
Confidence            98874322 2444433321110000 111123346999999874

RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=90.38  E-value=0.33  Score=56.73  Aligned_cols=50  Identities=16%  Similarity=0.196  Sum_probs=45.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~  510 (687)
                      ...|+|+|++++.+|++.-  .|+.+++.++.++|.++||+|++.|+.|.+.
T Consensus       527 L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~~~  576 (577)
T PRK14668        527 LDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIRER  576 (577)
T ss_pred             HhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHh
Confidence            4479999999999999975  5999999999999999999999999998764

>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

Probab=90.38  E-value=1.1  Score=45.73  Aligned_cols=42  Identities=21%  Similarity=0.093  Sum_probs=29.0

Q ss_pred             HHHHHHHHHCCCCCChHHHhcCChhhhhc---ccCccHHHHHHHHHH
Q psy11422        467 KKMIEKLVNANIVVTAVDLYKINFKNLLR---LDRVSNKLANNILLA  510 (687)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~---l~gfG~Ksa~~Ll~~  510 (687)
                      .+....|++.-  .+++|+..+..++|.+   -=||-..+|.+|++-
T Consensus        48 n~at~~Lf~~~--~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~   92 (211)
T COG0177          48 NKATPALFKRY--PTPEDLLNADEEELEELIKSIGLYRNKAKNIKEL   92 (211)
T ss_pred             HHHHHHHHHHc--CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHH
Confidence            45556666644  5999999988765543   248888888887753

>PRK10702 endonuclease III; Provisional

Probab=90.25  E-value=1.1  Score=45.70  Aligned_cols=78  Identities=15%  Similarity=0.223  Sum_probs=50.9

Q ss_pred             HHHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhc
Q psy11422        467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (687)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f  543 (687)
                      .+.+..|+...  .++++|..+..++|..+   -||-..+|.+|++..+.                         +.+.|
T Consensus        48 ~~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~-------------------------i~~~~  100 (211)
T PRK10702         48 NKATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRI-------------------------LLEQH  100 (211)
T ss_pred             HHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHH-------------------------HHHHc
Confidence            34455666542  58999999998888753   36767888888765432                         11222


Q ss_pred             CC-hHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        544 KN-LECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       544 ~s-ld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +. +    ..+.++|.+++|||+++|..|.-|.
T Consensus       101 ~~~~----p~~~~~Ll~lpGVG~ktA~~ill~a  129 (211)
T PRK10702        101 NGEV----PEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_pred             CCCC----CchHHHHhcCCcccHHHHHHHHHHH
Confidence            21 1    1246788888888888888887544

>KOG1929|consensus

Probab=89.56  E-value=0.53  Score=56.56  Aligned_cols=75  Identities=21%  Similarity=0.221  Sum_probs=68.0

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..+.|..||.||... ..|.+++.++..+||+.-.+.+..+.++++..... .|++.|..++++|++++++..-.+.
T Consensus       102 p~~~~~~Vc~tgl~~-~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~  177 (811)
T KOG1929|consen  102 PGFFGLKVCLTGLSG-DEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEK  177 (811)
T ss_pred             CcccceEEEecccch-HHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcc
Confidence            357899999999864 48999999999999999999999999999988766 9999999999999999999987754

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=89.09  E-value=0.68  Score=50.58  Aligned_cols=55  Identities=18%  Similarity=0.165  Sum_probs=48.5

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccC
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT  517 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~  517 (687)
                      .||++++..++.|+++-.  |+..++.++.++|..++|+|++.|..|.+.+.+.+..
T Consensus       291 ~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~  345 (352)
T PRK13482        291 KIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQ  345 (352)
T ss_pred             cCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence            489999999999999864  9999999999999999999999999988887765443

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=88.74  E-value=0.26  Score=46.30  Aligned_cols=23  Identities=17%  Similarity=0.541  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11422        414 IPNICPICNSKIIYIESNLIARCSG  438 (687)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (687)
                      +-+|||.||+||.+..|  ..||++
T Consensus        27 L~~hCp~Cg~PLF~KdG--~v~CPv   49 (131)
T COG1645          27 LAKHCPKCGTPLFRKDG--EVFCPV   49 (131)
T ss_pred             HHhhCcccCCcceeeCC--eEECCC
Confidence            34799999999998655  569987

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=88.67  E-value=0.76  Score=49.33  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=45.5

Q ss_pred             CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .|||||+.++++|.+. |.++++|..++.++|.++.|+++..|+.+.+...
T Consensus         3 ~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~   53 (310)
T TIGR02236         3 DLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR   53 (310)
T ss_pred             ccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence            5799999999999987 9999999999999999999999988888877664

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.

>KOG0967|consensus

Probab=87.89  E-value=6.1  Score=46.07  Aligned_cols=179  Identities=17%  Similarity=0.234  Sum_probs=108.5

Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEE-eCCEEEEEEecCCCCccchhhhhhhhhcc-
Q psy11422         87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK-  164 (687)
Q Consensus        87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-  164 (687)
                      .|||.  |  -...+.+.++|.+       +..|+||+|.||=-..+.+ ++|. +...+|    .+|+.|....-|-. 
T Consensus       345 KPMLA--k--pTK~i~evl~rf~-------~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi~~~  408 (714)
T KOG0967|consen  345 KPMLA--K--PTKGIQEVLERFQ-------DKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDIIEV  408 (714)
T ss_pred             cchhc--C--cchhHHHHHHHhh-------CceeEEEeecCceeeeeEEccCCc-EEEEec----ccccccccCccHHHH
Confidence            48975  2  2235666777764       3589999999999999986 6776 688999    78888887654332 


Q ss_pred             CCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccccEEEEEecccccCC
Q psy11422        165 IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGM  243 (687)
Q Consensus       165 iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~-~~~r~l~f~~y~~~~~~~~  243 (687)
                      +++....  --..+.+-||++--..+    |.     ---+|.     +.-+=++++-.. ...-..+.|+|++....|.
T Consensus       409 ~~~~~kp--~v~sFIlD~EvVA~Dr~----~~-----~IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~ng~  472 (714)
T KOG0967|consen  409 ISKLKKP--SVKSFILDCEVVAWDRE----KG-----KILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLNGE  472 (714)
T ss_pred             HHHhhCC--ccceeEEeeeEEEEecc----CC-----ccCchh-----hhhhhhccccchhhceEEEEEEEEeeeeeCCh
Confidence            3322221  01478999999854322    10     012232     111112222211 1122578899998876654


Q ss_pred             CCC-CCHHHHHHHHHhcCCCCCCCceE-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11422        244 NMP-SSHSELLNWYQKIGLSICGEYSV-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC  303 (687)
Q Consensus       244 ~~~-~~~~e~l~~L~~~Gf~~~~~~~~-----~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (687)
                      .+. ..-.+.-+.|.+-+=.+..+..+     +.++++|..|.++..      +--.-|+-||+=|
T Consensus       473 ~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv------~~~cEGlMvKtLd  532 (714)
T KOG0967|consen  473 SLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESV------QNSCEGLMVKTLD  532 (714)
T ss_pred             hhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhh------ccCcceeEEEeec
Confidence            321 45667777777764444444444     356889999887543      3445789988865

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=87.67  E-value=0.7  Score=54.49  Aligned_cols=59  Identities=17%  Similarity=0.229  Sum_probs=50.2

Q ss_pred             cccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccC
Q psy11422        454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT  517 (687)
Q Consensus       454 F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~  517 (687)
                      +-| ...+|+|+|+++..+|++.-  .|+.+|..++.++|.++  +|++.|++|++.+..+-..
T Consensus       550 ~~S-~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~~~~  608 (624)
T PRK14669        550 RTS-ELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAV--VGRAAAEAIIAHFTTEEAA  608 (624)
T ss_pred             HHH-HHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence            334 36689999999999999975  59999999999999997  9999999999998755443

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=87.54  E-value=1  Score=48.82  Aligned_cols=54  Identities=22%  Similarity=0.246  Sum_probs=48.5

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      |.-.|||+.++++|-++|+ .|+.|+...+..+|..+.|+.+..+++|++...+.
T Consensus         4 ~~~~g~~~~~~~~L~~~g~-~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~   57 (313)
T TIGR02238         4 LQAHGINAADIKKLKSAGI-CTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI   57 (313)
T ss_pred             hhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence            3346899999999999995 89999999999999999999999999999987654

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.

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=87.38  E-value=0.82  Score=47.77  Aligned_cols=52  Identities=21%  Similarity=0.356  Sum_probs=46.5

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      +.|||+|++.+..|++.-  .|+.++++++.+.|..++|+|+|.|..|..-+..
T Consensus       185 ~s~pgig~~~a~~ll~~f--gS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t  236 (254)
T COG1948         185 ESIPGIGPKLAERLLKKF--GSVEDVLTASEEELMKVKGIGEKKAREIYRFLRT  236 (254)
T ss_pred             HcCCCccHHHHHHHHHHh--cCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhc
Confidence            579999999999999864  5899999999999999999999999999887753

>PTZ00035 Rad51 protein; Provisional

Probab=86.83  E-value=1.1  Score=48.95  Aligned_cols=55  Identities=24%  Similarity=0.232  Sum_probs=48.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      .+.-+||++.++++|-++|+ .|+.||...+..+|..+.|+++..|++|++...+.
T Consensus        25 ~l~~~g~~~~~~~kL~~~g~-~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~   79 (337)
T PTZ00035         25 KLQSAGINAADIKKLKEAGI-CTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL   79 (337)
T ss_pred             HHhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence            34458999999999999995 89999999999999999999999999999877653

>PRK01172 ski2-like helicase; Provisional

Probab=86.76  E-value=2.6  Score=50.35  Aligned_cols=55  Identities=22%  Similarity=0.311  Sum_probs=48.1

Q ss_pred             HHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       521 r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      ..+.-+.|||+|..+|++|.+. +.|+.++..++.+++.++.|+|++.|++|.+..
T Consensus       610 ~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~  665 (674)
T PRK01172        610 DLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA  665 (674)
T ss_pred             HHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence            4444458999999999988864 899999999999999999999999999998863

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=86.66  E-value=0.65  Score=34.48  Aligned_cols=28  Identities=21%  Similarity=0.510  Sum_probs=21.7

Q ss_pred             CCCCCCCCcceeecC--ceeEEecCCCCCCH
Q psy11422        416 NICPICNSKIIYIES--NLIARCSGSWIECI  444 (687)
Q Consensus       416 ~~CP~C~~~l~~~~~--~~~~~C~n~~~~C~  444 (687)
                      ..||.||++|+...+  +.++-|+|.+. |.
T Consensus         2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~-C~   31 (39)
T PF01396_consen    2 EKCPKCGGPLVLRRGKKGKFLGCSNYPE-CK   31 (39)
T ss_pred             cCCCCCCceeEEEECCCCCEEECCCCCC-cC
Confidence            369999999986533  57888999766 85

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>PRK00420 hypothetical protein; Validated

Probab=86.05  E-value=0.5  Score=43.39  Aligned_cols=24  Identities=17%  Similarity=0.534  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11422        414 IPNICPICNSKIIYIESNLIARCSG  438 (687)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (687)
                      +..+||.||+||.+..+ ...+|++
T Consensus        22 l~~~CP~Cg~pLf~lk~-g~~~Cp~   45 (112)
T PRK00420         22 LSKHCPVCGLPLFELKD-GEVVCPV   45 (112)
T ss_pred             ccCCCCCCCCcceecCC-CceECCC
Confidence            46899999999987433 3679987

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=86.02  E-value=1.3  Score=48.03  Aligned_cols=52  Identities=19%  Similarity=0.183  Sum_probs=46.3

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      +--+|.-.+..-|-.+| |.++.||..++.++|+++++||+||.+.|.+.+++
T Consensus       252 ~~L~LS~R~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~  303 (310)
T PRK05182        252 EELELSVRSYNCLKRAG-INTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE  303 (310)
T ss_pred             HHhccchHHHHHHHHcC-CcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence            33478888888888887 69999999999999999999999999999998876

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=85.53  E-value=0.77  Score=39.03  Aligned_cols=26  Identities=27%  Similarity=0.488  Sum_probs=23.9

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKA  552 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~A  552 (687)
                      ||||||+++|..|...|++++.+..+
T Consensus        26 gv~giG~k~A~~ll~~~~~~~~~~~~   51 (75)
T cd00080          26 GVPGIGPKTALKLLKEYGSLENLLEN   51 (75)
T ss_pred             CCCcccHHHHHHHHHHhCCHHHHHHH
Confidence            79999999999999999999988864

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=85.30  E-value=1.1  Score=52.22  Aligned_cols=119  Identities=17%  Similarity=0.199  Sum_probs=73.6

Q ss_pred             HHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhh
Q psy11422        372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL  451 (687)
Q Consensus       372 ~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i  451 (687)
                      +.++++||.+- .|-|.|.-+      ..+..   +...++.+|..-|.=. -|.+.-++++.|-... +    +..+.=
T Consensus       462 ~vl~~l~~~~~-viglaK~~~------~~~~~---~~~~~~~l~~~~p~l~-~lq~irDEaHrfAi~~-h----R~~R~k  525 (581)
T COG0322         462 EVLKELGLDIP-VIGLAKGEE------ELLLP---GPGEEFDLPPNSPALY-LLQRIRDEAHRFAITY-H----RKKRSK  525 (581)
T ss_pred             HHHHHcCCCcc-EEEEEecCc------eeEec---CCCceecCCCCCHHHH-HHHHHHHHHHHHHHHH-H----HHHhhh
Confidence            44566666544 555555444      11111   1223455555333210 0112234455554442 2    333333


Q ss_pred             hhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11422        452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (687)
Q Consensus       452 ~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~  510 (687)
                      .++-| ...+|+|+|+++.++|.+.-  .|+.++..++.++|..+ |++++.|++|.+.
T Consensus       526 ~~~~s-~Ld~I~GiG~~r~~~LL~~F--gs~~~i~~As~eel~~v-gi~~~~a~~i~~~  580 (581)
T COG0322         526 AMLQS-SLDDIPGIGPKRRKALLKHF--GSLKGIKSASVEELAKV-GISKKLAEKIYEA  580 (581)
T ss_pred             hhhcC-ccccCCCcCHHHHHHHHHHh--hCHHHHHhcCHHHHHHc-CCCHHHHHHHHhh
Confidence            44444 46789999999999999865  48999999999999999 9999999999865

>PRK10736 hypothetical protein; Provisional

Probab=85.30  E-value=5.8  Score=44.06  Aligned_cols=113  Identities=9%  Similarity=0.102  Sum_probs=70.7

Q ss_pred             HHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCC--
Q psy11422        522 FIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN--  599 (687)
Q Consensus       522 ~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~--  599 (687)
                      +|.-..+||+|..+.++|.++|++..   .++.++|... |++++.+..+.++ ......+.++.+.+.|+.+-....  
T Consensus         7 ~l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~i~~~d~~   81 (374)
T PRK10736          7 WLRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQL-PRKSLESTLRWLEQPNHHLLTADSEF   81 (374)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhcc-CHHHHHHHHHHHHhcCCEEEccCchh
Confidence            34444789999999999999999887   4677888776 8999888888654 333334456667677776432100  


Q ss_pred             ----------CC------CCCCccCCeEEEEEcCCCc--CCHHHHHHH---HHhcCCEEcc
Q psy11422        600 ----------TK------GNKNYLKEKIFVFTGSLYA--FKRNEAIIL---IENLGGKVVN  639 (687)
Q Consensus       600 ----------~~------~~~~~l~g~~vv~TG~l~~--~~R~e~~~~---i~~~Gg~v~~  639 (687)
                                ..      ..-..+....|.+.|+-..  +.+.-++.+   +.+.|..|+|
T Consensus        82 YP~~L~~i~dpP~vLf~~G~~~~l~~~~iaiVGsR~~s~yg~~~~~~l~~~la~~g~~IVS  142 (374)
T PRK10736         82 YPPQLLAIADYPGALFVSGELAALHSPQLAVVGSRAHSWYGERWGRLFCEELAKNGLTITS  142 (374)
T ss_pred             chHHHhhCCCCCeEEEEeCCHHHccCCeEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEC
Confidence                      00      1111345578999999652  223333333   3344766666

>KOG3226|consensus

Probab=85.07  E-value=2.4  Score=46.18  Aligned_cols=71  Identities=15%  Similarity=0.085  Sum_probs=65.2

Q ss_pred             ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHH
Q psy11422        606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKI  677 (687)
Q Consensus       606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~  677 (687)
                      .|+|-.||++|.-. -.|.++...+-.+|++..-.-+...+.|||.-...-|+.+-+-+|=.||+-++..+.
T Consensus       317 lL~GVV~VlSGfqN-P~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~C  387 (508)
T KOG3226|consen  317 LLEGVVFVLSGFQN-PERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITEC  387 (508)
T ss_pred             hhhceEEEEecccC-chHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHH
Confidence            57999999999875 589999999999999999999999999999988789999999999999999988754

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=84.77  E-value=1.5  Score=47.14  Aligned_cols=53  Identities=17%  Similarity=0.201  Sum_probs=46.2

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ++--+|.-.+..-|-.+| |.++.||..++.++|+++++||+||.+.|.+.+++
T Consensus       237 I~~L~LSvR~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~~  289 (297)
T TIGR02027       237 IEELDLSVRSYNCLKRAG-IHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAE  289 (297)
T ss_pred             HHHhCccHHHHhHHHHcC-CcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHHH
Confidence            444567788888888887 69999999999999999999999999999988765

This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=84.71  E-value=1.5  Score=47.30  Aligned_cols=50  Identities=24%  Similarity=0.372  Sum_probs=44.3

Q ss_pred             CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+||||++++++|.+. |.++++|..++.++|.++.|+++..|+.+.+..+
T Consensus        10 ~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~   60 (317)
T PRK04301         10 DLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAR   60 (317)
T ss_pred             hcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence            5799999999988876 8999999999999999999999999998887554

>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]

Probab=84.42  E-value=5.2  Score=40.54  Aligned_cols=107  Identities=19%  Similarity=0.276  Sum_probs=54.8

Q ss_pred             HHHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHH----------HHHHHcccCCHHHHHHHcCCCCCCH
Q psy11422        467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNIL----------LAIQKSKLTTFSRFIYALGIRHVGE  533 (687)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll----------~~Ie~sk~~~l~r~L~aLGIp~vG~  533 (687)
                      ++-++.|-.++. -++..|..++.++|..+   -||=..+|..|.          .+++..++..++..|  |+|.|||+
T Consensus        49 ekAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R~~L--L~iKGIG~  125 (215)
T COG2231          49 EKALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREEL--LSIKGIGK  125 (215)
T ss_pred             HHHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHHHHH--HccCCcch
Confidence            455666666664 45777777777666554   567666666652          222222222233444  56777777


Q ss_pred             HHHHHHHhhc-CChHHHHhc-CHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        534 TTAKELANYF-KNLECMFKA-TEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       534 ~~Ak~La~~f-~sld~l~~A-s~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+|..|+-+. ....-+.++ +..=+..+-++-++.-+.|+.+|.
T Consensus       126 ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe  170 (215)
T COG2231         126 ETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFE  170 (215)
T ss_pred             hhHHHHHHHHhcCcccchhHHHHHHHHHhcccccccHHHHHHHHH
Confidence            7776665442 211112211 122233444444444555666664

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=84.34  E-value=0.66  Score=54.27  Aligned_cols=30  Identities=37%  Similarity=0.534  Sum_probs=28.4

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHH
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQ  556 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~ee  556 (687)
                      +|||||+++.+.|+++|||++++..||.++
T Consensus       545 ~I~GIG~kr~~~LL~~Fgs~~~i~~As~ee  574 (574)
T TIGR00194       545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE  574 (574)
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCccC
Confidence            899999999999999999999999999764

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=84.13  E-value=1.6  Score=47.88  Aligned_cols=56  Identities=25%  Similarity=0.231  Sum_probs=49.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      +.|.=.||++.++++|-++|+ .|+.||...+..+|..+.|+.+..|.+|++...+.
T Consensus        32 ~~l~~~g~~~~~~~kL~~~g~-~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~   87 (344)
T PLN03187         32 DKLISQGINAGDVKKLQDAGI-YTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL   87 (344)
T ss_pred             HHHhhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence            344458899999999999995 89999999999999999999999999999876553

>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

Probab=84.06  E-value=3.4  Score=39.67  Aligned_cols=23  Identities=30%  Similarity=0.629  Sum_probs=18.2

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        553 TEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       553 s~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      ..++|.+++|||+++|+.+.-|-
T Consensus        81 ~~~~L~~l~GIG~~tA~~~l~~~  103 (158)
T cd00056          81 AREELLALPGVGRKTANVVLLFA  103 (158)
T ss_pred             cHHHHHcCCCCCHHHHHHHHHHH
Confidence            35778889999999888877654

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=83.93  E-value=0.8  Score=30.72  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=13.4

Q ss_pred             hhhcccCccHHHHHHHHH
Q psy11422        492 NLLRLDRVSNKLANNILL  509 (687)
Q Consensus       492 ~L~~l~gfG~Ksa~~Ll~  509 (687)
                      +|.+++|+|+|+|++|++
T Consensus         2 ~L~~i~GiG~k~A~~il~   19 (26)
T smart00278        2 ELLKVPGIGPKTAEKILE   19 (26)
T ss_pred             hhhhCCCCCHHHHHHHHH
Confidence            466777888887777775

>PRK13766 Hef nuclease; Provisional

Probab=83.31  E-value=1.7  Score=52.65  Aligned_cols=51  Identities=12%  Similarity=0.212  Sum_probs=44.2

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .|+|+|++++.+|++.-  .++.+++.++.++|..++|+|++.|+.|.+.++.
T Consensus       719 ~ipgig~~~a~~Ll~~f--gs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~  769 (773)
T PRK13766        719 SLPDVGPVLARNLLEHF--GSVEAVMTASEEELMEVEGIGEKTAKRIREVVTS  769 (773)
T ss_pred             cCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhh
Confidence            68999999999999863  5899999999999999999999999998887764

>smart00478 ENDO3c endonuclease III

Probab=83.24  E-value=5.2  Score=38.00  Aligned_cols=66  Identities=23%  Similarity=0.329  Sum_probs=40.3

Q ss_pred             ChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhc-CChHHHHhcCHHH
Q psy11422        481 TAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF-KNLECMFKATEEQ  556 (687)
Q Consensus       481 ~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f-~sld~l~~As~ee  556 (687)
                      ++.+|..++.++|..+   -||....|+.|.+..+.                         +.+.+ +.++    ...++
T Consensus        23 ~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~-------------------------~~~~~~~~~~----~~~~~   73 (149)
T smart00478       23 TPEDLAAADEEELEELIRPLGFYRRKAKYLIELARI-------------------------LVEEYGGEVP----DDREE   73 (149)
T ss_pred             CHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHH-------------------------HHHHHCCCcc----HHHHH
Confidence            7888888888776332   27877888877754322                         11111 1111    13466


Q ss_pred             HhcCCCCCHHHHHHHHHHH
Q psy11422        557 LLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       557 L~~I~GIG~~~A~sI~~ff  575 (687)
                      |.+++|||+++|+.+.-|-
T Consensus        74 L~~l~GIG~~tA~~~l~~~   92 (149)
T smart00478       74 LLKLPGVGRKTANAVLSFA   92 (149)
T ss_pred             HHcCCCCcHHHHHHHHHHH
Confidence            7788888888888766543

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=83.17  E-value=1.3  Score=52.27  Aligned_cols=49  Identities=24%  Similarity=0.303  Sum_probs=44.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      ..+|+|+|+++...|.+.-  .|+.+|..++.++|.++  +|++.|++|.+.+
T Consensus       571 L~~I~GIG~k~a~~Ll~~F--gs~~~i~~As~eeL~~v--ig~k~A~~I~~~~  619 (621)
T PRK14671        571 LTDIAGIGEKTAEKLLEHF--GSVEKVAKASLEELAAV--AGPKTAETIYRYY  619 (621)
T ss_pred             hhcCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHh
Confidence            5689999999999999875  48899999999999998  9999999998875

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=83.11  E-value=3.4  Score=31.59  Aligned_cols=41  Identities=27%  Similarity=0.328  Sum_probs=33.7

Q ss_pred             HHHHHHHH-hhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11422        533 ETTAKELA-NYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       533 ~~~Ak~La-~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~  573 (687)
                      +..+..|. +.|.+++.+..++.++|..++|+++..+..+..
T Consensus         3 ~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~   44 (50)
T TIGR01954         3 EEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELIN   44 (50)
T ss_pred             HHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHH
Confidence            44555555 458999999999999999999999988887764

NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=82.56  E-value=1  Score=33.96  Aligned_cols=24  Identities=17%  Similarity=0.513  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11422        414 IPNICPICNSKIIYIESNLIARCSG  438 (687)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (687)
                      +-++||.||.||.+..++ ..+|++
T Consensus        16 L~~~Cp~C~~PL~~~k~g-~~~Cv~   39 (41)
T PF06677_consen   16 LDEHCPDCGTPLMRDKDG-KIYCVS   39 (41)
T ss_pred             hcCccCCCCCeeEEecCC-CEECCC
Confidence            457999999999985443 568976

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>KOG2841|consensus

Probab=82.42  E-value=1.8  Score=44.60  Aligned_cols=59  Identities=14%  Similarity=0.113  Sum_probs=51.1

Q ss_pred             hhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       449 ~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .++.+|..    .|+|++.--+..|...-  -|+..|.....++|...+|+|+.+|++|++.+..
T Consensus       191 s~~~~~Lt----~i~~VnKtda~~LL~~F--gsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~  249 (254)
T KOG2841|consen  191 SSLLGFLT----TIPGVNKTDAQLLLQKF--GSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ  249 (254)
T ss_pred             HHHHHHHH----hCCCCCcccHHHHHHhc--ccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence            36777764    79999999999888754  3889999999999999999999999999998864

>smart00483 POLXc DNA polymerase X family

Probab=82.05  E-value=0.62  Score=50.92  Aligned_cols=29  Identities=28%  Similarity=0.285  Sum_probs=26.1

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcC
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI  488 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L  488 (687)
                      .++|+|+||+++.+||+ ..|+|++||...
T Consensus        91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a  119 (334)
T smart00483       91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKN  119 (334)
T ss_pred             HHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence            46899999999999999 668999999874

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=81.93  E-value=5.2  Score=42.58  Aligned_cols=69  Identities=20%  Similarity=0.189  Sum_probs=38.3

Q ss_pred             HHHHHHHCCCCCChHHHhcCChhhhhcc-c--CccHHHHHHHHHHHHHccc---CCHHHHHHH-cCCCCCCHHHHHHHH
Q psy11422        469 MIEKLVNANIVVTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELA  540 (687)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~Ll~~Ie~sk~---~~l~r~L~a-LGIp~vG~~~Ak~La  540 (687)
                      ...+|++.  .-|+.+|..++.++|.++ .  |+- ..|.+|.+..+.-.+   ..+..-... +.+||||+.+|..++
T Consensus        47 ~~~rl~~~--fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il  122 (275)
T TIGR01084        47 YFERFLER--FPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAIL  122 (275)
T ss_pred             HHHHHHHh--CCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHH
Confidence            44445543  368999999998888443 2  554 357677665443211   111122222 366777777766554

This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=81.92  E-value=1  Score=37.01  Aligned_cols=30  Identities=27%  Similarity=0.491  Sum_probs=22.3

Q ss_pred             HHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        548 CMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       548 ~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      ++..|+.++|.++||||+..|++|.+|-..
T Consensus         7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~   36 (65)
T PF12836_consen    7 DINTASAEELQALPGIGPKQAKAIVEYREK   36 (65)
T ss_dssp             ETTTS-HHHHHTSTT--HHHHHHHHHHHHH
T ss_pred             cCccCCHHHHHHcCCCCHHHHHHHHHHHHh
Confidence            356788999999999999999999987543

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=81.72  E-value=0.9  Score=43.91  Aligned_cols=43  Identities=21%  Similarity=0.288  Sum_probs=33.4

Q ss_pred             HHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHh
Q psy11422        547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRD  589 (687)
Q Consensus       547 d~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~  589 (687)
                      =++..||.++|..++|||++.|+.|.+|-.......-++.|..
T Consensus        89 vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~  131 (149)
T COG1555          89 VNINTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK  131 (149)
T ss_pred             ccccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence            3678899999999999999999999998754433344666644

>PRK09482 flap endonuclease-like protein; Provisional

Probab=81.65  E-value=1.7  Score=45.82  Aligned_cols=26  Identities=35%  Similarity=0.709  Sum_probs=23.4

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKA  552 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~A  552 (687)
                      |+||||+++|..|++.|++++.+...
T Consensus       186 GVpGIG~KtA~~LL~~~gsle~i~~~  211 (256)
T PRK09482        186 GVAGIGPKSAAELLNQFRSLENIYES  211 (256)
T ss_pred             CCCCcChHHHHHHHHHhCCHHHHHHh
Confidence            78999999999999999999999753

>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate

Probab=80.96  E-value=4.5  Score=40.31  Aligned_cols=139  Identities=17%  Similarity=0.145  Sum_probs=76.4

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc--cCCccccc--CCCCceEEEEEEEEeehhhHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH--KIPLVLNI--KYPPELLEVRCEVLIYKKDFIKL  194 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~--~iP~~l~~--~~~~~~~evRGEi~~~~~~F~~~  194 (687)
                      .|+|.+|-||+-.-|...++ =+-++.|-         .++..+.  ..|.....  ........+-||+++....    
T Consensus        17 ~Y~V~eKaDG~Ryll~i~~~-~~ylidr~---------~~~~~v~~~~~p~~~~~~~~~~~~~TLLDGElV~d~~~----   82 (192)
T PF01331_consen   17 DYFVCEKADGTRYLLLITDN-GVYLIDRK---------NNVFKVDNLHFPSKKDSSDGRHHQDTLLDGELVLDKDP----   82 (192)
T ss_dssp             -EEEEEEESSEEEEEEEEEE-EEEEEETT---------S-EEEESSST-ECTTC--TTCEGCSEEEEEEEEEEECT----
T ss_pred             CcEEEECCCCcEEEEEEecc-eEEEEeCC---------CcEEEecCcccccccccccccccCCEEEEEEEEcccCC----
Confidence            69999999999997755443 23455553         3444444  24444320  0123468899999987432    


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc------------CC
Q psy11422        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI------------GL  261 (687)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~------------Gf  261 (687)
                                                  .   .+.+.|.+|++...+|... -....++|.+|++.            |-
T Consensus        83 ----------------------------~---~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~  131 (192)
T PF01331_consen   83 ----------------------------G---EKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGI  131 (192)
T ss_dssp             ----------------------------T---CEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTS
T ss_pred             ----------------------------C---CCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhcccccc
Confidence                                        0   2358999999887666432 13455666666421            10


Q ss_pred             -CC--CCCceEeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECCh
Q psy11422        262 -SI--CGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCL  304 (687)
Q Consensus       262 -~~--~~~~~~~~~~---~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~  304 (687)
                       ..  .+.......+   ..+....  .......+++++||+|+.=++.
T Consensus       132 ~~~~~~pf~i~~K~~~~~~~~~~~~--~~~~~~~l~h~~DGLIFtp~~~  178 (192)
T PF01331_consen  132 IKKKKEPFSIRIKDFFPIYQIEKLL--FEEFIPKLPHETDGLIFTPVNT  178 (192)
T ss_dssp             CTCTTSSSEEEE---EEGGGHHHHC--HHCCCCCTTSTEEEEEEEESSS
T ss_pred             ccccccceeeeccccHHHHhhHHHH--HHHhhccCCCCCCEEEEecCCC
Confidence             00  1111111111   2222211  3456788999999999987764

X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=80.78  E-value=2.4  Score=45.79  Aligned_cols=34  Identities=26%  Similarity=0.481  Sum_probs=25.2

Q ss_pred             CCCCCCCCC-cceeecCceeEEecCCCCCCHHHHHhhhh
Q psy11422        415 PNICPICNS-KIIYIESNLIARCSGSWIECIAQRKAGLQ  452 (687)
Q Consensus       415 P~~CP~C~~-~l~~~~~~~~~~C~n~~~~C~~q~~~~i~  452 (687)
                      +..||.||+ .++.+.....+.|.+    |-.-+-.++.
T Consensus        11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~----CG~Vl~e~~i   45 (310)
T PRK00423         11 KLVCPECGSDKLIYDYERGEIVCAD----CGLVIEENII   45 (310)
T ss_pred             CCcCcCCCCCCeeEECCCCeEeecc----cCCccccccc
Confidence            457999998 565555667899987    8766666665

>TIGR01083 nth endonuclease III

Probab=80.46  E-value=7.8  Score=38.77  Aligned_cols=76  Identities=17%  Similarity=0.244  Sum_probs=45.1

Q ss_pred             HHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC-
Q psy11422        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK-  544 (687)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~-  544 (687)
                      ...+|++. + .++.+|..++.++|.++   -||-..+|+.|.+-.+...                         +.|+ 
T Consensus        47 ~~~~l~~~-~-pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~-------------------------~~~~~   99 (191)
T TIGR01083        47 ATKKLFEV-Y-PTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILV-------------------------ERYGG   99 (191)
T ss_pred             HHHHHHHH-C-CCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHH-------------------------HHcCC
Confidence            34445543 2 48889998888887432   3776677777765433211                         1111 


Q ss_pred             ChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        545 NLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       545 sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .++.    +.++|.+++|||+++|..+.-|-
T Consensus       100 ~~~~----~~~~L~~l~GIG~ktA~~ill~~  126 (191)
T TIGR01083       100 EVPE----DREELVKLPGVGRKTANVVLNVA  126 (191)
T ss_pred             CCch----HHHHHHhCCCCcHHHHHHHHHHH
Confidence            1111    24678888888888888776654

This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.

>TIGR03491 RecB family nuclease, putative, TM0106 family

Probab=80.42  E-value=3.4  Score=47.09  Aligned_cols=65  Identities=17%  Similarity=0.179  Sum_probs=52.4

Q ss_pred             CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      |-+...+.      ++...++|++.+....|.++| |.|+.||-......|..+++++..++.+|..+.+..
T Consensus       199 C~~~~~~~------~~lslv~gi~~~~~~~L~~~G-I~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~a~  263 (457)
T TIGR03491       199 CEAVAKEE------GHLSLVPGIGPSRYRLLQELG-IHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARAQ  263 (457)
T ss_pred             HHHHHHhc------CCeeecCCCCHHHHHHHHHcC-CCcHHHHhcCCccccccccccCHHHHHHHHHHHHHH
Confidence            76655432      345579999999999999999 699999999876678888899999999988766543

Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.

>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]

Probab=80.41  E-value=3  Score=44.23  Aligned_cols=99  Identities=16%  Similarity=0.211  Sum_probs=61.8

Q ss_pred             EecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC--hhhhhcccCccHHHHHHHHHHHH
Q psy11422        435 RCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN--FKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       435 ~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~--~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ||.+... -+.-.++.|.+|.+++.||     +..|.+++--.-..++.|-+-..  .--|.++|++-..-++|++..+.
T Consensus       241 Y~~~~e~-d~~~~l~~l~~ls~~~lL~-----~~~i~kvlGY~~~~~~~d~~vspRGYR~l~kIpRlp~~iv~nlV~~F~  314 (349)
T COG1623         241 YHKEDEV-DIEAVLEELQSLSDEELLD-----PENIAKVLGYPKTTEADDSLVSPRGYRLLNKIPRLPFAIVENLVRAFG  314 (349)
T ss_pred             HhcCccc-CHHHHHHHHHhccchhhCC-----HHHHHHHhCCCCcchhcccccCchhhHHHhcCcCccHHHHHHHHHHHh
Confidence            5666433 6777888899988776654     66666666433333333311111  23477788888888888888775


Q ss_pred             HcccCCHHHHHHHc-----CCCCCCHHHHHHHHhhcC
Q psy11422        513 KSKLTTFSRFIYAL-----GIRHVGETTAKELANYFK  544 (687)
Q Consensus       513 ~sk~~~l~r~L~aL-----GIp~vG~~~Ak~La~~f~  544 (687)
                      .     |.+++.|.     .+.|||+..|+.|.+..+
T Consensus       315 ~-----l~~il~As~edL~~VeGIGe~rAr~i~~Gl~  346 (349)
T COG1623         315 T-----LDGILEASAEDLDAVEGIGEARARAIKEGLS  346 (349)
T ss_pred             h-----HHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence            4     34555543     567888888887775543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	687
2owo_A	671	Last Stop On The Road To Repair: Structure Of E.Col		1e-151
4glx_A	586	Dna Ligase A In Complex With Inhibitor Length = 586		1e-138
1dgs_A	667	Crystal Structure Of Nad+-Dependent Dna Ligase From		1e-109
1v9p_A	584	Crystal Structure Of Nad+-Dependent Dna Ligase Leng		1e-103
3sgi_A	615	Crystal Structure Of Dna Ligase A Brct Domain Delet		1e-103
3uq8_A	322	Structure Of Adenylation Domain Of Haemophilus Infl		1e-63
1b04_A	318	Structure Of The Adenylation Domain Of An Nad+ Depe		3e-63
3pn1_A	318	Novel Bacterial Nad+-Dependent Dna Ligase Inhibitor		3e-63
3jsl_A	318	Crystal Structure Of The Adenylation Domain Of Nad+		1e-55
1ta8_A	332	Structural Rearrangement Accompanying Nad+ Synthesi		4e-54
1tae_A	332	Structural Rearrangement Accompanying Nad+ Synthesi		5e-54
1zau_A	328	Adenylation Domain Of Nad+ Dependent Dna Ligase Fro		7e-53
3bac_A	270	Structural Basis For The Inhibition Of Bacterial Na		3e-51
4glw_A	305	Dna Ligase A In Complex With Inhibitor Length = 305		9e-46
2ebu_A	112	Solution Structure Of The Brct Domain From Human Re		4e-11
2k7f_A	109	Haddock Calculated Model Of The Complex Between The		5e-11
1l7b_A	92	Solution Nmr Structure Of Brct Domain Of T. Thermop		3e-07

>pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna Ligase Bound To Nicked Dna-Adenylate Length = 671

Iteration: 1
 Score =  531 bits (1369), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 269/665 (40%), Positives = 402/665 (60%), Gaps = 5/665 (0%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           ++TEL+  L  H   Y++ D P I D +YD+L+ EL+++E K+PEL+T DS TQ VG   
Sbjct: 7   QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAP 66
Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                 + H   M+SLDN F +E  + FNKR+ + LK  + + +  ELK DG+AV++ YE
Sbjct: 67  LAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYE 126
Query: 137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L  A+TRGD                 PL L+ +  P  LEVR EV + +  F K+N+
Sbjct: 127 NGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINE 186
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G K F NPRNAAAG LRQL+P+I   + L FF +GVG L G  +P +H   L  +
Sbjct: 187 DARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQF 246
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +K GL +    ++     +++ FY K+   R  L ++IDGVV K+N L+ Q++LGF +RA
Sbjct: 247 KKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARA 306
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+A+KF ++E +T ++ +  Q+GRTG ITPVA L+PV + G+ ++ ATLHN  EI R
Sbjct: 307 PRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIER 366
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
             ++IGD VV+ R+G+VIP++ + +LS RP D++    P  CP+C S +  +E   +ARC
Sbjct: 367 LGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARC 426
Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           +G  I C AQRK  L+HF SR+AM++ G+G K+I++LV    V T  DL+K+    L  L
Sbjct: 427 TGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGL 485
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           +R+  K A N++ A++K+K TTF+RF+YALGIR VGE TA  LA YF  LE +  A+ E+
Sbjct: 486 ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEE 545
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNP---NTKGNKNYLKEKIFV 613
           L  +P +G         F  +  +R +IS+L   G++W   P   N +   +    K  V
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHW-PAPIVINAEEIDSPFAGKTVV 604
Query: 614 FTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKN 673
            TGSL    R++A   +  LG KV   +SK T+ ++ G+  G KL KA +L I+++DE  
Sbjct: 605 LTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAE 664
Query: 674 FVKIV 678
            ++++
Sbjct: 665 MLRLL 669

>pdb|4GLX|A Chain A, Dna Ligase A In Complex With Inhibitor Length = 586

Iteration: 1
 Score =  489 bits (1260), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 242/578 (41%), Positives = 357/578 (61%), Gaps = 1/578 (0%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           ++TEL+  L  H   Y++ D P I D +YD+L+ EL+++E K+PEL+T DS TQ VG   
Sbjct: 7   QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAP 66
Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                 + H   M+SLDN F +E  + FNKR+ + LK  + + +  ELK DG+AV++ YE
Sbjct: 67  LAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYE 126
Query: 137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L  A+TRGD                 PL L+ +  P  LEVR EV + +  F K+N+
Sbjct: 127 NGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINE 186
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G K F NPRNAAAG LRQL+P+I   + L FF +GVG L G  +P +H   L  +
Sbjct: 187 DARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQF 246
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +K GL +    ++     +++ FY K+   R  L ++IDGVV K+N L+ Q++LGF +RA
Sbjct: 247 KKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARA 306
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+A+KF ++E +T ++ +  Q+GRTG ITPVA L+PV + G+ ++ ATLHN  EI R
Sbjct: 307 PRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIER 366
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
             ++IGD VV+ R+G+VIP++ + +LS RP D++    P  CP+C S +  +E   +ARC
Sbjct: 367 LGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARC 426
Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           +G  I C AQRK  L+HF SR+AM++ G+G K+I++LV    V T  DL+K+    L  L
Sbjct: 427 TGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGL 485
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           +R+  K A N++ A++K+K TTF+RF+YALGIR VGE TA  LA YF  LE +  A+ E+
Sbjct: 486 ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEE 545
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594
           L  +P +G         F  +  +R +IS+L   G++W
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHW 583

>pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T. Filiformis Length = 667

Iteration: 1
 Score =  392 bits (1006), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 249/669 (37%), Positives = 383/669 (57%), Gaps = 24/669 (3%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R+ EL+  +  HN  YY+  +P ISD +YD+LL ELK++EE++PE  + DS T+ VG   
Sbjct: 9   RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARP 68
Query: 77  GENS-KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
            E + + V H  +M SLDN F+ E+V+ F +R+  E +      Y  E K DG++V L Y
Sbjct: 69  LEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSL--YTVEHKVDGLSV-LYY 125
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
           E G     S  GD                 P    +K  P+ LEVR EV +  + F++LN
Sbjct: 126 EEGVWSTGS--GDGEVGEEVTQNLLTIPTIPR--RLKGVPDRLEVRGEVYMPIEAFLRLN 181
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILH--FFAHGVG---ELRGMNMPSSHS 250
           +     G K F NPRNAAAG LRQ +P++   + L   F+A G+G   E  G+    S  
Sbjct: 182 EELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLK---SQY 238
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
           ELL W ++ G  +   Y    G   + E Y++   +R  LP+E DGVV K++ L+   +L
Sbjct: 239 ELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGEL 298
Query: 311 GFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHN 370
           G+T+RAPRFALAYKF ++E  T++  +  Q+GRTG +TPV +L+PV I+G  ++R TLHN
Sbjct: 299 GYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHN 358
Query: 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIES 430
           ES I   +I+IGD V+VH++G VIP++   +   R    +  + P  CP C  ++  ++ 
Sbjct: 359 ESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRL--VKE 416
Query: 431 NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490
             + RC      C A+R   ++H++SRKAM+I GLG+K+IE+L+   +V    DLY +  
Sbjct: 417 GKVHRCPNPL--CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRK 474
Query: 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF 550
           ++LL L+R+  K A N+L  I++SK     R +YALG+  VGE  A+ LA  F  ++ + 
Sbjct: 475 EDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLL 534
Query: 551 KATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEK 610
           +A+ E+L+ + ++G  T +A ++ +  P  R L+ +L++ G+   +        + L   
Sbjct: 535 EASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEV---SDLLSGL 591
Query: 611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 670
            FV TG L +  R E   L+  LG KV + +S+ T+YLV G+ PG KLEKA  L + +L 
Sbjct: 592 TFVLTGEL-SRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLT 650
Query: 671 EKNFVKIVK 679
           E+ F + +K
Sbjct: 651 EEEFWRFLK 659

>pdb|1V9P|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase Length = 584

Iteration: 1
 Score =  373 bits (957), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 222/580 (38%), Positives = 344/580 (59%), Gaps = 13/580 (2%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R+ EL+  +  HN  YY+  +P ISD +YD+LL ELK++EE++PE  + DS T+ VG   
Sbjct: 9   RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARP 68
Query: 77  GENS-KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
            E + + V H  +M SLDN F+ E+V+ F +R+   L   +   Y  E K DG++VNL Y
Sbjct: 69  LEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYY 128
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
           E G L   +TRGD                 P    +K  P+ LEVR EV +  + F++LN
Sbjct: 129 EEGVLVFGATRGDGEVGEEVTQNLLTIPTIPR--RLKGVPDRLEVRGEVYMPIEAFLRLN 186
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILH--FFAHGVG-ELRGMNMPSSHSEL 252
           +     G K F NPRNAAAG LRQ +P++   + L   F+A G+G E  G+    S  EL
Sbjct: 187 EELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLEESGLK---SQYEL 243
Query: 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGF 312
           L W ++ G  +   Y    G   + E Y++   +R  LP+E DGVV K++ L+  ++LG+
Sbjct: 244 LLWLKEKGFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRELGY 303
Query: 313 TSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNES 372
           T+RAPRFALAYKF ++E  T++  +  Q+GRTG +TPV +L+PV I+G  ++R TLHNES
Sbjct: 304 TARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES 363
Query: 373 EIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNL 432
            I   +I+IGD V+VH++G VIP++   +   R  + +  + P  CP C  ++  ++   
Sbjct: 364 YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEERPIRWPETCPECGHRL--VKEGK 421
Query: 433 IARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKN 492
           + RC      C A+R   ++H++SRKAM+I GLG+K+IE+L+   +V    DLY +  ++
Sbjct: 422 VHRCPNPL--CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKED 479
Query: 493 LLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA 552
           LL L+R+  K A N+L  I++SK     R +YALG+  VGE  A+ LA  F  ++ + +A
Sbjct: 480 LLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEA 539
Query: 553 TEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
           + E+LL + ++G  T +A ++ +  P  R L+ +L++ G+
Sbjct: 540 SLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGV 579

>pdb|3SGI|A Chain A, Crystal Structure Of Dna Ligase A Brct Domain Deleted Mutant Of Mycobacterium Tuberculosis Length = 615

Iteration: 1
 Score =  372 bits (956), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 210/586 (35%), Positives = 320/586 (54%), Gaps = 21/586 (3%)
Query: 21  LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GEN 79
           L +E+  H   YY+ D PIISD ++D+LL  L+ +EE++PEL T DS TQ VG  G   +
Sbjct: 20  LAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATD 79
Query: 80  SKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGY 139
            + V H  +M+SLDN F+ +++  +  RI  E+    +  Y+ ELK DG+A++L Y  G 
Sbjct: 80  FEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGR 137
Query: 140 LKQASTRGDXXXXXXXXXXXXXXXXXP--LVLNIKYP-PELLEVRCEVLIYKKDFIKLNK 196
           L +ASTRGD                 P  L     YP PE+LEVR EV     DF  LN 
Sbjct: 138 LTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNA 197
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G   F NPRN+AAG LRQ +P +   + L    HG+G + G    + H   L   
Sbjct: 198 SLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLA-L 256
Query: 257 QKIGLSICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
           +  GL +    ++   L+GV + I+++ +    R  + +EIDGVV K++ ++ Q++LG T
Sbjct: 257 RAWGLPVSEHTTLATDLAGVRERIDYWGE---HRHEVDHEIDGVVVKVDEVALQRRLGST 313
Query: 314 SRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESE 373
           SRAPR+A+AYK+  +EA TK+  I + +GRTG ITP A + PV + G T+ +ATLHN SE
Sbjct: 314 SRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASE 373
Query: 374 IYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII-YIESNL 432
           I RK + IGDTVV+ ++G+VIP++   ++ LR    + F +P  CP C S +    E + 
Sbjct: 374 IKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDA 433
Query: 433 IARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKN 492
             RC  +   C  Q +  + H +SR  ++I  LG +    L+ A ++    +L+ +  ++
Sbjct: 434 DIRCPNA-RGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERD 492
Query: 493 LLRLDRVSNKLAN------NILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
           LLR D    K          +L+ + K+K     R + AL IRHVG T A+ LA  F +L
Sbjct: 493 LLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSL 552
Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
           + +  A+ +QL  +  +G T   A  ++     HR ++ + R  G+
Sbjct: 553 DAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGV 598

>pdb|3UQ8|A Chain A, Structure Of Adenylation Domain Of Haemophilus Influenzae Dna Ligases Bound To Nad+ In Adenylated State Length = 322

Iteration: 1
 Score =  241 bits (615), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 128/317 (40%), Positives = 184/317 (58%), Gaps = 1/317 (0%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           ++  L+K L ++   Y++ DNP + D++YD+L  +LK +E ++PE LT DS TQ VG   
Sbjct: 5   QLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKP 64
Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGIAVNLRY 135
                 + H   M+SLDN FSD +   F  RI + L  L   + +  E K DG+AV++ Y
Sbjct: 65  LSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILY 124
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
             G L QA+TRGD                 PL L    PP  LEVR EV +    F +LN
Sbjct: 125 VNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLN 184
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
           KY      K F NPRNAAAG LRQL+P I   + L   A+G+G   G+++P++H   L W
Sbjct: 185 KYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQW 244
Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
            + IG+ +  E  + +G ++++ FY+ I  KR +L Y+IDG V KIN ++ Q +LGF S+
Sbjct: 245 LKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISK 304
Query: 316 APRFALAYKFLSKEALT 332
           APR+A+AYKF ++E LT
Sbjct: 305 APRWAIAYKFPAQEELT 321

>pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent Ligase Length = 318

Iteration: 1
 Score =  239 bits (611), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 124/316 (39%), Positives = 186/316 (58%), Gaps = 7/316 (2%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  EL++ L+R+   YY+ D P + D +YD+L+ EL  IEE+YPEL T DS TQ +G   
Sbjct: 9   RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPP 68
Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            E  + V H   MMSL N F + D+  F++R+  E+       Y+ EL  DG+AV++RYE
Sbjct: 69  LEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEV---GEAAYVCELAIDGLAVSVRYE 125
Query: 137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            GY  Q +TRGD                 PL L     P  LE R E  + K  F++LN+
Sbjct: 126 DGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK---EPVSLEARGEAFMPKASFLRLNE 182
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G + F NPRNAAAG LRQL+PK+  ++ L  F +G+ +   + + +SHSE L++ 
Sbjct: 183 ERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGI-ASHSEALDYL 241
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           Q +G  +  E    + ++++I F  + + KR  LPYEIDG+V K++  + Q+ LG T+++
Sbjct: 242 QALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKS 301
Query: 317 PRFALAYKFLSKEALT 332
           PR+A+AYKF ++E +T
Sbjct: 302 PRWAIAYKFPAEEVVT 317

>pdb|3PN1|A Chain A, Novel Bacterial Nad+-Dependent Dna Ligase Inhibitors With Broad Spectrum Potency And Antibacterial Efficacy In Vivo Length = 318

Iteration: 1
 Score =  239 bits (610), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/316 (40%), Positives = 183/316 (57%), Gaps = 1/316 (0%)
Query: 11  FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQ 70
            + +  ++  L+K L ++   Y++ DNP + D++YD+L  +LK +E ++PE LT DS TQ
Sbjct: 1   MTNIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQ 60
Query: 71  HVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGI 129
            VG         + H   M+SLDN FSD +   F KRI + L  L K + +  E K DG+
Sbjct: 61  RVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGL 120
Query: 130 AVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKK 189
           AV++ Y  G L QA+TRGD                 PL L    PP  LEVR EV +   
Sbjct: 121 AVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHA 180
Query: 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
            F +LNKY      K F NPRNAAAG LRQL+P I   + L   A+G+G   G+++P++H
Sbjct: 181 GFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTH 240
Query: 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
              L W + IG+ +  E  + +G ++++ FY+ I  KR +L Y+IDG V KIN ++ Q +
Sbjct: 241 YARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNE 300
Query: 310 LGFTSRAPRFALAYKF 325
           LGF S+APR+A+AYKF
Sbjct: 301 LGFISKAPRWAIAYKF 316

>pdb|3JSL|A Chain A, Crystal Structure Of The Adenylation Domain Of Nad+- Dependent Dna Ligase From Staphylococcus Aureus Length = 318

Iteration: 1
 Score =  214 bits (545), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 120/319 (37%), Positives = 188/319 (58%), Gaps = 7/319 (2%)
Query: 11  FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQ 70
            + LS RV EL   L++++  YY+ DNP + D++YD+LL EL KIEE++PE  T DS T 
Sbjct: 1   MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTV 60
Query: 71  HVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIA 130
            VG     +   V+H   M+SL N F+++D+  F++RI  ++    N+EY+ ELK DG+A
Sbjct: 61  RVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQI---GNVEYMCELKIDGLA 117
Query: 131 VNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKD 190
           V+L+Y  GY  Q  TRGD                 PL +     P  +EVR E  + ++ 
Sbjct: 118 VSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMK---EPLNVEVRGEAYMPRRS 174
Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
           F++LN+ +     + F NPRNAAAG LRQL+ K+   + L  F + V +    N   S S
Sbjct: 175 FLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNA-RSQS 233
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
           E L+   K+G +     + ++ ++ ++E+ +K   +R +LPY+IDG+V K+N L  Q ++
Sbjct: 234 EALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEM 293
Query: 311 GFTSRAPRFALAYKFLSKE 329
           GFT ++PR+A+AYKF ++E
Sbjct: 294 GFTQKSPRWAIAYKFPAEE 312

>pdb|1TA8|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332

Iteration: 1
 Score =  209 bits (532), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 122/332 (36%), Positives = 184/332 (55%), Gaps = 12/332 (3%)
Query: 6   KKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTK 65
           ++ +  +  + R  EL+K+L++++  YY+ D P + D  YD+L  EL  IE ++P+L+T 
Sbjct: 3   QQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITP 62
Query: 66  DSLTQHVG---LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIA 122
           DS TQ VG   L G E +    H   M SL++GFS ED+  F++R+     + K + Y  
Sbjct: 63  DSPTQRVGGKVLSGFEKAP---HDIPMYSLNDGFSKEDIFAFDERVRK--AIGKPVAYCC 117
Query: 123 ELKFDGIAVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRC 182
           ELK DG+A++LRYE G   + +TRGD                 P+ L     P  +EVR 
Sbjct: 118 ELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRG 174
Query: 183 EVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242
           E  + K+ F+ LN+ R   G   F NPRNAAAG LRQL+ KI   + L+ F + V +   
Sbjct: 175 ECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGP 234
Query: 243 MNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302
           M    +  E L     IG     E  +   ++++  + ++ + KR  LPYEIDG+V K+N
Sbjct: 235 MKA-KTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVN 293
Query: 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALTKI 334
             + Q +LGFT +APR+A+AYKF  +EA T +
Sbjct: 294 EFALQDELGFTVKAPRWAIAYKFPPEEAETVV 325

>pdb|1TAE|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332

Iteration: 1
 Score =  209 bits (531), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 122/330 (36%), Positives = 183/330 (55%), Gaps = 12/330 (3%)
Query: 6   KKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTK 65
           ++ +  +  + R  EL+K+L++++  YY+ D P + D  YD+L  EL  IE ++P+L+T 
Sbjct: 3   QQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITP 62
Query: 66  DSLTQHVG---LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIA 122
           DS TQ VG   L G E +    H   M SL++GFS ED+  F++R+     + K + Y  
Sbjct: 63  DSPTQRVGGKVLSGFEKAP---HDIPMYSLNDGFSKEDIFAFDERVRK--AIGKPVAYCC 117
Query: 123 ELKFDGIAVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRC 182
           ELK DG+A++LRYE G   + +TRGD                 P+ L     P  +EVR 
Sbjct: 118 ELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRG 174
Query: 183 EVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242
           E  + K+ F+ LN+ R   G   F NPRNAAAG LRQL+ KI   + L+ F + V +   
Sbjct: 175 ECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGP 234
Query: 243 MNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302
           M    +  E L     IG     E  +   ++++  + ++ + KR  LPYEIDG+V K+N
Sbjct: 235 MKA-KTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVN 293
Query: 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALT 332
             + Q +LGFT +APR+A+AYKF  +EA T
Sbjct: 294 EFALQDELGFTVKAPRWAIAYKFPPEEAET 323

>pdb|1ZAU|A Chain A, Adenylation Domain Of Nad+ Dependent Dna Ligase From M.Tuberculosis Length = 328

Iteration: 1
 Score =  205 bits (522), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 119/312 (38%), Positives = 174/312 (55%), Gaps = 13/312 (4%)
Query: 21  LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GEN 79
           L +E+  H   YY+ D PIISD ++D+LL  L+ +EE++PEL T DS TQ VG  G   +
Sbjct: 20  LAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATD 79
Query: 80  SKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGY 139
            + V H  +M+SLDN F+ +++  +  RI  E+    +  Y+ ELK DG+A++L Y  G 
Sbjct: 80  FEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGR 137
Query: 140 LKQASTRGDXXXXXXXXXXXXXXXXXP--LVLNIKYP-PELLEVRCEVLIYKKDFIKLNK 196
           L +ASTRGD                 P  L     YP PE+LEVR EV     DF  LN 
Sbjct: 138 LTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNA 197
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G   F NPRN+AAG LRQ +P +   + L    HG+G + G    + H   L   
Sbjct: 198 SLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLA-L 256
Query: 257 QKIGLSICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
           +  GL +    ++   L+GV + I+++ +    R  + +EIDGVV K++ ++ Q++LG T
Sbjct: 257 RAWGLPVSEHTTLATDLAGVRERIDYWGE---HRHEVDHEIDGVVVKVDEVALQRRLGST 313
Query: 314 SRAPRFALAYKF 325
           SRAPR+A+AYK+
Sbjct: 314 SRAPRWAIAYKY 325

>pdb|3BAC|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+ Dependent Dna Ligase Length = 270

Iteration: 1
 Score =  199 bits (507), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/251 (42%), Positives = 147/251 (58%), Gaps = 1/251 (0%)
Query: 83  VHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGIAVNLRYEYGYLK 141
           + H   M+SLDN FSD +   F KRI + L  L K + +  E K DG+AV++ Y  G L 
Sbjct: 10  IRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGLAVSILYVNGELT 69
Query: 142 QASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHL 201
           QA+TRGD                 PL L    PP  LEVR EV +    F +LNKY    
Sbjct: 70  QAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEH 129
Query: 202 GLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGL 261
             K F NPRNAAAG LRQL+P I   + L   A+G+G   G+ +P++H   L W + IG+
Sbjct: 130 NEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVGLPTTHYARLQWLKSIGI 189
Query: 262 SICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFAL 321
            +  E  + +G +++++FY+ I  KR +L Y+IDG V KIN ++ Q +LGF S+APR+A+
Sbjct: 190 PVNPEIRLCNGADEVLDFYQDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAI 249
Query: 322 AYKFLSKEALT 332
           AYKF ++E LT
Sbjct: 250 AYKFPAQEELT 260

>pdb|4GLW|A Chain A, Dna Ligase A In Complex With Inhibitor Length = 305

Iteration: 1
 Score =  181 bits (460), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 113/313 (36%), Positives = 175/313 (55%), Gaps = 17/313 (5%)
Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVG--- 73
           R+ EL   L+R+   YY  DNP +SD++YD+L  EL ++E  YPE +  DS T  VG   
Sbjct: 4   RMNELVALLNRYATEYYTSDNPSVSDSEYDRLYRELVELETAYPEQVLADSPTHRVGGKV 63
Query: 74  LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
           L G E  KY H  + + SL + FS E++  F+ R+  E+    +  YI ELK DG++++L
Sbjct: 64  LDGFE--KYSHQ-YPLYSLQDAFSREELDAFDARVRKEVA---HPTYICELKIDGLSISL 117
Query: 134 RYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPEL-LEVRCEVLIYKKDFI 192
            YE G L    TRGD                 PL L    P EL + VR E  + +  F 
Sbjct: 118 TYEKGILVAGVTRGDGSIGENITENLKRVKDIPLTL----PEELDITVRGECYMPRASFD 173
Query: 193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL 252
           ++N+ R   G  +F NPRNAAAG LRQL+  +   + L  F +   +    +   S  + 
Sbjct: 174 QVNQARQENGEPEFANPRNAAAGTLRQLDTAVVAKRNLATFLY---QEASPSTRDSQEKG 230
Query: 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGF 312
           L + +++G  +  +  +   ++++  F +++  +R NLPY+IDGVV K+N L++Q++LGF
Sbjct: 231 LKYLEQLGFVVNPKRILAENIDEIWNFIQEVGQERENLPYDIDGVVIKVNDLASQEELGF 290
Query: 313 TSRAPRFALAYKF 325
           T +AP++A+AYKF
Sbjct: 291 TVKAPKWAVAYKF 303

>pdb|2EBU|A Chain A, Solution Structure Of The Brct Domain From Human Replication Factor C Large Subunit 1 Length = 112

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 1/80 (1%)
Query: 601 KGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGK-KLE 659
           KG +N L+  IFV TG L + +R+EA  LIE  GGKV   +SK TNYLV G+  G+ K +
Sbjct: 17  KGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD 76
Query: 660 KAIKLNIKILDEKNFVKIVK 679
           KA  L  KI+DE   + +++
Sbjct: 77  KAAALGTKIIDEDGLLNLIR 96

>pdb|2K7F|A Chain A, Haddock Calculated Model Of The Complex Between The Brct Region Of Rfc P140 And Dsdna Length = 109

Iteration: 1
 Score = 66.2 bits (160), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 1/80 (1%)
Query: 601 KGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGK-KLE 659
           KG +N L+  IFV TG L + +R+EA  LIE  GGKV   +SK TNYLV G+  G+ K +
Sbjct: 27  KGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD 86
Query: 660 KAIKLNIKILDEKNFVKIVK 679
           KA  L  KI+DE   + +++
Sbjct: 87  KAAALGTKIIDEDGLLNLIR 106

>pdb|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus: Northeast Structural Genomics Consortium Target Wr64tt Length = 92

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
           LK   FV TG L +  R E   L+  LG KV + +S+ T+YLV G+ PG KLEKA  L +
Sbjct: 8   LKGLTFVITGEL-SRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGV 66
Query: 667 KILDEKNFVKIVKG 680
             L E+   ++++ 
Sbjct: 67  PTLTEEELYRLLEA 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	687
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	0.0
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	0.0
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	0.0
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	1e-148
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	1e-144
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	1e-143
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	1e-142
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	1e-140
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	4e-24
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	4e-24
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	1e-22
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	2e-15
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	2e-14
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	5e-14
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	2e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	5e-06
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	1e-04
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	7e-04

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Length = 671

 Score =  870 bits (2251), Expect = 0.0
 Identities = 276/664 (41%), Positives = 412/664 (62%), Gaps = 3/664 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           ++TEL+  L  H   Y++ D P I D +YD+L+ EL+++E K+PEL+T DS TQ VG   
Sbjct: 7   QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAP 66

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
                 + H   M+SLDN F +E  + FNKR+ + LK  + + +  ELK DG+AV++ YE
Sbjct: 67  LAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYE 126

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G L  A+TRGDG  GE+IT+N+  I  IPL L+ +  P  LEVR EV + +  F K+N+
Sbjct: 127 NGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINE 186

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
                G K F NPRNAAAG LRQL+P+I   + L FF +GVG L G  +P +H   L  +
Sbjct: 187 DARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQF 246

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           +K GL +    ++     +++ FY K+   R  L ++IDGVV K+N L+ Q++LGF +RA
Sbjct: 247 KKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARA 306

Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
           PR+A+A+KF ++E +T ++ +  Q+GRTG ITPVA L+PV + G+ ++ ATLHN  EI R
Sbjct: 307 PRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIER 366

Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
             ++IGD VV+ R+G+VIP++ + +LS RP D++    P  CP+C S +  +E   +ARC
Sbjct: 367 LGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARC 426

Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
           +G  I C AQRK  L+HF SR+AM++ G+G K+I++LV    V T  DL+K+    L  L
Sbjct: 427 TGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGL 485

Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
           +R+  K A N++ A++K+K TTF+RF+YALGIR VGE TA  LA YF  LE +  A+ E+
Sbjct: 486 ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEE 545

Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW--LNNPNTKGNKNYLKEKIFVF 614
           L  +P +G         F  +  +R +IS+L   G++W      N +   +    K  V 
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVL 605

Query: 615 TGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 674
           TGSL    R++A   +  LG KV   +SK T+ ++ G+  G KL KA +L I+++DE   
Sbjct: 606 TGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEM 665

Query: 675 VKIV 678
           ++++
Sbjct: 666 LRLL 669

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Length = 667

 Score =  827 bits (2138), Expect = 0.0
 Identities = 251/669 (37%), Positives = 387/669 (57%), Gaps = 22/669 (3%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R+ EL+  +  HN  YY+  +P ISD +YD+LL ELK++EE++PE  + DS T+ VG   
Sbjct: 9   RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVG--A 66

Query: 77  GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
                    V H  +M SLDN F+ E+V+ F +R+  E +      Y  E K DG++V L
Sbjct: 67  RPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAE--APSLYTVEHKVDGLSV-L 123

Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIK 193
            YE G    ++  GDG +GE +T N+  I  IP  L  K  P+ LEVR EV +  + F++
Sbjct: 124 YYEEGVW--STGSGDGEVGEEVTQNLLTIPTIPRRL--KGVPDRLEVRGEVYMPIEAFLR 179

Query: 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN--MPSSHSE 251
           LN+     G K F NPRNAAAG LRQ +P++   + L    + +G   G+      S  E
Sbjct: 180 LNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYE 239

Query: 252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
           LL W ++ G  +   Y    G   + E Y++   +R  LP+E DGVV K++ L+   +LG
Sbjct: 240 LLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELG 299

Query: 312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
           +T+RAPRFALAYKF ++E  T++  +  Q+GRTG +TPV +L+PV I+G  ++R TLHNE
Sbjct: 300 YTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNE 359

Query: 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
           S I   +I+IGD V+VH++G VIP++   +   R    +  + P  CP C  +++     
Sbjct: 360 SYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGK- 418

Query: 432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
            + RC      C A+R   ++H++SRKAM+I GLG+K+IE+L+   +V    DLY +  +
Sbjct: 419 -VHRCPNP--LCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKE 475

Query: 492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
           +LL L+R+  K A N+L  I++SK     R +YALG+  VGE  A+ LA  F  ++ + +
Sbjct: 476 DLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLE 535

Query: 552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKI 611
           A+ E+L+ + ++G  T +A ++ +  P  R L+ +L++ G+      + +   + L    
Sbjct: 536 ASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSM---ESKEEVSDLLSGLT 592

Query: 612 FVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDE 671
           FV TG L +  R E   L+  LG KV + +S+ T+YLV G+ PG KLEKA  L + +L E
Sbjct: 593 FVLTGEL-SRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTE 651

Query: 672 KNFVKIVKG 680
           + F + +K 
Sbjct: 652 EEFWRFLKE 660

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} Length = 615

 Score =  757 bits (1957), Expect = 0.0
 Identities = 210/591 (35%), Positives = 322/591 (54%), Gaps = 19/591 (3%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           +   L +E+  H   YY+ D PIISD ++D+LL  L+ +EE++PEL T DS TQ VG  G
Sbjct: 16  QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVG--G 73

Query: 77  GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
              +     V H  +M+SLDN F+ +++  +  RI  E+       Y+ ELK DG+A++L
Sbjct: 74  AGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEV--GDAAHYLCELKIDGVALSL 131

Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL---NIKYPPELLEVRCEVLIYKKD 190
            Y  G L +ASTRGDG  GE++T N   I  +P  L   +    PE+LEVR EV     D
Sbjct: 132 VYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDD 191

Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
           F  LN      G   F NPRN+AAG LRQ +P +   + L    HG+G + G   P++  
Sbjct: 192 FQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR-PATLH 250

Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
           +     +  GL +    ++ + +  + E        R  + +EIDGVV K++ ++ Q++L
Sbjct: 251 QAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRL 310

Query: 311 GFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHN 370
           G TSRAPR+A+AYK+  +EA TK+  I + +GRTG ITP A + PV + G T+ +ATLHN
Sbjct: 311 GSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHN 370

Query: 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIY-IE 429
            SEI RK + IGDTVV+ ++G+VIP++   ++ LR    + F +P  CP C S +    E
Sbjct: 371 ASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKE 430

Query: 430 SNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489
            +   RC  +   C  Q +  + H +SR  ++I  LG +    L+ A ++    +L+ + 
Sbjct: 431 GDADIRCPNARG-CPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALT 489

Query: 490 FKNLLRLDRVSNKLA------NNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
            ++LLR D    K          +L+ + K+K     R + AL IRHVG T A+ LA  F
Sbjct: 490 ERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEF 549

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594
            +L+ +  A+ +QL  +  +G T   A  ++     HR ++ + R  G+  
Sbjct: 550 GSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM 600

>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A* Length = 322

 Score =  431 bits (1112), Expect = e-148
 Identities = 136/317 (42%), Positives = 194/317 (61%), Gaps = 1/317 (0%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           ++  L+K L ++   Y++ DNP + D++YD+L  +LK +E ++PE LT DS TQ VG   
Sbjct: 5   QLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKP 64

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLT-KNIEYIAELKFDGIAVNLRY 135
                 + H   M+SLDN FSD +   F  RI + L L    + +  E K DG+AV++ Y
Sbjct: 65  LSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILY 124

Query: 136 EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
             G L QA+TRGDG  GE+IT NI  I  +PL L    PP  LEVR EV +    F +LN
Sbjct: 125 VNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLN 184

Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
           KY      K F NPRNAAAG LRQL+P I   + L   A+G+G   G+++P++H   L W
Sbjct: 185 KYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQW 244

Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
            + IG+ +  E  + +G ++++ FY+ I  KR +L Y+IDG V KIN ++ Q +LGF S+
Sbjct: 245 LKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISK 304

Query: 316 APRFALAYKFLSKEALT 332
           APR+A+AYKF ++E LT
Sbjct: 305 APRWAIAYKFPAQEELT 321

>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A* Length = 332

 Score =  423 bits (1090), Expect = e-144
 Identities = 126/336 (37%), Positives = 194/336 (57%), Gaps = 6/336 (1%)

Query: 5   AKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLT 64
            ++ +  +  + R  EL+K+L++++  YY+ D P + D  YD+L  EL  IE ++P+L+T
Sbjct: 2   EQQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLIT 61

Query: 65  KDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAEL 124
            DS TQ VG       +   H   M SL++GFS ED+  F++R+   +   K + Y  EL
Sbjct: 62  PDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIG--KPVAYCCEL 119

Query: 125 KFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEV 184
           K DG+A++LRYE G   + +TRGDG +GENIT N+  +  +P+ L     P  +EVR E 
Sbjct: 120 KIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRGEC 176

Query: 185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN 244
            + K+ F+ LN+ R   G   F NPRNAAAG LRQL+ KI   + L+ F + V +   M 
Sbjct: 177 YMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK 236

Query: 245 MPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCL 304
              +  E L     IG     E  +   ++++  + ++ + KR  LPYEIDG+V K+N  
Sbjct: 237 -AKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEF 295

Query: 305 STQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ 340
           + Q +LGFT +APR+A+AYKF  +EA T ++  +  
Sbjct: 296 ALQDELGFTVKAPRWAIAYKFPPEEAETVVZHHHHH 331

>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB: 3jsn_A* Length = 318

 Score =  420 bits (1082), Expect = e-143
 Identities = 127/318 (39%), Positives = 196/318 (61%), Gaps = 7/318 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           RV EL   L++++  YY+ DNP + D++YD+LL EL KIEE++PE  T DS T  VG   
Sbjct: 7   RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEA 66

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
             +   V+H   M+SL N F+++D+  F++RI  ++    N+EY+ ELK DG+AV+L+Y 
Sbjct: 67  QASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIG---NVEYMCELKIDGLAVSLKYV 123

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            GY  Q  TRGDG  GE+IT N+  IH IPL +     P  +EVR E  + ++ F++LN+
Sbjct: 124 DGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMK---EPLNVEVRGEAYMPRRSFLRLNE 180

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            +     + F NPRNAAAG LRQL+ K+   + L  F + V +    N   S SE L+  
Sbjct: 181 EKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFN-ARSQSEALDEL 239

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
            K+G +     + ++ ++ ++E+ +K   +R +LPY+IDG+V K+N L  Q ++GFT ++
Sbjct: 240 DKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKS 299

Query: 317 PRFALAYKFLSKEALTKI 334
           PR+A+AYKF ++E     
Sbjct: 300 PRWAIAYKFPAEEHHHHH 317

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2 Length = 318

 Score =  416 bits (1073), Expect = e-142
 Identities = 131/316 (41%), Positives = 195/316 (61%), Gaps = 7/316 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  EL++ L+R+   YY+ D P + D +YD+L+ EL  IEE+YPEL T DS TQ +G   
Sbjct: 9   RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPP 68

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            E  + V H   MMSL N F + D+  F++R+  E+       Y+ EL  DG+AV++RYE
Sbjct: 69  LEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYE 125

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            GY  Q +TRGDG  GE+IT N+  I  +PL L     P  LE R E  + K  F++LN+
Sbjct: 126 DGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK---EPVSLEARGEAFMPKASFLRLNE 182

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G + F NPRNAAAG LRQL+PK+  ++ L  F +G+ +   +   +SHSE L++ 
Sbjct: 183 ERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHSEALDYL 241

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           Q +G  +  E    + ++++I F  + + KR  LPYEIDG+V K++  + Q+ LG T+++
Sbjct: 242 QALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKS 301

Query: 317 PRFALAYKFLSKEALT 332
           PR+A+AYKF ++E +T
Sbjct: 302 PRWAIAYKFPAEEVVT 317

>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Length = 328

 Score =  413 bits (1064), Expect = e-140
 Identities = 119/315 (37%), Positives = 176/315 (55%), Gaps = 11/315 (3%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           +   L +E+  H   YY+ D PIISD ++D+LL  L+ +EE++PEL T DS TQ VG  G
Sbjct: 16  QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVG--G 73

Query: 77  GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
              +     V H  +M+SLDN F+ +++  +  RI  E+       Y+ ELK DG+A++L
Sbjct: 74  AGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEV--GDAAHYLCELKIDGVALSL 131

Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL---NIKYPPELLEVRCEVLIYKKD 190
            Y  G L +ASTRGDG  GE++T N   I  +P  L   +    PE+LEVR EV     D
Sbjct: 132 VYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDD 191

Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
           F  LN      G   F NPRN+AAG LRQ +P +   + L    HG+G + G   P++  
Sbjct: 192 FQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR-PATLH 250

Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
           +     +  GL +    ++ + +  + E        R  + +EIDGVV K++ ++ Q++L
Sbjct: 251 QAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRL 310

Query: 311 GFTSRAPRFALAYKF 325
           G TSRAPR+A+AYK+
Sbjct: 311 GSTSRAPRWAIAYKY 325

>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 112

 Score = 96.7 bits (241), Expect = 4e-24
 Identities = 38/93 (40%), Positives = 52/93 (55%), Gaps = 1/93 (1%)

Query: 588 RDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNY 647
              G    +    KG +N L+  IFV TG L + +R+EA  LIE  GGKV   +SK TNY
Sbjct: 4   GSSGKALGSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNY 63

Query: 648 LVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 679
           LV G+  G  K +KA  L  KI+DE   + +++
Sbjct: 64  LVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 96

>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A Length = 109

 Score = 96.3 bits (240), Expect = 4e-24
 Identities = 41/105 (39%), Positives = 58/105 (55%), Gaps = 2/105 (1%)

Query: 577 QPLHRLLISQLRDVGIYWLNN-PNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGG 635
           +  ++   S L   G   L +    KG +N L+  IFV TG L + +R+EA  LIE  GG
Sbjct: 2   RTNYQAYRSYLNREGPKALGSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGG 61

Query: 636 KVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 679
           KV   +SK TNYLV G+  G  K +KA  L  KI+DE   + +++
Sbjct: 62  KVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 106

>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2 Length = 92

 Score = 91.6 bits (228), Expect = 1e-22
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 664
             LK   FV TG L +  R E   L+  LG KV + +S+ T+YLV G+ PG KLEKA  L
Sbjct: 6   EALKGLTFVITGEL-SRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARAL 64

Query: 665 NIKILDEKNFVKIVKG 680
            +  L E+   ++++ 
Sbjct: 65  GVPTLTEEELYRLLEA 80

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A Length = 113

 Score = 71.5 bits (175), Expect = 2e-15
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 599 NTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKG---QKPG 655
           +       L     +  G L +  ++E   +IE LGGK+    +K +  +      +K  
Sbjct: 3   SGSSGDKPLSNMKILTLGKL-SRNKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMN 61

Query: 656 KKLEKAIKLNIKILDEKNFVKIVKG 680
           KK+E+  + NI+++ E     +   
Sbjct: 62  KKMEEVKEANIRVVSEDFLQDVSAS 86

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 91

 Score = 68.3 bits (167), Expect = 2e-14
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 501 NKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLN 559
              A+ ++   +K +    SR    L  ++ V +T ++ L   F +LE +  A+ E L  
Sbjct: 12  QDPADLLM---EKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLAL 68

Query: 560 IPKIGSTTVKAFIKFINQPLHRL 582
            P +G    +     +++P  ++
Sbjct: 69  CPGLGPQKARRLFDVLHEPFLKV 91

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Length = 89

 Score = 67.2 bits (164), Expect = 5e-14
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 503 LANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIP 561
           +A+ ++   +K +    SR    L  ++ V +T ++ L   F +LE +  A+ E L   P
Sbjct: 1   MADLLM---EKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCP 57

Query: 562 KIGSTTVKAFIKFINQPLHR 581
            +G    +     +++P  +
Sbjct: 58  GLGPQKARRLFDVLHEPFLK 77

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Length = 75

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 511 IQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569
           ++K  LT   R    + G+ HV  T A+ L  +F ++E +F A+  +L+ +  IG    K
Sbjct: 1   MEKKALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAK 60

Query: 570 AFIKFINQPLHR 581
              + I  P   
Sbjct: 61  EIRRVITAPYIE 72

>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 = 71.0 bits (173), Expect = 8e-13
 Identities = 99/670 (14%), Positives = 201/670 (30%), Gaps = 192/670 (28%)

Query: 26  HRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHH 85
           H H++           D +  +  ++ K I   + +    +   + V             
Sbjct: 3   HHHHM-----------DFETGEHQYQYKDILSVFEDAFVDNFDCKDV-------QDMPKS 44

Query: 86  TFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQAST 145
                 +D+    +D +    R+   L L+K  E + +   + +   LR  Y +L     
Sbjct: 45  ILSKEEIDHIIMSKDAVSGTLRLFWTL-LSKQ-EEMVQKFVEEV---LRINYKFLMSP-- 97

Query: 146 RGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKD--------FIKLNKY 197
                        I    + P ++   Y            I ++D        F K N  
Sbjct: 98  -------------IKTEQRQPSMMTRMY------------IEQRDRLYNDNQVFAKYNVS 132

Query: 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGE-------LRG-------- 242
           R    L+ +   R A    L +L P   KN ++     G G+                  
Sbjct: 133 R----LQPYLKLRQA----LLELRP--AKNVLIDGVL-GSGKTWVALDVCLSYKVQCKMD 181

Query: 243 -----MNMPSSHSE------LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRF--N 289
                +N+ + +S       L     +I  +        S +   I   +   ++R   +
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA-ELRRLLKS 240

Query: 290 LPYE-----IDGV-------VYKINCLSTQKKLGFTSRAPRFA-----LAYKFLS----K 328
            PYE     +  V        + ++C    K L  T+R  +            +S     
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSC----KIL-LTTRFKQVTDFLSAATTTHISLDHHS 295

Query: 329 EALTKIKAINIQIGRTGIIT---PVALLK--PVLIDGITITRATLHNE---SEIYRKNIQ 380
             LT  +  ++ +          P  +L   P  +  I     ++ +     + ++    
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA---ESIRDGLATWDNWKHV-- 350

Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSK-------IF----KIP-NICPICNSKIIYI 428
                       +   I SS+  L P + +       +F     IP  +  +    +I  
Sbjct: 351 --------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402

Query: 429 ESNLIAR--CSGSWIECIAQRKA------GLQHFSSRKAMNIIGLGKKMIE------KLV 474
           +  ++       S +E   Q K        +      K  N   L + +++         
Sbjct: 403 DVMVVVNKLHKYSLVEK--QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460

Query: 475 NANIVVTAVDLYKINF-----KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIR 529
           + +++   +D Y  +      KN+   +R++  L   + L         F RF+    IR
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMT--LFRMVFL--------DF-RFLEQ-KIR 508

Query: 530 HVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRD 589
           H    TA   +    N     K  +  + +        V A + F+ +    L+ S+  D
Sbjct: 509 HDS--TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTD 566

Query: 590 VGIYWLNNPN 599
           +    L   +
Sbjct: 567 LLRIALMAED 576

>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 = 56.0 bits (134), Expect = 3e-08
 Identities = 63/475 (13%), Positives = 125/475 (26%), Gaps = 186/475 (39%)

Query: 268 SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF---ALA-- 322
           S+LS      E    I          + G +     L ++++        +F    L   
Sbjct: 44  SILSK-----EEIDHI----IMSKDAVSGTLRLFWTLLSKQE----EMVQKFVEEVLRIN 90

Query: 323 YKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI-TRATLHNESEIYRK-NIQ 380
           YKFL    ++ IK    Q              P ++  + I  R  L+N+++++ K N+ 
Sbjct: 91  YKFL----MSPIKTEQRQ--------------PSMMTRMYIEQRDRLYNDNQVFAKYNVS 132

Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSW 440
                +         K+  ++L LRP         N+       +I              
Sbjct: 133 RLQPYL---------KLRQALLELRPA-------KNV-------LID------------- 156

Query: 441 IECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS 500
                    G         +  +G GK            V           ++    +V 
Sbjct: 157 ---------G---------V--LGSGKT----------WVAL---------DVCLSYKVQ 177

Query: 501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI 560
            K+   I              F   L   +  ET  + L      ++  + +  +   NI
Sbjct: 178 CKMDFKI--------------FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 561 PKIGSTTVKAFIKFINQPLHR--LLISQLRDVGIYWLNNPNT----------------KG 602
                +      + +    +   LL+  L +V      N                   K 
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLV--LLNV---Q--NAKAWNAFNLSCKILLTTRFKQ 276

Query: 603 NKNYL---KEKIFVFTGSLYAFKRNEAIILIEN-----------------------LGGK 636
             ++L                   +E   L+                         +   
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES 336

Query: 637 VVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDE----KNFVKIVKGFSTETKI 687
           + + ++   N+         KL   I+ ++ +L+     K F ++   F     I
Sbjct: 337 IRDGLATWDNWK---HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV-FPPSAHI 387

>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 129

 Score = 45.6 bits (108), Expect = 5e-06
 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 666
           L+  + V +G      R+E       LG K     ++++ +L+       K  + + L  
Sbjct: 23  LQGVVVVLSG-FQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGG 81

Query: 667 KI 668
           +I
Sbjct: 82  RI 83

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Length = 219

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 12/66 (18%), Positives = 25/66 (37%)

Query: 513 KSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFI 572
           +       +         +G  TA+ +   F +LE  F A++ ++  +  IG    +   
Sbjct: 152 RLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIK 211

Query: 573 KFINQP 578
           K +  P
Sbjct: 212 KILMTP 217

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Length = 107

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 9/56 (16%), Positives = 22/56 (39%)

Query: 613 VFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKI 668
           V++ +            + ++G KV    +K   +++         +KA K  +K+
Sbjct: 17  VWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKL 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	687
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	100.0
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	100.0
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	100.0
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	100.0
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	100.0
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	100.0
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	100.0
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	100.0
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	100.0
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	100.0
2vug_A	389	PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transfe	100.0
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	99.83
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	99.82
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	99.82
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	99.71
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	99.31
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	99.29
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	98.94
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	98.86
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	98.77
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	98.74
4id3_A	92	DNA repair protein REV1; BRCT domain, protein bind	98.74
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	98.69
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	98.64
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	98.57
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	98.56
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	98.41
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	98.33
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	98.28
1fvi_A	297	Chlorella virus DNA ligase-adenylate; adenylated D	98.25
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	98.16
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	98.12
3gde_A	558	DNA ligase; DNA-binding domain, adenylation domain	98.06
1vs0_A	310	Putative DNA ligase-like protein RV0938/MT0965; OB	98.05
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	98.02
2cfm_A	561	Thermostable DNA ligase; protein-nucleotide comple	97.95
1a0i_A	348	DNA ligase; DNA replication; HET: DNA ATP; 2.60A {	97.9
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	97.89
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	97.89
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	97.86
3l2p_A	579	DNA ligase 3; DNA ligase, DNA repair, ATP-binding,	97.86
3qwu_A	370	DNA ligase; structural genomics, PSI-2, midwest ce	97.84
2hiv_A	621	Thermostable DNA ligase; ATP-dependent, open confo	97.8
1x9n_A	688	DNA ligase I; 5'-adenylated nicked DNA, protein-DN	97.78
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	97.76
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	97.7
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	97.66
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	97.6
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	97.58
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	97.54
1ckm_A	330	MRNA capping enzyme; nucleotidyltransferase; HET:	97.45
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	97.44
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	97.38
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	97.35
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	97.32
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	97.32
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	97.28
3vnn_A	139	DNA ligase 4; non-homologous END joining, DNA repa	97.23
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	97.18
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	97.18
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	97.03
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	97.02
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	96.99
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	96.98
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	96.97
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	96.95
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	96.82
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	96.79
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	96.61
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	96.59
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	96.59
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	96.56
3b0x_A	575	DNA polymerase beta family (X family); structural	96.55
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	96.48
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	96.46
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	96.45
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	96.39
2duy_A	75	Competence protein comea-related protein; helix-ha	96.35
1u9l_A	70	Transcription elongation protein NUSA; escherichia	96.33
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	96.32
3b0x_A	575	DNA polymerase beta family (X family); structural	96.32
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	96.28
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	96.12
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	95.98
2hvq_A	335	ORF1, hypothetical 37.6 kDa protein in GP24-HOC in	95.97
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	95.84
1z3e_B	73	DNA-directed RNA polymerase alpha chain; bacterial	95.84
1p16_A	395	GTP--RNA, mRNA capping enzyme alpha subunit; guany	95.83
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	95.8
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	95.63
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	95.6
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	95.6
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	95.48
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	95.47
3gfk_B	79	DNA-directed RNA polymerase subunit alpha; protein	95.43
1s68_A	249	RNA ligase 2; ribonucleic acid ligase, RNA repair;	95.29
3k4g_A	86	DNA-directed RNA polymerase subunit alpha; bacteri	95.24
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	95.24
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	95.17
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	95.06
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	94.96
2duy_A	75	Competence protein comea-related protein; helix-ha	94.7
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	94.59
3kyh_C	461	MRNA-capping enzyme subunit alpha; 5' modification	94.48
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	94.3
3rtx_A	343	MRNA-capping enzyme; guanylyltransferase, RNA poly	94.24
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	94.14
1coo_A	98	RNA polymerase alpha subunit; transcription regula	93.94
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	93.92
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	93.88
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	93.74
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	93.58
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	93.55
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	93.42
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	93.32
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	93.04
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	92.97
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	92.89
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	92.69
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	92.06
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	92.01
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	91.93
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	91.86
1u9l_A	70	Transcription elongation protein NUSA; escherichia	91.42
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	91.19
2ep8_A	100	Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r	91.19
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	91.06
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	90.53
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	89.97
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	89.19
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	89.16
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	89.02
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	88.77
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	88.71
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	87.61
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	87.32
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	87.27
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	86.99
2kz3_A	83	Putative uncharacterized protein RAD51L3; RAD51D,	86.84
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	86.67
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	86.41
3oq4_A	134	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	86.29
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	86.15
3pc7_A	88	DNA ligase 3; DNA repair, BRCT domain, protein:pro	86.11
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	85.65
1xdn_A	277	RNA editing ligase MP52; HET: MSE ATP; 1.20A {Tryp	84.89
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	84.86
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	84.33
2coe_A	120	Deoxynucleotidyltransferase, terminal variant; BRC	83.59
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	82.84
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	82.72
3bqs_A	93	Uncharacterized protein; 10114F, NYSGXRC, PSI-2, s	81.58
3im1_A	328	Protein SNU246, PRE-mRNA-splicing helicase BRR2; A	81.17
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	80.79
1rxw_A	336	Flap structure-specific endonuclease; helical clam	80.69
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	80.51
3huf_A	325	DNA repair and telomere maintenance protein NBS1;	80.29

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=100.00  E-value=8.6e-194  Score=1646.29  Aligned_cols=665  Identities=41%  Similarity=0.691  Sum_probs=560.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCC
Q psy11422         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSL   92 (687)
Q Consensus        13 ~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL   92 (687)
                      ++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.++|||||+||+.+.++|.||+|++|||||
T Consensus         3 ~~~~~~~~L~~~l~~~~~~YY~~d~p~isD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~f~kv~H~~pMlSL   82 (671)
T 2owo_A            3 SIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAPLAAFSQIRHEVPMLSL   82 (671)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHHHHHHHCTTSCCTTSGGGCCSCCCCBCCCEEECSSCCCCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCcccccCcccccCCCceECCCcCcCc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccC
Q psy11422         93 DNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (687)
Q Consensus        93 ~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (687)
                      +|+||.+||.+|++|+.+.++...++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|.+.
T Consensus        83 ~n~~~~~el~~f~~rv~~~l~~~~~~~~~~e~KiDGlaisL~Ye~G~Lv~a~TRGDG~~GEdvT~n~rtI~~IP~~l~~~  162 (671)
T 2owo_A           83 DNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGE  162 (671)
T ss_dssp             EEECSHHHHHHHHHHHHHHSSSCCCCCEEEEEEESSEEEEEEEETTEEEEEECCTTSSEEEBCHHHHHTCTTSCSBCCSS
T ss_pred             cccCCHHHHHHHHHHHHHhcCCCcCceEEEEEecceEEEEEEEeCCEEEEEEecCCCcchhhHHHHHhhhcCCCccccCC
Confidence            99999999999999999887521236899999999999999999999999999999999999999999999999999752


Q ss_pred             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC-CCCCCCHHH
Q psy11422        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG-MNMPSSHSE  251 (687)
Q Consensus       173 ~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~-~~~~~~~~e  251 (687)
                      +.|..+|||||+||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++ .. +.+|++
T Consensus       163 ~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaaAGsLrqld~~~~a~R~L~~~~y~~~~~~~~~~-~~t~~e  241 (671)
T 2owo_A          163 NIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGEL-PDTHLG  241 (671)
T ss_dssp             SCCSEEEEEEEEECCHHHHHHHHHHHHHSSCCCCSCHHHHHHHHHTCSCHHHHHTSCCEEEEEEEEEEESSCC-CSBHHH
T ss_pred             CCCCeEEEEEEEEEEHHHHHHHHHHHHhcCCCcccChHHHHHHHHHhcChhhHhcCCCEEEEEECcccCCCCC-CCCHHH
Confidence            2588999999999999999999999999999999999999999999999999999999999999964232 22 489999


Q ss_pred             HHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceee
Q psy11422        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEAL  331 (687)
Q Consensus       252 ~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~  331 (687)
                      .|++|++|||+++++.+.|.+.+++++|+++|.+.|..|||+|||+||||||+.+|+.||+|+|+||||||||||+++++
T Consensus       242 ~l~~L~~~Gf~v~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGvViKv~~~~~q~~LG~t~k~PrWAiA~Kfpae~~~  321 (671)
T 2owo_A          242 RLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARAPRWAVAFKFPAQEQM  321 (671)
T ss_dssp             HHHHHHHHTCCCCTTCEEESSHHHHHHHHHHHHHHGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEEECCCCEEE
T ss_pred             HHHHHHHCCCCCCCcceeeCCHHHHHHHHHHHHHHHhcCCCCCccEEEEecCHHHHHHhCcccCCCCceEEEcCCCceEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCcc
Q psy11422        332 TKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKI  411 (687)
Q Consensus       332 T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~  411 (687)
                      |+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||+|||+|.|+|||||||+|++|+.+.|++++.+
T Consensus       322 T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLHN~d~i~~~di~iGD~V~V~rAGdvIP~i~~vv~~~r~~~~~~  401 (671)
T 2owo_A          322 TFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTRE  401 (671)
T ss_dssp             EEEEEEEEEECTTSBEEEEEEEEEEEETTEEEEEEECCSHHHHHHHTCCBTCEEEEEEETTTEEEEEEECGGGCCSSCBC
T ss_pred             EEEEEEEEecCCCceeeeEEEEEeEEECCEEEEeccCCCHHHHHHcCCCCCCEEEEEECCCcccceeccccccCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999899


Q ss_pred             ccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChh
Q psy11422        412 FKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK  491 (687)
Q Consensus       412 ~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~  491 (687)
                      |.+|++||+||++|++.+|++.+||+|... ||+|++++|.||+||++|||+|||+|+|++|+++|+|++++|||.|+.+
T Consensus       402 ~~~P~~CP~Cgs~l~~~~~~~~~rC~n~~~-Cpaq~~~~l~hf~sr~aldI~GLG~k~i~~L~~~g~I~~~aDL~~L~~~  480 (671)
T 2owo_A          402 VVFPTHCPVCGSDVERVEGEAVARCTGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAG  480 (671)
T ss_dssp             CCCCSBCTTTCCBEEECTTCSCEEECCGGG-CHHHHHHHHHHHHSTTTTCCTTCCHHHHHHHHHTTCCSSGGGGGTCCHH
T ss_pred             CcCCCCCCCCCCEeEEecCCEEEECCCCCC-CHHHHHHHHHHHhhhhhcCCCCCCHHHHHHHHHcCCCCCHHHHHhhCHH
Confidence            999999999999999988899999998656 9999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHH
Q psy11422        492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAF  571 (687)
Q Consensus       492 ~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI  571 (687)
                      +|..++|||+|+++||+++|+.+|+.+|+|||+||||||||+++|+.|+++|+++++|..|+.++|.+++|||+++|++|
T Consensus       481 ~L~~l~gfG~Ksa~nLl~aIe~sk~~~l~R~L~algi~~VG~~~Ak~La~~Fgsl~~l~~As~eeL~~i~GIG~~~A~sI  560 (671)
T 2owo_A          481 KLTGLERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHV  560 (671)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHH
T ss_pred             HhhcccccchhHHHHHHHHHHHHhcCChhheehhhcccCccHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcchhHHHHHHHHHhcCcccccCCC--CCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEE
Q psy11422        572 IKFINQPLHRLLISQLRDVGIYWLNNPN--TKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLV  649 (687)
Q Consensus       572 ~~ff~~~~n~~~i~~L~~~Gv~~~~~~~--~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV  649 (687)
                      ++||++++|+++|++|.+.|+++.....  ....+++|+|++|||||+|+.|+|++++++|+++||+|++|||++|||||
T Consensus       561 ~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV  640 (671)
T 2owo_A          561 HNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVLTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVI  640 (671)
T ss_dssp             HHHHTCHHHHHHHHHHHHHTCBCCCC------------------------------------------------------
T ss_pred             HHHHHhHHHHHHHHHHHHcCCcccccccccccccCCcccCcEEEEcCCCCCCCHHHHHHHHHHcCCEEeCcccCceeEEE
Confidence            9999999999999999999998753211  11235689999999999999999999999999999999999999999999


Q ss_pred             EcCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        650 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       650 ~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      +|+++|+|++||++|||+||+|++|++||+
T Consensus       641 ~G~~~gsKl~KA~~lgI~Ii~E~~f~~~l~  670 (671)
T 2owo_A          641 AGEAAGSKLAKAQELGIEVIDEAEMLRLLG  670 (671)
T ss_dssp             ------------------------------
T ss_pred             ECCCCChHHHHHHHCCCcEEcHHHHHHHhc
Confidence            999999999999999999999999999984

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=100.00  E-value=6.9e-188  Score=1596.68  Aligned_cols=654  Identities=39%  Similarity=0.657  Sum_probs=551.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCC-Ccceecccccc
Q psy11422         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGEN-SKYVHHTFKMM   90 (687)
Q Consensus        12 ~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~-~~kv~H~~pMl   90 (687)
                      +++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.++|||||+||+.+.++ |.||+|++|||
T Consensus         4 ~~~~~~~~~L~~~l~~~~~~YY~~d~p~isD~eYD~l~~eL~~lE~~~P~l~~~dSpt~rVG~~~~~~~f~~v~H~~pMl   83 (667)
T 1dgs_A            4 EEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMY   83 (667)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHHHTTSSGGGCCTTSGGGGCSSSCCCCCCCEEECSSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCCccccCCccceECCCcCc
Confidence            45568999999999999999999999999999999999999999999999999999999999999888 99999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11422         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (687)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (687)
                      ||+|+||.+||.+|++|+.+.++  .++.|+|||||||+|| |+|+||+  +|+|||||.+|||||+|+++|++||++|.
T Consensus        84 SL~n~~~~~el~~f~~rv~~~~~--~~~~~~~e~KiDGlai-L~Ye~G~--~a~TRGDG~~GedvT~n~rtI~~iP~~l~  158 (667)
T 1dgs_A           84 SLDNAFTYEEVLAFEERLEREAE--APSLYTVEHKVDGLSV-LYYEEGV--WSTGSGDGEVGEEVTQNLLTIPTIPRRLK  158 (667)
T ss_dssp             CCCEECSHHHHHHHHHHTTSSSC--SCCEEEEEECCSCEEE-EEEETTE--EEEEECSSSEEEBCTGGGTSSTTSCSBCS
T ss_pred             CccccCCHHHHHHHHHHHHHhcC--CCceEEEEEccceeEE-EEEcCCC--EEEeeCCCcchhhHHHHHhhhcCCCcccC
Confidence            99999999999999999988775  2478999999999999 9999999  99999999999999999999999999997


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccccccccc--EEEEEeccc-ccCCCCCC
Q psy11422        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKIL--HFFAHGVGE-LRGMNMPS  247 (687)
Q Consensus       171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l--~f~~y~~~~-~~~~~~~~  247 (687)
                      +.  |..+|||||+||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|  +||+|+|.. .++.. +.
T Consensus       159 ~~--p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaaAGsLrqld~~~~a~r~L~~~~~~y~~~~~~~~~~-~~  235 (667)
T 1dgs_A          159 GV--PDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESG-LK  235 (667)
T ss_dssp             SC--CSEEEEEEEEECCHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHSCSSHHHHHHSCCEEECCCBCTTTTTTSCC-CC
T ss_pred             CC--CCeEEEEEEEEEEHHHHHHHHHHHHhcCCCcccChHHHHHHHHHhcChhhhhhCCCCCEEEEEEeeccCCCCC-CC
Confidence            52  88999999999999999999999999999999999999999999999999999999  999999931 12222 48


Q ss_pred             CHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11422        248 SHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (687)
Q Consensus       248 ~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (687)
                      +|++.|++|++|||+|+++.+.|.+.+++++|+++|.+.|..|||+|||+||||||+.+|+.||+|+|+||||||||||+
T Consensus       236 t~~e~l~~L~~~Gf~v~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGvViKv~~~~~q~~LG~t~k~PrWAiA~Kfpa  315 (667)
T 1dgs_A          236 SQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPA  315 (667)
T ss_dssp             BHHHHHHHHHHTTCCCCSCEEEEEHHHHHHHHHHHHHHTTTTSSSCCCEEEEEESBTHHHHHSCBCSSCBSSEEEEECCC
T ss_pred             CHHHHHHHHHHCCCCCCccceEeCCHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHHhCcccCCCCceEEecCCC
Confidence            99999999999999999998999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCC
Q psy11422        328 KEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPN  407 (687)
Q Consensus       328 ~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~  407 (687)
                      ++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++
T Consensus       316 e~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrAtLhN~d~i~~~di~iGD~V~V~rAGdvIP~i~~vv~~~R~~  395 (667)
T 1dgs_A          316 EEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTG  395 (667)
T ss_dssp             CCEEEEEEEEEEEECTTSBEEEEEEEEEEEETTEEEEEEECCSHHHHHHTTCBSSCEEEEEEETTTEEEEEEECGGGCCS
T ss_pred             ceEEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEcccCCHHHHHHcCCCCCCEEEEEECCCcchhhhccccccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11422        408 DSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (687)
Q Consensus       408 ~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (687)
                      ++.+|.+|++||+||+++  .+|++.+||+|. . ||+|++++|.||+||++|||+|||+|+|++|+++|+|++++|||.
T Consensus       396 ~~~~~~~P~~CP~Cgs~l--~~g~~~~~C~n~-~-Cpaq~~~~l~hf~sr~aldI~GLG~k~i~~L~~~g~I~~~~DL~~  471 (667)
T 1dgs_A          396 KERPIRWPEACPECGHRL--VKEGKVHRCPNP-L-CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYH  471 (667)
T ss_dssp             CCCBCCCCSBCTTTCCBC--EEETTEEECCCT-T-CGGGHHHHHHHHHSTTSSCCTTCCHHHHHHHHHTTSCSSGGGGGG
T ss_pred             cCCcccCCCCCCCCCCCc--cCCCeEEEeCCC-C-ChhHHHHHHHHHhcccccCcCcCCHHHHHHHHHcCCCCCHHHHHh
Confidence            889999999999999999  567799999996 6 999999999999999999999999999999999999999999999


Q ss_pred             CChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHH
Q psy11422        488 INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT  567 (687)
Q Consensus       488 L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~  567 (687)
                      |+.++|..++|||+|+++||+++|+++|+.+|+|||+||||||||+++|+.|+++|+++++|..|+.++|.+++|||+++
T Consensus       472 L~~e~L~~l~g~G~Ksa~nLl~aIe~sk~~~l~R~L~alGI~~VG~~~Ak~La~~Fgsl~~l~~As~eeL~~I~GIG~~~  551 (667)
T 1dgs_A          472 LRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELT  551 (667)
T ss_dssp             GCCHHHHTTSSCCSTTHHHHHHHHHHGGGCCHHHHHHHTTCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHHTSTTCCHHH
T ss_pred             cCHHHHhcccccchhhHHHHHHHHHHHhcCcHHHhhHhhccCCccHHHHHHHHHHcCCHHHHHhCCHHHHHhccCcCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccE
Q psy11422        568 VKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNY  647 (687)
Q Consensus       568 A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~  647 (687)
                      |++|.+||+++.|+++|++|.+.|+++...  .. .+++|+|++|||||+|+. +|++++++|+++||+|++|||++|||
T Consensus       552 A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~--~~-~~~~l~G~~~v~TG~l~~-~R~e~~~~i~~~Ggkv~~sVSkkTd~  627 (667)
T 1dgs_A          552 ARAILETLKDPAFRDLVRRLKEAGVSMESK--EE-VSDLLSGLTFVLTGELSR-PREEVKALLGRLGAKVTDSVSRKTSY  627 (667)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHTTCCCBCC--------------------------------------------------
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHcCCccccc--cc-cccccCCCEEEEeCCCCC-CHHHHHHHHHHcCCEEcCcccCCeeE
Confidence            999999999999999999999999987531  11 356899999999999987 99999999999999999999999999


Q ss_pred             EEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11422        648 LVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       648 LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      ||+|+++|+|++||++|||+||+|++|++||+..
T Consensus       628 lV~G~~~gsKl~KA~~lgI~Ii~E~~f~~~l~~~  661 (667)
T 1dgs_A          628 LVVGENPGSKLEKARALGVAVLTEEEFWRFLKEK  661 (667)
T ss_dssp             ----------------------------------
T ss_pred             EEECCCCChHHHHHHHCCCeEEeHHHHHHHHhcC
Confidence            9999999999999999999999999999999753

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=100.00  E-value=4.4e-175  Score=1474.53  Aligned_cols=585  Identities=43%  Similarity=0.722  Sum_probs=561.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11422         11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM   90 (687)
Q Consensus        11 ~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl   90 (687)
                      |+++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+.++|.||+|++|||
T Consensus         1 me~~~~~i~~L~~~i~~~~~~Yy~~~~p~IsD~eYD~L~~eL~~lE~~~p~l~~~dSPtqrVG~~~~~~f~kv~H~~pMl   80 (586)
T 4glx_A            1 MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAPLAAFSQIRHEVPML   80 (586)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHHHHHHHSGGGCCTTSGGGC----CCBCCCEEECSSCCC
T ss_pred             CchHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCcccccccccCCCCcccCCCCCC
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11422         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (687)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (687)
                      ||+|+||.+||.+|++|+.+.|+..++..|+|||||||+|++|+|+||+|++|+|||||.+|||||+|+++|++||++|.
T Consensus        81 SL~n~~~~~el~~~~~r~~~~l~~~~~~~~~~epKiDGlavsL~Ye~G~Lv~a~TRGDG~~GeDiT~nvrtI~~IPl~l~  160 (586)
T 4glx_A           81 SLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLH  160 (586)
T ss_dssp             CCCEECSHHHHHHHHHHHHHC-------CEEEEEEESSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSBCC
T ss_pred             CccccCCHHHHHHHHHHHHHHhccCCCceEEEEEeecceEEEEEEeCCEEEEEEccCCCcccccHHHHHHhccCcccccc
Confidence            99999999999999999999887555678999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHH
Q psy11422        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS  250 (687)
Q Consensus       171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~  250 (687)
                      +.++|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++...++..++.+|+
T Consensus       161 ~~~~p~~leVRGEv~m~~~~F~~ln~~~~~~g~~~faNpRNaaAGslrqld~~~~a~r~L~f~~y~v~~~~~~~~~~t~~  240 (586)
T 4glx_A          161 GENIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHL  240 (586)
T ss_dssp             SSSCCSEEEEEEEEECCHHHHHHHHHHHHHTTCCCCSCHHHHHHHHHTCSCHHHHHTSCCEEEEEEEEEEESSCCCSBHH
T ss_pred             cCCCCceEEEEEEEEEEhhhccccchhhhhccCccchhhHHHHhccccccchhhhhccccceeEeeeeeeecccccccHH
Confidence            76789999999999999999999999999999999999999999999999999999999999999998766656678999


Q ss_pred             HHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCcee
Q psy11422        251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEA  330 (687)
Q Consensus       251 e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~  330 (687)
                      +.|++|++|||+++++...+.+.+++.+|+++|...|..+||+|||||||+|++.+|+.||+|+|+||||||||||++++
T Consensus       241 e~l~~L~~~Gf~v~~~~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~~~lG~ts~~PrwAiA~Kfp~e~~  320 (586)
T 4glx_A          241 GRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARAPRWAVAFKFPAQEQ  320 (586)
T ss_dssp             HHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHHGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEECCCCCEE
T ss_pred             HHHHHHHHcCCCCccceeeeccHHHHHHHHHHHHHhhhcccccCCceEEEecchhhhhccCCccCCCCeeEEEcccchhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCc
Q psy11422        331 LTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSK  410 (687)
Q Consensus       331 ~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~  410 (687)
                      +|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+++.|++++.
T Consensus       321 ~T~v~~I~~qVGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~I~~~di~iGD~V~V~rAGdVIP~I~~Vv~~~r~~~~~  400 (586)
T 4glx_A          321 MTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTR  400 (586)
T ss_dssp             EEEEEEEEEEECTTSBEEEEEEEEEEEETTEEEEEEECCCHHHHHHHTCEETCEEEEEEETTTEEEEEEECGGGCCSSCE
T ss_pred             eeEeEEEEEecCCceEEEEEEEEeeEEeCCEEEEecccCCHHHHHhcCCCcCCEEEEEECCCcCccceeeecccCCccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCCh
Q psy11422        411 IFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF  490 (687)
Q Consensus       411 ~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~  490 (687)
                      +|.+|++||+||+++++.++++.+||+|+.. ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|+.
T Consensus       401 ~~~~P~~CP~Cgs~~~~~~~~~~~rC~n~~~-Cpaq~~~~l~hf~sr~amdI~GlG~~~i~~L~~~g~i~~~~Dly~L~~  479 (586)
T 4glx_A          401 EVVFPTHCPVCGSDVERVEGEAVARCTGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTA  479 (586)
T ss_dssp             ECCCCSBCTTTCCBEECCTTCSCCEESCGGG-CHHHHHHHHHHHHSTTTTCCTTCCHHHHHHHHHTTCCSSGGGGGTCCH
T ss_pred             CCcCCCcCCCCCCchhhhhcccccEeCCCcC-cHHHHHhHHHhhhccccccCCCcCHHHHHHHHhcCCCCCHHHHhCCCH
Confidence            9999999999999999999999999999766 999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHH
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA  570 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~s  570 (687)
                      ++|++++|||+|+|+||+++|++||+.+|+|||+|||||+||+.+|+.|+++|+++++|.+|+.++|.+|+|||+++|++
T Consensus       480 ~~L~~l~g~geKsa~nL~~aIe~sk~~~l~r~l~aLGI~~vG~~~a~~La~~f~sl~~l~~a~~e~l~~i~giG~~~A~s  559 (586)
T 4glx_A          480 GKLTGLERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASH  559 (586)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHH
T ss_pred             HHHhcccCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCCchhHHHHHHHHHHcCCHHHHHccCHHHHhcCCCccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcchhHHHHHHHHHhcCccccc
Q psy11422        571 FIKFINQPLHRLLISQLRDVGIYWLN  596 (687)
Q Consensus       571 I~~ff~~~~n~~~i~~L~~~Gv~~~~  596 (687)
                      |.+||++++|+++|++|.+.||+|+.
T Consensus       560 i~~ff~~~~n~~~i~~L~~~Gv~~~~  585 (586)
T 4glx_A          560 VHNFFAEESNRNVISELLAEGVHWPA  585 (586)
T ss_dssp             HHHHHHSHHHHHHHHHHHHTTCBCCC
T ss_pred             HHHHHcCHHHHHHHHHHHHcCCCCCC
Confidence            99999999999999999999999864

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=100.00  E-value=3.4e-175  Score=1474.22  Aligned_cols=585  Identities=36%  Similarity=0.575  Sum_probs=388.1

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCccc-CCCCcceeccc
Q psy11422          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GENSKYVHHTF   87 (687)
Q Consensus         9 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~-~~~~~kv~H~~   87 (687)
                      ....++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+ ..+|.||+|.+
T Consensus         8 ~~~~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVGg~~~~~~f~kV~H~~   87 (615)
T 3sgi_A            8 QTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLE   87 (615)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHHSCCCSSCCSSCSSSSHHHHHHTSSGGGCCTTCTTSCCCCCCCSSSCCBCCCSS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhCcCcCCCCCCcccCCCcccccCCCceecCC
Confidence            34466788999999999999999999999999999999999999999999999999999999999999 79999999999


Q ss_pred             cccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCc
Q psy11422         88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPL  167 (687)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~  167 (687)
                      |||||+|+||.+||.+|++|+.+.++.  ++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||+
T Consensus        88 pMlSL~n~f~~eel~~f~~rv~~~l~~--~~~~~~EpKiDGlavsL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~  165 (615)
T 3sgi_A           88 RMLSLDNAFTADELAAWAGRIHAEVGD--AAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPE  165 (615)
T ss_dssp             CCCCCEEECSSSCCSTTTTTSTTTTCS--CCCEEEEEEECSEEEEEEEETTEEEEEECCTTSSSCBCCHHHHHSCSSSCS
T ss_pred             ccCCccccCCHHHHHHHHHHHHHhcCC--CCeEEEEEEecceEEEEEEECCEEEEEEecCCCcchhhHHHHHHhhcCcch
Confidence            999999999999999999999988762  468999999999999999999999999999999999999999999999999


Q ss_pred             ccccCC---CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCC
Q psy11422        168 VLNIKY---PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN  244 (687)
Q Consensus       168 ~l~~~~---~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~  244 (687)
                      +|.+.+   +|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++..
T Consensus       166 ~L~~~~~~~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqld~~ita~R~L~~f~y~~~~~~~~~  245 (615)
T 3sgi_A          166 RLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR  245 (615)
T ss_dssp             SCCCCSSCCCCSEEEEEEEEECCHHHHHHHHTTCSSSSSCCCSSHHHHHHHHHTCSSTTHHHHSCCEEEEEEEEEEESCC
T ss_pred             hhcCCcccCCCCeEEEEEEEEEeHHHHHHHHHHHHHcCCCcCCChHHHHHHHHHcCChhhHhhCcceEEEEeccccCCCC
Confidence            998642   58899999999999999999999999999999999999999999999999999999999999998655443


Q ss_pred             CCCCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11422        245 MPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK  324 (687)
Q Consensus       245 ~~~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K  324 (687)
                       +.+|++.|++|++|||+|+++.+.|.+++++.+|+++|.+.|..|||+|||||||||++.+|+.||+|+|+||||||||
T Consensus       246 -~~t~~e~l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~lG~t~k~PRWAiA~K  324 (615)
T 3sgi_A          246 -PATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYK  324 (615)
T ss_dssp             -CSBTTTHHHHHHHTTCCCCCCCCCBSSHHHHHHHHTTTTTSGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEEE
T ss_pred             -CcCHHHHHHHHHHCCCCCCCCeEeeCCHHHHHHHHHHHHHHhhcCCCCCCeEEEEecCHHHHHHhCCCCCCCCceEEEc
Confidence             4799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCC
Q psy11422        325 FLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSL  404 (687)
Q Consensus       325 f~~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~  404 (687)
                      ||+++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||+|||+|.|+|||||||+|++|+.+.
T Consensus       325 fpaee~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLHN~d~i~~~di~iGD~V~V~rAGdVIP~V~~vv~~~  404 (615)
T 3sgi_A          325 YPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVEL  404 (615)
T ss_dssp             CCCSEEEEECCEECCCBCSSSCBCCBEECCCEECSSSEECCCBCCSTTTTTTTCCCBTCEEEEECCSSSSCCCCEECTTC
T ss_pred             CCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEEEEEecCCCHHHHHHcCCCCCCEEEEEEcCCCccceeeecccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccccCCCCCCCCCCccee-ecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChH
Q psy11422        405 RPNDSKIFKIPNICPICNSKIIY-IESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAV  483 (687)
Q Consensus       405 r~~~~~~~~~P~~CP~C~~~l~~-~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~  483 (687)
                      |++++.+|.+|++||+||++|++ .++++.+||+|+.. ||+|++++|.||+||+||||+|||+++|++|++.|+|++++
T Consensus       405 R~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~rC~n~~~-CpaQ~~~~l~hf~Sr~amdI~GlG~~~i~~L~~~g~i~~~a  483 (615)
T 3sgi_A          405 RDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARG-CPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEG  483 (615)
T ss_dssp             CCCCCBCCCCC---------------------------------------------------------------------
T ss_pred             CCCCCccCCCCCCCCCCCCeeeecCCCCEEEEcCCCCC-CHHHHHHHHHHHhccCccCccccCHHHHHHHHHCCCcCCHH
Confidence            99988999999999999999998 67889999999656 99999999999999999999999999999999999999999


Q ss_pred             HHhcCChhhhhcccCc------cHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHH
Q psy11422        484 DLYKINFKNLLRLDRV------SNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQL  557 (687)
Q Consensus       484 DL~~L~~~~L~~l~gf------G~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL  557 (687)
                      |||+|+.++|+.++||      |+|+|+||+++|++||+.+|+|||+||||||||+++|+.|+++|+++++|..|+.++|
T Consensus       484 Dly~L~~~~L~~l~~~~~~~g~g~ksa~nLl~aIe~sk~~~l~r~L~aLGIp~VG~~~ak~La~~Fgsle~L~~As~eeL  563 (615)
T 3sgi_A          484 ELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQL  563 (615)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhhCCHHHHhhccccccccCccchHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHH
Confidence            9999999999999977      5899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccC
Q psy11422        558 LNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN  597 (687)
Q Consensus       558 ~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~  597 (687)
                      .+++|||+++|++|++||++++|+++|++|.++||++...
T Consensus       564 ~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~  603 (615)
T 3sgi_A          564 AAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDE  603 (615)
T ss_dssp             ----------------------------------------
T ss_pred             hhCCCCCHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccc
Confidence            9999999999999999999999999999999999988653

>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A*

Probab=100.00  E-value=2.3e-103  Score=829.04  Aligned_cols=320  Identities=43%  Similarity=0.696  Sum_probs=305.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11422         14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD   93 (687)
Q Consensus        14 ~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~   93 (687)
                      +++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+..+|.||+|++|||||+
T Consensus         2 ~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~f~kv~H~~pMlSL~   81 (322)
T 3uq8_A            2 IQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLD   81 (322)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTSGGGCSCSSCCSSCCEEECSSCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcCCCCCCCcccccCcccccCCCceecCCcccCcc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHhhcc-CCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccC
Q psy11422         94 NGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (687)
Q Consensus        94 k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (687)
                      |+||.+||.+|++|+.+.|+. .+++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|.+.
T Consensus        82 n~~~~eel~~f~~rv~~~l~~~~~~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IPl~L~~~  161 (322)
T 3uq8_A           82 NAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTD  161 (322)
T ss_dssp             EECSHHHHHHHHHHHHHHCSSCCSSCEEEEEEEESSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHHTCTTSCSBCSCS
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCcCceEEEEEeeceEEEEEEEeCCEEEEEEecCCCccchhHHHHHHHhcCCCccccCC
Confidence            999999999999999998863 1347899999999999999999999999999999999999999999999999999864


Q ss_pred             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHH
Q psy11422        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL  252 (687)
Q Consensus       173 ~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~  252 (687)
                      ++|..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++..++.+|++.
T Consensus       162 ~~p~~leVRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLRqld~~ita~R~L~ff~y~~~~~~~~~~~~t~~e~  241 (322)
T 3uq8_A          162 NPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYAR  241 (322)
T ss_dssp             SCCSEEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHTCSCHHHHTTSCCEEEEEEEEEEESCCCCSBHHHH
T ss_pred             CCCceEEEEEEEEeeHHHHHHHHHHHHHhCCccccchhHHHHHHHhhcChhhhhcCccEEEEEeccccCCCCCCCCHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999765543345899999


Q ss_pred             HHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeE
Q psy11422        253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALT  332 (687)
Q Consensus       253 l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T  332 (687)
                      |++|++|||+|+++.+.|.+++++.+|+++|.+.|..|||+|||||||||++.+|+.||+|+|+||||||||||+++++|
T Consensus       242 l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiA~Kfpaee~~T  321 (322)
T 3uq8_A          242 LQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAIAYKFPAQEELT  321 (322)
T ss_dssp             HHHHHHTTCCCCTTCEEEESHHHHHHHHHHHHHTTTTTSSCEEEEEEEESBHHHHHHHCEETTEETTEEEEECCCGGGCC
T ss_pred             HHHHHHcCCCCCCCcEEeCCHHHHHHHHHHHHHHHhcCCCCCCeEEEEecCHHHHHHcCccCCCCCceEEEcCCcccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             E
Q psy11422        333 K  333 (687)
Q Consensus       333 ~  333 (687)
                      .
T Consensus       322 ~  322 (322)
T 3uq8_A          322 L  322 (322)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A*

Probab=100.00  E-value=9.2e-102  Score=814.60  Aligned_cols=312  Identities=41%  Similarity=0.677  Sum_probs=297.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccC
Q psy11422         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMS   91 (687)
Q Consensus        12 ~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlS   91 (687)
                      +++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+..+|.||+|++||||
T Consensus         2 ~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~p~l~~~dSPTqrVG~~~~~~f~kv~H~~pMlS   81 (318)
T 3jsl_A            2 ADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLS   81 (318)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCCSCCCCCCEEECSSCCCC
T ss_pred             chHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhCcCCCCCCCCccccCccccccCceeecCCcCcC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccccc
Q psy11422         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (687)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (687)
                      |+|+||.+||.+|++|+.+.|+   ++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++
T Consensus        82 L~n~f~~eel~~f~~r~~~~l~---~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~L~~  158 (318)
T 3jsl_A           82 LGNAFNEDDLRKFDQRIREQIG---NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE  158 (318)
T ss_dssp             CEEECSHHHHHHHHHHHHHHTC---SCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSBCSS
T ss_pred             ccccCCHHHHHHHHHHHHhhcC---CceEEEEEeecceEEEEEEECCEEEEEEeCCCCccchhHHHHHHHhcCCccccCC
Confidence            9999999999999999998886   4789999999999999999999999999999999999999999999999999974


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHH
Q psy11422        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (687)
Q Consensus       172 ~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e  251 (687)
                         |..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+.+++.. +.+|++
T Consensus       159 ---~~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLRqld~~ita~R~L~ff~y~~~~~~~~~-~~t~~e  234 (318)
T 3jsl_A          159 ---PLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFN-ARSQSE  234 (318)
T ss_dssp             ---CCCEEEEEEEECCHHHHHHHHHHHBTTBCCCCSSHHHHHHHHHSCSCHHHHHHSCCEEEEEEESCCTTCC-CSBHHH
T ss_pred             ---CCcEEEEEEEEEcHHHHHHHHHHHHHhCCccccChHHHHHHHHHccChhhhhhCcceEEEEecccccCCC-CCCHHH
Confidence               5679999999999999999999999999999999999999999999999999999999999998766544 489999


Q ss_pred             HHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCcee
Q psy11422        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEA  330 (687)
Q Consensus       252 ~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~  330 (687)
                      .|++|++|||+|+++..+|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||||+++-
T Consensus       235 ~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiAyKfp~~~~  313 (318)
T 3jsl_A          235 ALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEH  313 (318)
T ss_dssp             HHHHHHHHTCCCCTTCEEESSHHHHHHHHHHHHHHGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBTTEEEEECC----
T ss_pred             HHHHHHHCCCCcCCcceEeCCHHHHHHHHHHHHHHHhcCCCCCCcEEEEEeCHHHHHHhCCCCCCCCceEEECCCCccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999863

>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*

Probab=100.00  E-value=5.8e-101  Score=813.78  Aligned_cols=322  Identities=39%  Similarity=0.634  Sum_probs=297.8

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccc
Q psy11422          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFK   88 (687)
Q Consensus         9 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~p   88 (687)
                      ..+++++++|++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.++|.||+|++|
T Consensus         6 ~~~~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~f~kv~H~~p   85 (332)
T 1ta8_A            6 LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIP   85 (332)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCCCBCSSCCEEECSSC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCccccccCCccCCCCc
Confidence            35566778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcc
Q psy11422         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (687)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (687)
                      ||||+|+||.+||.+|++|+.+.++  .++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++
T Consensus        86 MlSL~n~f~~eel~~w~~rv~~~l~--~~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~  163 (332)
T 1ta8_A           86 MYSLNDGFSKEDIFAFDERVRKAIG--KPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMR  163 (332)
T ss_dssp             CCCCCEECSHHHHHHHHHHHHHHHS--SCCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSB
T ss_pred             CCCccccCCHHHHHHHHHHHHHhcC--CCceEEEeeeecceEEEEEEECCEEEEEEcCCCCccchhHHHHHHHhcCCccc
Confidence            9999999999999999999998876  24789999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCC
Q psy11422        169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS  248 (687)
Q Consensus       169 l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~  248 (687)
                      |..   |..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+
T Consensus       164 L~~---p~~leVRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLrqld~~ita~R~L~ff~y~i~~~~~~~-~~t  239 (332)
T 1ta8_A          164 LTE---PISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK-AKT  239 (332)
T ss_dssp             CSS---CCCEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHTCSBHHHHHTSCCEEEEEEESCCTTCC-CSB
T ss_pred             cCC---CCeEEEEEEEEEEHHHHHHHHHHHHhcCCccccChHHHHHHHHHccChhhHhhCCCEEEEEecccccCCC-CCC
Confidence            972   7889999999999999999999999999999999999999999999999999999999999997433323 489


Q ss_pred             HHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCc
Q psy11422        249 HSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (687)
Q Consensus       249 ~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (687)
                      |++.|++|++|||+++++..+|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||||++
T Consensus       240 ~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~tsk~PRWAiAyKfpae  319 (332)
T 1ta8_A          240 QFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPE  319 (332)
T ss_dssp             HHHHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHTGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEEECC--
T ss_pred             HHHHHHHHHHcCCCCCCcceEeCCHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHHhCCcCCCCCceeEecCCCc
Confidence            99999999999999999899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeEEEEE
Q psy11422        329 EALTKIKA  336 (687)
Q Consensus       329 ~~~T~v~~  336 (687)
                      +++|+|..
T Consensus       320 e~~T~l~~  327 (332)
T 1ta8_A          320 EAETVVZH  327 (332)
T ss_dssp             --------
T ss_pred             eEEEEEec
Confidence            99999874

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2

Probab=100.00  E-value=8e-101  Score=809.34  Aligned_cols=315  Identities=42%  Similarity=0.690  Sum_probs=295.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccC
Q psy11422         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMS   91 (687)
Q Consensus        12 ~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlS   91 (687)
                      ++++++|++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.++|.||+|++||||
T Consensus         4 ~~~~~~~~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~f~kv~H~~pMlS   83 (318)
T 1b04_A            4 QQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMS   83 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHHHHHHCGGGCCTTCGGGGTCCCCCSCCCEECCSSCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCccccccCCccCCCCcCcC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccccc
Q psy11422         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (687)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (687)
                      |+|+||.+||.+|++|+.+.++   .+.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus        84 L~n~f~~eel~~f~~rv~~~l~---~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~L~~  160 (318)
T 1b04_A           84 LANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKE  160 (318)
T ss_dssp             CCEECSTTHHHHHHHHHHHHHS---SCCEEEEEEESSEEEEEEEETTEEEEEEECTTSSCEEBCHHHHHTCTTSCSBCSS
T ss_pred             ccccCCHHHHHHHHHHHHHhcc---CceEEEEEecccEEEEEEEECCEEEEEEccCCCcccHHHHHhHHHhcCCCcccCC
Confidence            9999999999999999998886   3689999999999999999999999999999999999999999999999999972


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHH
Q psy11422        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (687)
Q Consensus       172 ~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e  251 (687)
                         |..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+|++
T Consensus       161 ---p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaAAGsLrqld~~ita~R~L~ff~y~~~~~~~~~-~~t~~e  236 (318)
T 1b04_A          161 ---PVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHSE  236 (318)
T ss_dssp             ---CCCEEEEEEEECCHHHHHHHHHHHHHC--CCCSCHHHHHHHHHHSSCHHHHHHTCCEEEEEEETTTTTTT-CCBHHH
T ss_pred             ---CCeEEEEEEEEEEHHHHHHHHHHHHHcCCCccchhhHHHHHHHHccChhhHhhCCCEEEEEecccccCCC-CCCHHH
Confidence               7889999999999999999999999999999999999999999999999999999999999997433323 489999


Q ss_pred             HHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceee
Q psy11422        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEAL  331 (687)
Q Consensus       252 ~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~  331 (687)
                      .|++|++|||+++++.++|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||||+++++
T Consensus       237 ~l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiA~Kfpaee~~  316 (318)
T 1b04_A          237 ALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAEEVV  316 (318)
T ss_dssp             HHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHHSTTCSSCEEEEEEEECBHHHHHHHCCCSSSCTTEEEEECCCC---
T ss_pred             HHHHHHHcCCCCCCcceEeCCHHHHHHHHHHHHHHHhhCCCCCCcEEEEecCHHHHHHhCCcCCCCCceeeecCCcceee
Confidence            99999999999999899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EE
Q psy11422        332 TK  333 (687)
Q Consensus       332 T~  333 (687)
                      |+
T Consensus       317 T~  318 (318)
T 1b04_A          317 TT  318 (318)
T ss_dssp             --
T ss_pred             cC
Confidence            85

>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}

Probab=100.00  E-value=2.2e-99  Score=801.47  Aligned_cols=316  Identities=37%  Similarity=0.571  Sum_probs=298.9

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcc-cCCCCcceecccc
Q psy11422         10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTFK   88 (687)
Q Consensus        10 ~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~p   88 (687)
                      .+..++++|++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+. +.++|.||+|++|
T Consensus         9 ~~~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~~f~kv~H~~p   88 (328)
T 1zau_A            9 TAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLER   88 (328)
T ss_dssp             CHHHHHTTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHHHHHHTSSTTCCTTCTTTTCSSCCCCCCCCCEECSSC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCCccccccCCccCCCCC
Confidence            456667899999999999999999999999999999999999999999999999999999999999 9999999999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcc
Q psy11422         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (687)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (687)
                      ||||+|+||.+||.+|++|+.+.++  .++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++
T Consensus        89 MlSL~n~f~~eel~~f~~rv~~~l~--~~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~  166 (328)
T 1zau_A           89 MLSLDNAFTADELAAWAGRIHAEVG--DAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPER  166 (328)
T ss_dssp             CCCCCCBSSHHHHHHHHHGGGTTTC--SCSCEEEEEEECSEEEEEECGGGBCCBCBBCTTSSEECBCHHHHHHSSSCCSB
T ss_pred             CCCccccCCHHHHHHHHHHHHHhcC--CCcceEEeeecceEEEEEEEECCEEEEEEccCCCcccHHHHHHHHHhcCCChh
Confidence            9999999999999999999998875  24689999999999999999999999999999999999999999999999999


Q ss_pred             c-ccC--CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC
Q psy11422        169 L-NIK--YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM  245 (687)
Q Consensus       169 l-~~~--~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~  245 (687)
                      | .+.  +.|..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||+++++|+|+||+|+++..++.. 
T Consensus       167 L~~g~~~~~p~~leVRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLrqld~~ita~R~L~f~~y~i~~~~~~~-  245 (328)
T 1zau_A          167 LTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR-  245 (328)
T ss_dssp             CCCBTTBCCCSCCEEEEEEBCCHHHHHHHHHSCSSTTSCCCSSHHHHHHHHHTCSSHHHHHHSCCBCCCCBCCCCSSCC-
T ss_pred             hccCCcCCCCCeEEEEEEEEEEHHHHHHHHHHHHHcCCccccChHHHHHHHHHccChhhhhcCcceEEEEeccccCCCC-
Confidence            9 532  257889999999999999999999999999999999999999999999999999999999999997433222 


Q ss_pred             CCCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecC
Q psy11422        246 PSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKF  325 (687)
Q Consensus       246 ~~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf  325 (687)
                      +.+|++.|++|++|||+|+++.++|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+|||||||||
T Consensus       246 ~~t~~e~l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiAyKf  325 (328)
T 1zau_A          246 PATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKY  325 (328)
T ss_dssp             CSBHHHHHHHHHTTTCCCCCCCCCBCHHHHHHHHHHHTTTTCSSCSSCEEEEEEEECBHHHHTTSCBCSSSBSSCCCEEC
T ss_pred             CCCHHHHHHHHHHcCCCCCCceEEeCCHHHHHHHHHHHHHHHhcCCCCCceEEEEecCHHHHHHhCccCCCCCceeEeCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCc
Q psy11422        326 LSK  328 (687)
Q Consensus       326 ~~~  328 (687)
                      |++
T Consensus       326 pae  328 (328)
T 1zau_A          326 PPE  328 (328)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            985

>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae}

Probab=100.00  E-value=8.7e-98  Score=786.72  Aligned_cols=305  Identities=37%  Similarity=0.600  Sum_probs=265.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11422         14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD   93 (687)
Q Consensus        14 ~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~   93 (687)
                      +++||++|+++|++||++||+.|+|+|||++||+|+++|++||++||++.+++|||++||+.+..+|.||+|++|||||+
T Consensus         1 i~~ri~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~le~~~P~~~~~~sPt~~VG~~~~~~f~kv~H~~pMlSL~   80 (305)
T 4glw_A            1 MNKRMNELVALLNRYATEYYTSDNPSVSDSEYDRLYRELVELETAYPEQVLADSPTHRVGGKVLDGFEKYSHQYPLYSLQ   80 (305)
T ss_dssp             -CHHHHC-----------------------------CHHHHHHHHSGGGCCTTCGGGGSCCCBCSSCEEEECSSCCCCCC
T ss_pred             ChHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCccccccccceeeeeeeeccC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCC
Q psy11422         94 NGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKY  173 (687)
Q Consensus        94 k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~  173 (687)
                      |+|+.+||.+|++|+.+.++   ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.  
T Consensus        81 n~~~~~el~~f~~r~~~~l~---~~~~~~epKiDGlavsL~Y~~G~L~~a~TRGDG~~GeDiT~n~~tI~~IP~~l~~--  155 (305)
T 4glw_A           81 DAFSREELDAFDARVRKEVA---HPTYICELKIDGLSISLTYEKGILVAGVTRGDGSIGENITENLKRVKDIPLTLPE--  155 (305)
T ss_dssp             EECSHHHHHHHHHHHTTTCS---SCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEECHHHHTTSTTSCSBCSS--
T ss_pred             CcCCHHHHHHHHHHHHHhcC---CCcEEEEeeecceEEEEEEeCCeEEEEEecCCCcchhhHHHHHhhccCCcccCCC--
Confidence            99999999999999998876   4689999999999999999999999999999999999999999999999999974  


Q ss_pred             CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHH
Q psy11422        174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL  253 (687)
Q Consensus       174 ~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l  253 (687)
                       |..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++..+++   +.+|++.|
T Consensus       156 -~~~levRGEv~m~~~~F~~~n~~~~~~g~~~faNpRNaaAGslrq~d~~~~~~r~L~f~~y~~~~~~~---~~s~~e~l  231 (305)
T 4glw_A          156 -ELDITVRGECYMPRASFDQVNQARQENGEPEFANPRNAAAGTLRQLDTAVVAKRNLATFLYQEASPST---RDSQEKGL  231 (305)
T ss_dssp             -CCCEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHSSSBHHHHHHSCCEEEEEEESSSCS---SSBHHHHH
T ss_pred             -cccccccceEEeehhhHHHHHHHHHhcCCccchhhhHHHhhhhhccCchhhhhhcceEEEeeeccccc---cchHHHHH
Confidence             67899999999999999999999999999999999999999999999999999999999999886654   57999999


Q ss_pred             HHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11422        254 NWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (687)
Q Consensus       254 ~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (687)
                      ++|++|||+++++..+|.+++++++|+++|.+.|..+||+|||||||||++.+|+.||+|+|+|||||||||||
T Consensus       232 ~~L~~~Gf~~~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiVikvn~~~~q~~lG~tsk~PrWAiA~KfpA  305 (305)
T 4glw_A          232 KYLEQLGFVVNPKRILAENIDEIWNFIQEVGQERENLPYDIDGVVIKVNDLASQEELGFTVKAPKWAVAYKFPA  305 (305)
T ss_dssp             HHHHHHTCCCCCCCEEESSHHHHHHHHHHHHHHGGGSSSCEEEEEEEECBHHHHHHHCBCSSSBSSEEEEECCC
T ss_pred             HHHHhCCCccCCceEEeCCHHHHHHHHHHHHHHhhcCCCCCCeEEEEEeCHHHHHHcCCcCCCCCceEEeCccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997

>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP; 2.9A {Pyrococcus abyssi GE5}

Probab=100.00  E-value=5e-38  Score=341.81  Aligned_cols=223  Identities=15%  Similarity=0.141  Sum_probs=190.4

Q ss_pred             CCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHHHHHHHHHHHHhhccCCC
Q psy11422         38 PIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKN  117 (687)
Q Consensus        38 p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~  117 (687)
                      +.-.|++||+|+++|+.||++| ++.        ||+.+..+|+++   .||+||+|+++.     |.+ +         
T Consensus        42 ~~~~D~eyd~l~~el~~lE~~~-~~~--------vg~~~~~~fpkv---~~mlsL~~~~~~-----~~~-~---------   94 (389)
T 2vug_A           42 DEFDGIRYVRFKDSAGKLRRGT-VVI--------DEEYVIPGFPHI---KRIINLRSGIRR-----IFK-R---------   94 (389)
T ss_dssp             CCTTSCCEEECSSCBTTBCTTC-EEE--------ETTEEECCCCCC---EEESSSHHHHHH-----HSS-S---------
T ss_pred             cccCCHHHHHHHHHHHHHHhhc-eee--------eCcEEccCCCCc---ccccCchhhhhh-----hcc-C---------
Confidence            4567999999999999999998 765        898888899988   899999999643     542 1         


Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~  196 (687)
                      ..|+||+|+||+++++.|++|+ ++|.|||+|.  +|||+|  +|++ ||..|...  |..++||||+||+...|+++| 
T Consensus        95 ~~~vvEeKlDG~~v~l~y~~G~-v~a~TRg~g~--e~iT~n--~i~~wip~~L~~~--~~~l~L~GEvv~~~~~f~~~n-  166 (389)
T 2vug_A           95 GEFYVEEKVDGYNVRVVMYKGK-MLGITRGGFI--CPFTTE--RIPDFVPQEFFKD--NPNLILVGEMAGPESPYLVEG-  166 (389)
T ss_dssp             CEEEEEEECCSEEEEEEEETTE-EEEEETTSCB--CHHHHH--HGGGTSCTHHHHH--CTTEEEEEEEESSSCSSCSCC-
T ss_pred             CeEEEEEeecCcEEEEEEECCE-EEEEeCCCCC--CCCchh--hhhHhHHHHHhcC--CCcEEEEEEEEecCChHHHhc-
Confidence            3799999999999999999999 8999999999  999999  8888 89777532  567999999999999886433 


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCCCCCceEeC--CHH
Q psy11422        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLS--GVN  274 (687)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~~~~~~~~~--~~~  274 (687)
                               ++||                 .|++.||+|++...++..+ .++.+.+++|+++||++++....+.  +.+
T Consensus       167 ---------~~np-----------------~r~l~F~vFDV~~~~~g~~-~s~~er~~~L~~lG~~~vp~~~~~~~~~~e  219 (389)
T 2vug_A          167 ---------PPYV-----------------KEDIQFFLFDVQEIKTGRS-LPVEERLKIAEEYGINHVEVFGKYTKDDVD  219 (389)
T ss_dssp             ---------CTTC-----------------CSSCEEEEEEEEETTTCCB-CCHHHHHHHHHHHTCCBCCEEEEEEGGGHH
T ss_pred             ---------ccCc-----------------ccCCEEEEEEeeccCCCCc-CCHHHHHHHHHHcCCCCCCeEEEEcCCCHH
Confidence                     2444                 5789999999964332223 6899999999999999998776666  789


Q ss_pred             HHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc---eEeecCCCcee
Q psy11422        275 KLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF---ALAYKFLSKEA  330 (687)
Q Consensus       275 ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw---aiA~Kf~~~~~  330 (687)
                      ++.++++.|.      +|.+||+|+|+++..  +.+|+|+++|||   |+|||||+++.
T Consensus       220 el~~~i~~~~------~~~~EGvViK~~d~~--~~lkyt~~~pr~~dlaiA~Kfp~e~~  270 (389)
T 2vug_A          220 ELYQLIERLS------KEGREGIIMKSPDMK--KIVKYVTPYANINDIKIGARVFYELP  270 (389)
T ss_dssp             HHHHHHHHHH------HTTCCEEEEECTTSC--CEEEEECHHHHHHHHHHHHTTGGGSC
T ss_pred             HHHHHHHHhc------CCCCCeEEEEECChh--hhcCceecCCCCcceEEEEecccccc
Confidence            9999999886      899999999999977  789999999999   99999999974

>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.7e-20  Score=169.45  Aligned_cols=80  Identities=44%  Similarity=0.679  Sum_probs=75.9

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      ..++|.|++|||||+|..++|++++++|+++||+|++|||++|||||+|+++| +|++||++|||+||+|++|++||+..
T Consensus        19 ~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~LV~G~~~g~sKl~KA~~lgI~IisE~~f~~ll~~~   98 (112)
T 2ebu_A           19 AENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRTM   98 (112)
T ss_dssp             CSSSSTTCEEEECSCCSSSCHHHHHHHHHHTTCEECSSCCSSCCEEEECSSCCSHHHHHHHHHTCEEEEHHHHHHHHHHS
T ss_pred             CCCCcCCCEEEEeeeCCCCCHHHHHHHHHHcCCEEeccccCCeeEEEecCCCChHHHHHHHHcCCeEEeHHHHHHHHhhC
Confidence            34689999999999999899999999999999999999999999999999999 99999999999999999999999754


Q ss_pred             c
Q psy11422        682 S  682 (687)
Q Consensus       682 s  682 (687)
                      .
T Consensus        99 ~   99 (112)
T 2ebu_A           99 P   99 (112)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2

Probab=99.82  E-value=8e-21  Score=166.15  Aligned_cols=80  Identities=38%  Similarity=0.584  Sum_probs=75.8

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhccc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS  682 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~~s  682 (687)
                      ..++|.|++|||||+|+. +|++++++|+++||+|++|||++|||||+|+++|+|++||+++||+||+|++|++||...+
T Consensus         4 ~~~~l~G~~~v~TG~l~~-~R~e~~~~i~~~Gg~v~~sVskkt~~LV~g~~~gsK~~kA~~lgI~Ii~E~~f~~~l~~~~   82 (92)
T 1l7b_A            4 GGEALKGLTFVITGELSR-PREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEART   82 (92)
T ss_dssp             CCCSSTTCEEECSTTTTS-CHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHHH
T ss_pred             CCCCcCCcEEEEecCCCC-CHHHHHHHHHHcCCEEeCcccCCeeEEEeCCCCChHHHHHHHcCCcEEeHHHHHHHHHhcc
Confidence            356899999999999987 9999999999999999999999999999999999999999999999999999999998665


Q ss_pred             C
Q psy11422        683 T  683 (687)
Q Consensus       683 ~  683 (687)
                      +
T Consensus        83 g   83 (92)
T 1l7b_A           83 G   83 (92)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A

Probab=99.82  E-value=1.9e-20  Score=168.74  Aligned_cols=78  Identities=45%  Similarity=0.695  Sum_probs=74.8

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+++|.|++|||||+|+.++|++++++|+++||+|++|||++|||||+|+++| +|++||+++||+||+|++|++||+.
T Consensus        29 ~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Gg~v~~sVSkkTd~LV~G~~~g~sK~~kA~~lgI~Ii~E~~f~~ll~~  107 (109)
T 2k6g_A           29 AENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRN  107 (109)
T ss_dssp             CTTTTTTCEEEEESBCSSCCHHHHHHHHHHTTCEEESSCCTTCCEEEECBCCCHHHHHHHHHHTCEEECHHHHHHHHHH
T ss_pred             CCCCCCCCEEEEeeeCCCCCHHHHHHHHHHcCCEeeCcccCCceEEEECCCCChHHHHHHHHcCCeEEeHHHHHHHHHh
Confidence            45689999999999999899999999999999999999999999999999999 9999999999999999999999964

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A

Probab=99.71  E-value=8.2e-18  Score=152.24  Aligned_cols=74  Identities=24%  Similarity=0.360  Sum_probs=67.4

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC---CCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK---PGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~---~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      ..+|.|++|||||+|.. +|++++++|+++||+|++|||++|||||+|+.   +|+|++||++|||+||+|++ +.++.
T Consensus         8 ~~~l~G~~~ViTG~l~~-~R~e~k~~ie~~Ggkv~~sVskkT~~lV~g~~~e~~gsKl~kA~~lgI~IvsE~~-l~~~~   84 (113)
T 2cok_A            8 DKPLSNMKILTLGKLSR-NKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDF-LQDVS   84 (113)
T ss_dssp             CCSSSSCEEEECSCCSS-CHHHHHHHHHHTTCEEESCSTTCSEEECCHHHHHHCCHHHHHHHHTTCCEECTHH-HHHHH
T ss_pred             CCCcCCCEEEEEecCCC-CHHHHHHHHHHCCCEEcCccccCccEEEECCCCCCCChHHHHHHHCCCcEEeHHH-HHHHH
Confidence            45899999999999975 99999999999999999999999999999954   88999999999999999995 44443

>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=2.7e-12  Score=119.01  Aligned_cols=76  Identities=16%  Similarity=0.114  Sum_probs=71.5

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..+|.|++|||||.+ ..+|++++++|+.+||++..+|+++||+||+++..++|+++|.++||+||++++|.+++..
T Consensus        20 ~~~f~g~~i~itG~~-~~~r~~l~~~i~~~Gg~v~~~~s~~~ThLI~~~~~~~K~~~A~~~gi~IV~~~Wl~d~~~~   95 (129)
T 2d8m_A           20 GKILQGVVVVLSGFQ-NPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGRIVRKEWVLDCHRM   95 (129)
T ss_dssp             TTTSTTEEEEEESCC-TTHHHHHHHHHHHTTEEEESSCCTTCCEEEESSSSCHHHHHHHHHTCEEEETHHHHHHHHT
T ss_pred             cccCCCeEEEEeCCC-cHHHHHHHHHHHHcCCEEeCCcCCCCeEEEecCCCChHHHHHHHCCCcEecHHHHHHHHHh
Confidence            347999999999998 4689999999999999999999999999999999999999999999999999999998853

>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe}

Probab=98.94  E-value=2e-09  Score=116.53  Aligned_cols=76  Identities=20%  Similarity=0.233  Sum_probs=70.2

Q ss_pred             CccCCeEEEEEcCCCcCC---HHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHc-CCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFK---RNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL-NIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~---R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~l-gI~Ii~E~~f~~~l~~  680 (687)
                      .+|.|.+|||||.++.++   |.++..+++.+||+++++||++|++||+|...|+|+++|+++ ||+|+++++|.+.+..
T Consensus       281 ~~L~G~~ivfSG~~~~~~~~~~~~l~~l~~~lGa~v~~~vs~~vTHLVa~~~~t~K~~~A~~~~~I~IV~~~Wl~~c~~~  360 (372)
T 3ef0_A          281 KVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQ  360 (372)
T ss_dssp             TTSTTCEEEEESSSCTTSCTTTSHHHHHHHHTTCEEESSSSSCCSEEEECSCCCHHHHHHHHSSSCCEEEHHHHHHHHHT
T ss_pred             hhcCCcEEEEecccCCCcchhHHHHHHHHHHcCCEEeCcCCCCceEEEEcCCCchHHHHHHhcCCCEEEcHHHHHHHHHh
Confidence            479999999999997544   599999999999999999999999999999889999999999 8999999999998853

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A*

Probab=98.86  E-value=2.6e-09  Score=112.50  Aligned_cols=76  Identities=20%  Similarity=0.250  Sum_probs=71.0

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccc-ccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFIS-KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVs-k~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..+|.|.+|||||... .+|++++++|+.+||+++++++ ++||+||+++..|+|+++|+++||+|+++++|.+.+..
T Consensus       197 ~~~f~g~~i~~tG~~~-~~r~~l~~li~~~GG~~~~~ls~~~~THLI~~~~~g~K~~~A~~~gi~IV~~~Wl~dsi~~  273 (298)
T 3olc_X          197 CPIFLGCIICVTGLCG-LDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEK  273 (298)
T ss_dssp             CCTTTTCEEEECSCCH-HHHHHHHHHHHHTTCEECSSCCTTTCCEEECSSSCSHHHHHHHHTTCEEECHHHHHHHHHH
T ss_pred             ccccCCeEEEEeCCCC-ccHHHHHHHHHHcCCEEeceecCCCceEEEEeCCCchHHHHHHHCCCeEEeHHHHHHHHHC
Confidence            3579999999999876 4899999999999999999999 89999999999999999999999999999999998863

>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe}

Probab=98.77  E-value=9.8e-09  Score=112.85  Aligned_cols=76  Identities=20%  Similarity=0.232  Sum_probs=70.4

Q ss_pred             CccCCeEEEEEcCCCcC---CHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHc-CCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAF---KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL-NIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~---~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~l-gI~Ii~E~~f~~~l~~  680 (687)
                      .+|.|.+|||||.++..   .|.++..+++.+||+++++||++|++||++...|+|+++|+++ ||+||++++|.+.+..
T Consensus       351 ~~L~G~~IvfSG~~p~~~~~~r~~l~~~~~~lGa~~~~~vs~~vTHLVa~~~~t~K~~~A~~~g~IkIVs~~WL~dcl~~  430 (442)
T 3ef1_A          351 KVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQ  430 (442)
T ss_dssp             TTSTTCEEEEESSSCTTSCSTTSHHHHHHHTTTCEECSSSSSCCSEEEECSCCCHHHHHHHHHSSSEEEEHHHHHHHHHH
T ss_pred             cccCCcEEEEecccCCCCCccHHHHHHHHHHcCCEEeCCCCCCceEEEeCCCCCHHHHHHHhcCCCEEEeHHHHHHHHHc
Confidence            37999999999999654   5899999999999999999999999999999889999999999 5999999999998863

>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens}

Probab=98.74  E-value=5.7e-09  Score=94.23  Aligned_cols=75  Identities=16%  Similarity=0.145  Sum_probs=69.5

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+|.|.+|||||. +...|.+++++|+.+||+++..++++++.||+.+..+.|++.|.+.+|+|++.++|++-++.
T Consensus        20 p~F~g~~Ic~sGf-~~~er~~l~~~i~~~GG~~~~~l~~~cTHLV~~~~~~~K~~~A~~~~i~IVs~eWl~dsi~~   94 (112)
T 3l46_A           20 PPFQDCILSFLGF-SDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKKLYVVKQEWFWGSIQM   94 (112)
T ss_dssp             CTTTTCEECEESC-CHHHHHHHHHHHHHTTCEECCTTCTTCSEEEECTTTBSSCSSCCCSSCEEEEHHHHHHHHHH
T ss_pred             CccCCeEEEEeCC-CHHHHHHHHHHHHHcCCEECcccCCCceEEEecCCchhhHHHHHHCCeeEecHHHHHHHHHc
Confidence            4899999999994 45689999999999999999999999999999998889999999999999999999998863

>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C}

Probab=98.74  E-value=1.6e-08  Score=87.21  Aligned_cols=75  Identities=24%  Similarity=0.261  Sum_probs=64.5

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccc--ccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFIS--KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVs--k~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+.+|.|.+|||+|... .+|.+++++|+.+||++..+++  +++++||++...+.|..++  .|++|++++++.+.+..
T Consensus         4 ~~~~f~g~~~~i~g~~~-~~~~~l~~~i~~~GG~~~~~~~~~~~~THlI~~~~~~~K~~~~--~~~~iV~~~Wi~dci~~   80 (92)
T 4id3_A            4 SSKIFKNCVIYINGYTK-PGRLQLHEMIVLHGGKFLHYLSSKKTVTHIVASNLPLKKRIEF--ANYKVVSPDWIVDSVKE   80 (92)
T ss_dssp             --CTTTTCEEEECSCCS-SCHHHHHHHHHHTTCEEESSCCCTTTCCEEECSCCCHHHHHHT--TTSCEECTHHHHHHHHH
T ss_pred             cccccCCEEEEEeCCCC-cCHHHHHHHHHHCCCEEEEEecCCCceEEEEecCCCHHHHHHc--CCCCEEcccHHHHHHHc
Confidence            35689999999999533 3899999999999999999999  8999999999877776544  79999999999998864

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=98.69  E-value=1.5e-08  Score=87.95  Aligned_cols=66  Identities=23%  Similarity=0.405  Sum_probs=60.3

Q ss_pred             cccCCHHHHHHHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchh
Q psy11422        514 SKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (687)
Q Consensus       514 sk~~~l~r~L~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~  579 (687)
                      .+...+.+++.+| +|||||+++|+.|+++|++++++..++.++|.+++|||+++|++|..+|+++.
T Consensus        22 ~~~~~~~~~~~~L~~IpgIG~~~A~~Ll~~fgs~~~l~~as~~eL~~i~GIG~~~a~~I~~~l~~~~   88 (91)
T 2a1j_B           22 LEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPF   88 (91)
T ss_dssp             HHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCS
T ss_pred             ccCCHHHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhh
Confidence            3445678999999 99999999999999999999999999999999999999999999999997653

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A*

Probab=98.64  E-value=3.9e-08  Score=103.57  Aligned_cols=75  Identities=20%  Similarity=0.197  Sum_probs=70.4

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      +.+|.|.+||+||.... .|+++.++|+.+||++.++++++||+||+|...+.|+.+|.++||+|++++++.+++.
T Consensus       103 ~~~l~g~~~~~tG~~~~-~r~~l~~~i~~~GG~v~~~~t~~tTHLI~~~~~t~Ky~~A~~~gi~IV~~~Wl~~c~~  177 (298)
T 3olc_X          103 NMVMSDVTISCTSLEKE-KREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWE  177 (298)
T ss_dssp             CCTTTTCEEEEESCCHH-HHHHHHHHHHHTTCEECSSCCTTCCEEEESSSCSHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             ccccCCeEEEeCCCcHH-hHHHHHHHHHHCCCEEecCcCCCeeEEEEeCCCChHHHHHHHCCCeEeeHHHHHHHHH
Confidence            34789999999999865 8999999999999999999999999999999989999999999999999999998875

>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.57  E-value=2.9e-08  Score=89.16  Aligned_cols=76  Identities=13%  Similarity=0.119  Sum_probs=69.3

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      -.+|.|.+|||||. ....|.+++.+|+.+||+++..++++++.||+.+..+.|++.|.+.+|+|++.++|.+-+..
T Consensus        10 ~~~F~g~~i~~sg~-~~~~r~~l~~~i~~~GG~~~~~~~~~~THLV~~~~~~~K~~~a~~~~i~IV~~~Wl~dsi~~   85 (109)
T 2cou_A           10 VPPFQDCILSFLGF-SDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPSKKLFVVKQEWFWGSIQM   85 (109)
T ss_dssp             CCTTTTCBEEEESS-CHHHHHHHHHHHHHHTCBCCCTTCTTCSEEEECTTTCSSCSSCCCTTSEEECHHHHHHHHHT
T ss_pred             CCcCCCeEEEecCC-CHHHHHHHHHHHHHcCCEEecccCCCccEEEEeCCccHHHHHHHHCCCeEecHHHHHHHHHc
Confidence            34799999999995 44689999999999999999999999999999988789999999999999999999998753

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=98.56  E-value=1.2e-07  Score=81.93  Aligned_cols=60  Identities=25%  Similarity=0.460  Sum_probs=55.6

Q ss_pred             HHHHHHHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        519 FSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       519 l~r~L~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      +.++..+| +|||||+++|+.|+++|++++++..++.++|.+++|||+++|++|..+|.++
T Consensus        14 ~~~~~~~L~~IpgIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~~   74 (89)
T 1z00_A           14 VSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             HHHHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            46777788 9999999999999999999999999999999999999999999999998654

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=98.41  E-value=3.9e-07  Score=75.56  Aligned_cols=55  Identities=29%  Similarity=0.485  Sum_probs=52.1

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhH
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n  580 (687)
                      .+|||||+.+|+.|+++|++++.+..++.++|..++|||+++|.+|..+|.++.+
T Consensus        17 ~~i~giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~~~   71 (75)
T 1x2i_A           17 EGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYI   71 (75)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCC
T ss_pred             cCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCccc
Confidence            5999999999999999999999999999999999999999999999999987654

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=98.33  E-value=3.5e-07  Score=73.99  Aligned_cols=51  Identities=22%  Similarity=0.414  Sum_probs=48.0

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHH-HHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT-VKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~-A~sI~~ff~~~  578 (687)
                      ..|||||+++++.|+++|+|++++..|+.++|.++  +|... |+.|++||+.+
T Consensus         7 ~~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~v--ig~~~~A~~I~~~l~~~   58 (63)
T 2a1j_A            7 LKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTS   58 (63)
T ss_dssp             HTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHH--HSCHHHHHHHHHHHHCC
T ss_pred             HcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--cCchHHHHHHHHHHhcc
Confidence            47999999999999999999999999999999999  89999 99999999754

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=98.28  E-value=5.2e-07  Score=75.93  Aligned_cols=51  Identities=20%  Similarity=0.299  Sum_probs=48.9

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+|||||+++|+.|+++|++++++..++.++|.+++|||+++|++|..+|+
T Consensus        27 ~~I~gIG~~~A~~Ll~~fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~~~   77 (78)
T 1kft_A           27 ETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             GGCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHh
Confidence            489999999999999999999999999999999999999999999999985

>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A*

Probab=98.25  E-value=8.5e-06  Score=85.64  Aligned_cols=200  Identities=13%  Similarity=0.095  Sum_probs=123.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~  197 (687)
                      ..|++|+|+||+-+.+   +|   ++.||    .|+|+|.  ..|.   ..+..  .+ ...+-||+++...+|+.+...
T Consensus        19 ~~~~~E~K~DG~R~~~---~g---~l~SR----~g~~~t~--p~l~---~~~~~--~~-~~iLDGElv~~~~~F~~l~~~   80 (297)
T 1fvi_A           19 FPCLATPKIAGIRSVK---QT---QMLSR----TFKPIRN--SVMN---RLLTE--LL-PEGSDGEISIEGATFQDTTSA   80 (297)
T ss_dssp             SSEEEEECCCSEEEEE---SS---SEECT----TSCBCSC--HHHH---HHHHH--HS-CTTEEEEEECTTSCHHHHHHH
T ss_pred             CcEEEEeeEeeeeEEe---cC---EEECC----CCcccCc--HHHH---HHHHh--cC-CeeEEEEEEECCCCHHHHHHH
Confidence            3699999999999876   88   88999    5888885  2111   11110  01 356889999988888876443


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhc----C-------CCCCC-
Q psy11422        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI----G-------LSICG-  265 (687)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~----G-------f~~~~-  265 (687)
                                         +++.++.  ...++.|++|++...+ .  .....+..+.|+++    +       +.+++ 
T Consensus        81 -------------------~~~~~~~--~~~~~~~~vFDll~l~-~--~~pl~eRr~~L~~~~~~~~~~~~~~~i~~~~~  136 (297)
T 1fvi_A           81 -------------------VMTGHKM--YNAKFSYYWFDYVTDD-P--LKKYIDRVEDMKNYITVHPHILEHAQVKIIPL  136 (297)
T ss_dssp             -------------------HHSCC------CCEEEEEEEECSSC-T--TSCHHHHHHHHHHHHHHCGGGGGCSSEEEEEC
T ss_pred             -------------------hccCCCC--CccceEEEEEeccCCC-C--CCCHHHHHHHHHHHHhhcCCccccceEEEcCc
Confidence                               2232322  2357999999998533 2  25677888777765    1       11122 


Q ss_pred             CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCC----CceEeecCCCceeeEEEEEEEEe-
Q psy11422        266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAP----RFALAYKFLSKEALTKIKAINIQ-  340 (687)
Q Consensus       266 ~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~P----rwaiA~Kf~~~~~~T~v~~I~~q-  340 (687)
                      ....+.+.+++.++++...+      --.+|||+|--+..++.  |   +.+    .| +-+|- ...+...|.+..+- 
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--G---Rs~~~~g~w-lK~K~-~~~~d~vVig~~~g~  203 (297)
T 1fvi_A          137 IPVEINNITELLQYERDVLS------KGFEGVMIRKPDGKYKF--G---RSTLKEGIL-LKMKQ-FKDAEATIISMTALF  203 (297)
T ss_dssp             CCEEECSHHHHHHHHHHHHH------TTCCSEEEECTTCCCCS--S---BCCTTTTSS-EEECC-CEEEEEEEEEEEESC
T ss_pred             ceEecCCHHHHHHHHHHHHH------CCCcEEEEECCCCCcCC--C---CCCCCCCCe-EEECC-CCCEEEEEEEEEeCc
Confidence            02234678899998877643      34699999986654442  2   344    56 45553 45678888888886 


Q ss_pred             --------------------ecC--cceeeeEEEEEEEEECCEEEEEecCCCHHHHHh
Q psy11422        341 --------------------IGR--TGIITPVALLKPVLIDGITITRATLHNESEIYR  376 (687)
Q Consensus       341 --------------------vGR--TG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~  376 (687)
                                          -||  +|.+--...-.|    |..+.-.|..+-+..++
T Consensus       204 ~~~~~~~~~~~g~~~r~~~~~G~~~~g~~g~ll~~~~----g~~~~vgtGftd~~~~~  257 (297)
T 1fvi_A          204 KNTNTKTKDNFGYSKRSTHKSGKVEEDVMGSIEVDYD----GVVFSIGTGFDADQRRD  257 (297)
T ss_dssp             C-------------------CCCTTCCCEEEEEECST----TCCEEECSSCCHHHHHH
T ss_pred             cccccccccccccccccccCCCcccCCcEEEEEEccC----CeEEEECCCCCHHHHHH
Confidence                                665  454322211112    66554448888887774

>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens}

Probab=98.16  E-value=4.4e-06  Score=72.79  Aligned_cols=75  Identities=16%  Similarity=0.190  Sum_probs=65.4

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccc-ccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFIS-KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVs-k~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ....|+|..||++|... .+|++++.+|+.+||++....+ .++++||++...+.|++.|+  +++|++.+++.+-+..
T Consensus         9 ~~~lF~g~~~~isg~~~-~~~~~L~~~i~~~GG~~~~~~~~~~~THlI~~~~~~~k~~~~~--~~~iV~p~Wl~dci~~   84 (97)
T 2ebw_A            9 SSTIFSGVAIYVNGYTD-PSAEELRKLMMLHGGQYHVYYSRSKTTHIIATNLPNAKIKELK--GEKVIRPEWIVESIKA   84 (97)
T ss_dssp             CCCTTTTCEEEECSSCS-SCHHHHHHHHHHTTCEECSSCCSSSCCEEECSCCCTTHHHHTS--SSCCBCTHHHHHHHHH
T ss_pred             CCCCCCCeEEEEeCCCc-ccHHHHHHHHHHcCCEEeeecCCCCCEEEEecCCChHHHHHhc--CCCEeChHHHHHHHHc
Confidence            45689999999999754 5899999999999999988776 68999999988788888776  9999999999998753

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=98.12  E-value=2e-06  Score=73.53  Aligned_cols=52  Identities=21%  Similarity=0.419  Sum_probs=48.9

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHH-HHHHHHHHcchh
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT-VKAFIKFINQPL  579 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~-A~sI~~ff~~~~  579 (687)
                      ..|||||+++++.|+++|+++++|..|+.++|.++  ||... |+.|++||+.+.
T Consensus        21 ~~IpGIG~kr~~~LL~~FgSl~~i~~AS~eEL~~v--ig~~~~A~~I~~~l~~~~   73 (84)
T 1z00_B           21 LKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTSF   73 (84)
T ss_dssp             HTCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHH--HSCHHHHHHHHHHHTSBH
T ss_pred             HhCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--hCchHHHHHHHHHHHhhh
Confidence            48999999999999999999999999999999999  99999 999999998654

>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus}

Probab=98.06  E-value=5.1e-05  Score=86.29  Aligned_cols=215  Identities=18%  Similarity=0.164  Sum_probs=136.3

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKK----DFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~----~F~~  193 (687)
                      .|++|+|+||.-+.+.+.+|. ++..||+    |+|+|+....|.. +...+     |..+.+-||++.-..    .|+.
T Consensus       246 ~~~~E~K~DG~R~qi~~~g~~-v~l~SR~----g~d~t~~fPel~~~~~~~l-----~~~~iLDGElv~~~~g~~~~F~~  315 (558)
T 3gde_A          246 TAAVEWKFDGSRVQVHWDGSR-VTIYSRR----LENVTNALPDIVEEIKKSV-----KPGVILDGEVIAVKEGKPMPFQH  315 (558)
T ss_dssp             SEEEEEECSSEEEEEEECSSC-CEEEETT----CCBCGGGCHHHHHHHHHHB-----CSSEEEEEEEEEEETTEEECHHH
T ss_pred             ceEEEEeEeeEEEEEEEeCCE-EEEEcCC----CCcccccchHHHHHHHhhC-----CCCeEEEeEEEEcCCCcCCCHHH
Confidence            599999999999998776665 6999995    8999987654432 22123     334899999999632    6877


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcc--cccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc---
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY---  267 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~--~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~---  267 (687)
                      +-.+.                   +++.+.  .....++.|++|++...+| ++ ..+..+..+.|.++--+ .+..   
T Consensus       316 L~~r~-------------------~~~~~~~~~~~~~pv~~~vFDlL~l~G-~l~~~pl~eRr~~L~~~~~~-~~~i~~~  374 (558)
T 3gde_A          316 VLRRF-------------------RRKHDVAKMVEKIPLEAHFFDILYHDG-ECIDLPLRERRKLLESAVNE-SEKIKLA  374 (558)
T ss_dssp             HHHHH-------------------HC--CTHHHHHHSCEEEEEEEEEEESS-BCTTSBHHHHHHHHHHHBCC-CSSEEEC
T ss_pred             HHHHh-------------------ccccchhhHhhcCCeEEEEEEEEeeCC-CccCCCHHHHHHHHHHhcCC-CCeEEEe
Confidence            64321                   111100  0123468999999987665 43 24788888888876322 2221   


Q ss_pred             --eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-c
Q psy11422        268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-T  344 (687)
Q Consensus       268 --~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-T  344 (687)
                        ..+.+.+++.++++...+      -..+|+|+|--|..++  -|.  +...| +=+|-........|.+..|--|| +
T Consensus       375 ~~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~--~G~--Rs~~W-lK~K~~~~t~D~vViG~~~g~Gkr~  443 (558)
T 3gde_A          375 KQIVTDSVDEVRKMYDEAIS------AGHEGVMIKLPSSPYI--PGK--RGKNW-LKVKAIMETLDLVVVGGEWGEGKRS  443 (558)
T ss_dssp             CEEEESCHHHHHHHHHHHHH------TTCCEEEEECTTCBCC--TTC--EEEEE-EEEESSCCCEEEEEEEEEECCTTGG
T ss_pred             eeEecCCHHHHHHHHHHHHH------cCCceeEEecCCCCCC--CCC--cCCce-EEEecccceEEEEEEEEEeCCCCcc
Confidence              235688899998877653      2469999997654443  121  23345 45553356789999999998765 5


Q ss_pred             ceeee--EEEEEEEEECCE--EEEEe-cCCCHHHHHhc
Q psy11422        345 GIITP--VALLKPVLIDGI--TITRA-TLHNESEIYRK  377 (687)
Q Consensus       345 G~iTP--vA~lePV~l~G~--tVsra-TLhN~~~i~~~  377 (687)
                      |.++.  ++..+|-  +|.  +|-++ |..+-+..+++
T Consensus       444 g~~g~lllg~~d~~--~g~l~~vgkvgsGftd~~~~~l  479 (558)
T 3gde_A          444 HWLSSFELACLDPV--TGKLLKVGRVATGFTEEDLEEL  479 (558)
T ss_dssp             GSEEEEEEEEECTT--TCCEEEEEEECSSCCHHHHHHH
T ss_pred             CccceEEEEEeeCC--CCEEEEEeeeCCCCCHHHHHHH
Confidence            56654  2233220  243  34554 78888777664

>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis}

Probab=98.05  E-value=5.7e-05  Score=79.80  Aligned_cols=203  Identities=15%  Similarity=0.166  Sum_probs=119.7

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~  193 (687)
                      ..|++|+|+||.-+.+...+|. +++.||    .|+|+|+....+..+-..++    +..+.+-||+++.    ..+|+.
T Consensus        25 ~~~~~E~K~DG~R~~~~~~~g~-v~l~SR----~g~~~t~~fPel~~~~~~l~----~~~~iLDGElv~~d~~g~~~F~~   95 (310)
T 1vs0_A           25 SQWAFEGXWDGYRLLVEADHGA-VRLRSR----SGRDVTAEYPQLRALAEDLA----DHHVVLDGEAVVLDSSGVPSFSQ   95 (310)
T ss_dssp             TTEEEEEECCSEEEEEEEETTE-EEEEET----TCCBCGGGCGGGHHHHHHTT----TCEEEEEEEEECBCTTSCBCHHH
T ss_pred             CCEEEEEccCcEEEEEEEECCE-EEEEcC----CCCCchhhchhHHHHHHhCC----CccEEEeeEEEEECCCCCcCHHH
Confidence            3699999999999999888887 689999    57899886554333222221    2478999999994    336665


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc----CCCCCCCce
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI----GLSICGEYS  268 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~----Gf~~~~~~~  268 (687)
                      +...                   +++        ..+.|++|++...++.++ .....+..+.|.++    -+.+++...
T Consensus        96 l~~r-------------------~~~--------~~~~~~vFDll~~~g~~l~~~pl~eRr~~L~~~~~~~~i~~~~~~~  148 (310)
T 1vs0_A           96 MQNR-------------------GRD--------TRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELLP  148 (310)
T ss_dssp             HHTC-------------------CTT--------SCCEEEEEEEEEETTEECTTSCHHHHHHHHHHHHHHSCCCCCCCCC
T ss_pred             HHhh-------------------ccC--------CcEEEEEEEeEEECCcCcccCCHHHHHHHHHHhccCCcEEECccCc
Confidence            4210                   010        138999999987655332 24677777777664    233333221


Q ss_pred             EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-ccee
Q psy11422        269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGII  347 (687)
Q Consensus       269 ~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~i  347 (687)
                           .++.++++...+      -..+|+|+|--+..++.  |.  +.+.| +-+|- ...+...|.+..+.-|| +|.+
T Consensus       149 -----~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--G~--Rs~~W-lK~K~-~~~~D~vv~G~~~g~G~r~g~~  211 (310)
T 1vs0_A          149 -----GDGAQAFACSRK------HGWEGVIAKRRDSRYQP--GR--RCASW-VKDKH-WNTQEVVIGGWRAGEGGRSSGV  211 (310)
T ss_dssp             -----SSHHHHHHHHHH------TTCCEEEEEETTCCCCT--TC--EEEEE-EEEES-SEEEEEEEEEEEC--------C
T ss_pred             -----hHHHHHHHHHHH------cCCceEEEeCCCCCcCC--CC--cChHH-hccch-heEEEEEEEEEEcCCCCccCcc
Confidence                 135556555432      34699999987754432  21  23334 45553 35677788777666654 3555


Q ss_pred             ee--EEEEEEEEECC-EEEEEe-cCCCHHHHHh
Q psy11422        348 TP--VALLKPVLIDG-ITITRA-TLHNESEIYR  376 (687)
Q Consensus       348 TP--vA~lePV~l~G-~tVsra-TLhN~~~i~~  376 (687)
                      +.  ++..++   +| ..|.++ |..+.+..++
T Consensus       212 g~lllg~~d~---~g~~~vgkvgtGftd~~~~~  241 (310)
T 1vs0_A          212 GSLLMGIPGP---GGLQFAGRVGTGLSERELAN  241 (310)
T ss_dssp             CEEEEEEEET---TEEEEEEEECSSCCHHHHHH
T ss_pred             ceEEEEEEcC---CCCEEEEEECCCCCHHHHHH
Confidence            43  222222   23 244466 7778777765

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A*

Probab=98.02  E-value=1.7e-05  Score=70.87  Aligned_cols=76  Identities=14%  Similarity=0.060  Sum_probs=66.7

Q ss_pred             CccCCeEEEEEcCCCc---CCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYA---FKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~---~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..|.|.+++|.+....   ...+.+..+++.+||+++.+++++++.||+.+..++|+++|++++|+|++.+++.+.+.+
T Consensus         6 p~f~g~vvyvd~~~~~g~~~~s~~l~~~l~~~GA~v~~~l~~~vTHvV~~~~~~~~~~~A~~~~i~iV~~~Wv~~C~~~   84 (107)
T 3pa6_A            6 PILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTA   84 (107)
T ss_dssp             CTTTTCEEEEEEBCTTSCCBCHHHHHHHHHHTTCEECSSCCTTCCEEEEESCCHHHHHHHHHHTCEEECHHHHHHHHHH
T ss_pred             cccCCEEEEEeccCCCChhhHHHHHHHHHHHcCCEEecccCCCccEEEEeCCCChHHHHHhcCCCEEECHHHHHHHHHh
Confidence            4799999999887532   135789999999999999999999999999887779999999999999999999988753

>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A*

Probab=97.95  E-value=0.00012  Score=83.39  Aligned_cols=216  Identities=17%  Similarity=0.150  Sum_probs=135.2

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeeh-----hhHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYK-----KDFI  192 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~-----~~F~  192 (687)
                      .|++|+|+||.-+.+.+.+|. ++..||+    |+|+|+....+.. +...++    ...+.+-||+++-.     -.|+
T Consensus       243 ~~~~E~K~DG~R~~i~~~~g~-v~l~SR~----g~~~t~~fPel~~~~~~~l~----~~~~iLDGElv~~d~~g~~~~F~  313 (561)
T 2cfm_A          243 EAEFEIKYDGARVQVHKDGSK-IIVYSRR----LENVTRAIPEIVEALKEAII----PEKAIVEGELVAIGENGRPLPFQ  313 (561)
T ss_dssp             CEEEEEECCSEEEEEEEETTE-EEEECTT----CCBCGGGCHHHHHHHHHHBC----SSEEEEEEEEEEBCTTSSBCCTH
T ss_pred             cEEEEEeEceEEEEEEEECCE-EEEEeCC----CCCchhhhhhHHHHHHHhCC----CcceEeeeEEEEEcCCCcccCHH
Confidence            699999999999999888886 6899996    8999976544322 111221    14689999999963     1577


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCcc--cccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC---
Q psy11422        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---  266 (687)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~--~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~---  266 (687)
                      .+....                   +++.+.  .....++.|++|++...+|.++ .....+..+.|.++--+. +.   
T Consensus       314 ~L~~r~-------------------~~~~~~~~~~~~~~~~~~vFDlL~l~g~~l~~~pl~eRr~~L~~~~~~~-~~i~~  373 (561)
T 2cfm_A          314 YVLRRF-------------------RRKHNIEEMMEKIPLELNLFDVLYVDGQSLIDTKFIDRRRTLEEIIKQN-EKIKV  373 (561)
T ss_dssp             HHHHHH-------------------HCCSCHHHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCC-SSEEE
T ss_pred             HHHHHh-------------------hcccchhhhcccCceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhCcC-CcEEE
Confidence            664431                   111110  1123479999999987665332 256888888998763321 11   


Q ss_pred             --ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-
Q psy11422        267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-  343 (687)
Q Consensus       267 --~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-  343 (687)
                        ...+.+.+++.++++...+      -..+|+|+|--+..++-  |  .+...| +=+|-..+.....|.+..|--|| 
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--G--~Rs~~W-lK~K~~~dt~D~vViG~~~g~Gkr  442 (561)
T 2cfm_A          374 AENLITKKVEEAEAFYKRALE------MGHEGLMAKRLDAVYEP--G--NRGKKW-LKIKPTMENLDLVIIGAEWGEGRR  442 (561)
T ss_dssp             CCEEEESCHHHHHHHHHHHHH------TTCCEEEEECTTCCCCT--T--CEEEEE-EEECSSCCCEEEEEEEEEECSGGG
T ss_pred             eeeEEcCCHHHHHHHHHHHHH------cCCceeEEeCCCCCCCC--C--CcCCCe-EEEcccCcceeEEEEEEEeCCCCC
Confidence              1235688899998877653      34699999987644431  2  123335 34443335788899998887765 


Q ss_pred             cceeeeEE--EEEEEEECCE--EEEE-ecCCCHHHHHh
Q psy11422        344 TGIITPVA--LLKPVLIDGI--TITR-ATLHNESEIYR  376 (687)
Q Consensus       344 TG~iTPvA--~lePV~l~G~--tVsr-aTLhN~~~i~~  376 (687)
                      +|.++..-  ..+|=  +|.  +|.+ .|..+-+..++
T Consensus       443 ~g~~g~lllg~~d~~--~~~~~~vgkvgsGftd~~~~~  478 (561)
T 2cfm_A          443 AHLFGSFILGAYDPE--TGEFLEVGKVGSGFTDDDLVE  478 (561)
T ss_dssp             TTSEEEEEEEEECTT--TCCEEEEEEECSSCCHHHHHH
T ss_pred             CCccceEEEEEEeCC--CCeEEEEeEeCCCCCHHHHHH
Confidence            56655422  23220  132  3334 36677766665

>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1

Probab=97.90  E-value=0.00017  Score=77.25  Aligned_cols=230  Identities=15%  Similarity=0.064  Sum_probs=131.0

Q ss_pred             eEEEEEccceeEEEEEEe-CCEEEEEEecCCCCccchhhhhhhhhccCCc---cccc--CCCCceEEEEEEEEeehhhHH
Q psy11422        119 EYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPL---VLNI--KYPPELLEVRCEVLIYKKDFI  192 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~---~l~~--~~~~~~~evRGEi~~~~~~F~  192 (687)
                      .|.+|+|+||.-+.+.+. +|. ++..||.    |.|+++........|.   .|..  ...|..+.+-||+++....|+
T Consensus        27 ~~~~E~K~DG~R~~~~~~~~g~-v~l~SR~----g~~~~~l~~~~~~~p~~~~~l~~~~~~~~~~~iLDGElv~~~~~F~  101 (348)
T 1a0i_A           27 YLIAEIKYDGVRGNICVDNTAN-SYWLSRV----SKTIPALEHLNGFDVRWKRLLNDDRCFYKDGFMLDGELMVKGVDFN  101 (348)
T ss_dssp             SEEEEECCCSEEEEEEEETTSE-EEEECTT----SCBCGGGGGGCEECHHHHHHHHSTTCCCTTEEEEEEEEEESSSCTT
T ss_pred             cEEEEEeeceeEEEEEEeCCCe-EEEEcCC----CCCCcchhhhhcccchHHHHHhhhhccCCCCEEEEEEEEEeCCCHH
Confidence            699999999999999887 565 6899994    5566653321110111   1111  013568999999999766777


Q ss_pred             HHHHHHHHcC--C----CCCCChhhhHHhHhhhcCcc---cccccccEEEEEeccccc----CCCC----CCCHHHHHHH
Q psy11422        193 KLNKYRYHLG--L----KKFTNPRNAAAGILRQLNPK---INKNKILHFFAHGVGELR----GMNM----PSSHSELLNW  255 (687)
Q Consensus       193 ~~n~~~~~~g--~----~~f~NpRN~aaG~lr~~~~~---~~~~r~l~f~~y~~~~~~----~~~~----~~~~~e~l~~  255 (687)
                      .+........  .    ..+.+-|...     ...+.   .....++.|++|++...+    |.++    .....+..+.
T Consensus       102 ~l~~~~~~k~~~~k~v~~~~~~~r~~~-----~~~~~i~~~~~~~~~~~~vFDll~l~~~~~G~~l~~~~~~pl~eRr~~  176 (348)
T 1a0i_A          102 TGSGLLRTKWTDTKNQEFHEELFVEPI-----RKKDKVPFKLHTGHLHIKLYAILPLHIVESGEDCDVMTLLMQEHVKNM  176 (348)
T ss_dssp             THHHHHHCCSCCSSBSSCC-------------CCCSCCCCCBCTTTEEEEEEEEEEHHHHHHCCCEEEEHHHHHHHHHHH
T ss_pred             HHHHHhccccccccccccccccccccc-----ccccccccccccCcEEEEEEeeEeeCCCCCCccchhhccCCHHHHHHH
Confidence            6544321100  0    0011111110     00110   123567999999998755    4332    1245666666


Q ss_pred             HHhc--CCC-----CCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCc
Q psy11422        256 YQKI--GLS-----ICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (687)
Q Consensus       256 L~~~--Gf~-----~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (687)
                      |.++  .++     +++ ...+.+.+++.++++...+      -..+|||+|--+..++.  |..   ..|- =+| +..
T Consensus       177 L~~l~~~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--Grr---~~wl-K~K-~~~  242 (348)
T 1a0i_A          177 LPLLQEYFPEIEWQAAE-SYEVYDMVELQQLYEQKRA------EGHEGLIVKDPMCIYKR--GKK---SGWW-KMK-PEN  242 (348)
T ss_dssp             HHHHHHHCTTSEEEECC-EEEESSHHHHHHHHHHHHT------TTCCCEEEECTTCEECS--EEE---EEEE-EES-CCE
T ss_pred             HHHHhhhCCCCeEEEec-cEecCCHHHHHHHHHHHHH------cCCceEEEeCCCCCCCC--CCc---cCcE-EEe-ecc
Confidence            6653  222     122 2235678899988876643      33599999997755542  222   1253 455 344


Q ss_pred             eeeEEEEEEEEeecC---cceeeeEEEEEEEEECCEEEEEecCCCHHHHHh
Q psy11422        329 EALTKIKAINIQIGR---TGIITPVALLKPVLIDGITITRATLHNESEIYR  376 (687)
Q Consensus       329 ~~~T~v~~I~~qvGR---TG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~  376 (687)
                      .+...|.+..|--||   +|.+....-..   =+|.-+ .+|..+.+..++
T Consensus       243 ~~D~vViG~~~g~g~r~~~g~~~~~~~~~---~~g~~~-~gtGftd~~~~~  289 (348)
T 1a0i_A          243 EADGIIQGLVWGTKGLANEGKVIGFEVLL---ESGRLV-NATNISRALMDE  289 (348)
T ss_dssp             EEEEEEEEEECCCTTTSSCSSCCEEEEEC---TTSCEE-EEBCCCSHHHHH
T ss_pred             cEEEEEEEEEeCCCCccCCceEEEEEEEe---CCCCEE-EccCCCHHHHHH
Confidence            788899999998887   57665543211   155433 478887765554

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}

Probab=97.89  E-value=1.6e-06  Score=87.15  Aligned_cols=50  Identities=30%  Similarity=0.365  Sum_probs=0.0

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .+|||||+++++.|+++|+|++++..|+.++|.++ |||+++|++|++||+
T Consensus       176 ~~IpGIG~k~ak~Ll~~FGSl~~i~~As~eeL~~V-GIG~~~A~~I~~~f~  225 (226)
T 3c65_A          176 DDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKLH  225 (226)
T ss_dssp             ---------------------------------------------------
T ss_pred             cccCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhh
Confidence            48999999999999999999999999999999999 999999999999985

>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A

Probab=97.89  E-value=5.8e-06  Score=82.75  Aligned_cols=49  Identities=22%  Similarity=0.388  Sum_probs=46.8

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCH-HHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGS-TTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~-~~A~sI~~ff~  576 (687)
                      .||||||+++++.|+++|+|++++..|+.++|.++  ||+ ++|++|++||+
T Consensus       171 dgIpGIG~k~ak~Ll~~FgSl~~i~~As~EeL~~V--IG~~~~A~~I~~~f~  220 (220)
T 2nrt_A          171 DNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARV--IGSTEIARRVLDILG  220 (220)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHTSCHHHHHHH--HTCHHHHHHHHHHC-
T ss_pred             cCCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hChHHHHHHHHHHhC
Confidence            59999999999999999999999999999999999  999 99999999984

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=97.86  E-value=1.5e-05  Score=79.88  Aligned_cols=53  Identities=23%  Similarity=0.433  Sum_probs=50.7

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      .+|||||++.|+.|+++|++++++..|+.++|.+++|||+++|++|.+||+.+
T Consensus       165 ~~i~gVg~~~a~~Ll~~fgs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~~~~  217 (219)
T 2bgw_A          165 QSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP  217 (219)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSC
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHhcc
Confidence            39999999999999999999999999999999999999999999999999765

>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens}

Probab=97.86  E-value=0.00022  Score=81.38  Aligned_cols=234  Identities=15%  Similarity=0.149  Sum_probs=143.7

Q ss_pred             cccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhh-hhhhc-
Q psy11422         86 TFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIH-  163 (687)
Q Consensus        86 ~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~-  163 (687)
                      -.|||.- .+.+.+++   +++.        +..|++|+|+||.-+.+.+.+|. ++..||+    |+|++.- +..+. 
T Consensus       227 v~PMLA~-~~~~~~~~---~~~~--------~~~~~~E~K~DG~R~qih~~g~~-v~l~SR~----g~~~~p~~~~~l~~  289 (579)
T 3l2p_A          227 VQPMLAE-ACKSVEYA---MKKC--------PNGMFSEIKYDGERVQVHKNGDH-FSYFSRS----LKPVLPHKVAHFKD  289 (579)
T ss_dssp             CCCCEEE-ECCCHHHH---HHHC--------TTCEEEEECCCSEEEEEEEETTE-EEEECTT----SCBCCGGGTTTGGG
T ss_pred             CCCccCC-cCCCHHHH---HhhC--------CCCeEEEEccCcEEEEEEEECCE-EEEECCC----CCccChhHHHHHHH
Confidence            4589753 24455553   2221        23689999999999998887775 7999996    6777533 22221 


Q ss_pred             cCCcccccCCCCceEEEEEEEEeehh------hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEec
Q psy11422        164 KIPLVLNIKYPPELLEVRCEVLIYKK------DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGV  237 (687)
Q Consensus       164 ~iP~~l~~~~~~~~~evRGEi~~~~~------~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~  237 (687)
                      .||..++.   ...+.+-||++.-..      .|+.+..           +.|+.            ....++.|++|++
T Consensus       290 ~l~~~~~~---~~~~iLDGElv~~d~~~g~~~~F~~L~~-----------~~~~~------------~~~~~v~~~vFDl  343 (579)
T 3l2p_A          290 YIPQAFPG---GHSMILDSEVLLIDNKTGKPLPFGTLGV-----------HKKAA------------FQDANVCLFVFDC  343 (579)
T ss_dssp             THHHHSTT---CSEEEEEEEEEEBCTTTCCBCCGGGGSH-----------HHHHH------------CSSCCEEEEEEEE
T ss_pred             HHHHhcCc---CCceEEEeEEEEEeCCCCcccCHHHHHH-----------Hhhhh------------cccCCeEEEEEEe
Confidence            13333321   236899999998542      4654311           01110            0124789999999


Q ss_pred             ccccCCCC-CCCHHHHHHHHHhcCCCCCCCce-----EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhC
Q psy11422        238 GELRGMNM-PSSHSELLNWYQKIGLSICGEYS-----VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG  311 (687)
Q Consensus       238 ~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~-----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG  311 (687)
                      ...+|.++ ..+..+..+.|.++--+.+....     .+.+.+++.++++...+.      -..|||+|--+..++-  |
T Consensus       344 L~l~G~~L~~~Pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~a~~~------g~EGlv~K~~ds~Y~~--G  415 (579)
T 3l2p_A          344 IYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQE------GLEGLVLKDVKGTYEP--G  415 (579)
T ss_dssp             EEETTEECTTSCHHHHHHHHHHHCCCBTTTEEECCEEEECSHHHHHHHHHHHHHT------TCCCEEEEESSCCCCT--T
T ss_pred             eccCCCccccCCHHHHHHHHHHHhhcCCCeEEEeeeEEcCCHHHHHHHHHHHHHh------CCCceEEecCcCCCCC--C
Confidence            87655332 24788999999887544433332     345778888888766432      4699999987755442  2


Q ss_pred             CCCCCCCceEeecCC-------CceeeEEEEEEEEeec-CcceeeeE--EEEEEEEECC--EEEEEe-cCCCHHHHHhc
Q psy11422        312 FTSRAPRFALAYKFL-------SKEALTKIKAINIQIG-RTGIITPV--ALLKPVLIDG--ITITRA-TLHNESEIYRK  377 (687)
Q Consensus       312 ~ts~~PrwaiA~Kf~-------~~~~~T~v~~I~~qvG-RTG~iTPv--A~lePV~l~G--~tVsra-TLhN~~~i~~~  377 (687)
                      .   . .| +=+|-.       .......|.+-.|--| |+|.++..  +..+|-  +|  ++|-++ |.++-+.++++
T Consensus       416 r---r-~W-lK~K~~y~~~g~~~~t~D~vViG~~~G~Gkr~g~~g~lllg~~d~~--~~~l~~vgkvgtGftd~~l~~l  487 (579)
T 3l2p_A          416 K---R-HW-LKVKKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPG--SQKWCTVTKCAGGHDDATLARL  487 (579)
T ss_dssp             C---E-EE-EEECTTTCC---CCEEEEEEEEEEECCCTTSCSSCCEEEEEEECTT--TSSEEEEEEECTTCCHHHHHHT
T ss_pred             C---e-ee-EEEechhhccccccccccEEEEEEEeCCCCCCCceeEEEEEEEeCC--CCeEEEecCccCCCCHHHHHHH
Confidence            2   1 34 344433       1467778888888776 56666643  444430  23  345555 89999888886

>3qwu_A DNA ligase; structural genomics, PSI-2, midwest center for structural GE MCSG; HET: DNA ADN; 2.35A {Aquifex aeolicus}

Probab=97.84  E-value=0.00013  Score=78.04  Aligned_cols=143  Identities=22%  Similarity=0.226  Sum_probs=98.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchh---hhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENI---TTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKL  194 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDv---T~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~  194 (687)
                      -.|++|+|+||-.+.+.|-+|+ +.|.||| |.+   +   |..++.+...  .+.. ++| .+.+-||++.+...|.. 
T Consensus        73 ~~~~veEKLDG~NVRi~~~dG~-ilA~TRg-G~i---cP~tT~r~~~~~~~--~f~~-~~P-~l~LdGEl~g~~npy~~-  142 (370)
T 3qwu_A           73 APFWVEEKVDGYNTRIFKYGDN-YYALSRG-GFI---CPFTTDRLPDLIDL--RILD-ENP-DLVICAEVAGPENPYIE-  142 (370)
T ss_dssp             SCEEEEEECSSEEEEEEEETTE-EEEECTT-SCB---CHHHHHHHHHHCCC--HHHH-HCT-TEEEEEEEECTTCSSCS-
T ss_pred             CcEEEEEeeCCeEEEEEEECCE-EEEEcCC-Ccc---cCcchhhhhhhcCc--hhhh-cCC-CeEEEEEEEcCCCCccc-
Confidence            3799999999999998889998 5899997 322   2   4444443322  2322 234 68999999987655420 


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCCCCCceE--eC-
Q psy11422        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSV--LS-  271 (687)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~~~~~~~--~~-  271 (687)
                                              +. +.. ...++.|++|++.+.+... +-+..+.+++|..+|++.++....  +. 
T Consensus       143 ------------------------~s-~~y-~~~~i~F~VFDV~d~~~~~-~L~~~eR~~ll~~~~lp~V~ii~~~~~~~  195 (370)
T 3qwu_A          143 ------------------------ES-PPY-VKEDVQLFVFDFMKKNEQG-FLSQEEKMELIEKYNLPHVEILGRFTASE  195 (370)
T ss_dssp             ------------------------CC-CTT-CCSSCEEEEEEEEETTCCS-CCCHHHHHHHHHHHTCCBCCEEEEECSSH
T ss_pred             ------------------------cC-Ccc-cccCceEEEEeCccccCCC-cCCHHHHHHHHHHCCCCCccEEEEeCCCC
Confidence                                    11 111 1357999999998643322 358899999999999998875443  34 


Q ss_pred             -CHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11422        272 -GVNKLIEFYKKINIKRFNLPYEIDGVVYKINC  303 (687)
Q Consensus       272 -~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (687)
                       +.+++.++++++.+.      .--|||+|-.+
T Consensus       196 ~~~~~l~~~l~~l~~~------g~EGVVlK~~~  222 (370)
T 3qwu_A          196 EGIKKIKEILKRFNEE------GREGVVFKEDS  222 (370)
T ss_dssp             HHHHHHHHHHHHHHHT------TCCEEEEEESS
T ss_pred             CCHHHHHHHHHHHHhC------CCcEEEEecCc
Confidence             466777788777654      34799999876

>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A*

Probab=97.80  E-value=0.0002  Score=82.51  Aligned_cols=217  Identities=14%  Similarity=0.104  Sum_probs=134.2

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeehh------hH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKK------DF  191 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~------~F  191 (687)
                      .|++|+|+||.-+.+.+.+|. ++..||    .|+|+|+....+.. +...++    ...+.+-||+++-..      .|
T Consensus       274 ~~~~E~K~DG~R~qi~~~g~~-v~l~SR----~g~~~t~~fP~l~~~~~~~l~----~~~~iLDGElv~~d~~~g~~l~F  344 (621)
T 2hiv_A          274 NAIVDYKYDGERAQIHKKEDK-IFIFSR----RLENITSQYPDVVDYVSKYIE----GKEFIIEGEIVAIDPESGEMRPF  344 (621)
T ss_dssp             CEEEEEECSSEEEEEEEETTE-EEEECT----TCCBCGGGCHHHHHHHHHHBC----CSSEEEEEEEEEBCTTTCCBCCT
T ss_pred             cEEEEEEEcceeEEEEEcCCE-EEEEcC----CCcCcHhhhhhHHHHHHHhCC----CcCeEEeEEEEEeecCCCCcCCH
Confidence            699999999999999887776 699999    48899976554321 111221    146899999999641      57


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc---
Q psy11422        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY---  267 (687)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~---  267 (687)
                      +.+...+.+  .    .    +.        ......++.|++|++...+|.++ ..+..+..+.|.++--+. ...   
T Consensus       345 ~~L~~r~~~--~----~----~~--------~~~~~~~v~~~vFDlL~l~G~~l~~~pl~eRr~~L~~~~~~~-~~i~~~  405 (621)
T 2hiv_A          345 QELMHRKRK--S----D----IY--------EAIKEYPVNVFLFDLMYYEDVDYTTKPLEARRKLLESIVKPN-DYVKIA  405 (621)
T ss_dssp             HHHHHHHHC--S----C----HH--------HHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCC-SSEEEC
T ss_pred             HHHhhhccc--c----c----hh--------hhcccCceEEEEEeccccCCCccccCCHHHHHHHHHHHhCcC-CcEEEe
Confidence            766443110  0    0    00        01123479999999987655332 257888889998873221 221   


Q ss_pred             --eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCCC-----ceeeEEEEEEE
Q psy11422        268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKAIN  338 (687)
Q Consensus       268 --~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~I~  338 (687)
                        ..+.+.+++.++++...+      -..+|+|+|--  +..++.  |  .+...| +=+|-..     +.....|.+..
T Consensus       406 ~~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~~~ds~Y~~--G--~Rs~~W-lK~K~~~~~~~~dt~D~vViG~~  474 (621)
T 2hiv_A          406 HHIQANNVEDLKSFFYRAIS------EGGEGVMVKAIGKDAIYQA--G--ARGWLW-IKLKRDYQSEMADTVDLVVVGGF  474 (621)
T ss_dssp             CEEEESSHHHHHHHHHHHHH------TTCCEEEEECCSTTCCCCT--T--CEEEEE-EEEETTCTTSSCEEEEEEEEEEE
T ss_pred             eeEEeCCHHHHHHHHHHHHh------cCCceEEEEecCCCCCccC--C--CcCCCe-EEEechhccCcCceeEEEEEEEE
Confidence              235688899998877653      34699999986  433331  2  123335 4555444     47888998888


Q ss_pred             EeecC-cceeeeEE--EEEEEEECCE--EEEE-ecCCCHHHHHh
Q psy11422        339 IQIGR-TGIITPVA--LLKPVLIDGI--TITR-ATLHNESEIYR  376 (687)
Q Consensus       339 ~qvGR-TG~iTPvA--~lePV~l~G~--tVsr-aTLhN~~~i~~  376 (687)
                      |--|| +|.++..-  ..+|=  +|.  +|.+ .|..+-+..++
T Consensus       475 ~g~Gkr~g~~g~lllg~~d~~--~~~l~~vgkvgtGftd~~~~~  516 (621)
T 2hiv_A          475 YGKGKRGGKISSLLMAAYNPK--TDSFESVCKVASGFSDEQLDE  516 (621)
T ss_dssp             ECSGGGTTSEEEEEEEEEETT--TTEEEEEEEECBSCCHHHHHH
T ss_pred             cCCCCCCCcccceEEEEEeCC--CCeEEEEeeeCCCCCHHHHHH
Confidence            87764 56665432  33320  133  3334 46777666654

>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1

Probab=97.78  E-value=0.00035  Score=81.31  Aligned_cols=220  Identities=15%  Similarity=0.134  Sum_probs=132.6

Q ss_pred             eeEEEEEccceeEEEEEE-eCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeeh------h
Q psy11422        118 IEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYK------K  189 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~------~  189 (687)
                      ..|++|+|+||.-+.+.+ .+|. ++..||    .|+|+|+....+.. ++..+.. . ...+.+-||+++-.      .
T Consensus       330 ~~~~~E~K~DG~R~qih~~~~g~-v~l~SR----~g~d~t~~fPel~~~l~~~~~~-~-~~~~ILDGElV~~d~~~g~~~  402 (688)
T 1x9n_A          330 AAFTCEYKYDGQRAQIHALEGGE-VKIFSR----NQEDNTGKYPDIISRIPKIKLP-S-VTSFILDTEAVAWDREKKQIQ  402 (688)
T ss_dssp             SCEEEEEEESSEEEEEEECTTSC-EEEECT----TSCBCTTTCHHHHHTSGGGBCT-T-CCCEEEEEEEEEECTTTCSBC
T ss_pred             CeEEEEEccccEeEEEEEcCCCe-EEEEeC----CCCcccccchHHHHHHHHhhcc-C-CCCeEEeEEEEEEeCCCCCcC
Confidence            369999999999999988 4665 689999    68899976654432 3322211 0 23689999999943      2


Q ss_pred             hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce
Q psy11422        190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS  268 (687)
Q Consensus       190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~  268 (687)
                      .|+.+...    .       |.        .-+......++.|++|++...+|.++ .....++.+.|.++--+......
T Consensus       403 ~F~~L~~r----~-------r~--------~~~~~~~~~~v~~~vFDlL~l~G~~l~~~Pl~eRr~~L~~~~~~~~~~i~  463 (688)
T 1x9n_A          403 PFQVLTTR----K-------RK--------EVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFV  463 (688)
T ss_dssp             CHHHHTTS----C-------SS--------CCCGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBTTTEE
T ss_pred             CHHHHHHH----h-------hc--------ccchhhcccceEEEEEechhhcCCccccCCHHHHHHHHHHhhccCCCcEE
Confidence            57654211    0       00        00111124579999999987655332 25788999999887433322222


Q ss_pred             -----EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCC-----CceeeEEEEE
Q psy11422        269 -----VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFL-----SKEALTKIKA  336 (687)
Q Consensus       269 -----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~-----~~~~~T~v~~  336 (687)
                           .+.+.+++.++++...+      -..+|+|+|--  +..++-  |  .+...| +=+|-.     ..+....|.+
T Consensus       464 ~~~~~~~~~~~~~~~~~~~a~~------~g~EGlV~K~~~~ds~Y~~--G--kRs~~W-lK~K~~y~~~~~dt~D~vVIG  532 (688)
T 1x9n_A          464 FATSLDTKDIEQIAEFLEQSVK------DSCEGLMVKTLDVDATYEI--A--KRSHNW-LKLKKDYLDGVGDTLDLVVIG  532 (688)
T ss_dssp             ECCEECCCCHHHHHHHHHHHHH------TSEEEEEEEESSSSCSSCT--T--TCSEEE-EEEEHHHHHSSCEEEEEEEEE
T ss_pred             EEeeEecCCHHHHHHHHHHHHh------cCCceeEEeecccCCCCCC--C--CcCchH-heeehhhhccccccccEEEEE
Confidence                 24578888888876643      34699999986  433321  1  123345 444543     1466778888


Q ss_pred             EEEeecC-cceeeeEE--EEEEEEECCE--EEEE-ecCCCHHHHHh
Q psy11422        337 INIQIGR-TGIITPVA--LLKPVLIDGI--TITR-ATLHNESEIYR  376 (687)
Q Consensus       337 I~~qvGR-TG~iTPvA--~lePV~l~G~--tVsr-aTLhN~~~i~~  376 (687)
                      ..|--|| +|.++..-  ..+|-  +|.  +|.+ .|.++-+..++
T Consensus       533 ~~~g~Gkr~g~~gslllg~~d~~--~~~l~~vgkvgtGftd~~~~~  576 (688)
T 1x9n_A          533 AYLGRGKRAGRYGGFLLASYDED--SEELQAICKLGTGFSDEELEE  576 (688)
T ss_dssp             EEEBCTTSBTSEEEEEEEEEETT--TTEEEEEEEECCSCCHHHHHH
T ss_pred             EEeCCCCCCCceeeEEEEEEeCC--CCeEEEEeeeCCCCCHHHHHH
Confidence            8887665 56555432  22220  132  3444 35677766665

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=97.76  E-value=3.9e-05  Score=81.73  Aligned_cols=100  Identities=15%  Similarity=0.276  Sum_probs=76.2

Q ss_pred             cccC-CCCHHHHHHHHHCCCCCChHHHhc----CChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHH
Q psy11422        460 MNII-GLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGET  534 (687)
Q Consensus       460 l~I~-GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~  534 (687)
                      |-++ |+|..|.+.|...-  .++..+-.    ...++|..++|+|+|.+..+..++         ..|  -.|||||+.
T Consensus       413 LAvkfG~g~eTAe~L~~~a--gr~l~leqi~rdrEvgkL~SVpGikek~sktL~eqe---------amL--tAIaGIGp~  479 (685)
T 4gfj_A          413 LTKKEGVGRKTAERLLRAF--GNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGY---------ASL--ISIRGIDRE  479 (685)
T ss_dssp             HHTSTTCCHHHHHHHHHHH--SSHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHSTTH---------HHH--HTSTTCCHH
T ss_pred             hhhhcCCchHHHHHHHHHh--cchhhhhhhhhhhhhhcccccccchhhhhcccccce---------eee--eccCCCCHH
Confidence            3444 88888888775531  12222222    456789999999999887776651         111  379999999


Q ss_pred             HHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11422        535 TAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       535 ~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~  573 (687)
                      +|++|+++|||++.++.|+.++|.. +|||++.|..|..
T Consensus       480 tAeRLLEkFGSVe~Vm~AteDELRe-dGIGekqarrI~g  517 (685)
T 4gfj_A          480 RAERLLKKYGGYSKVREAGVEELRE-DGLTDAQIRELKG  517 (685)
T ss_dssp             HHHHHHHHHTSHHHHHHSCHHHHHH-TTCCHHHHHHHHT
T ss_pred             HHHHHHHHhcCHHHHHhCCHHHHHH-ccccHHHHHHHhh
Confidence            9999999999999999999999977 9999999988764

>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B

Probab=97.70  E-value=7.4e-05  Score=76.90  Aligned_cols=78  Identities=13%  Similarity=0.122  Sum_probs=65.4

Q ss_pred             CCCccCCeEEEEEcCCCc----------------------------CCHHHHHHHHHhcCCEEccccccc------ccEE
Q psy11422        603 NKNYLKEKIFVFTGSLYA----------------------------FKRNEAIILIENLGGKVVNFISKN------TNYL  648 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~----------------------------~~R~e~~~~i~~~Gg~v~~sVsk~------t~~L  648 (687)
                      ..+.|.|+.|++|+....                            ++|.+++++|+++||+|..+++..      +.+|
T Consensus        12 ~~~iF~g~~F~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~l~~~I~~~GG~v~~~~~~~~~~~~~~t~L   91 (259)
T 1kzy_C           12 NKTLFLGYAFLLTMATTSDKLASRSKLPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCLL   91 (259)
T ss_dssp             STTTTTTEEEEECCCC---------------------------CCCCCHHHHHHHHHTTTCEECSSCCTTTTTTTCEEEE
T ss_pred             CCcCcCCcEEEEEcccccccccccccccccccccccccccccccCcccHHHHHHHHHHCCCEEecCccccccccCCCeEE
Confidence            456899999999999753                            588999999999999999998865      5678


Q ss_pred             EEcCC-CCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        649 VKGQK-PGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       649 V~G~~-~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      |+... -+.|...|...|++||+.+++.+.++.
T Consensus        92 Ia~~~~rt~K~l~ala~g~~iVs~~Wl~dc~~~  124 (259)
T 1kzy_C           92 IADQHCRTRKYFLCLASGIPCVSHVWVHDSCHA  124 (259)
T ss_dssp             EESSCCCSHHHHHHHHHTCCEEETHHHHHHHHH
T ss_pred             EcCCCCCcHHHHHHHhcCCCCccHHHHHHHHHc
Confidence            88763 347999999999999999999998753

>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens}

Probab=97.66  E-value=6.1e-05  Score=75.64  Aligned_cols=74  Identities=18%  Similarity=0.169  Sum_probs=64.5

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .|+.|..|||||.- .-.++++.++++.+||.+.+++ .++++||++.... .|+..|...|++|++.+++.+.++.
T Consensus        12 ~~~~~~~i~~SG~~-~~~~~~l~~~i~~lGg~v~~~~-~~~THLI~~~~~rT~K~l~A~~~g~~IVs~~Wl~~c~~~   86 (219)
T 3sqd_A           12 TPELTPFVLFTGFE-PVQVQQYIKKLYILGGEVAESA-QKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRC   86 (219)
T ss_dssp             CGGGCCEEEECSCC-HHHHHHHHHHHHHTTCEECSSG-GGCSEEECSSCCCCHHHHHHTTTCSEEECHHHHHHHHHH
T ss_pred             CCCCCeEEEEeCCC-hHHHHHHHHHHHHCCCEEeCCC-CCceEEEECCCCCCHHHHHHHHcCCCEecHHHHHHHHHc
Confidence            37899999999954 3467899999999999999997 7999999987555 5999999999999999999988753

>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A*

Probab=97.60  E-value=0.00012  Score=74.57  Aligned_cols=75  Identities=19%  Similarity=0.306  Sum_probs=62.6

Q ss_pred             ccCCeEEEEEcC--CCcCCHHHHHHHHHhcCCEEccc-------ccc-----------------c--ccEEEEcCCC-Cc
Q psy11422        606 YLKEKIFVFTGS--LYAFKRNEAIILIENLGGKVVNF-------ISK-----------------N--TNYLVKGQKP-GK  656 (687)
Q Consensus       606 ~l~g~~vv~TG~--l~~~~R~e~~~~i~~~Gg~v~~s-------Vsk-----------------~--t~~LV~G~~~-g~  656 (687)
                      .|+|+.|||||.  +...+|.+++++|+++||+|...       .+.                 .  .++||+.... ..
T Consensus         2 lF~g~~F~ls~~~~~~~~~k~~L~~~I~~~GG~v~~~g~~~lf~~~~~~~~~~~~~~k~~~~~~~~~~t~lia~~~~rt~   81 (241)
T 2vxb_A            2 IFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRKV   81 (241)
T ss_dssp             TTTTEEEEECCCSSTTSSCHHHHHHHHHHTTCEECTTCSGGGBCCSCC----CCCSCCBCGGGGGCSEEEEECSSCCCCH
T ss_pred             CCCCcEEEEecCCCCchhhHHHHHHHHHHCCCEEecCcchhhccCccccccccccccccccccccccceEEEcCCCCCcH
Confidence            689999999999  76789999999999999999886       111                 1  2777777644 48


Q ss_pred             cHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        657 KLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       657 Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      |..+|..+||+||+.+++.+.++.
T Consensus        82 K~~~ala~gipiV~~~Wi~dc~~~  105 (241)
T 2vxb_A           82 KYLEALAFNIPCVHPQFIKQCLKM  105 (241)
T ss_dssp             HHHHHHHHTCCEECTHHHHHHHHH
T ss_pred             HHHHHHHcCCCEecHHHHHHHHHc
Confidence            999999999999999999998853

>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} SCOP: c.15.1.1 PDB: 3pc8_A* 3qvg_B* 1cdz_A

Probab=97.58  E-value=0.00028  Score=62.59  Aligned_cols=77  Identities=12%  Similarity=0.307  Sum_probs=68.3

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHc--CCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL--NIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~l--gI~Ii~E~~f~~~l~~  680 (687)
                      .+.|+|++|+|.|....-.|..+..+|.+.||.++...+.+++++|+....+.|++.|.+.  ++++++.+++.+.+..
T Consensus         5 pd~F~g~~f~l~~~~p~~~r~~l~ryiia~GG~v~~~~~~~vTHvIt~~~~d~~~~~a~~~~p~~~~V~P~WI~~Ci~~   83 (104)
T 3pc6_A            5 PDFFEGKHFFLYGEFPGDERRRLIRYVTAFNGELEDYMNERVQFVITAQEWDPNFEEALMENPSLAFVRPRWIYSCNEK   83 (104)
T ss_dssp             CCTTTTCEEEEESCCSTTHHHHHHHHHHHTTCEECSSCCTTCCEEEESSCCCHHHHHHHTTCTTCEEECHHHHHHHHHH
T ss_pred             chhhCCeEEEEcCCCcHHHHHHHHHHHHHcCCEEEcccCCCceEEEeCCCCChhHHHHhhhCCCCeEEccHHHHHHHhc
Confidence            3578999999999984347999999999999999999999999999998877899988765  7999999999998864

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=97.54  E-value=0.0001  Score=72.46  Aligned_cols=73  Identities=12%  Similarity=0.183  Sum_probs=58.3

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCC---hHHHHhcCHHHHhcCCCCCHHH
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTT  567 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~s---ld~l~~As~eeL~~I~GIG~~~  567 (687)
                      ++-..|-||..+....+.            +.|  ..|+|||+++|..|+++|++   .+++..++.++|.++||||+++
T Consensus        54 eda~~l~gf~~~~ek~~f------------~~L--~~v~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~  119 (191)
T 1ixr_A           54 EEGLSLYGFPDEENLALF------------ELL--LSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRL  119 (191)
T ss_dssp             SSCCCEEEESSHHHHHHH------------HHH--HSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHH
T ss_pred             hhhHHhhccCCHHHHHHH------------HHH--hcCCCcCHHHHHHHHHhCChHHHHHHHHhCCHHHHHhCCCCCHHH
Confidence            333347777766444333            222  35999999999999999998   7889999999999999999999


Q ss_pred             HHHHHHHHcc
Q psy11422        568 VKAFIKFINQ  577 (687)
Q Consensus       568 A~sI~~ff~~  577 (687)
                      |+.|...|++
T Consensus       120 A~rI~~~lk~  129 (191)
T 1ixr_A          120 AERIALELKG  129 (191)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHHH
Confidence            9999888754

>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} SCOP: b.40.4.6 d.142.2.3 PDB: 1ckn_A* 1cko_A* 1ckn_B*

Probab=97.45  E-value=0.00077  Score=71.73  Aligned_cols=151  Identities=13%  Similarity=0.017  Sum_probs=91.5

Q ss_pred             eEEEEEccceeEEEEEEe---CCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN  195 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n  195 (687)
                      .|.+|+|.||+-+.+...   ++.-+.+.||+    |+++|.-.   +.++..     .+....+-||+++...      
T Consensus        76 ~y~ve~K~DG~R~ll~~~~~~g~g~v~L~sR~----~~~~t~~f---p~~~~~-----~~~~~vLDGElv~~~~------  137 (330)
T 1ckm_A           76 KYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRA----MTVYLLPF---KNIPRV-----LFQGSIFDGELCVDIV------  137 (330)
T ss_dssp             CEEEEEEECSEEEEEEEEEETTEEEEEEECTT----CCEEECCC---SCCCTT-----GGGCEEEEEEEEEETT------
T ss_pred             CEEEEECcceEEEEEEEEecCCCCEEEEEeCC----CCEEeccC---hhhhhc-----cCCCeeEEEEEEEEcC------
Confidence            699999999999988776   22347899996    78888632   223211     2346889999998431      


Q ss_pred             HHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc--CC---CCCCC-ce
Q psy11422        196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI--GL---SICGE-YS  268 (687)
Q Consensus       196 ~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~--Gf---~~~~~-~~  268 (687)
                                        .|             .+.|++|++...+|.++ .....++++.|+++  +.   ...+. ..
T Consensus       138 ------------------~~-------------~~~f~vFDlL~~~G~dl~~~pl~eRr~~L~~~l~~~~~~~~~~~~i~  186 (330)
T 1ckm_A          138 ------------------EK-------------KFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILR  186 (330)
T ss_dssp             ------------------TT-------------EEEEEEEEEEEETTEECTTSCHHHHHHHHHHHHTTCCCCTTSSSEEE
T ss_pred             ------------------CC-------------eEEEEEEeeeeeCCcccccCCHHHHHHHHHHHHhhhcccCCCCeEEE
Confidence                              01             17899999987665432 24677888888764  21   11111 11


Q ss_pred             EeC--CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11422        269 VLS--GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (687)
Q Consensus       269 ~~~--~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (687)
                      ...  .. ++.++++++..... ..|..||||+|-.+..++-  |   +...| +-||.+
T Consensus       187 ~~~~~~~-~~~~~~~~~~~~~~-~~yg~EGlI~K~~dspY~~--G---r~~~~-lKwK~~  238 (330)
T 1ckm_A          187 YKEWIPL-EHPTIIKDHLKKAN-AIYHTDGLIIMSVDEPVIY--G---RNFNL-FKLKPG  238 (330)
T ss_dssp             ECCCEET-TCHHHHHHHHHHHH-HHSCEEEEEEEESSSCCCC--E---EEEEE-EEECST
T ss_pred             EEEEEeh-hHHHHHHHHHHHHh-ccCCCceEEEeeCCCcccC--C---CccCe-EEEEeC
Confidence            111  11 34444432222111 1468999999998755542  2   33456 777764

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=97.44  E-value=0.00012  Score=72.76  Aligned_cols=73  Identities=16%  Similarity=0.235  Sum_probs=59.0

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCC---hHHHHhcCHHHHhcCCCCCHHH
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTT  567 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~s---ld~l~~As~eeL~~I~GIG~~~  567 (687)
                      ++-..|-||..+....+..            .|  ..|+|||+++|..|+.+|++   .+++..++.++|.++||||+++
T Consensus        55 eda~~l~gf~~~~ek~~f~------------~L--~~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~  120 (203)
T 1cuk_A           55 EDAQLLYGFNNKQERTLFK------------EL--IKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT  120 (203)
T ss_dssp             TTEEEEEEESSHHHHHHHH------------HH--HHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHH
T ss_pred             ehhhhhhccCCHHHHHHHH------------HH--hcCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence            3334477888776654443            22  23999999999999999999   8899999999999999999999


Q ss_pred             HHHHHHHHcc
Q psy11422        568 VKAFIKFINQ  577 (687)
Q Consensus       568 A~sI~~ff~~  577 (687)
                      |+.|...|++
T Consensus       121 A~rI~~elk~  130 (203)
T 1cuk_A          121 AERLIVEMKD  130 (203)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999887753

>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3

Probab=97.38  E-value=0.00029  Score=70.47  Aligned_cols=74  Identities=12%  Similarity=0.007  Sum_probs=65.1

Q ss_pred             ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC------CCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK------PGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~------~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      .+.+..||+||... ..|+.++++++.+||.+.+.++.++++||++..      -+.|+..|...|++|++.+++.+.++
T Consensus         4 ~~~~~~i~~sg~~~-~~~~~l~~~~~~~G~~~~~~~~~~~THlI~~~~~~~~~~rt~K~~~a~~~g~~IV~~~Wl~~~~~   82 (229)
T 1l0b_A            4 AERDISMVVSGLTP-KEVMIVQKFAEKYRLALTDVITEETTHVIIKTDAEFVCERTLKYFLGIAGGKWIVSYSWVIKSIQ   82 (229)
T ss_dssp             CCCCCEEEEESCCH-HHHHHHHHHHHHTTCEECSSCCSSCCEEEECBCTTSEECCCHHHHHHHHTTCEEEETHHHHHHHT
T ss_pred             CCCCeEEEEcCCCH-HHHHHHHHHHHHcCCEEeCCcCCCCCEEEEcCCccccccccHHHHHHHHCCCcEecHHHHHHHHH
Confidence            46788999999754 368899999999999999999999999999975      34799999999999999999998875


Q ss_pred             c
Q psy11422        680 G  680 (687)
Q Consensus       680 ~  680 (687)
                      .
T Consensus        83 ~   83 (229)
T 1l0b_A           83 E   83 (229)
T ss_dssp             T
T ss_pred             C
Confidence            3

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*

Probab=97.35  E-value=0.0002  Score=76.82  Aligned_cols=52  Identities=21%  Similarity=0.308  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      .||.+|++.|++|.++|++++++.+|+.+||.+++|||++.|..|++.+..-
T Consensus       319 ~IPrl~~~iae~Lv~~FGsLq~Il~AS~eEL~~VeGIGe~rAr~IregL~r~  370 (377)
T 3c1y_A          319 TVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSL  370 (377)
T ss_dssp             HTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhccCccHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999999999999887543

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A*

Probab=97.32  E-value=0.00057  Score=70.41  Aligned_cols=76  Identities=16%  Similarity=0.243  Sum_probs=63.9

Q ss_pred             CCCccCCeEEEE-EcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcC-CeEEeHHHHHHHHhc
Q psy11422        603 NKNYLKEKIFVF-TGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLN-IKILDEKNFVKIVKG  680 (687)
Q Consensus       603 ~~~~l~g~~vv~-TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lg-I~Ii~E~~f~~~l~~  680 (687)
                      .++.|+|+.||+ +|. ...+|++++.+|.++||++..+.++.|.++|++. .+.|.+.|.+.| ++||+.+++.+.++.
T Consensus         7 ~s~lF~G~~f~V~sg~-~~~~k~~L~~lI~~~GG~v~~n~~~~t~~iIa~~-~~~k~~~~~~~g~~~IV~p~Wv~Dci~~   84 (263)
T 3ii6_X            7 ISNIFEDVEFCVMSGT-DSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGS-ENIRVKNIILSNKHDVVKPAWLLECFKT   84 (263)
T ss_dssp             CCCTTTTCEEEECCCC---CCHHHHHHHHHHTTCEECSSCCTTEEEEECSS-CCHHHHHHHHSCSCCEECHHHHHHHHHH
T ss_pred             CcccCCCeEEEEEcCC-CCCCHHHHHHHHHHcCCEEEecCCCCEEEEEeCC-CCHHHHHHHhcCCCCEeehHHHHHHHhc
Confidence            456899999998 564 3469999999999999999999988888778765 448889999987 999999999998753

>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5

Probab=97.32  E-value=0.00085  Score=61.81  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=63.5

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHH---cCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIK---LNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~---lgI~Ii~E~~f~~~l~~  680 (687)
                      ...|.|.+|+|.|.-. ..+..++.+++.+||++...++..+++||+++. ..+++++..   .+++|++.+++.+.+..
T Consensus        38 ~~lF~g~~i~i~G~~~-~~~~~L~~~i~~~Gg~v~~~l~~~vTHvI~~~~-~~~~~~~~~~~~~~~~iV~~~Wv~dsi~~  115 (132)
T 1wf6_A           38 EDLLDGCRIYLCGFSG-RKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDY-DDELKQFWNKSAHRPHVVGAKWLLECFSK  115 (132)
T ss_dssp             TTTTTTCEEEEESCCS-HHHHHHHHHHHHTTCEEESSCCSSCCEEEESSC-CSHHHHHHHHSCCCCCEEEHHHHHHHHHH
T ss_pred             ccccCCEEEEEECCCh-HHHHHHHHHHHHCCCEEeCcCCCCCeEEEECCc-hHHHHHHHHhhCCCCeEechHHHHHHHHc
Confidence            4679999999999754 588999999999999999999999999999864 456666543   47999999999998753

>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A

Probab=97.28  E-value=0.00034  Score=68.95  Aligned_cols=72  Identities=14%  Similarity=-0.010  Sum_probs=62.9

Q ss_pred             CCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCC------CccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        608 KEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKP------GKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       608 ~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~------g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+..||+||... ..|+.+.++++.+||.+.+.++.++++||++...      +.|+..|...|++|++.+++.+.++.
T Consensus         3 ~~~~~~~sg~~~-~~~~~l~~~~~~~G~~~~~~~~~~~THli~~~~~~~~~~rt~k~~~a~~~g~~IV~~~Wl~~~~~~   80 (214)
T 1t15_A            3 KRMSMVVSGLTP-EEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKE   80 (214)
T ss_dssp             -CCEEEEESCCH-HHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHHT
T ss_pred             CcEEEEECCCCH-HHHHHHHHHHHHhCCEEeCccCCCCcEEEEeCCcccchhhhHHHHHHHhcCCEEeCHHHHHHHHHC
Confidence            477899999654 4788999999999999999999999999999753      47989999999999999999988753

>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens}

Probab=97.23  E-value=0.00068  Score=63.16  Aligned_cols=117  Identities=12%  Similarity=0.134  Sum_probs=70.7

Q ss_pred             EEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-------CCcccccCCCCceEEEEEEEEeehhhHH
Q psy11422        120 YIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-------IPLVLNIKYPPELLEVRCEVLIYKKDFI  192 (687)
Q Consensus       120 ~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-------iP~~l~~~~~~~~~evRGEi~~~~~~F~  192 (687)
                      |++|+|+||.-+.+.+.+|. ++..||    -|+|+|+....+..       |...+..  ....+.+-||++.-...  
T Consensus         1 f~~E~K~DG~R~q~~~~g~~-v~l~SR----~g~d~t~~fPel~~~~~l~~~i~~~~~~--~~~~~iLDGEiv~~d~~--   71 (139)
T 3vnn_A            1 FYIETKLDGERMQMHKDGDV-YKYFSR----NGYNYTDQFGASPTEGSLTPFIHNAFKA--DIQICILDGEMMAYNPN--   71 (139)
T ss_dssp             CCCCCCCCCEEEEEEEETTE-EEEECS----SCCBCTTTSCSSTTC--CCSGGGSCCCT--TCCEEEEEEEEEEEETT--
T ss_pred             CEEEEEECeEEEEEEEECCE-EEEEeC----CCCCchhhccchhhhcchhHHHHHHHhc--cCCceEeeeEEEEecCC--
Confidence            57899999999999887776 799999    58999987644321       2222221  13579999999995321  


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc
Q psy11422        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI  259 (687)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~  259 (687)
                                ...|. ++...   ++.+........++.|++|++...+|.++ ..+..+..+.|.++
T Consensus        72 ----------~~~f~-~~~~~---~~~~~~~~~~~~~~~~~vFDlL~l~G~~L~~~pl~eRr~~L~~l  125 (139)
T 3vnn_A           72 ----------TQTFM-QKGTK---FDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSI  125 (139)
T ss_dssp             ----------TTEEC-CC----------------CCEEEEEEEEEEEETTEECSSSCHHHHHHHHHHH
T ss_pred             ----------CCCHH-HHHhh---hhhhhhhhccCceEEEEEEEEEeECCcCcccCCHHHHHHHHHHH
Confidence                      01122 11000   01111111123478999999987665432 24688888888776

>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A

Probab=97.18  E-value=0.00053  Score=67.86  Aligned_cols=71  Identities=13%  Similarity=-0.049  Sum_probs=62.4

Q ss_pred             CeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcC---CCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        609 EKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQ---KPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       609 g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~---~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      |..||+||... -.|+.+.++++.+||.+.+.++.++++||++.   ..+.|+..|...|++|++.+++.+.++.
T Consensus         2 ~~vi~~sg~~~-~~~~~l~~~~~~~G~~~~~~~~~~~THlV~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~~   75 (210)
T 2nte_A            2 PLVLIGSGLSS-EQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRR   75 (210)
T ss_dssp             CCEEEESSCCH-HHHHHHHHHHHHTTCEEESSCCTTCCEEEESSSSCCCSHHHHHHHHTTCEEEETHHHHHHHHH
T ss_pred             CEEEEECCCCH-HHHHHHHHHHHHcCCEEeCCCCCCCeEEEEcCCCcchHHHHHHHHhcCCEEecHHHHHHHHHc
Confidence            56899999654 47889999999999999999999999999987   3358999999999999999999987753

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=97.18  E-value=0.00017  Score=60.37  Aligned_cols=53  Identities=19%  Similarity=0.284  Sum_probs=47.5

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ....|+|+|++++.+|++.  ..++.+|+..+.++|..++|+|++.|+.|++.+.
T Consensus        25 ~L~~I~gIG~~~A~~Ll~~--fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~~~   77 (78)
T 1kft_A           25 SLETIEGVGPKRRQMLLKY--MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             GGGGCTTCSSSHHHHHHHH--HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             HHhcCCCCCHHHHHHHHHH--cCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHh
Confidence            4668999999999999997  3589999999999999999999999999998763

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=97.03  E-value=0.00069  Score=55.63  Aligned_cols=56  Identities=11%  Similarity=0.275  Sum_probs=49.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~  516 (687)
                      ...|+|+|++++..|++.  ..++.+|+..+.++|..++|+|++.|+.|+..++...+
T Consensus        16 L~~i~giG~~~a~~Ll~~--fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~~~   71 (75)
T 1x2i_A           16 VEGLPHVSATLARRLLKH--FGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYI   71 (75)
T ss_dssp             HTTSTTCCHHHHHHHHHH--HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCC
T ss_pred             HcCCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCccc
Confidence            457999999999999995  36789999999999999999999999999999876543

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=97.02  E-value=0.00091  Score=55.02  Aligned_cols=56  Identities=18%  Similarity=0.367  Sum_probs=50.3

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       456 sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      +.+..+++|+|+.++.+|.++|+ .|+.||-.++.++|..+.|+++..|++|+..-.
T Consensus         6 ~~~l~~L~Gi~~~~~~kL~e~Gi-~TvedlA~~~~~eL~~i~gise~kA~~ii~aAr   61 (70)
T 1wcn_A            6 ADDLLNLEGVDRDLAFKLAARGV-CTLEDLAEQGIDDLADIEGLTDEKAGALIMAAR   61 (70)
T ss_dssp             CHHHHSSTTCCHHHHHHHHTTTC-CSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHH
T ss_pred             hhHHHHcCCCCHHHHHHHHHcCC-CcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHH
Confidence            34567899999999999999995 899999999999999999999999999997654

>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...

Probab=96.99  E-value=9.9e-05  Score=75.10  Aligned_cols=58  Identities=21%  Similarity=0.260  Sum_probs=0.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~  516 (687)
                      ..++|+|+||+++.+|++.| +.++.+|...+.++|..++|||+|+|++|+..++....
T Consensus        16 ~L~~IpGIGpk~a~~Ll~~g-f~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~l~~~~~   73 (241)
T 1vq8_Y           16 ELTDISGVGPSKAESLREAG-FESVEDVRGADQSALADVSGIGNALAARIKADVGGLEV   73 (241)
T ss_dssp             -----------------------------------------------------------
T ss_pred             HHhcCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHhccCCCHHHHHHHHHHHHHHHh
Confidence            36789999999999999995 58999998889999999999999999999999875444

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=96.98  E-value=0.00087  Score=57.39  Aligned_cols=52  Identities=10%  Similarity=0.092  Sum_probs=47.7

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..|+|+|++++.+|++.-  .++.+++..+.++|..++|+|++.|+.|+..++.
T Consensus        22 ~~IpgIG~~~A~~Ll~~f--gsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~   73 (89)
T 1z00_A           22 TTVKSVNKTDSQTLLTTF--GSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   73 (89)
T ss_dssp             TTSSSCCHHHHHHHHHHT--CBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHS
T ss_pred             HcCCCCCHHHHHHHHHHC--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            489999999999999863  5789999999999999999999999999999975

>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A

Probab=96.97  E-value=0.0011  Score=65.65  Aligned_cols=71  Identities=20%  Similarity=0.161  Sum_probs=58.7

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCC-CccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKP-GKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~-g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ..+.+..|||||...    ++++++++.+||.+..++++ +++||++... +.|+..|...|++|++.+++.+.++.
T Consensus         8 ~~~~~~~v~~sG~~~----~~~~~~i~~lGg~~~~~~~~-~THlI~~~~~rt~K~l~a~~~g~~IV~~~Wl~~~~~~   79 (209)
T 2etx_A            8 QESTAPKVLFTGVVD----ARGERAVLALGGSLAGSAAE-ASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKA   79 (209)
T ss_dssp             ----CCEEEECSSCC----HHHHHHHHHTTCEECSSTTT-CSEEECSSCCCSHHHHHHHHHTCCEECTHHHHHHHHH
T ss_pred             ccCCCcEEEEeCCCc----HHHHHHHHHCCCEEeCCCCC-ceEEEECCCCCCHHHHHHHhcCCccccHHHHHHHHHc
Confidence            457799999999753    45799999999999999985 9999998743 58999999999999999999998753

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=96.95  E-value=0.00078  Score=58.03  Aligned_cols=52  Identities=10%  Similarity=0.092  Sum_probs=47.2

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..|+|+|++++.+|++.-  .++.+|+..+.++|..++|+|++.|+.|++.+..
T Consensus        35 ~~IpgIG~~~A~~Ll~~f--gs~~~l~~as~~eL~~i~GIG~~~a~~I~~~l~~   86 (91)
T 2a1j_B           35 TTVKSVNKTDSQTLLTTF--GSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   86 (91)
T ss_dssp             TTSTTCCHHHHHHHHHHH--SSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS
T ss_pred             HcCCCCCHHHHHHHHHHC--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhh
Confidence            389999999999999862  4789999999999999999999999999999864

>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3

Probab=96.82  E-value=0.0022  Score=63.98  Aligned_cols=76  Identities=5%  Similarity=0.003  Sum_probs=52.8

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccc------ccEEEEcCCC---CccHHH-HHHcCCeEEeHHHH
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKN------TNYLVKGQKP---GKKLEK-AIKLNIKILDEKNF  674 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~------t~~LV~G~~~---g~Kl~k-A~~lgI~Ii~E~~f  674 (687)
                      ..|.|.+|+|+|.+...++++++++|+..||++..+.+..      +.++|++...   ..+++. |...+++|++.+++
T Consensus       116 ~lF~g~~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~~vvv~~~~~~~~~~~~~l~~~~~i~iVs~~Wl  195 (229)
T 1l0b_A          116 KLFEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCKGRLVMWDWV  195 (229)
T ss_dssp             -CCTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC-------------------CEEETHHH
T ss_pred             hhhcCceEEEEecCCCCCHHHHHHHHHHCCCEEeCCcccccccCCCceEEEEcCCccchhhhHHHHHHHcCCeEeehhHH
Confidence            4799999999998877789999999999999999998764      4467777542   345443 35679999999999


Q ss_pred             HHHHhc
Q psy11422        675 VKIVKG  680 (687)
Q Consensus       675 ~~~l~~  680 (687)
                      ++.+..
T Consensus       196 ldsI~~  201 (229)
T 1l0b_A          196 LDSISV  201 (229)
T ss_dssp             HHHHHT
T ss_pred             HHHHhc
Confidence            998854

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=96.79  E-value=0.00067  Score=77.54  Aligned_cols=56  Identities=25%  Similarity=0.189  Sum_probs=49.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      ..+.|+|+|||++.+|++. .+.|++||.. +..+.|..+||||+|++++|+.+|+..
T Consensus        98 ~L~~v~GVGpk~A~~i~~~-G~~s~edL~~a~~~~~L~~~~GiG~Ktaq~I~~~l~~~  154 (578)
T 2w9m_A           98 DLLGVRGLGPKKIRSLWLA-GIDSLERLREAAESGELAGLKGFGAKSAATILENVVFL  154 (578)
T ss_dssp             HHTTSTTCCHHHHHHHHHT-TCCSHHHHHHHHHHTTTTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHhCCCCcCHHHHHHHHHc-CCCCHHHHHHHHhhCccccCCCCCHHHHHHHHHHHHHH
Confidence            4678999999999999999 4699999998 466789999999999999999888753

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=96.61  E-value=0.0028  Score=63.13  Aligned_cols=51  Identities=14%  Similarity=0.211  Sum_probs=43.0

Q ss_pred             CCCCCCHHHHHHHHhhcCC---hHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        527 GIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~s---ld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      .++|||+++|..|..+|+.   ..++...+.+.|.++||||+++|+.|..-+.+
T Consensus        92 sv~GIGpk~A~~Ils~~~~~~l~~aI~~~d~~~L~~vpGIG~KtA~rIi~elk~  145 (212)
T 2ztd_A           92 SVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRD  145 (212)
T ss_dssp             TSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTT
T ss_pred             CcCCcCHHHHHHHHHhCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            5999999999999999974   23466779999999999999999998766554

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=96.59  E-value=0.0025  Score=72.83  Aligned_cols=84  Identities=14%  Similarity=0.278  Sum_probs=64.2

Q ss_pred             hhhcccCccHHHHHHHHHHHHHcccCCH--------HHHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhc-CHHHHhcCC
Q psy11422        492 NLLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELANY-FKNLECMFKA-TEEQLLNIP  561 (687)
Q Consensus       492 ~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l--------~r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~A-s~eeL~~I~  561 (687)
                      .+..+||+|++.+.++...++.-....+        .-|+.-+.|+|||+++|+.|.+. |.++++|..| ....|.+++
T Consensus        58 ~~~~lp~iG~~~~~~i~~~v~~g~~~~~~~~~~~~~~~~~~L~~v~GVGpk~A~~i~~~G~~s~edL~~a~~~~~L~~~~  137 (578)
T 2w9m_A           58 EFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLK  137 (578)
T ss_dssp             -CCSSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTTSTTCCHHHHHHHHHTTCCSHHHHHHHHHHTTTTTST
T ss_pred             hhhhcCCCChhHHHHHHHHHcCChHHHHHHHhhhhHHHHHHHhCCCCcCHHHHHHHHHcCCCCHHHHHHHHhhCccccCC
Confidence            3899999999999988888764221111        12344469999999999988764 7899999876 345899999


Q ss_pred             CCCHHHHHHHHHHH
Q psy11422        562 KIGSTTVKAFIKFI  575 (687)
Q Consensus       562 GIG~~~A~sI~~ff  575 (687)
                      |||++++++|...+
T Consensus       138 GiG~Ktaq~I~~~l  151 (578)
T 2w9m_A          138 GFGAKSAATILENV  151 (578)
T ss_dssp             TCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999995544

>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A

Probab=96.59  E-value=0.0034  Score=61.73  Aligned_cols=77  Identities=10%  Similarity=0.107  Sum_probs=59.0

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccc-----c-EEEEcCCC--C-ccH-HHHHHcCCeEEeHHH
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNT-----N-YLVKGQKP--G-KKL-EKAIKLNIKILDEKN  673 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t-----~-~LV~G~~~--g-~Kl-~kA~~lgI~Ii~E~~  673 (687)
                      ...|.|.+|+|+|.+...+|++++.+|+..||++..+++..+     . ++|+....  . .|. ..|...|++|++.++
T Consensus       113 ~~lF~g~~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~ivi~~~~~~~~~~~~~~~a~~~~~~iV~~~W  192 (214)
T 1t15_A          113 RKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREW  192 (214)
T ss_dssp             SCTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTCSSCEEEHHH
T ss_pred             CcccCCCEEEEEecCCCCCHHHHHHHHHHCCCEEecCccccccCCCCccEEEECCCcccchhhHHHHHHhcCCcEEeccH
Confidence            357999999999988777899999999999999999987632     3 33443221  1 233 245678999999999


Q ss_pred             HHHHHhc
Q psy11422        674 FVKIVKG  680 (687)
Q Consensus       674 f~~~l~~  680 (687)
                      +++-+..
T Consensus       193 i~dsi~~  199 (214)
T 1t15_A          193 VLDSVAL  199 (214)
T ss_dssp             HHHHHHH
T ss_pred             HHHhHhh
Confidence            9998864

>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A

Probab=96.56  E-value=0.0047  Score=61.14  Aligned_cols=76  Identities=11%  Similarity=0.072  Sum_probs=61.0

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccc--ccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKN--TNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~--t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      ..|.|++|++|+... .++++++++|+..||++.......  .+.+|++.... .+++.+.+.|+++++.+++++-+..+
T Consensus       114 ~lF~g~~~~~~~~~~-~~~~~l~~li~~~GG~v~~~~~~~~~~~~ivI~~~~d~~~~~~~~~~~i~vvs~eWi~~sI~~q  192 (209)
T 2etx_A          114 RLLEGYEIYVTPGVQ-PPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQ  192 (209)
T ss_dssp             CTTTTCEEEECTTCS-SCHHHHHHHHHHTTCEECSSCCCSCCTTEEEECCGGGGGGCHHHHHHTCCEECTHHHHHHHHHT
T ss_pred             CCcCCcEEEEeCCCC-CCHHHHHHHHHHCCCEEECCCCCCCCCceEEEECcccHHHHHHHHHCCCeEEcHHHHHHHHHhc
Confidence            479999999999875 489999999999999999877653  24555554433 67778888899999999999887543

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=96.55  E-value=0.0013  Score=75.19  Aligned_cols=57  Identities=21%  Similarity=0.224  Sum_probs=50.5

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      ..+.|+|+|||++.++++...+.+++||.. +..++|.++||||+|+|++|+.+++..
T Consensus        94 ~l~~v~GvGpk~A~~~~~~lg~~~~~~l~~a~~~~~l~~~~GiG~k~a~~i~~~l~~~  151 (575)
T 3b0x_A           94 EVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALA  151 (575)
T ss_dssp             HHHTSTTTCHHHHHHHHHTSCCCSHHHHHHHHHHTGGGGSTTCCHHHHHHHHHHHHHH
T ss_pred             HHhcCCCcCHHHHHHHHHhcCCCCHHHHHHHHHcCCcccCCCCCccHHHHHHHHHHHH
Confidence            467899999999999999856799999998 556789999999999999998888753

>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A*

Probab=96.48  E-value=0.0047  Score=62.47  Aligned_cols=72  Identities=21%  Similarity=0.227  Sum_probs=62.1

Q ss_pred             cCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcc--cccccccEEEEcCCC-CccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVN--FISKNTNYLVKGQKP-GKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       607 l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~--sVsk~t~~LV~G~~~-g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      -.+..|+|||..+ -.|+++.++|+.+||.+..  +++.++++||++... +-|+-.|...|..|++.+++.+.++
T Consensus         7 ~~~~~~~~Sg~~~-~~~~~l~~~i~~LGg~~~~~~~~~~~~THlV~~~~~RT~K~l~aia~G~wIvs~~wl~~s~~   81 (235)
T 3al2_A            7 KKQYIFQLSSLNP-QERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVAAGKWVLHRSYLEACRT   81 (235)
T ss_dssp             -CCCEEEEESCCH-HHHHHHHHHHHHTTCEECCSSSCCTTCCEEEESSCCCSHHHHHHHHTTCEEECTHHHHHHHH
T ss_pred             CCCEEEEEcCCCH-HHHHHHHHHHHHcCCEEeccCCCCCCCcEEEECCCCCCHHHHHHHHcCCcCccHHHHHHHHH
Confidence            3578999999653 4688999999999999975  588999999999853 5899999999999999999998774

>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens}

Probab=96.46  E-value=0.0056  Score=61.22  Aligned_cols=75  Identities=15%  Similarity=0.122  Sum_probs=60.9

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccc------------ccEEEEcCC-CCccHHHHHHcCCeEEeH
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKN------------TNYLVKGQK-PGKKLEKAIKLNIKILDE  671 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~------------t~~LV~G~~-~g~Kl~kA~~lgI~Ii~E  671 (687)
                      ..|.|++|++||.+. .++++++++|+.+||++.....+.            .+++|+... .-...+++.+.|++|++-
T Consensus       121 ~LF~G~~f~it~~~~-~~~~~l~~lI~~~GG~v~~~~p~~~~~~~~~~~~~~~~~ivis~~~d~~~~~~~~~~~~~v~s~  199 (219)
T 3sqd_A          121 PLFKAKYFYITPGIC-PSLSTMKAIVECAGGKVLSKQPSFRKLMEHKQNSSLSEIILISCENDLHLCREYFARGIDVHNA  199 (219)
T ss_dssp             CTTTTEEEEECTTCS-SCHHHHHHHHHHTTCEEESSCCCHHHHHHHHHCTTSCEEEEEECGGGGGGGHHHHHTTCCCEET
T ss_pred             cccCCcEEEEeCCCC-CCHHHHHHHHHHCCCEEECCCCchHHhhhhhcccCCCCEEEEecccHHHHHHHHHHCCCcEEeH
Confidence            478999999999886 589999999999999999987542            356665554 337778888899999999


Q ss_pred             HHHHHHHhc
Q psy11422        672 KNFVKIVKG  680 (687)
Q Consensus       672 ~~f~~~l~~  680 (687)
                      +.+++-+-.
T Consensus       200 E~il~~Il~  208 (219)
T 3sqd_A          200 EFVLTGVLT  208 (219)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999986543

>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...

Probab=96.45  E-value=0.00047  Score=70.11  Aligned_cols=52  Identities=21%  Similarity=0.288  Sum_probs=0.0

Q ss_pred             cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      +.|||||+++|+.|.++ |++++.|..++.++|.+++|||+++|+.|..++..
T Consensus        18 ~~IpGIGpk~a~~Ll~~gf~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~l~~   70 (241)
T 1vq8_Y           18 TDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGG   70 (241)
T ss_dssp             -----------------------------------------------------
T ss_pred             hcCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHhccCCCHHHHHHHHHHHHH
Confidence            46899999999998887 99999999999999999999999999999888753

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=96.39  E-value=0.0026  Score=51.07  Aligned_cols=50  Identities=16%  Similarity=0.243  Sum_probs=45.4

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHH-HHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKL-ANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ks-a~~Ll~~Ie~  513 (687)
                      .+|||+|+++..+|++.-  .|+.+|..++.++|.++  +|.+. |++|++.++.
T Consensus         7 ~~IpGIG~kr~~~LL~~F--gs~~~i~~As~eeL~~v--ig~~~~A~~I~~~l~~   57 (63)
T 2a1j_A            7 LKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSI--LGNAANAKQLYDFIHT   57 (63)
T ss_dssp             HTSTTCCHHHHHHHHHHC--SSHHHHHTCCHHHHHHH--HSCHHHHHHHHHHHHC
T ss_pred             HcCCCCCHHHHHHHHHHc--CCHHHHHHCCHHHHHHH--cCchHHHHHHHHHHhc
Confidence            479999999999999865  69999999999999999  88999 9999998864

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=96.35  E-value=0.0017  Score=53.75  Aligned_cols=24  Identities=29%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             cCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        552 ATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       552 As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      ++.++|.+++|+|+++++.|..|+
T Consensus        50 ~s~~eL~~v~Gig~k~~~~i~~~l   73 (75)
T 2duy_A           50 ARVEDLLKVKGIGPATLERLRPYL   73 (75)
T ss_dssp             SSGGGGGGSTTCCHHHHHHHGGGE
T ss_pred             CCHHHHHhCCCCCHHHHHHHHHhc
Confidence            567888899999999999888775

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=96.33  E-value=0.0045  Score=50.84  Aligned_cols=53  Identities=13%  Similarity=0.241  Sum_probs=48.8

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      |++.|+++..+++|+++|+ .|+.++-..+.++|+.++||.+..+++|.+.-.+
T Consensus         9 ~~~lgI~e~~a~~L~~~Gf-~tve~vA~~~~~eL~~I~G~dE~~a~~l~~~A~~   61 (70)
T 1u9l_A            9 TKYLDIDEDFATVLVEEGF-STLEELAYVPMKELLEIEGLDEPTVEALRERAKN   61 (70)
T ss_dssp             HHHHTCCHHHHHHHHHTTC-CCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             HHhCCCCHHHHHHHHHcCc-CcHHHHHcCCHHHHhhccCCCHHHHHHHHHHHHH
Confidence            5788999999999999997 8999999999999999999999999999987643

>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A*

Probab=96.32  E-value=0.0058  Score=60.16  Aligned_cols=71  Identities=15%  Similarity=0.171  Sum_probs=61.7

Q ss_pred             CCeEEEEEcCCCcCCHHHHHHHHHhcCC-EEcccccccccEEEEcCC-CCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        608 KEKIFVFTGSLYAFKRNEAIILIENLGG-KVVNFISKNTNYLVKGQK-PGKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       608 ~g~~vv~TG~l~~~~R~e~~~~i~~~Gg-~v~~sVsk~t~~LV~G~~-~g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      ....||+||.-. -.|+++.++++.+|| .++++++..|++||++.. -+.|+..|...|+.|++.+++.+.++
T Consensus        10 ~~~~~~~sgl~~-~~~~~l~~~i~~lgG~~~~~~~~~~~THlv~~~~~rT~K~l~ai~~g~~Iv~~~Wv~~~~~   82 (199)
T 3u3z_A           10 PTRTLVMTSMPS-EKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIARGCWVLSYDWVLWSLE   82 (199)
T ss_dssp             CCCEEEEESCCH-HHHHHHHHHHHHHCSCEEESSCCTTEEEEEESSCCCBHHHHHHHHTTCEEEETHHHHHHHH
T ss_pred             CCeEEEEcCCCH-HHHHHHHHHHHHcCCcEEecCCCCCCeEEEECCCCCCHHHHHHHHCCCcEEeHHHHHHHhh
Confidence            367899999754 478889999999977 677999999999999885 44899999999999999999998775

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=96.32  E-value=0.0092  Score=68.06  Aligned_cols=118  Identities=17%  Similarity=0.190  Sum_probs=79.0

Q ss_pred             ccccCCCCHHHHHHHHHC-----CCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccC--------CHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNA-----NIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT--------TFSRFIYA  525 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~-----g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~--------~l~r~L~a  525 (687)
                      .|.+.|-.+=.+...-.+     .+=..+.++.....+.+..|||+|++.+.++...++.-.-.        ...-|..-
T Consensus        16 ~~e~~g~~~~r~~aYr~Aa~~l~~~~~~i~~~~~~~~~~~~~lp~iG~~~~~~i~~~v~~g~~~l~~~~~~~~~~~~~~l   95 (575)
T 3b0x_A           16 MSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEV   95 (575)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHCCSCHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHH
T ss_pred             HHHhcCCCchhHHHHHHHHHHHHhCCcchhhHhhcchhHHHhCCCCCHHHHHHHHHHHHcCcHHHHhhhhhhhHHHHHHH
Confidence            455666554444433321     11134444444322229999999999999998888652211        11234444


Q ss_pred             cCCCCCCHHHHHHHHhh--cCChHHHHhcC-HHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANY--FKNLECMFKAT-EEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~--f~sld~l~~As-~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      +.|+|||+++|..+...  +.++++|..|- ..+|.+++|||+++|+.|..-+.
T Consensus        96 ~~v~GvGpk~A~~~~~~lg~~~~~~l~~a~~~~~l~~~~GiG~k~a~~i~~~l~  149 (575)
T 3b0x_A           96 MEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLA  149 (575)
T ss_dssp             HTSTTTCHHHHHHHHHTSCCCSHHHHHHHHHHTGGGGSTTCCHHHHHHHHHHHH
T ss_pred             hcCCCcCHHHHHHHHHhcCCCCHHHHHHHHHcCCcccCCCCCccHHHHHHHHHH
Confidence            69999999999998875  57899998764 35799999999999999966554

>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B

Probab=96.28  E-value=0.009  Score=61.26  Aligned_cols=77  Identities=10%  Similarity=0.046  Sum_probs=62.2

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccc----------ccccEEEEcCC-CCccHHHHHHcCCeEEeHH
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFIS----------KNTNYLVKGQK-PGKKLEKAIKLNIKILDEK  672 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVs----------k~t~~LV~G~~-~g~Kl~kA~~lgI~Ii~E~  672 (687)
                      ...|.|.+|++||....-.++.+..+++.+||++.....          ..++++|+... +..+.+.|.+.||+|++.+
T Consensus       153 ~~LF~G~~I~i~~~~~~~~~~~~~~Il~~~Ga~vv~~~~s~~~~~d~~~~~~~viv~d~~~~~~~~~~a~~~~i~iVs~E  232 (259)
T 1kzy_C          153 ENPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQE  232 (259)
T ss_dssp             CCTTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTTCCHHHHHHHHHHTCCEECHH
T ss_pred             CCCCCCeEEEEecCCCCCHHHHHHHHHHhcCCEEEeccccchhhhhccCCCCeEEEECCCChHHHHHHHHhcCCCEecHH
Confidence            468999999999997543577888899999999887763          46788888543 3467788999999999999


Q ss_pred             HHHHHHhc
Q psy11422        673 NFVKIVKG  680 (687)
Q Consensus       673 ~f~~~l~~  680 (687)
                      ++++.+..
T Consensus       233 Wv~~sI~~  240 (259)
T 1kzy_C          233 WVIQCLIV  240 (259)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99998753

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=96.12  E-value=0.0046  Score=55.62  Aligned_cols=50  Identities=24%  Similarity=0.281  Sum_probs=46.9

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      |+|+.++++|.++|+ .|+.++-..+.++|..++|+++.+|++|+++..+.
T Consensus        32 GIg~~~i~kL~eAG~-~Tve~va~a~~~eL~~i~GIse~ka~kIi~aA~kl   81 (114)
T 1b22_A           32 GINANDVKKLEEAGF-HTVEAVAYAPKKELINIKGISEAKADKILAEAAKL   81 (114)
T ss_dssp             TCSHHHHHHHHTTCC-SSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCc-CcHHHHHhCCHHHHHHccCCCHHHHHHHHHHHHHH
Confidence            999999999999997 89999999999999999999999999999987653

>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A

Probab=95.98  E-value=0.0086  Score=59.05  Aligned_cols=78  Identities=17%  Similarity=0.235  Sum_probs=56.7

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc------------------------cccEEEEcCCCCccHH
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK------------------------NTNYLVKGQKPGKKLE  659 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk------------------------~t~~LV~G~~~g~Kl~  659 (687)
                      ...|.|.+|+++|.+...+|++++++|+..||++.+...+                        -|.|+|.......+.+
T Consensus       102 ~~lF~g~~~~l~~~~~~~~~~~l~~lI~~~GG~v~~~~p~~~~~~~~~~~~v~~~~~~~~~~~~~t~~iv~~~~~~~~~~  181 (210)
T 2nte_A          102 PKLFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPE  181 (210)
T ss_dssp             CCTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEEESSCCCGGGCGGGSSCCCCTTSCTTCGGGTCCEEEEECSCSSCCCS
T ss_pred             ccccCceEEEEeccCCCCCHHHHHHHHHHCCCEEEecCCCCccccccccceeeeccCCCcccccceEEEEeccccccCHH
Confidence            3479999999999887778999999999999999863211                        1345554332112223


Q ss_pred             HHHHcCCeEEeHHHHHHHHhcc
Q psy11422        660 KAIKLNIKILDEKNFVKIVKGF  681 (687)
Q Consensus       660 kA~~lgI~Ii~E~~f~~~l~~~  681 (687)
                      .|...+|++++.++|++.+...
T Consensus       182 ~~~~~~v~~V~~~Wl~dcI~~~  203 (210)
T 2nte_A          182 RVRQGKVWKAPSSWFIDCVMSF  203 (210)
T ss_dssp             CSEETTEEEEEHHHHHHHHHHT
T ss_pred             HHhccCcccccHHHHHHHHHhC
Confidence            4566789999999999988653

>2hvq_A ORF1, hypothetical 37.6 kDa protein in GP24-HOC intergenic region; RNA, ligase, lysine adenylate; HET: APK; 2.40A {Enterobacteria phage T4} PDB: 2hvr_A* 2hvs_A*

Probab=95.97  E-value=0.034  Score=59.14  Aligned_cols=138  Identities=13%  Similarity=0.065  Sum_probs=83.0

Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccch--------hhhhhh
Q psy11422         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGEN--------ITTNIH  160 (687)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeD--------vT~n~~  160 (687)
                      .-||.|-++.    .|++.+... + .....++++.|+||-++++.+.+|. +.+.|||--. -.+        +++...
T Consensus         6 Y~si~n~~~~----~~i~~~~~~-~-l~~~~vvvtEKlDG~N~~i~~~~~~-i~~~sR~~~l-~~~~~~~~~~~~~~~~~   77 (335)
T 2hvq_A            6 YSSLENHYNS----KFIEKLYSL-G-LTGGEWVAREXIHGTNFSLIIERDK-VTCAKRTGPI-LPAEDFFGYEIILKNYA   77 (335)
T ss_dssp             CCCCEETTCH----HHHHHHHHT-T-CSCSCEEEEECCSSEEEEEEEETTE-EEEEETTEEC-CTTCCCTTTHHHHHHHH
T ss_pred             CCCCcchhhh----hHHHHHHhh-c-cCCCcEEEEEEecCcceEEEEECCE-EEEecCCccc-CCccccchHHHHHHHHH
Confidence            3467777752    344444321 1 1134799999999999999998888 5799998333 222        555543


Q ss_pred             -hhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecc-
Q psy11422        161 -IIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVG-  238 (687)
Q Consensus       161 -~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~-  238 (687)
                       .|..+-..|... .+..+.|-||.+=+.                             -|.+-...   +..|++|+|- 
T Consensus        78 ~~i~~L~~~l~~~-~~~~~~i~GE~~G~~-----------------------------Iq~~i~Y~---~~~FyvFDI~~  124 (335)
T 2hvq_A           78 DSIKAVQDIMETS-AVVSYQVFGEFAGPG-----------------------------IQKNVDYG---DKDFYVFDIIV  124 (335)
T ss_dssp             HHHHHHHTTHHHH-TEEEEEEEEEEESBT-----------------------------TBSSCCCC---SSEEEEEEEEE
T ss_pred             HHHHHHHHHhhcc-CCCcEEEEEEEccCc-----------------------------ccCCcccC---CCeEEEEEEEE
Confidence             233333233210 135799999998321                             11111111   4589999975 


Q ss_pred             cccCC-CCCCCHHHHHHHHHhcCCCCCCCc
Q psy11422        239 ELRGM-NMPSSHSELLNWYQKIGLSICGEY  267 (687)
Q Consensus       239 ~~~~~-~~~~~~~e~l~~L~~~Gf~~~~~~  267 (687)
                      ..++. ...-+..+..+++..+||++++..
T Consensus       125 ~~~~~~~~~l~~~~~~~l~~~~gl~~VP~L  154 (335)
T 2hvq_A          125 TTESGDVTYVDDYMMESFCNTFKFKMAPLL  154 (335)
T ss_dssp             EETTCCEEECCHHHHHHHHHHHTCEESCEE
T ss_pred             ecCCCceeeCCHHHHHHHHHHcCCCeecee
Confidence            32220 012578888899999999988743

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=95.84  E-value=0.0055  Score=69.72  Aligned_cols=80  Identities=19%  Similarity=0.249  Sum_probs=48.1

Q ss_pred             cccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11422        458 KAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v  531 (687)
                      +.+.++|+|+|.+++|+++-   .-.++.-++.     =+.++++|++.|..|.+.+   +.-.+.+...+   ..|+||
T Consensus       481 ~L~~l~g~geKsa~nL~~aIe~sk~~~l~r~l~-----aLGI~~vG~~~a~~La~~f~sl~~l~~a~~e~l---~~i~gi  552 (586)
T 4glx_A          481 KLTGLERMGPKSAQNVVNALEKAKETTFARFLY-----ALGIREVGEATAAGLAAYFGTLEALEAASIEEL---QKVPDV  552 (586)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHHHHTBCCHHHHHH-----HTTCTTCCHHHHHHHHHHHCSHHHHHHCCHHHH---TTSTTC
T ss_pred             HHhcccCccHHHHHHHHHHHHHHcCCCHHHHHH-----HcCCCchhHHHHHHHHHHcCCHHHHHccCHHHH---hcCCCc
Confidence            56778899999999988631   1112222221     1456778888887776654   22222332221   368888


Q ss_pred             CHHHHHHHHhhcCC
Q psy11422        532 GETTAKELANYFKN  545 (687)
Q Consensus       532 G~~~Ak~La~~f~s  545 (687)
                      |+.+|..|.+.|..
T Consensus       553 G~~~A~si~~ff~~  566 (586)
T 4glx_A          553 GIVVASHVHNFFAE  566 (586)
T ss_dssp             CHHHHHHHHHHHHS
T ss_pred             cHHHHHHHHHHHcC
Confidence            88888888777754

>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B

Probab=95.84  E-value=0.015  Score=48.06  Aligned_cols=52  Identities=12%  Similarity=0.210  Sum_probs=46.7

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      +--+|+.....-|-.+| |.++.||...+.++|.+++|||+|+.+.|.+.+++
T Consensus        12 e~L~LS~Ra~NcLkrag-I~Tv~dL~~~s~~dLlki~n~G~kSl~EI~~~L~~   63 (73)
T 1z3e_B           12 EELDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   63 (73)
T ss_dssp             GGSCCBHHHHHHHHHTT-CCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHcC-CCcHHHHHcCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            33478999999999888 79999999999999999999999999999988764

>1p16_A GTP--RNA, mRNA capping enzyme alpha subunit; guanylyltransferase, transcription, capping, CTD, mRNA; HET: SEP G GTP; 2.70A {Candida albicans} SCOP: b.40.4.6 d.142.2.3

Probab=95.83  E-value=0.018  Score=62.55  Aligned_cols=174  Identities=11%  Similarity=-0.003  Sum_probs=97.4

Q ss_pred             eEEEEEccceeEEEEEEe----CCEEEEEEecCCCCccchhhhhhhhhccCCccccc-CCCCceEEEEEEEEeehhhHHH
Q psy11422        119 EYIAELKFDGIAVNLRYE----YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI-KYPPELLEVRCEVLIYKKDFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~----~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~-~~~~~~~evRGEi~~~~~~F~~  193 (687)
                      .|++|+|.||+-+.+...    +|.=+.+.||+    |++++-.-...+.+...... ...+....+-||+++....   
T Consensus        61 ~~~ve~K~DG~R~ll~~~~~~~~g~~v~L~sR~----~~~~~i~~~~FP~~~~~~~~~~~~~~~~vLDGElV~~~~~---  133 (395)
T 1p16_A           61 DYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRE----NDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRN---  133 (395)
T ss_dssp             CEEEEEEECSEEEEEEEEEETTTEEEEEEEETT----CCEEECCSCCCCSCTTCCSSSCCCCSSEEEEEEEEEECCS---
T ss_pred             CEEEEECccceEEEEEEeecccCCCEEEEEeCC----CceEEeccccCCcccccccchhccCCcceeeeEEEEeccC---
Confidence            699999999999988662    44557999996    56644211111211111100 0124468899999986421   


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCC---------
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI---------  263 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~---------  263 (687)
                                                     ....++.|++|++...+|.++ .....+.++.|+++=+..         
T Consensus       134 -------------------------------~~~~~~~f~~FDlL~~~G~dl~~~pl~eR~~~L~~~i~~~~~~~~~~~~  182 (395)
T 1p16_A          134 -------------------------------VSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNP  182 (395)
T ss_dssp             -------------------------------SSCCEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHTHHHHHHHHHHCH
T ss_pred             -------------------------------CCcceeEEEEEEEEEECCeEcccCCHHHHHHHHHHHhhcccHhhhhcCc
Confidence                                           012578999999987766432 146778888887742110         


Q ss_pred             -------CCC-ceEe--CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC-ceeeE
Q psy11422        264 -------CGE-YSVL--SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS-KEALT  332 (687)
Q Consensus       264 -------~~~-~~~~--~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~-~~~~T  332 (687)
                             .+. ....  .....+.++++.    -..+.+..||||+|--+..++-  |   +.+ --+=||.+. .++..
T Consensus       183 ~~~~~~~~pf~v~~~~~~~~~~~~~~~~~----~~~~~~g~EGlI~K~~ds~Y~~--G---r~~-~wlKwK~~~~~TvDf  252 (395)
T 1p16_A          183 DIVNSPEFPFKVGFKTMLTSYHADDVLSK----MDKLFHASDGLIYTCAETPYVF--G---TDQ-TLLKWKPAEENTVDF  252 (395)
T ss_dssp             HHHSCTTSCCEEEECCCEEGGGTHHHHTT----GGGCSSCEEEEEEEESSSCCCS--E---EEE-EEEEECCGGGCCEEE
T ss_pred             cccccccCceEEEEecchhHHHHHHHHHH----HHhcCCCCCeEEEEeCCCCcCC--C---Ccc-ceEEEecCCCeEEEE
Confidence                   000 0111  112333344332    2345789999999987755442  2   222 335667644 34444


Q ss_pred             EEEEEEEe
Q psy11422        333 KIKAINIQ  340 (687)
Q Consensus       333 ~v~~I~~q  340 (687)
                      +|.....|
T Consensus       253 vl~~~~~~  260 (395)
T 1p16_A          253 QLEFVFNE  260 (395)
T ss_dssp             EEEEECEE
T ss_pred             EEEEEecc
Confidence            55544444

>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A*

Probab=95.80  E-value=0.01  Score=58.34  Aligned_cols=70  Identities=17%  Similarity=0.253  Sum_probs=54.3

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ...|+|+.|++.+.+...+|++++++|+.+||++..++. +++++| |+...     ++..++++++++++++-+..
T Consensus       117 ~~LF~g~~~~~v~~~~~~~~~~L~~lI~~~GG~v~~~~~-~~~iiI-~~~~~-----~~~~~~~~V~p~Wi~DsI~~  186 (199)
T 3u3z_A          117 GTLFADQPVMFVSPASSPPVAKLCELVHLCGGRVSQVPR-QASIVI-GPYSG-----KKKATVKYLSEKWVLDSITQ  186 (199)
T ss_dssp             CCTTTTSCCEEECTTCSSCHHHHHHHHHHTTCCBCSSGG-GCSEEE-SCCCS-----CCCTTCEEECHHHHHHHHHH
T ss_pred             chhhCCCeEEEECCCCCCCHHHHHHHHHHcCCEEeccCC-CCEEEE-eCCch-----hccCCCcEEChhHHHHHHHc
Confidence            457999964444444457999999999999999999985 677765 55433     24679999999999998864

>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A*

Probab=95.63  E-value=0.011  Score=59.17  Aligned_cols=68  Identities=16%  Similarity=0.071  Sum_probs=58.2

Q ss_pred             CCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCC-CccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        608 KEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKP-GKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       608 ~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~-g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+..|+|||.-..    +.+++++.+||.+.++++ ++++||++... +.|+-.|...|++|++.+++.+.++.
T Consensus         7 ~~~~v~fSG~~~~----~~~~~i~~lGg~v~~~~~-~~THlV~~~~~RT~K~l~Aia~g~~IVs~~Wl~~~~~~   75 (220)
T 3l41_A            7 KRVYITFTGYDKK----PSIDNLKKLDMSITSNPS-KCTHLIAPRILRTSKFLCSIPYGPCVVTMDWINSCLKT   75 (220)
T ss_dssp             CCEEEEECSCSSC----CCCGGGGGGTEEECSCTT-TCSEEECSSCCCBHHHHHHGGGCCEEECHHHHHHHHHH
T ss_pred             ceEEEEEeccCCC----CCcchHhhcceeeccCch-hhhhhhhhhHhhhcceeecCCCCCeEEEhHHHHhhhhh
Confidence            4779999998653    348999999999999986 59999998754 48999999999999999999988753

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=95.60  E-value=0.0075  Score=51.32  Aligned_cols=51  Identities=16%  Similarity=0.231  Sum_probs=45.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHH-HHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKL-ANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ks-a~~Ll~~Ie~  513 (687)
                      ..+|||+|+++..+|++.-  .|+.+|..++.++|..+  +|.+. |++|++.+..
T Consensus        20 L~~IpGIG~kr~~~LL~~F--gSl~~i~~AS~eEL~~v--ig~~~~A~~I~~~l~~   71 (84)
T 1z00_B           20 LLKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSI--LGNAANAKQLYDFIHT   71 (84)
T ss_dssp             HHTCSSCCHHHHHHHHHHS--SCHHHHHHSCHHHHHHH--HSCHHHHHHHHHHHTS
T ss_pred             HHhCCCCCHHHHHHHHHHc--CCHHHHHHCCHHHHHHH--hCchHHHHHHHHHHHh
Confidence            3479999999999999854  69999999999999999  88998 9999998853

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=95.60  E-value=0.0069  Score=69.93  Aligned_cols=80  Identities=19%  Similarity=0.300  Sum_probs=40.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhh---hcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v  531 (687)
                      +.+.++|+|+|+.++|+++     +..--.-.-.++   +.++|+|++.|+.|++.+   +.-++.+...+   ..|+||
T Consensus       481 ~L~~l~gfG~Ksa~nLl~a-----Ie~sk~~~l~R~L~algi~~VG~~~Ak~La~~Fgsl~~l~~As~eeL---~~i~GI  552 (671)
T 2owo_A          481 KLTGLERMGPKSAQNVVNA-----LEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEEL---QKVPDV  552 (671)
T ss_dssp             HHHTSTTCCHHHHHHHHHH-----HHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHCSHHHHHTCCHHHH---TTSTTC
T ss_pred             HhhcccccchhHHHHHHHH-----HHHHhcCChhheehhhcccCccHHHHHHHHHHcCCHHHHHhCCHHHH---hhcCCC
Confidence            3455667777777777652     111111111221   256667777776666643   22233332211   256677


Q ss_pred             CHHHHHHHHhhcCC
Q psy11422        532 GETTAKELANYFKN  545 (687)
Q Consensus       532 G~~~Ak~La~~f~s  545 (687)
                      |+.+|+.|.+.|..
T Consensus       553 G~~~A~sI~~ff~~  566 (671)
T 2owo_A          553 GIVVASHVHNFFAE  566 (671)
T ss_dssp             CHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHh
Confidence            77777666666643

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=95.48  E-value=0.0024  Score=72.87  Aligned_cols=68  Identities=13%  Similarity=0.069  Sum_probs=0.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCC
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGI  528 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGI  528 (687)
                      ||+|+|+|+++.+.|.+.-  .|+..|..++.++|.+++|+|++.|+.|++.++...+..+..-|.+.|+
T Consensus       531 aLGIp~VG~~~ak~La~~F--gsle~L~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv  598 (615)
T 3sgi_A          531 ALSIRHVGPTAARALATEF--GSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGV  598 (615)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             HcCCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHcCHHHHHHHHHHHHcCC
Confidence            4555555555555554431  3455555555555666666666666666655555555444333334443

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=95.47  E-value=0.012  Score=67.75  Aligned_cols=68  Identities=19%  Similarity=0.339  Sum_probs=33.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCC
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGI  528 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGI  528 (687)
                      +|+|+|+|+++..+|.+.-  .++..|...+.++|..++|+|++.|++|.+.+....+..+..-|.+.|+
T Consensus       509 alGI~~VG~~~Ak~La~~F--gsl~~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv  576 (667)
T 1dgs_A          509 ALGLPGVGEVLARNLARRF--GTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGV  576 (667)
T ss_dssp             HTTCSSCCHHHHHHHHHTT--SBHHHHTTCCHHHHHTSTTCCHHHHHHHHHHHHCHHHHHHHHHHHHTTC
T ss_pred             hhccCCccHHHHHHHHHHc--CCHHHHHhCCHHHHHhccCcCHHHHHHHHHHHhhHHHHHHHHHHHHcCC
Confidence            3455555555555555431  3444555555555555555555555555555544333333333333444

>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1

Probab=95.43  E-value=0.024  Score=47.52  Aligned_cols=50  Identities=12%  Similarity=0.230  Sum_probs=45.8

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        463 IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      =+|+.....-|-.+| |.++.||...+.++|+++.+||+|+.+.|.+.+++
T Consensus        21 L~LS~Ra~NcLk~ag-I~Tv~dL~~~se~dLlki~n~G~kSl~EI~~~L~e   70 (79)
T 3gfk_B           21 LDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   70 (79)
T ss_dssp             SCCBHHHHHHHHHTT-CCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHhC-CCCHHHHHhCCHHHHHHcCCCCHhHHHHHHHHHHH
Confidence            378899999999998 69999999999999999999999999999888764

>1s68_A RNA ligase 2; ribonucleic acid ligase, RNA repair; HET: AMP; 1.90A {Enterobacteria phage T4} SCOP: d.142.2.4

Probab=95.29  E-value=0.067  Score=54.46  Aligned_cols=148  Identities=16%  Similarity=0.116  Sum_probs=83.3

Q ss_pred             cCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCcc-c------hhhhhh-hh
Q psy11422         90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIG-E------NITTNI-HI  161 (687)
Q Consensus        90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~G-e------DvT~n~-~~  161 (687)
                      -||+|-|+.    .|++++... +. ....++++.|+||-++++.+.+|. +.+.|||-=... +      .+.+.. ..
T Consensus         6 ~~i~n~~~~----~~~~~~~~~-~~-~~~~vvvtEKldG~N~~i~~~~~~-i~~~sR~~~l~~~~~f~~~~~~~~~~~~~   78 (249)
T 1s68_A            6 SSLENHYNS----KFIEKLYSL-GL-TGGEWVAREKIHGTNFSLIIERDK-VTCAKRTGPILPAEDFFGYEIILKNYADS   78 (249)
T ss_dssp             CCCEETTCH----HHHHHHHHH-TC-SCSCEEEEECCCSEEEEEEEESSC-EEEEETTEECCTTCCCTTTHHHHHHTHHH
T ss_pred             Ccccchhhh----HHHHHHHhh-cc-CCCCEEEEEEECCcceEEEEECCE-EEEEeCCcccCCCCccchHHHHHHHHHHH
Confidence            467777752    345555321 11 134799999999999999998887 569999833211 1      222221 11


Q ss_pred             hccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecc-cc
Q psy11422        162 IHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVG-EL  240 (687)
Q Consensus       162 i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~-~~  240 (687)
                      |..+=..|... .+..+.|-||++=+.                             -|.+-...   +..|++|+|- +.
T Consensus        79 ~~~l~~~l~~~-~~~~~~i~GE~~G~~-----------------------------Iq~~v~Y~---~~~FyvFdI~~~~  125 (249)
T 1s68_A           79 IKAVQDIMETS-AVVSYQVFGEFAGPG-----------------------------IQKNVDYC---DKDFYVFDIIVTT  125 (249)
T ss_dssp             HHHHHHHHHHH-TEEEEEEEEEEESTT-----------------------------TSSSCCCC---SCEEEEEEEEEEE
T ss_pred             HHHHHHHhccc-CCCcEEEEEEEcccc-----------------------------ccCCcccC---CCeEEEEEEEEec
Confidence            11111112100 135799999998221                             11111111   4589999975 42


Q ss_pred             cCC-CCCCCHHHHHHHHHhcCCCCCCCceEeCCHHHHHH
Q psy11422        241 RGM-NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIE  278 (687)
Q Consensus       241 ~~~-~~~~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~  278 (687)
                      ++. ...-+..+..+++..+||++++.... .+.+++.+
T Consensus       126 ~~g~~~~l~~~~~~~l~~~~gl~~VP~l~~-g~~~e~~~  163 (249)
T 1s68_A          126 ESGDVTYVDDYMMESFCNTFKFKMAPLLGR-GKFEELIK  163 (249)
T ss_dssp             TTCCEEECCHHHHHHHHHHHTCEESCEEEE-ECHHHHTT
T ss_pred             CCCccccCCHHHHHHHHHHCCCCeecEEeE-EcHHHHhh
Confidence            211 01247778889999999998875322 34555444

>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D

Probab=95.24  E-value=0.027  Score=48.01  Aligned_cols=50  Identities=14%  Similarity=0.074  Sum_probs=46.1

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        463 IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      =+|+.....-|-.+| |.++.||...+.++|+++++||+||.+.|.+.+++
T Consensus        17 L~LSvRa~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   66 (86)
T 3k4g_A           17 LELTVRSANCLXAEA-IHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLAS   66 (86)
T ss_dssp             GCCCHHHHHHHHHTT-CCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHT
T ss_pred             hCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHhhccccCcccHHHHHHHHHH
Confidence            378999999999988 79999999999999999999999999999988865

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=95.24  E-value=0.012  Score=57.78  Aligned_cols=54  Identities=22%  Similarity=0.252  Sum_probs=42.7

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCh-HHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ...|+|+|||+..+|++.-....+ ..+..-+.++|.++||+|+|+|++|+..+.
T Consensus        74 L~~v~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~~lk  128 (191)
T 1ixr_A           74 LLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELK  128 (191)
T ss_dssp             HHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HhcCCCcCHHHHHHHHHhCChHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence            457999999999999986532222 234556788999999999999999998875

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=95.17  E-value=0.016  Score=62.05  Aligned_cols=108  Identities=15%  Similarity=0.185  Sum_probs=71.4

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH--HHHHc--------------------ccC
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL--AIQKS--------------------KLT  517 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~--~Ie~s--------------------k~~  517 (687)
                      -.|+|+||.+++.|.++-.  |++.+-+++.++|.. +|+|+|.|..|+.  .+...                    +..
T Consensus       471 tAIaGIGp~tAeRLLEkFG--SVe~Vm~AteDELRe-dGIGekqarrI~gl~~l~~~~~d~~~a~elkr~ygs~savr~~  547 (685)
T 4gfj_A          471 ISIRGIDRERAERLLKKYG--GYSKVREAGVEELRE-DGLTDAQIRELKGLKTLESIVGDLEKADELKRKYGSASAVRRL  547 (685)
T ss_dssp             HTSTTCCHHHHHHHHHHHT--SHHHHHHSCHHHHHH-TTCCHHHHHHHHTCHHHHHHSSSHHHHHHHHHHSSCHHHHHHS
T ss_pred             eccCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHH-ccccHHHHHHHhhHHHHHHHhcchhhHHHHHHhhccHHHHHhc
Confidence            3699999999999999743  788888899999977 9999999988862  11110                    011


Q ss_pred             CHHHHHHHc-----------CCC-----CCCHHHHHHHHhhcCChHHHHhc-CHHHHhcCCCCCHHHHHHHH
Q psy11422        518 TFSRFIYAL-----------GIR-----HVGETTAKELANYFKNLECMFKA-TEEQLLNIPKIGSTTVKAFI  572 (687)
Q Consensus       518 ~l~r~L~aL-----------GIp-----~vG~~~Ak~La~~f~sld~l~~A-s~eeL~~I~GIG~~~A~sI~  572 (687)
                      |.. =|..|           |||     +..-.+|..|.+.|+++..+..+ +.++|.. +|.|++.+..|.
T Consensus       548 pv~-elrelg~sd~~ia~ikgip~~~~~~~~~e~a~~l~er~~~~~~~~~~~~~~~l~~-~g~~~~~~~eik  617 (685)
T 4gfj_A          548 PVE-ELRELGFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYDDLLE-LGATPKAAAEIK  617 (685)
T ss_dssp             CHH-HHHTTSCCHHHHHHHHTCCHHHHHHSCHHHHHHHHHHHSSSTGGGGSCGGGCCSS-SCCGGGC-----
T ss_pred             cHH-HHHHcCCchhhHHHhcCCcHHHHhhcCHHHHHHHHHHhccHHHHhhcCCHHHHhc-cCCCHHHHHHhc
Confidence            111 11112           454     12335677888899999988876 6667766 777777776665

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=95.06  E-value=0.017  Score=57.53  Aligned_cols=53  Identities=11%  Similarity=0.265  Sum_probs=47.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+.|+|+|++++..|.+.-  .++.+|+..+.++|..++|+|++.|++|.+.+..
T Consensus       164 L~~i~gVg~~~a~~Ll~~f--gs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~~~  216 (219)
T 2bgw_A          164 LQSFPGIGRRTAERILERF--GSLERFFTASKAEISKVEGIGEKRAEEIKKILMT  216 (219)
T ss_dssp             HHTSTTCCHHHHHHHHHHH--SSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHS
T ss_pred             HhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHhc
Confidence            3479999999999999963  5799999999999999999999999999998864

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=94.96  E-value=0.02  Score=56.58  Aligned_cols=55  Identities=13%  Similarity=0.257  Sum_probs=44.1

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCh-HHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ...|+|+|||+..+|++.-....+ ..+..-+.++|.++||+|+|+|++|+..+..
T Consensus        75 L~~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~elk~  130 (203)
T 1cuk_A           75 LIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKD  130 (203)
T ss_dssp             HHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HhcCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            457999999999999996532222 3455577899999999999999999988853

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=94.70  E-value=0.0088  Score=49.37  Aligned_cols=42  Identities=14%  Similarity=0.339  Sum_probs=20.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNIL  508 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll  508 (687)
                      ...|+|+|+++++++++.-..        -+.++|..++|+|++.+++|.
T Consensus        29 L~~ipGIG~~~A~~Il~~r~~--------~s~~eL~~v~Gig~k~~~~i~   70 (75)
T 2duy_A           29 LMALPGIGPVLARRIVEGRPY--------ARVEDLLKVKGIGPATLERLR   70 (75)
T ss_dssp             HTTSTTCCHHHHHHHHHTCCC--------SSGGGGGGSTTCCHHHHHHHG
T ss_pred             HHhCCCCCHHHHHHHHHHccc--------CCHHHHHhCCCCCHHHHHHHH
Confidence            344555555555555554311        223444455555555555543

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=94.59  E-value=0.061  Score=44.03  Aligned_cols=48  Identities=21%  Similarity=0.184  Sum_probs=43.1

Q ss_pred             CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11422        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      .+||+|+..+.+|.+. |.|++.|..++.++|..|.||++..|..|+.-
T Consensus        11 ~L~Gi~~~~~~kL~e~Gi~TvedlA~~~~~eL~~i~gise~kA~~ii~a   59 (70)
T 1wcn_A           11 NLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMA   59 (70)
T ss_dssp             SSTTCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHH
Confidence            6789999999988865 89999999999999999999999999988753

>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae}

Probab=94.48  E-value=0.18  Score=55.73  Aligned_cols=146  Identities=17%  Similarity=0.105  Sum_probs=85.5

Q ss_pred             eeEEEEEccceeEEEEEEeC----C-EEEEEEecCCCCccchhhhhhhhhccCCcc-----cccCCCCceEEEEEEEEee
Q psy11422        118 IEYIAELKFDGIAVNLRYEY----G-YLKQASTRGDGNIGENITTNIHIIHKIPLV-----LNIKYPPELLEVRCEVLIY  187 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~----G-~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~-----l~~~~~~~~~evRGEi~~~  187 (687)
                      -.|++++|.||+-+.+....    | .=+.++||++-    +++-+-...+.++..     +.  ..+....+-||+++.
T Consensus        65 ~dY~V~eK~DGiR~Ll~i~~~~~~g~g~v~LidR~~~----~~~v~~~~FP~~~~~~~~~~l~--~~~~~TlLDGElV~d  138 (461)
T 3kyh_C           65 HDYYVCEKTDGLRVLMFIVINPVTGEQGCFMIDRENN----YYLVNGFRFPRLPQKKKEELLE--TLQDGTLLDGELVIQ  138 (461)
T ss_dssp             SCEEEEEEECSEEEEEEEEECTTTCCEEEEEECSSSC----EEEECCCCCCCCSSCCSSGGGT--CCCCSEEEEEEEEEE
T ss_pred             CCEEEEEcccceEEEEEEeccccCCCceEEEEeCCCC----eEEcccccCCcccccchhhhhh--ccCCCeEEEEEEEec
Confidence            47999999999999886652    2 34788999654    454220111222221     11  134567899999995


Q ss_pred             hhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCC----
Q psy11422        188 KKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLS----  262 (687)
Q Consensus       188 ~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~----  262 (687)
                      ...                   .   +           ....+.|++|++...+|.++ .....+.++.|.++=..    
T Consensus       139 ~~~-------------------~---~-----------~~~~~~y~~FDlL~~~G~dl~~~pl~eR~~~Le~~I~~P~~~  185 (461)
T 3kyh_C          139 TNP-------------------M---T-----------KLQELRYLMFDCLAINGRCLTQSPTSSRLAHLGKEFFKPYFD  185 (461)
T ss_dssp             ECT-------------------T---T-----------CCEEEEEEEEEEEEETTEECSSSBHHHHHHHHHHTTHHHHHH
T ss_pred             cCC-------------------C---C-----------CccceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhcccchh
Confidence            321                   0   0           12478999999987665432 14677888888755110    


Q ss_pred             ----------CCCCceEeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        263 ----------ICGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       263 ----------~~~~~~~~~~~---~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                                ..+......++   .++.++++    .-..+.+..||+|+|--+..+
T Consensus       186 ~~~~~p~~~~~~pF~V~~K~~~~~~~~~~l~~----~~~~l~~~~EGLv~k~~~spY  238 (461)
T 3kyh_C          186 LRAAYPNRCTTFPFKISMKHMDFSYQLVKVAK----SLDKLPHLSDGLIFTPVKAPY  238 (461)
T ss_dssp             HHHHCSTTCSCCCSEEEECCCEEGGGHHHHHH----HHTTCSSCEEEEEEEESSSBC
T ss_pred             hhhccccccccCCcEEEeccchhhhhHHHHHH----hhhhccCCCCeEEEEeCCCCC
Confidence                      01111112222   23444433    124688999999999866433

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=94.30  E-value=0.02  Score=57.03  Aligned_cols=54  Identities=15%  Similarity=0.249  Sum_probs=42.5

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChH-HHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAV-DLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~-DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..|+|+|||++..+++......+. .+..-+.+.|.++||+|+|+|++|+..+..
T Consensus        91 ~sv~GIGpk~A~~Ils~~~~~~l~~aI~~~d~~~L~~vpGIG~KtA~rIi~elk~  145 (212)
T 2ztd_A           91 LSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRD  145 (212)
T ss_dssp             HTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTT
T ss_pred             cCcCCcCHHHHHHHHHhCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            349999999999999865333332 233456788999999999999999998864

>3rtx_A MRNA-capping enzyme; guanylyltransferase, RNA polymerase II CTD, lysyl-N-GMP, NUC mRNA capping, transferase; HET: SEP GUN; 2.81A {Mus musculus} PDB: 3s24_A

Probab=94.24  E-value=0.068  Score=57.01  Aligned_cols=155  Identities=15%  Similarity=0.079  Sum_probs=82.4

Q ss_pred             eEEEEEccceeEEEEEEe-CCEEEEEEecCCCCccchhhh-hhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITT-NIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~-n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~  196 (687)
                      .|++++|.||.-+.+... +|. +.+.||+    |+++|. +.+. +.+.. +.  ..+....+-||+++...+      
T Consensus        64 ~y~v~~K~DG~R~ll~i~~~~~-v~L~sR~----~~~~~~~~~~F-P~~~~-~~--~~~~~tvLDGElV~~~~~------  128 (343)
T 3rtx_A           64 PYKVSWKADGTRYMMLIDGTNE-VFMIDRD----NSVFHVSNLEF-PFRKD-LR--MHLSNTLLDGEMIIDKVN------  128 (343)
T ss_dssp             CEEEEEECCCEEEEEEECSTTC-EEEECTT----CCEEEETTCCC-EETTE-EE--EECCSEEEEEEEEEEESS------
T ss_pred             CEEEEECCCceEEEEEEEcCCE-EEEEeCC----CCeEEeccccC-Ccchh-hh--ccCCCeEEEEEEEEecCC------
Confidence            699999999999988666 454 6889995    455653 2211 11110 11  013457899999986421      


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc-----------CCC--
Q psy11422        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI-----------GLS--  262 (687)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~-----------Gf~--  262 (687)
                                        |           ...+.|++|++...+|.++ .....+.++.|.+.           |..  
T Consensus       129 ------------------g-----------~~~~~~~~FDlL~~~G~dl~~~pl~eR~~~L~~~i~~p~~~~~~~~~~~~  179 (343)
T 3rtx_A          129 ------------------G-----------QAVPRYLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDK  179 (343)
T ss_dssp             ------------------S-----------SEEEEEEEEEEEEBTTBCGGGSCHHHHHHHHHHHTHHHHHHHHHHSSCCT
T ss_pred             ------------------C-----------cEeeEEEEEEEEeECCcCcccCCHHHHHHHHHHHhhhHHHHHhhcccccc
Confidence                              1           1246999999988766442 14677777777642           210  


Q ss_pred             -CCCCc------eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11422        263 -ICGEY------SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (687)
Q Consensus       263 -~~~~~------~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (687)
                       ..+..      ......+.+..  .   +....+.+..||+|++-.+ .+.      ++....-+-||.+...
T Consensus       180 ~~~pf~vr~K~~~~~~~~~~ll~--~---~~~~~l~~~~dGlIf~~~~-~Y~------~G~~~~~lKwKp~~~~  241 (343)
T 3rtx_A          180 TQEPFSVRPKQFFDINISRKLLE--G---NFAKEVSHEMDGLIFQPIG-KYK------PGRCDDILKWKPPSLN  241 (343)
T ss_dssp             TTSSSEEEECCCEEGGGHHHHSC--C-------------CEEEEEESS-CCC------CEEEEEEEEECCSTTC
T ss_pred             cCCCcEEEEEEeEehhhHHHHHh--h---hhHhhcCCCCCeEEEEECc-cCc------CCCCcceEEEecCcce
Confidence             01111      11122233221  0   1234678899999999877 432      2222344667766543

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=94.14  E-value=0.022  Score=52.23  Aligned_cols=56  Identities=20%  Similarity=0.310  Sum_probs=40.7

Q ss_pred             hHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCC
Q psy11422        482 AVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIP  561 (687)
Q Consensus       482 i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~  561 (687)
                      .-||-+.+.++|..+||+|++.|++|++      +.                        .|.+        .|||.+++
T Consensus        54 kIniNtA~~~eL~~LpGiGp~~A~~II~------~G------------------------pF~s--------vedL~~V~   95 (134)
T 1s5l_U           54 KIDLNNTNIAAFIQYRGLYPTLAKLIVK------NA------------------------PYES--------VEDVLNIP   95 (134)
T ss_dssp             SEETTTSCGGGGGGSTTCTHHHHHHHHH------TC------------------------CCSS--------GGGGGGCT
T ss_pred             eeeCcccCHHHHHHCCCCCHHHHHHHHH------cC------------------------CCCC--------HHHHHhCC
Confidence            3477778889999999999999999881      11                        2553        36677777


Q ss_pred             CCCHHHHHHHHHHH
Q psy11422        562 KIGSTTVKAFIKFI  575 (687)
Q Consensus       562 GIG~~~A~sI~~ff  575 (687)
                      |||+++.+.+..+.
T Consensus        96 GIg~k~~e~l~~~~  109 (134)
T 1s5l_U           96 GLTERQKQILRENL  109 (134)
T ss_dssp             TCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhh
Confidence            88877776665554

>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A

Probab=93.94  E-value=0.05  Score=47.47  Aligned_cols=50  Identities=16%  Similarity=0.103  Sum_probs=45.2

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        463 IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      -+|+.....-|-.+| |.++.||...+.++|+++++||+|+.+.|.+.++.
T Consensus        29 L~LSvRs~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   78 (98)
T 1coo_A           29 LELTVRSANCLKAEA-IHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   78 (98)
T ss_dssp             GTCCTTTHHHHHTTT-CCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            367888888998887 79999999999999999999999999999988864

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=93.92  E-value=0.051  Score=57.78  Aligned_cols=63  Identities=16%  Similarity=0.271  Sum_probs=47.6

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccCCHH------HHHHHc-CCCCCCHHHHHHHHh-hcCChHHHHhcC
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS------RFIYAL-GIRHVGETTAKELAN-YFKNLECMFKAT  553 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~------r~L~aL-GIp~vG~~~Ak~La~-~f~sld~l~~As  553 (687)
                      ++|..|||+|++.|++|.+-++.-+-..+.      .++.-| .|||||+++|+.+-+ .+.|+++|..+.
T Consensus        57 ~~l~~lpGIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k~a~~l~~~Gi~tledL~~a~  127 (335)
T 2bcq_A           57 QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQA  127 (335)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHHHHC
T ss_pred             HHHhcCCCccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHHHHHHHHHcCCCCHHHHHHHh
Confidence            458999999999999999988742211121      356666 999999999998865 467888888753

>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae}

Probab=93.88  E-value=0.0044  Score=63.39  Aligned_cols=75  Identities=17%  Similarity=0.194  Sum_probs=58.0

Q ss_pred             CCccCCeEEEE-EcCCC-----cCCHHHHHHHHHhcCCEEcccccccc-----cEEEEcCCCCccHHHHHHcCCeEEeHH
Q psy11422        604 KNYLKEKIFVF-TGSLY-----AFKRNEAIILIENLGGKVVNFISKNT-----NYLVKGQKPGKKLEKAIKLNIKILDEK  672 (687)
Q Consensus       604 ~~~l~g~~vv~-TG~l~-----~~~R~e~~~~i~~~Gg~v~~sVsk~t-----~~LV~G~~~g~Kl~kA~~lgI~Ii~E~  672 (687)
                      ++.|+|.+||+ +|.+.     ..+|++++.+|+++||++.......|     +++|+ ++...|.+.+...|++||+.+
T Consensus         3 s~lF~g~~f~v~~~~~~p~~~~~~~~~~L~~li~~~GG~~~~~~~~~t~~~~~~~iI~-~~~t~k~~~~~~~~~~vV~p~   81 (264)
T 1z56_C            3 SNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLIS-CKTTTECKALIDRGYDILHPN   81 (264)
T ss_dssp             CCCCCTTCCCCSEEEECCCCCSSSSCCCTHHHHHHHHTTSCCCSSCCCCCSSCCEEEE-CSCCGGGGGGTTTTCCCBCSS
T ss_pred             cccCCCcEEEEEcCCCCccccccCCHHHHHHHHHHcCCEEeecCCCCccCccceEEEe-cCCcHHHHHHHhCCCCEEech
Confidence            45799999977 66542     25899999999999998876555555     44555 456678888888889999999


Q ss_pred             HHHHHHh
Q psy11422        673 NFVKIVK  679 (687)
Q Consensus       673 ~f~~~l~  679 (687)
                      ++.+.+.
T Consensus        82 Wv~dci~   88 (264)
T 1z56_C           82 WVLDCIA   88 (264)
T ss_dssp             TTHHHHS
T ss_pred             HHHHHhh
Confidence            9998875

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=93.74  E-value=0.056  Score=46.95  Aligned_cols=31  Identities=23%  Similarity=0.075  Sum_probs=22.6

Q ss_pred             hHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        482 AVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       482 i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      +.||.+++.++|..++|+|++.|++|++..+
T Consensus        31 ~i~iN~a~~~~L~~ipGIG~~~A~~Il~~r~   61 (98)
T 2edu_A           31 LDLLNEGSARDLRSLQRIGPKKAQLIVGWRE   61 (98)
T ss_dssp             HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             CeehhhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            3467777777787888888888877777654

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=93.58  E-value=0.1  Score=45.27  Aligned_cols=42  Identities=17%  Similarity=0.374  Sum_probs=28.3

Q ss_pred             CCCCCCHHHHHHHHhhc---CChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11422        527 GIRHVGETTAKELANYF---KNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f---~sld~l~~As~eeL~~I~GIG~~~A~sI~~  573 (687)
                      .|||||+++|+.|.+++   +.+     .+.++|.+++|||+++++.|..
T Consensus        44 ~ipGIG~~~A~~Il~~r~~~g~f-----~s~edL~~v~Gig~k~~~~l~~   88 (98)
T 2edu_A           44 SLQRIGPKKAQLIVGWRELHGPF-----SQVEDLERVEGITGKQMESFLK   88 (98)
T ss_dssp             HSTTCCHHHHHHHHHHHHHHCCC-----SSGGGGGGSTTCCHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHhcCCc-----CCHHHHHhCCCCCHHHHHHHHH
Confidence            46777777777777665   222     4566677777777777777654

>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*

Probab=93.55  E-value=0.36  Score=48.03  Aligned_cols=82  Identities=24%  Similarity=0.313  Sum_probs=51.9

Q ss_pred             HHHHHHHHCCCCCC------hHHHhcCChhhhhc---ccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHH
Q psy11422        468 KMIEKLVNANIVVT------AVDLYKINFKNLLR---LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKE  538 (687)
Q Consensus       468 k~i~~L~~~g~I~~------i~DL~~L~~~~L~~---l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~  538 (687)
                      +.+..|.+.|+ -+      +++|..++.++|..   --||...+|.+|.+.-+.                         
T Consensus        50 ~~~~~L~~~~~-pt~~~~~t~~~la~~~~e~L~~~ir~~G~~~~KA~~L~~~a~~-------------------------  103 (218)
T 1pu6_A           50 KSLENLKNAFI-LENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGN-------------------------  103 (218)
T ss_dssp             HHHHHHHHTTS-SCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHH-------------------------
T ss_pred             HHHHHHHHccC-CCccccccHHHHHhCCHHHHHHHHHHCCCcHHHHHHHHHHHHH-------------------------
Confidence            45566666655 35      88999988877743   247887788777764332                         


Q ss_pred             HHhhcCChHHH-HhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        539 LANYFKNLECM-FKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       539 La~~f~sld~l-~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.+.++.++.+ ...+.++|.+++|||+++|..|..|-
T Consensus       104 i~~~~~~l~~~~~~~~~~~L~~lpGIG~kTA~~il~~a  141 (218)
T 1pu6_A          104 ILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYA  141 (218)
T ss_dssp             HHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             HHHhcCChhhccchHHHHHHHcCCCcCHHHHHHHHHHH
Confidence            12222222222 12356788899999999998887654

>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc genomics, PSI-2, protein structure initiative, joint center structural genomics; 2.55A {Bacillus halodurans}

Probab=93.42  E-value=0.23  Score=49.94  Aligned_cols=81  Identities=19%  Similarity=0.188  Sum_probs=51.8

Q ss_pred             HHHHHHHHC-CC-CCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCC
Q psy11422        468 KMIEKLVNA-NI-VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (687)
Q Consensus       468 k~i~~L~~~-g~-I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~s  545 (687)
                      +.+..|++. |. --++.+|..++.++|..+ ||+..+|..|.+.-+..                         .+.+.+
T Consensus        71 ~~~~rL~~~~G~~fPtp~~la~~~~e~Lr~~-G~~~~KA~~I~~~A~~i-------------------------~~~~~~  124 (233)
T 2h56_A           71 AIYGRVEQLVGGALEKPEQLYRVSDEALRQA-GVSKRKIEYIRHVCEHV-------------------------ESGRLD  124 (233)
T ss_dssp             HHHHHHHHHHTSCCCCTHHHHTSCHHHHHHT-TCCHHHHHHHHHHHHHH-------------------------HTTSSC
T ss_pred             HHHHHHHHHhCCCCCCHHHHHcCCHHHHHHc-CCCHHHHHHHHHHHHHH-------------------------HhCCCC
Confidence            455556554 42 138889998888888665 88888888777654322                         222223


Q ss_pred             hHHHHhc----CHHHHhcCCCCCHHHHHHHHHH
Q psy11422        546 LECMFKA----TEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       546 ld~l~~A----s~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      ++.+...    ..++|.+++|||+++|+.|.-|
T Consensus       125 ~~~l~~~p~~~~~~~L~~lpGIG~kTA~~ill~  157 (233)
T 2h56_A          125 FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMF  157 (233)
T ss_dssp             HHHHTTSCHHHHHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHH
Confidence            3333222    2467888888888888888776

>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A

Probab=93.32  E-value=0.25  Score=49.97  Aligned_cols=113  Identities=20%  Similarity=0.285  Sum_probs=75.3

Q ss_pred             CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH---cc
Q psy11422        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK---SK  515 (687)
Q Consensus       443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~---sk  515 (687)
                      .|.-.-.-|.||-|..  .|-.-.-.-|+.+|++|-++.  +-|..    .-.+|.+-+|.|.|+|+.|+.++-+   .|
T Consensus       363 spdaadeliehfesia--gilatdleeiermyeegrlse--eayraaveiqlaeltkkegvgrktaerllrafgnpervk  438 (519)
T 2csb_A          363 SPDAADELIEHFESIA--GILATDLEEIERMYEEGRLSE--EAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVK  438 (519)
T ss_dssp             CHHHHHHHHHHHSSHH--HHHTSCHHHHHHHHHHTSSCH--HHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSHHHHH
T ss_pred             CcchHHHHHHHHHHHH--HHHhccHHHHHHHHHcccccH--HHHHHHHHHHHHHHhhhcccchhHHHHHHHHhCCHHHHH
Confidence            5666778899998843  444455677899999997653  34442    3456788899999999999988732   11


Q ss_pred             ----cCCH----------HHHHHHc--------CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhc
Q psy11422        516 ----LTTF----------SRFIYAL--------GIRHVGETTAKELANYFKNLECMFKATEEQLLN  559 (687)
Q Consensus       516 ----~~~l----------~r~L~aL--------GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~  559 (687)
                          .-..          .|+|.+|        .|+||....|.+|+++||....+..|..++|..
T Consensus       439 qlarefeieklasvegvgervlrslvpgyaslisirgidreraerllkkyggyskvreagveelre  504 (519)
T 2csb_A          439 QLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELRE  504 (519)
T ss_dssp             HHHHTTCHHHHHTSTTCSHHHHHHHSTTHHHHHTSTTCCHHHHHHHHHHHTSHHHHHTSCHHHHHH
T ss_pred             HHHHHHhHHHHhhccchHHHHHHHhccchhhheeeccccHHHHHHHHHHhCChhHHHHhhHHHHHH
Confidence                1111          1344332        567777777777777777777777777666653

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*

Probab=93.04  E-value=0.081  Score=56.76  Aligned_cols=52  Identities=15%  Similarity=0.146  Sum_probs=48.1

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      .||+||+++++.|+++-  .|+..|++.+.++|.+++|+|++.|..|.+.+..-
T Consensus       319 ~IPrl~~~iae~Lv~~F--GsLq~Il~AS~eEL~~VeGIGe~rAr~IregL~r~  370 (377)
T 3c1y_A          319 TVARIPLSIGYNVVRMF--KTLDQISKASVEDLKKVEGIGEKRARAISESISSL  370 (377)
T ss_dssp             HTSCCCHHHHHHHHHHH--CSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHhccCccHHHHHHHHHHHHHH
Confidence            49999999999999975  49999999999999999999999999999998764

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=92.97  E-value=0.15  Score=54.25  Aligned_cols=62  Identities=23%  Similarity=0.286  Sum_probs=47.2

Q ss_pred             hhhhcccCccHHHHHHHHHHHHHcccC--------C-HHHHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhc
Q psy11422        491 KNLLRLDRVSNKLANNILLAIQKSKLT--------T-FSRFIYALGIRHVGETTAKELANY-FKNLECMFKA  552 (687)
Q Consensus       491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~--------~-l~r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~A  552 (687)
                      .+|..|||+|++.|++|.+-++.-+-.        + ..-+..=+.|||||+++|+.+-+. +.|+++|..+
T Consensus        57 ~~l~~LpGIG~~~A~kI~E~l~tG~~~~le~l~~~~~~~~l~~l~~V~GiGpk~a~~l~~~Gi~tledL~~a  128 (335)
T 2fmp_A           57 AEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKN  128 (335)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHHHHHHTTCCSHHHHHTC
T ss_pred             HHHhcCCCCcHHHHHHHHHHHHhCCcHHHHHHHcccchhHHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHHh
Confidence            468999999999999999988743211        1 223444469999999999988754 6789999886

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=92.89  E-value=0.047  Score=47.63  Aligned_cols=56  Identities=20%  Similarity=0.317  Sum_probs=42.3

Q ss_pred             HHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCC
Q psy11422        483 VDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPK  562 (687)
Q Consensus       483 ~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~G  562 (687)
                      -||-+++.++|..+||+|++.|++|++      +               |         .|.+        .++|.+++|
T Consensus        18 vdiNtAs~~eL~~lpGIG~~~A~~IV~------~---------------G---------pF~s--------~edL~~V~G   59 (97)
T 3arc_U           18 IDLNNTNIAAFIQYRGLYPTLAKLIVK------N---------------A---------PYES--------VEDVLNIPG   59 (97)
T ss_dssp             EETTTSCGGGGGGSTTCTTHHHHHHHH------H---------------C---------CCSS--------GGGGGGCTT
T ss_pred             eeCCcCCHHHHhHCCCCCHHHHHHHHH------c---------------C---------CCCC--------HHHHHhccC
Confidence            467777888898999999998888886      0               1         3553        467778888


Q ss_pred             CCHHHHHHHHHHHc
Q psy11422        563 IGSTTVKAFIKFIN  576 (687)
Q Consensus       563 IG~~~A~sI~~ff~  576 (687)
                      ||+++.+.+..++.
T Consensus        60 ig~~~~e~l~~~l~   73 (97)
T 3arc_U           60 LTERQKQILRENLE   73 (97)
T ss_dssp             CCHHHHHHHHHTGG
T ss_pred             CCHHHHHHHHHHhc
Confidence            88888888877653

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}

Probab=92.69  E-value=0.021  Score=57.35  Aligned_cols=51  Identities=20%  Similarity=0.272  Sum_probs=0.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ..+|+|+|+++.++|.+.-  .|+..|...+.++|.++ |+|++.|++|++.+.
T Consensus       175 L~~IpGIG~k~ak~Ll~~F--GSl~~i~~As~eeL~~V-GIG~~~A~~I~~~f~  225 (226)
T 3c65_A          175 LDDIPGVGEKRKKALLNYF--GSVKKMKEATVEELQRA-NIPRAVAEKIYEKLH  225 (226)
T ss_dssp             ------------------------------------------------------
T ss_pred             ccccCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhh
Confidence            4579999999999999863  57888999999999999 999999999988763

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=92.06  E-value=0.17  Score=54.62  Aligned_cols=101  Identities=15%  Similarity=0.106  Sum_probs=63.1

Q ss_pred             CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh-cC-ChhhhhcccCccHHHHHHHHHHHHHcccCCHH
Q psy11422        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY-KI-NFKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (687)
Q Consensus       443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~-~L-~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~  520 (687)
                      -.+..++.|..     .|.+.| .+-.+...-.+-  ..+..+= .+ +.++|.+|||+|++.|++|.+-++.-+-..+.
T Consensus        38 ~i~~~L~~ia~-----~~e~~g-~~~rv~AYr~Aa--~~l~~l~~~i~~~~~l~~lpGIG~~ia~kI~E~l~tG~~~~le  109 (381)
T 1jms_A           38 LFTDALDILAE-----NDELRE-NEGSCLAFMRAS--SVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAK  109 (381)
T ss_dssp             HHHHHHHHHHH-----HHHHTT-CHHHHHHHHHHH--HHHHTCSSCCCSGGGGTTCSSCCHHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHHHHHHHHH-----HHHhhC-CcHHHHHHHHHH--HHHHhCCccccCHHHHhcCCCCcHHHHHHHHHHHHcCCcHHHH
Confidence            34555566654     456778 777766654421  1111110 12 13469999999999999999988753322222


Q ss_pred             H---------HHHHcCCCCCCHHHHHHHHhh-cCChHHHHh
Q psy11422        521 R---------FIYALGIRHVGETTAKELANY-FKNLECMFK  551 (687)
Q Consensus       521 r---------~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~  551 (687)
                      .         +..=++|+|||+++|+.+-+. +.|+++|..
T Consensus       110 ~l~~d~~~~~l~~l~~I~GvGpk~a~~ly~~Gi~tledL~~  150 (381)
T 1jms_A          110 AVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQS  150 (381)
T ss_dssp             HHHHCHHHHHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHHH
T ss_pred             HHhcCcchhHHHHHHccCCCCHHHHHHHHHcCCCcHHHHHh
Confidence            2         233359999999999988754 667777764

>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A

Probab=92.01  E-value=0.48  Score=47.31  Aligned_cols=83  Identities=17%  Similarity=0.164  Sum_probs=51.2

Q ss_pred             HHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCCh
Q psy11422        467 KKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL  546 (687)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sl  546 (687)
                      .+.+..|.+.-.--++++|..++.++|..+ ||+..+|..|.+.-+...+                         ...++
T Consensus        80 ~~~~~rL~~~~G~ptp~~la~~~~e~Lr~~-G~~~~KA~~i~~lA~~~~~-------------------------g~~~l  133 (225)
T 2yg9_A           80 QAIYGRLEGLPGGVVPAALLKVSGDDLRGV-GLSWAKVRTVQAAAAAAVS-------------------------GQIDF  133 (225)
T ss_dssp             HHHHHHHHTSTTCSCHHHHTTSCHHHHHHT-TCCHHHHHHHHHHHHHHHT-------------------------TSSCG
T ss_pred             HHHHHHHHHHhCcCCHHHHHcCCHHHHHHC-CCcHHHHHHHHHHHHHHHh-------------------------CCcCH
Confidence            344555555422258888888888888665 8888778777664332211                         11123


Q ss_pred             HHHHhcC----HHHHhcCCCCCHHHHHHHHHHH
Q psy11422        547 ECMFKAT----EEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       547 d~l~~As----~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.+...+    .++|.+++|||+++|+.+.-|-
T Consensus       134 ~~l~~~~~~e~~~~L~~l~GIG~~TA~~ill~~  166 (225)
T 2yg9_A          134 AHLSGQPDELVIAELVQLPGIGRWTAEMFLLFA  166 (225)
T ss_dssp             GGCTTSCHHHHHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             HHHhcCCHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence            3333222    3578888888888888887763

>4b21_A Probable DNA-3-methyladenine glycosylase 2; hydrolase-DNA complex, helix-hairpin-helix; HET: BGC 3DR; 1.45A {Schizosaccharomyces pombe} PDB: 4b22_A* 4b23_A* 4b24_A*

Probab=91.93  E-value=0.71  Score=46.36  Aligned_cols=82  Identities=15%  Similarity=0.159  Sum_probs=54.2

Q ss_pred             HHHHHHHC-CC---CCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC
Q psy11422        469 MIEKLVNA-NI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK  544 (687)
Q Consensus       469 ~i~~L~~~-g~---I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~  544 (687)
                      .+.+|.+. |-   .-++++|..++.++|..+ ||+..+|..|.+.-+.         +.. |              .++
T Consensus        81 ~~~rL~~~~G~~~~fPtpe~la~~~~e~Lr~~-Gl~~~Ka~~l~~~A~~---------~~~-g--------------~~p  135 (232)
T 4b21_A           81 IINKFCTQCSDNDEFPTPKQIMETDVETLHEC-GFSKLKSQEIHIVAEA---------ALN-K--------------QIP  135 (232)
T ss_dssp             HHHHHHHHHCSSSSCCCHHHHHTSCHHHHHTT-TCCHHHHHHHHHHHHH---------HHT-T--------------CSC
T ss_pred             HHHHHHHHhCCCCCCCCHHHHHcCCHHHHHHc-CCcHHHHHHHHHHHHH---------HHh-C--------------CCC
Confidence            44455554 31   368999999998888775 9998888877764322         111 0              122


Q ss_pred             ChHHHHhcC----HHHHhcCCCCCHHHHHHHHHHH
Q psy11422        545 NLECMFKAT----EEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       545 sld~l~~As----~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +++.+...+    .++|.+++|||+.+|+.|.-|-
T Consensus       136 ~l~~l~~~~~~~~~~~L~~l~GIG~~TA~~ill~a  170 (232)
T 4b21_A          136 SKSEIEKMSEEELMESLSKIKGVKRWTIEMYSIFT  170 (232)
T ss_dssp             CHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHHHT
T ss_pred             CHHHHHcCCHHHHHHHHHhCCCcCHHHHHHHHHHh
Confidence            344444333    4679999999999999988764

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=91.86  E-value=0.21  Score=53.50  Aligned_cols=100  Identities=12%  Similarity=0.095  Sum_probs=63.1

Q ss_pred             CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh-cC-ChhhhhcccCccHHHHHHHHHHHHHcccCCHH
Q psy11422        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY-KI-NFKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (687)
Q Consensus       443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~-~L-~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~  520 (687)
                      -.+..++.|..     .|.+.| .+-.+...-.+-  ..+..+= .+ +.++|..|||+|++.|++|.+-++.-+-..+.
T Consensus        19 ~i~~~L~~ia~-----~~e~~g-~~~r~~AYr~Aa--~~l~~l~~~i~~~~~l~~lpGIG~~~A~kI~E~l~tG~~~~le   90 (360)
T 2ihm_A           19 LLSEALETLAE-----AAGFEA-NEGRLLSFSRAA--SVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVK   90 (360)
T ss_dssp             HHHHHHHHHHH-----HHHHTT-CHHHHHHHHHHH--HHHHHCSSCCCSGGGGTTCTTCCHHHHHHHHHHHHHSCCHHHH
T ss_pred             HHHHHHHHHHH-----HHHHcC-CcHHHHHHHHHH--HHHHhCCcccCCHHHHhcCCCCCHHHHHHHHHHHHcCChHHHH
Confidence            34555666654     456777 777766654321  1111111 12 23469999999999999999988753322222


Q ss_pred             H---------HHHHcCCCCCCHHHHHHHHhh-cCChHHHH
Q psy11422        521 R---------FIYALGIRHVGETTAKELANY-FKNLECMF  550 (687)
Q Consensus       521 r---------~L~aLGIp~vG~~~Ak~La~~-f~sld~l~  550 (687)
                      .         +..=++|||||+++|+.+-+. +.|+++|.
T Consensus        91 ~L~~d~~~~~l~~l~~I~GvG~kta~~l~~~Gi~tledL~  130 (360)
T 2ihm_A           91 QVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELR  130 (360)
T ss_dssp             HHHHSHHHHHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHH
T ss_pred             HHhcccchHHHHHHhCCCCCCHHHHHHHHHcCCCCHHHHH
Confidence            2         222359999999999988654 66787777

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=91.42  E-value=0.36  Score=39.43  Aligned_cols=52  Identities=29%  Similarity=0.294  Sum_probs=42.7

Q ss_pred             HHHHHcCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        521 RFIYALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       521 r~L~aLGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      -|+..+||   ++..+++|.+ -|.|++.+..++.++|..|+||++.+++.|++--
T Consensus         7 ~f~~~lgI---~e~~a~~L~~~Gf~tve~vA~~~~~eL~~I~G~dE~~a~~l~~~A   59 (70)
T 1u9l_A            7 TFTKYLDI---DEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERA   59 (70)
T ss_dssp             HHHHHHTC---CHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhCCC---CHHHHHHHHHcCcCcHHHHHcCCHHHHhhccCCCHHHHHHHHHHH
Confidence            45556654   4677877765 5999999999999999999999999999988643

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=91.19  E-value=0.28  Score=44.97  Aligned_cols=46  Identities=9%  Similarity=0.167  Sum_probs=36.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ...++|+||+++++.+++|--+++        +||.+++|+|+|..+.|-+...
T Consensus        65 L~~LpGiGp~~A~~II~~GpF~sv--------edL~~V~GIg~k~~e~l~~~~~  110 (134)
T 1s5l_U           65 FIQYRGLYPTLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLE  110 (134)
T ss_dssp             GGGSTTCTHHHHHHHHHTCCCSSG--------GGGGGCTTCCHHHHHHHHHHHT
T ss_pred             HHHCCCCCHHHHHHHHHcCCCCCH--------HHHHhCCCCCHHHHHHHHHhhc
Confidence            346999999999999999887776        4556689999998876655443

>2ep8_A Pescadillo homolog 1; A/B/A 3 layers, nucleolus, ribosome biogenesis, DNA damage, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.19  E-value=0.54  Score=41.03  Aligned_cols=71  Identities=11%  Similarity=0.138  Sum_probs=54.9

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccc-----------cccccEEEEcCCCCccHHHHHHcCCeEEeH
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFI-----------SKNTNYLVKGQKPGKKLEKAIKLNIKILDE  671 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sV-----------sk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E  671 (687)
                      ..+.|+|++|++.+.   .+|++++.+|+.+||+|....           ....+++|+....-.+    +..+..+|..
T Consensus         9 ~~~LF~g~~F~i~~e---~p~~~le~~I~~~GG~v~~~~~~~~g~~~~~~~~~iTh~I~drp~~~~----~~~~r~~VqP   81 (100)
T 2ep8_A            9 HKKLFEGLKFFLNRE---VPREALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQT----SVIGRCYVQP   81 (100)
T ss_dssp             SCCTTSSCEEECCSS---SCHHHHHHHHHHTTCEEECCTTTSSCCCSCTTCTTCCEEECSCTTTSC----CBTTBEEECT
T ss_pred             hHHHcCCcEEEEecC---CCHHHHHHHHHHcCCEEEeccccccCcccccCCCceEEEEecccchhh----hcCCCeEEcc
Confidence            345799999999775   489999999999999998642           4688899887533222    2246789999


Q ss_pred             HHHHHHHhc
Q psy11422        672 KNFVKIVKG  680 (687)
Q Consensus       672 ~~f~~~l~~  680 (687)
                      .+..+.++.
T Consensus        82 qWV~Dcin~   90 (100)
T 2ep8_A           82 QWVFDSVNA   90 (100)
T ss_dssp             HHHHHHHHH
T ss_pred             hHHHHHHhc
Confidence            999988764

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=91.06  E-value=0.18  Score=43.91  Aligned_cols=48  Identities=8%  Similarity=0.162  Sum_probs=38.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.++|+|+++++++++.|-.+++        ++|.+++|+|++..++|...+..
T Consensus        27 eL~~lpGIG~~~A~~IV~~GpF~s~--------edL~~V~Gig~~~~e~l~~~l~~   74 (97)
T 3arc_U           27 AFIQYRGLYPTLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLEH   74 (97)
T ss_dssp             GGGGSTTCTTHHHHHHHHHCCCSSG--------GGGGGCTTCCHHHHHHHHHTGGG
T ss_pred             HHhHCCCCCHHHHHHHHHcCCCCCH--------HHHHhccCCCHHHHHHHHHHhce
Confidence            3456999999999999998876665        55667899999999888776653

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=90.53  E-value=0.12  Score=55.88  Aligned_cols=44  Identities=16%  Similarity=0.092  Sum_probs=36.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .|+|+|+|+|++.+||++ .|+|++||..          +-|.|..++++.+|+.
T Consensus       123 l~~I~GvGpk~a~~ly~~-Gi~tledL~~----------~~g~kl~~~q~~Gl~~  166 (381)
T 1jms_A          123 FTSVFGVGLKTAEKWFRM-GFRTLSKIQS----------DKSLRFTQMQKAGFLY  166 (381)
T ss_dssp             HHTSTTCCHHHHHHHHHT-TCCSHHHHHH----------CSSCCCCHHHHHHHHT
T ss_pred             HHccCCCCHHHHHHHHHc-CCCcHHHHHh----------CcccchHHHHHHHHHH
Confidence            468999999999999999 5799999986          2256777777777764

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=89.97  E-value=0.23  Score=44.57  Aligned_cols=46  Identities=20%  Similarity=0.325  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        530 HVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       530 ~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      |||+..+++|.+. |.|++.+..++.++|.+++|||+..|+.|.+.-
T Consensus        32 GIg~~~i~kL~eAG~~Tve~va~a~~~eL~~i~GIse~ka~kIi~aA   78 (114)
T 1b22_A           32 GINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEA   78 (114)
T ss_dssp             TCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCcCcHHHHHhCCHHHHHHccCCCHHHHHHHHHHH
Confidence            7889999988864 899999999999999999999999999988753

>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A

Probab=89.19  E-value=0.17  Score=50.44  Aligned_cols=49  Identities=16%  Similarity=0.310  Sum_probs=43.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccH-HHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAI  511 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~-Ksa~~Ll~~I  511 (687)
                      ..+|+|+|+++.++|.+.-  .|+..|..++.++|.++  +|+ +.|++|++.+
T Consensus       170 LdgIpGIG~k~ak~Ll~~F--gSl~~i~~As~EeL~~V--IG~~~~A~~I~~~f  219 (220)
T 2nrt_A          170 LDNVPGIGPIRKKKLIEHF--GSLENIRSASLEEIARV--IGSTEIARRVLDIL  219 (220)
T ss_dssp             HTTSTTCCHHHHHHHHHHH--CSHHHHHTSCHHHHHHH--HTCHHHHHHHHHHC
T ss_pred             ccCCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hChHHHHHHHHHHh
Confidence            4579999999999999963  48999999999999999  999 9999998754

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=89.16  E-value=0.38  Score=51.58  Aligned_cols=50  Identities=14%  Similarity=0.214  Sum_probs=37.9

Q ss_pred             HHcCCCCCCHHHHHHHHhh--cCChHHHHhc-------CHHHHhcCCCCCHHHHHHHHH
Q psy11422        524 YALGIRHVGETTAKELANY--FKNLECMFKA-------TEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       524 ~aLGIp~vG~~~Ak~La~~--f~sld~l~~A-------s~eeL~~I~GIG~~~A~sI~~  573 (687)
                      ....|||||+++|++|.+.  -|.+..+...       ...+|.+|+|||+++|..+++
T Consensus        62 ~l~~lpGIG~~~A~kI~E~l~tG~~~~le~L~~d~~~~~l~~l~~I~GvG~kta~~l~~  120 (360)
T 2ihm_A           62 QLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQ  120 (360)
T ss_dssp             GGTTCTTCCHHHHHHHHHHHHHSCCHHHHHHHHSHHHHHHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHHHcCChHHHHHHhcccchHHHHHHhCCCCCCHHHHHHHHH
Confidence            3568999999999988764  3555544322       246899999999999998865

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=89.02  E-value=0.34  Score=51.39  Aligned_cols=34  Identities=26%  Similarity=0.263  Sum_probs=28.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhh
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL  493 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L  493 (687)
                      ..++|+|+||+++.+||++ .|+|++||... ...|
T Consensus        99 ~l~~V~GiGpk~a~~l~~~-Gi~tledL~~a-~~~l  132 (335)
T 2fmp_A           99 FLTRVSGIGPSAARKFVDE-GIKTLEDLRKN-EDKL  132 (335)
T ss_dssp             HHTTSTTCCHHHHHHHHHT-TCCSHHHHHTC-GGGS
T ss_pred             HHhCCCCCCHHHHHHHHHc-CCCCHHHHHHh-hhhh
Confidence            3578999999999999999 57999999986 4333

>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae}

Probab=88.77  E-value=0.19  Score=51.03  Aligned_cols=77  Identities=13%  Similarity=0.145  Sum_probs=41.8

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHH---------cCC-e
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIK---------LNI-K  667 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~---------lgI-~  667 (687)
                      ...|.|.+|+|.|......++-+..+|..+||++++.+++.|+.+|++....      .++++...         .++ .
T Consensus       158 ~~lF~g~~~yl~~~~~~~~~~~l~~~i~~~GG~v~~~l~~~t~hVV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (264)
T 1z56_C          158 LFLFSNRIAYVPRRKISTEDDIIEMKIKLFGGKITDQQSLCNLIIIPYTDPILRKDCMNEVHEKIKEQIKASDTIPKIAR  237 (264)
T ss_dssp             CC--------------------CHHHHHHHTTSCCCCSSSCSEEECCCSSTTTHHHHSSHHHHTTTTTTTSSSSCCCCCE
T ss_pred             hhhhCCeEEEEecCCCchhHHHHHHHHHHcCCEEecccCCCEEEEEeCCCccchHHHHHHHHHHHHhhcccccccCCCCE
Confidence            4468999999999754445566788899999999999998888888865321      23333211         244 9


Q ss_pred             EEeHHHHHHHHhc
Q psy11422        668 ILDEKNFVKIVKG  680 (687)
Q Consensus       668 Ii~E~~f~~~l~~  680 (687)
                      |++.+++.+.+..
T Consensus       238 iV~~~Wv~dci~~  250 (264)
T 1z56_C          238 VVAPEWVDHSINE  250 (264)
T ss_dssp             EECTHHHHHHHTT
T ss_pred             EecHHHHHHHHHc
Confidence            9999999998864

>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=88.71  E-value=0.55  Score=48.83  Aligned_cols=56  Identities=20%  Similarity=0.362  Sum_probs=50.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      +..+++|+++.++.+|-++|+ .|+.|+..+...+|..+.|+.++.|.+++....+.
T Consensus         4 ~~~~l~gi~~~~~~kL~~~gi-~t~~~~~~~~~~~L~~~~gis~~~a~~~i~~a~~~   59 (322)
T 2i1q_A            4 NLTDLPGVGPSTAEKLVEAGY-IDFMKIATATVGELTDIEGISEKAAAKMIMGARDL   59 (322)
T ss_dssp             -CTTSTTCCHHHHHHHHHHTC-CSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             cHhhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhhCcCHHHHHHHHHHHHHh
Confidence            466789999999999999994 89999999999999999999999999999887553

>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation; 2.00A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.96.1.2

Probab=87.61  E-value=1.5  Score=43.50  Aligned_cols=76  Identities=16%  Similarity=0.201  Sum_probs=47.0

Q ss_pred             HHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC-
Q psy11422        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK-  544 (687)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~-  544 (687)
                      .+..|++.  .-++++|..++.++|.++   -||...+|.+|.+.-+...                         +.|+ 
T Consensus        56 ~~~~l~~~--fptp~~la~a~~e~l~~~i~~~G~~~~KA~~l~~~a~~i~-------------------------~~~~g  108 (221)
T 1kea_A           56 IYDKFFVK--YKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVI-------------------------NDYGG  108 (221)
T ss_dssp             HHHHHHHH--CCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHH-------------------------HHHTT
T ss_pred             HHHHHHHH--CCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-------------------------HHhCC
Confidence            33444443  258888888887777332   2777777777766543211                         1111 


Q ss_pred             ChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        545 NLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       545 sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .++    .+.++|.+++|||+++|..|..|-
T Consensus       109 ~~p----~~~~~L~~lpGIG~~TA~~il~~~  135 (221)
T 1kea_A          109 RVP----RNRKAILDLPGVGKYTCAAVMCLA  135 (221)
T ss_dssp             SCC----SCHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             Cch----HHHHHHHhCCCCcHHHHHHHHHHh
Confidence            111    346788889999999998887764

>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A

Probab=87.32  E-value=1.3  Score=45.96  Aligned_cols=68  Identities=18%  Similarity=0.149  Sum_probs=45.7

Q ss_pred             CChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcC----HH
Q psy11422        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKAT----EE  555 (687)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As----~e  555 (687)
                      -++++|..++.++|..+ |+|- .|..|.+.-                         +.+.+...+++.+...+    .+
T Consensus       159 Ptpe~la~~~~e~L~~~-g~g~-Ra~~I~~~A-------------------------~~i~~g~~~l~~l~~~~~~~~~~  211 (290)
T 3i0w_A          159 PTVDKLHEFTEKDFEEC-TAGF-RAKYLKDTV-------------------------DRIYNGELNLEYIKSLNDNECHE  211 (290)
T ss_dssp             CCHHHHTTCCHHHHHHT-TCGG-GHHHHHHHH-------------------------HHHHTTSSCHHHHHHSCHHHHHH
T ss_pred             CcHHHHHCCCHHHHHHc-CCch-HHHHHHHHH-------------------------HHHHhCCCCHHHHhcCCHHHHHH
Confidence            58899988988888885 7886 466666532                         22222223344443333    46


Q ss_pred             HHhcCCCCCHHHHHHHHHH
Q psy11422        556 QLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       556 eL~~I~GIG~~~A~sI~~f  574 (687)
                      +|.+++|||+++|+.|.-|
T Consensus       212 ~L~~lpGIG~~TA~~ill~  230 (290)
T 3i0w_A          212 ELKKFMGVGPQVADCIMLF  230 (290)
T ss_dssp             HHTTSTTCCHHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHHH
Confidence            7889999999999988776

>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A*

Probab=87.27  E-value=1.4  Score=44.08  Aligned_cols=74  Identities=14%  Similarity=0.092  Sum_probs=55.1

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc----cccEEEEcCC------CCccHHHHHHcCCeEEeHHHH
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK----NTNYLVKGQK------PGKKLEKAIKLNIKILDEKNF  674 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk----~t~~LV~G~~------~g~Kl~kA~~lgI~Ii~E~~f  674 (687)
                      ..|.|.+|+|++.-  ...+.++.+|+..||+|..+.+.    ..+.++++.+      ...++..+.+.||+|++.+.+
T Consensus       134 ~lF~g~~v~l~~~~--~~~~~l~~ii~agGg~vl~~~~~~~~~~~t~~~vd~~~~~~~~~~~~~~~~~~~~i~~v~~ewl  211 (235)
T 3al2_A          134 GAFSGWKVILHVDQ--SREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDLNKLKPDDSGVNIAEAAAQNVYCLRTEYI  211 (235)
T ss_dssp             STTTTCEEEEECCH--HHHHHHHHHHHHTTCEECSSCCGGGGGGCSEEEECC--------CCCHHHHHHTTCEEEETHHH
T ss_pred             CCCCCcEEEEecCC--CcHHHHHHHHHcCCcEEecCCCCCccccCceEEEecccCCccchhHHHHHHHHcCCcEEcHHHH
Confidence            57999999999973  35688999999999999876432    2234444431      124677788889999999999


Q ss_pred             HHHHhc
Q psy11422        675 VKIVKG  680 (687)
Q Consensus       675 ~~~l~~  680 (687)
                      ++.+-.
T Consensus       212 ld~i~~  217 (235)
T 3al2_A          212 ADYLMQ  217 (235)
T ss_dssp             HHHHHC
T ss_pred             HHHHhc
Confidence            988753

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=86.99  E-value=0.69  Score=53.69  Aligned_cols=52  Identities=17%  Similarity=0.286  Sum_probs=45.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      .|.|||+|..++.+|+++| ++|+.||-.++.++|..++++|++.++.+...+
T Consensus       648 L~qlp~v~~~rar~L~~~G-~~s~~dl~~~~~~~l~~~~~~~~~i~~~~~~~~  699 (720)
T 2zj8_A          648 LMQLPLVGRRRARALYNSG-FRSIEDISQARPEELLKIEGIGVKTVEAIFKFL  699 (720)
T ss_dssp             GTTSTTCCHHHHHHHHTTT-CCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hhhCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHhHhHHHHHHHHHHHhc
Confidence            5789999999999999988 599999999999999999999988877666554

>2kz3_A Putative uncharacterized protein RAD51L3; RAD51D, homologous recombination, unknown function; NMR {Homo sapiens}

Probab=86.84  E-value=1.3  Score=37.41  Aligned_cols=53  Identities=21%  Similarity=0.260  Sum_probs=47.6

Q ss_pred             ccc-CCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNI-IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I-~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+. |||.+..++.|-.++ |.|..|++.++..+|.++-|.+-+.+..|.+.+.+
T Consensus         6 ~~~~p~Lse~~~~~L~~~~-I~Tv~Dfl~~d~~eL~~~~~ls~~~v~~l~r~l~~   59 (83)
T 2kz3_A            6 VGLCPGLTEEMIQLLRSHR-IKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLA   59 (83)
T ss_dssp             TTSSTTCCHHHHHHHHHTT-CCCHHHHTTSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cccCCCCCHHHHHHHHHCC-CCCHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            566 999999999998888 69999999999999999999999999888887754

>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens}

Probab=86.67  E-value=0.68  Score=40.74  Aligned_cols=77  Identities=6%  Similarity=-0.000  Sum_probs=53.7

Q ss_pred             CCccCCeEEEEEcC-CCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc-HH---HHHH--cCCeEEeHHHHHH
Q psy11422        604 KNYLKEKIFVFTGS-LYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK-LE---KAIK--LNIKILDEKNFVK  676 (687)
Q Consensus       604 ~~~l~g~~vv~TG~-l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K-l~---kA~~--lgI~Ii~E~~f~~  676 (687)
                      ...|.|.+|.|--. +....|+-....+..+||+++++++.+++.+|+.+..+.+ ..   +++.  .++.|++++++.+
T Consensus         9 ~~~F~g~~v~~~p~~~~~~r~~i~~~~a~~~Ga~v~~~~~~~vTHVVvd~~~s~~~~l~~l~~~~l~~~~~iV~~~Wv~d   88 (106)
T 2jw5_A            9 EEWLSSLRAHVVRTGIGRARAELFEKQIVQHGGQLCPAQGPGVTHIVVDEGMDYERALRLLRLPQLPPGAQLVKSAWLSL   88 (106)
T ss_dssp             GGCGGGSCCCBCTTTCCSSSTTHHHHHHHHTTCCCCSTTCTTCCEEEECSSSCHHHHHHHTTCSSCCSSCEEEEHHHHHH
T ss_pred             cCEeCCeEEEEEecCCchHHHHHHHHHHHHcCCEEeeccCCCccEEEEcCCCCHHHHHHHHhhcccCCCcEEecCchHHH
Confidence            45688888887321 2223455567799999999999999999999997544311 11   1111  2578999999999


Q ss_pred             HHhc
Q psy11422        677 IVKG  680 (687)
Q Consensus       677 ~l~~  680 (687)
                      .+..
T Consensus        89 ci~~   92 (106)
T 2jw5_A           89 CLQE   92 (106)
T ss_dssp             HHHT
T ss_pred             HHhc
Confidence            8864

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=86.41  E-value=0.75  Score=48.76  Aligned_cols=74  Identities=15%  Similarity=0.121  Sum_probs=46.5

Q ss_pred             ccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhh--cCChHHHHhcC-----HHHHhcCCCCCHHHHHHH
Q psy11422        499 VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY--FKNLECMFKAT-----EEQLLNIPKIGSTTVKAF  571 (687)
Q Consensus       499 fG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~--f~sld~l~~As-----~eeL~~I~GIG~~~A~sI  571 (687)
                      |.-..-.+-...|+.. ..++........|||||+++|++|.+.  -|.+..+....     .+-|.+|+|||+++|..+
T Consensus        34 ~r~~AYr~Aa~~l~~l-~~~i~~~~~l~~lpGIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k~a~~l  112 (335)
T 2bcq_A           34 WRALGYAKAINALKSF-HKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMW  112 (335)
T ss_dssp             HHHHHHHHHHHHHHSC-CSCCCCHHHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHHHHHHH
T ss_pred             HhHHHHHHHHHHHHhC-CccccCHHHHhcCCCccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHHHHHHH
Confidence            4444444444445432 223334444579999999999988764  35555544332     234569999999999988


Q ss_pred             HH
Q psy11422        572 IK  573 (687)
Q Consensus       572 ~~  573 (687)
                      ++
T Consensus       113 ~~  114 (335)
T 2bcq_A          113 YQ  114 (335)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>3oq4_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.40A {Saccharomyces cerevisiae}

Probab=86.29  E-value=2  Score=39.28  Aligned_cols=58  Identities=16%  Similarity=0.233  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhcCCEEcccccccccEEEEcCCCC--------ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG--------KKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g--------~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ++-++..+..+||+|..=-+.+++++|.-....        -=+.+|+++|++|++-+-+.++|..
T Consensus        32 ~~llk~~f~~LGa~I~~FFd~~VTiiITrR~~~~~~~~p~~DIL~rAr~~~mKIWs~EKl~RfL~~   97 (134)
T 3oq4_A           32 RDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKN   97 (134)
T ss_dssp             HHHHHHHHHHTTCEEESSCCTTCCEEEESSCGGGGGGSCTTSHHHHHHHTTCEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCEEeeecCCceEEEEeCCcCcccccCCcchHHHHHHHcCCeeeeHHHHHHHHHh
Confidence            455777888999999999999999999876432        2379999999999999999998864

>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair, helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF); HET: 3DR; 2.28A {Schizosaccharomyces pombe}

Probab=86.15  E-value=1.7  Score=43.41  Aligned_cols=71  Identities=17%  Similarity=0.192  Sum_probs=46.2

Q ss_pred             CCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcC----H
Q psy11422        479 VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKAT----E  554 (687)
Q Consensus       479 I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As----~  554 (687)
                      .-++.+|..++.++|..+ ||+..+|..|.+.-+..         ..=               .+.+++.+...+    .
T Consensus        84 fPtp~~la~~~~e~Lr~~-G~~~rKa~~i~~~A~~~---------~~g---------------~~p~~~~l~~~~~~e~~  138 (228)
T 3s6i_A           84 FPTPEEIRDMDFEIMRAC-GFSARKIDSLKSIAEAT---------ISG---------------LIPTKEEAERLSNEELI  138 (228)
T ss_dssp             CCCHHHHHHSCHHHHHHH-TCCHHHHHHHHHHHHHH---------HHT---------------SSCCHHHHTTSCHHHHH
T ss_pred             CCCHHHHHcCCHHHHHHc-CCCHHHHHHHHHHHHHH---------HcC---------------CCCChHHHhcCCHHHHH
Confidence            358889988888888765 89988888777643321         110               111233333333    3


Q ss_pred             HHHhcCCCCCHHHHHHHHHH
Q psy11422        555 EQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       555 eeL~~I~GIG~~~A~sI~~f  574 (687)
                      ++|.+++|||+.+|+.+.-|
T Consensus       139 ~~L~~l~GIG~~TA~~ill~  158 (228)
T 3s6i_A          139 ERLTQIKGIGRWTVEMLLIF  158 (228)
T ss_dssp             HHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHhCCCcCHHHHHHHHHH
Confidence            67888888888888887765

>3pc7_A DNA ligase 3; DNA repair, BRCT domain, protein:protein interactions, XRCC1 domain, DNA binding protein; HET: DNA MSE; 1.65A {Homo sapiens} SCOP: c.15.1.2 PDB: 3pc8_C* 1imo_A* 1in1_A* 3qvg_A*

Probab=86.11  E-value=1.7  Score=37.09  Aligned_cols=67  Identities=4%  Similarity=-0.002  Sum_probs=54.2

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc-cccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK-NTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk-~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      .+.|+|++|.+-+.++  ....+..+|.+.||.|..+-.+ +++++|....        +..+.+.++.+++.+.++.
T Consensus        14 pdiFsg~~~~l~~~v~--~~~~l~RyiiAfgG~v~~~~~~~~vTHvI~~~~--------~~~~~~~V~p~WI~dcI~k   81 (88)
T 3pc7_A           14 LDIFTGVRLYLPPSTP--DFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD--------KNPAAQQVSPEWIWACIRK   81 (88)
T ss_dssp             CCCSTTCEECCCTTST--THHHHHHHHHHTTCEECCGGGGGGCSEEESCCT--------TCTTSEEECHHHHHHHHHH
T ss_pred             ChhhcCeEEEccCCcC--chhhheeeeeecCCEEecccCCCcCeEEecCCC--------cCCCCcEEchHHHHHHHhC
Confidence            4579999999999885  3579999999999999776554 8889885442        3558999999999998864

>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=85.65  E-value=0.92  Score=48.12  Aligned_cols=54  Identities=24%  Similarity=0.202  Sum_probs=48.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .-.++|+|+.++++|-++|+ .|+.++...+..+|..+.|+.+..++++++...+
T Consensus        37 l~~l~Gi~~~~~~kL~~ag~-~t~~~~~~~~~~~L~~~~~~s~~~~~~~l~~~~~   90 (349)
T 1pzn_A           37 IEDLPGVGPATAEKLREAGY-DTLEAIAVASPIELKEVAGISEGTALKIIQAARK   90 (349)
T ss_dssp             SSCCTTCCHHHHHHHHTTTC-CSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHhhcCCCHHHHHHHHHHHhh
Confidence            45679999999999999996 8999999999999999999999999999887754

>1xdn_A RNA editing ligase MP52; HET: MSE ATP; 1.20A {Trypanosoma brucei} SCOP: d.142.2.4

Probab=84.89  E-value=1.4  Score=45.17  Aligned_cols=199  Identities=17%  Similarity=0.125  Sum_probs=104.4

Q ss_pred             cccCCCCCCChHHHHHHHHHHHH-hhccCCCeeEEEEEccceeEEEEEE-eCCEE--EEEEecCCCCccch---------
Q psy11422         88 KMMSLDNGFSDEDVIIFNKRITN-ELKLTKNIEYIAELKFDGIAVNLRY-EYGYL--KQASTRGDGNIGEN---------  154 (687)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~-~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l--~~a~TRGdG~~GeD---------  154 (687)
                      ..-||+|-|..     |++++.. .+.   ...|+++.||||.-.++++ ++|..  ++.+.| +|..+++         
T Consensus        10 ~Y~sieNh~~~-----~i~~~~~~~l~---~~ewvatEKIHGaNFsii~~~d~~~~~i~~akR-s~~l~~~e~FfGy~~i   80 (277)
T 1xdn_A           10 PYIEIDLPSES-----RIQSLHKSGLA---AQEWVACEKVHGTNFGIYLINQGDHEVVRFAKR-SGIMDPNENFFGYHIL   80 (277)
T ss_dssp             CCCCCCCCCHH-----HHHHHHHTTGG---GSCEEEEEECCSEEEEEEEEEETTEEEEEEEET-TEECCTTCCCTTGGGG
T ss_pred             CcccccchHHH-----HHHHHHhcCCC---CCcEEEEEeeccccEEEEEecCCCeeEEEEeec-ccccCcccccccHHHH
Confidence            45688888755     3344432 221   3579999999999999988 46777  888888 5655533         


Q ss_pred             ---hhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH---HHcCCCCCCChhhhHHhHhhhcCc--cccc
Q psy11422        155 ---ITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR---YHLGLKKFTNPRNAAAGILRQLNP--KINK  226 (687)
Q Consensus       155 ---vT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~---~~~g~~~f~NpRN~aaG~lr~~~~--~~~~  226 (687)
                         .+..++.+..+........-+..+.|-||++=..=.+-.....+   ...+++  ..||-+   +-=|+..  .-+ 
T Consensus        81 ~~~l~~~~~~l~~~l~~~~~~~~~~~v~VyGELfGg~y~hp~v~~~~~~~~~~~~~--~~p~~~---~~IQ~~i~~~Y~-  154 (277)
T 1xdn_A           81 IDEFTAQIRILNDLLKQKYGLSRVGRLVLNGELFGAKYKHPLVPKSEKWCTLPNGK--KFPIAG---VQIQREPFPQYS-  154 (277)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCSCCSEEEEEEEEEEEECCCTTSCCCCCEEECTTSC--EEEGGG---CCSCCCSSCCCE-
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCccEEEEEEEEecCccCCccccccccccccCccc--cCcccc---cccccccccccC-
Confidence               22233333333221110001468999999993210000000000   000000  012211   1012222  221 


Q ss_pred             ccccEEEEEecccccC-CC---CCCCHHHHHHHHHhc-CCCCCCCceEeCCHHHHHHHHHH-----HHHhhc-----CCC
Q psy11422        227 NKILHFFAHGVGELRG-MN---MPSSHSELLNWYQKI-GLSICGEYSVLSGVNKLIEFYKK-----INIKRF-----NLP  291 (687)
Q Consensus       227 ~r~l~f~~y~~~~~~~-~~---~~~~~~e~l~~L~~~-Gf~~~~~~~~~~~~~ei~~~~~~-----~~~~r~-----~l~  291 (687)
                       ..++|++|+|..... .+   .--+..+..+.+.+. ||.+.+.. ...+++++++|--+     +.+.=.     .-+
T Consensus       155 -p~~~FYaFDI~~~~~~~~~~~~~L~fd~~~~~~~~~~gl~~ap~L-~rGt~~e~~~~~~~~f~s~ip~~~g~~~~~~~~  232 (277)
T 1xdn_A          155 -PELHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARAL-VRGTLDECLAFDVENFMTPLPALLGLGNYPLEG  232 (277)
T ss_dssp             -EEEEEEEEEEEEESSCCGGGEEECCHHHHHHHHHTSTTCEECCCS-EEESHHHHHTCCGGGCBCSHHHHTTCTTSCCTT
T ss_pred             -CCceEEEEEEEEecCCCccccccCCHHHHHHHHHHhcCCCeeeee-eecCHHHHhhcccccccccchhhcCCCccCCCC
Confidence             269999999865431 11   013567888888885 99988743 45577777774221     111001     112


Q ss_pred             CccceEEEEECC
Q psy11422        292 YEIDGVVYKINC  303 (687)
Q Consensus       292 y~iDGiVikv~~  303 (687)
                      .---|+|||-..
T Consensus       233 NiaEGvViKp~~  244 (277)
T 1xdn_A          233 NLAEGVVIRHVR  244 (277)
T ss_dssp             CBCCEEEEEETT
T ss_pred             CeeeeEEEeecc
Confidence            235699999875

>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A*

Probab=84.86  E-value=2.8  Score=41.74  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=27.0

Q ss_pred             HHHHHHCCCCCChHHHhcCChhhhhc---ccCccHHHHHHHHHHHH
Q psy11422        470 IEKLVNANIVVTAVDLYKINFKNLLR---LDRVSNKLANNILLAIQ  512 (687)
Q Consensus       470 i~~L~~~g~I~~i~DL~~L~~~~L~~---l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ...|++.  .-++.+|..++.++|..   --||...+|.+|.+.-+
T Consensus        55 ~~~l~~~--fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~   98 (226)
T 1orn_A           55 TKRLFEK--YRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCA   98 (226)
T ss_dssp             HHHHHHH--CCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHH
T ss_pred             HHHHHHH--CCCHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            3444444  25899999998887543   13777778877776543

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A*

Probab=84.33  E-value=1.8  Score=44.14  Aligned_cols=77  Identities=13%  Similarity=0.164  Sum_probs=55.4

Q ss_pred             CCccCCeEEEEEcCC------C--cCCHHH-HHHHHHhcCCEEcccccccccEEEEcCCCC-cc-HHHHHH---cCCeEE
Q psy11422        604 KNYLKEKIFVFTGSL------Y--AFKRNE-AIILIENLGGKVVNFISKNTNYLVKGQKPG-KK-LEKAIK---LNIKIL  669 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l------~--~~~R~e-~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~K-l~kA~~---lgI~Ii  669 (687)
                      ...|.|.+|.|-+.-      .  ...|-+ ++.++..+||++++.++.+++++|+++... .. ++..+.   .+++|+
T Consensus       162 ~~lF~~~~vy~~~~~~~~~~~~~i~~~~l~~~~~~i~~~GG~v~~~l~~~vTHVVv~~~~~r~~~~~~~~~~~~~~~~iV  241 (263)
T 3ii6_X          162 LSMFRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKIL  241 (263)
T ss_dssp             GGTTTTCEEEECCBSSTTCGGGBCCSSHHHHHHHHHHHTTCEEESSCCTTCCEEEECSCCTTHHHHHHHHHTCSSCCEEE
T ss_pred             chhhCCeEEEEecccccCCcccccchhHHHHHHHHHHccCCEEecCCCCCceEEEECCCCccHHHHHHHHhhcCCCCEEe
Confidence            357899999995521      0  123444 488999999999999999999999987432 11 222222   378999


Q ss_pred             eHHHHHHHHhc
Q psy11422        670 DEKNFVKIVKG  680 (687)
Q Consensus       670 ~E~~f~~~l~~  680 (687)
                      +.+++.+-+.+
T Consensus       242 ~~~Wv~dci~~  252 (263)
T 3ii6_X          242 KESWVTDSIDK  252 (263)
T ss_dssp             ETHHHHHHHHT
T ss_pred             ChHHHHHHHHc
Confidence            99999988864

>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.59  E-value=4.1  Score=36.64  Aligned_cols=77  Identities=16%  Similarity=0.207  Sum_probs=56.4

Q ss_pred             CCccCCeEEEEEcC-CCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHH---HHHHc----CCeEEeHHHHH
Q psy11422        604 KNYLKEKIFVFTGS-LYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLE---KAIKL----NIKILDEKNFV  675 (687)
Q Consensus       604 ~~~l~g~~vv~TG~-l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~---kA~~l----gI~Ii~E~~f~  675 (687)
                      ..-|.|.++-|-.. +....|+-++.++...||+|.+..+..++.+|+++.....+.   ++..+    +..|++.++|.
T Consensus        18 ~~~F~g~~iy~v~~~~g~~R~~~l~~l~r~~G~~V~~~ls~~VTHVVve~~~~~e~~~~l~~~~l~~~~~~~lv~i~Wl~   97 (120)
T 2coe_A           18 DIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENELSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDVSWLI   97 (120)
T ss_dssp             CCSCTTCEEEEECTTTCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEESSCCHHHHHHHHHHCCCCCSSCCEEEEHHHHH
T ss_pred             ccccCCeEEEEeecccchHHHHHHHHHHHHcCCEEeeccCCCcCEEEecCCCHHHHHHHHhccccccccccEEeecHHHH
Confidence            35689999988654 222345668889999999999999999999999754222222   32222    57899999999


Q ss_pred             HHHhc
Q psy11422        676 KIVKG  680 (687)
Q Consensus       676 ~~l~~  680 (687)
                      +-++.
T Consensus        98 esmk~  102 (120)
T 2coe_A           98 ECIGA  102 (120)
T ss_dssp             HHHHT
T ss_pred             HHHHc
Confidence            98864

>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A*

Probab=82.84  E-value=2.2  Score=42.85  Aligned_cols=72  Identities=14%  Similarity=0.041  Sum_probs=50.9

Q ss_pred             CCccCCeEEEEEcCCCcCC------------HHHHHHHHHhcCCEE--ccccc-ccccEEEEcCCCCccHHHHHHcCCeE
Q psy11422        604 KNYLKEKIFVFTGSLYAFK------------RNEAIILIENLGGKV--VNFIS-KNTNYLVKGQKPGKKLEKAIKLNIKI  668 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~------------R~e~~~~i~~~Gg~v--~~sVs-k~t~~LV~G~~~g~Kl~kA~~lgI~I  668 (687)
                      ...|.|.+|+|++.-....            ++.+..+++.+||++  ...++ ..+|++++.+..     .|.+++++|
T Consensus       149 ~~Lf~g~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~i~~~~Ga~~~~v~~~~~~~~d~v~~~~~~-----~~~~~~~~i  223 (241)
T 2vxb_A          149 KGPLFGKKILFIIPEAKSWQKKIENTEQGQKALAHVYHALALGADVEIRPNVAHLECDLILTMDGN-----IVDETNCPV  223 (241)
T ss_dssp             CCTTTTCEEEECCCC------------CHHHHHHHHHHHHHTTCEEECCSCCSSCCCSEEECSSSC-----CCSSCSSCE
T ss_pred             CcCCCCcEEEEEeCCCcccccccccccccchHHHHHHHHHHcCCceecccccccCCccEEEECCcc-----ccccCCCCE
Confidence            3579999999875421111            378899999999999  33333 367877774432     256789999


Q ss_pred             EeHHHHHHHHhc
Q psy11422        669 LDEKNFVKIVKG  680 (687)
Q Consensus       669 i~E~~f~~~l~~  680 (687)
                      ++.+++.+.+-.
T Consensus       224 V~~eWv~~~i~~  235 (241)
T 2vxb_A          224 VDPEWIVECLIS  235 (241)
T ss_dssp             ECHHHHHHHHHH
T ss_pred             ecHHHHHHHHHh
Confidence            999999998754

>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A*

Probab=82.72  E-value=2.3  Score=42.22  Aligned_cols=74  Identities=14%  Similarity=0.182  Sum_probs=50.3

Q ss_pred             CccCCeEEEEEcCCC-cCCHHHHHHHHHhcCCEEcc--cccc--------cccEEEEcCCCC---ccHHHHH--HcCCeE
Q psy11422        605 NYLKEKIFVFTGSLY-AFKRNEAIILIENLGGKVVN--FISK--------NTNYLVKGQKPG---KKLEKAI--KLNIKI  668 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~-~~~R~e~~~~i~~~Gg~v~~--sVsk--------~t~~LV~G~~~g---~Kl~kA~--~lgI~I  668 (687)
                      ..|.|++|++|+... ..++++++++|+..||++..  +.+.        .-.|||.+++.-   .++.+..  ..+++|
T Consensus       112 ~LF~G~~f~it~~~~~~p~~~~l~~iI~~~GG~v~~~p~~~~~~~~~~~~~~~~vis~~~d~~~~~~f~~~~~~~~~~~i  191 (220)
T 3l41_A          112 SLLEDYVVYLTSKTVAPENVPAVISIVKSNGGVCSTLNVYNKRLARHLEDGNVVLITCNEDSHIWTNFLDNASQNKTIFL  191 (220)
T ss_dssp             CTTTTSEEEEETTSSCGGGHHHHHHHHHHTTCEEEEECSCCHHHHHHHHHCCEEEEECGGGHHHHTTTHHHHTTCTTEEE
T ss_pred             hhhhheeEEEeccccCCCCCceEEEEEecCCcEechhhHHHHHHHHhcccCCEEEEEeCCcchHHHHhhccccccceEEE
Confidence            479999999999872 24799999999999999987  1111        113666664321   2332321  235679


Q ss_pred             EeHHHHHHHH
Q psy11422        669 LDEKNFVKIV  678 (687)
Q Consensus       669 i~E~~f~~~l  678 (687)
                      ++-+.++.-+
T Consensus       192 ~~~e~ll~~i  201 (220)
T 3l41_A          192 QNYDWLIKTV  201 (220)
T ss_dssp             EEHHHHHHHH
T ss_pred             echhHHHHHH
Confidence            9999999865

>3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular model mRNA splicing; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A

Probab=81.17  E-value=2.7  Score=44.12  Aligned_cols=55  Identities=15%  Similarity=0.163  Sum_probs=46.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ..+.+||+|+..+.+|.++| ++++.||..++.+++..+-|++++..+.+.+.++.
T Consensus       158 pL~Qlp~i~~~~~~~l~~~~-i~s~~~l~~~~~~e~~~ll~~~~~~~~~v~~~~~~  212 (328)
T 3im1_A          158 PLRQIPHFNNKILEKCKEIN-VETVYDIMALEDEERDEILTLTDSQLAQVAAFVNN  212 (328)
T ss_dssp             GGGGSTTCCHHHHHHHHHTT-CCSHHHHHHSCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_pred             ceeCCCCCCHHHHHHHHhCC-CCCHHHHhcCCHHHHHhHhCCCHHHHHHHHHHHHh
Confidence            57899999999999999887 58999999999888888778888777777776654

>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A

Probab=80.79  E-value=4.6  Score=40.88  Aligned_cols=105  Identities=16%  Similarity=0.238  Sum_probs=67.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHc-CCCCCCHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAK  537 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aL-GIp~vG~~~Ak  537 (687)
                      .+|=-||+|.....|++.-  .+++.|+.-+-+++..+---|.-+.+.--.+.+        --|..| .-.|+|.++|.
T Consensus       356 lidehglspdaadeliehf--esiagilatdleeiermyeegrlseeayraave--------iqlaeltkkegvgrktae  425 (519)
T 2csb_A          356 LIDEHGLSPDAADELIEHF--ESIAGILATDLEEIERMYEEGRLSEEAYRAAVE--------IQLAELTKKEGVGRKTAE  425 (519)
T ss_dssp             HHHHHCCCHHHHHHHHHHH--SSHHHHHTSCHHHHHHHHHHTSSCHHHHHHHHH--------HHHHHHHTSTTCCHHHHH
T ss_pred             HHHhcCCCcchHHHHHHHH--HHHHHHHhccHHHHHHHHHcccccHHHHHHHHH--------HHHHHHhhhcccchhHHH
Confidence            3466789999999998853  688888765444333221011111111111111        112222 34689999999


Q ss_pred             HHHhhcCChHHHHhc----CHHHHhcCCCCCHHHHHHHHH
Q psy11422        538 ELANYFKNLECMFKA----TEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       538 ~La~~f~sld~l~~A----s~eeL~~I~GIG~~~A~sI~~  573 (687)
                      +|+..||+.+.+.+.    ..+.|.++.|+|+.+..++..
T Consensus       426 rllrafgnpervkqlarefeieklasvegvgervlrslvp  465 (519)
T 2csb_A          426 RLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVP  465 (519)
T ss_dssp             HHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHHST
T ss_pred             HHHHHhCCHHHHHHHHHHHhHHHHhhccchHHHHHHHhcc
Confidence            999999999888764    468899999999987777654

>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A

Probab=80.69  E-value=2.9  Score=44.06  Aligned_cols=93  Identities=15%  Similarity=0.100  Sum_probs=56.3

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCC----hHHHhcCChhhh-hcccCccH----------------HHHHHHHHHHHHc
Q psy11422        456 SRKAMNIIGLGKKMIEKLVNANIVVT----AVDLYKINFKNL-LRLDRVSN----------------KLANNILLAIQKS  514 (687)
Q Consensus       456 sr~~l~I~GLG~k~i~~L~~~g~I~~----i~DL~~L~~~~L-~~l~gfG~----------------Ksa~~Ll~~Ie~s  514 (687)
                      .-..+..||-+++++..|.+.|++.-    =.|++.+-.+.+ ..+.-.|.                -..+.+++..   
T Consensus       142 gi~~i~apgeAEA~lA~la~~g~~~~I~S~D~Dllql~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~---  218 (336)
T 1rxw_A          142 GIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRL---  218 (336)
T ss_dssp             TCCEEECSSCHHHHHHHHHHTTSSSEEECSSSHHHHTTCSEEEESCCC-------------CCCCEEEEHHHHHHHH---
T ss_pred             CCCEEEcCchHHHHHHHHHHcCCeeEEEcCCCCcceecCCeEEEeccccccccCCccccccccceEEeEHHHHHHHc---
Confidence            34566778988999999998886442    358887643332 11111111                0122333332   


Q ss_pred             ccCCHHHHH-----HHc----CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11422        515 KLTTFSRFI-----YAL----GIRHVGETTAKELANYFKNLECMFKA  552 (687)
Q Consensus       515 k~~~l~r~L-----~aL----GIp~vG~~~Ak~La~~f~sld~l~~A  552 (687)
                       ..+-.+|+     .+.    ||||||+++|..|.+.|++++++...
T Consensus       219 -gl~~~q~id~~~L~GsD~ipGv~GiG~KtA~kLl~~~gsle~i~~~  264 (336)
T 1rxw_A          219 -GLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKA  264 (336)
T ss_dssp             -TCCHHHHHHHHHHHCBTTBCCCTTCCHHHHHHHHHHHSSHHHHHHH
T ss_pred             -CCCHHHHHHHHhhcCCCCCCCCCCcCHHHHHHHHHHcCCHHHHHHh
Confidence             23323322     222    89999999999999999999988764

>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1

Probab=80.51  E-value=2.4  Score=41.69  Aligned_cols=66  Identities=14%  Similarity=0.200  Sum_probs=39.0

Q ss_pred             CChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC-ChHHHHhcCHH
Q psy11422        480 VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK-NLECMFKATEE  555 (687)
Q Consensus       480 ~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~-sld~l~~As~e  555 (687)
                      -++.+|..++.++|.++   -||...+|.+|.+.-+...                         +.|+ .+    ..+.+
T Consensus        59 pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~~~-------------------------~~~~g~~----~~~~~  109 (211)
T 2abk_A           59 NTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILL-------------------------EQHNGEV----PEDRA  109 (211)
T ss_dssp             CSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH-------------------------HHTTTSC----CSCHH
T ss_pred             CCHHHHHCCCHHHHHHHHHHcCCChHHHHHHHHHHHHHH-------------------------HHcCCCc----hHHHH
Confidence            57888888777776442   3666667777765433211                         1111 11    12456


Q ss_pred             HHhcCCCCCHHHHHHHHHH
Q psy11422        556 QLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       556 eL~~I~GIG~~~A~sI~~f  574 (687)
                      +|.+++|||+++|..|.-|
T Consensus       110 ~L~~l~GIG~~tA~~il~~  128 (211)
T 2abk_A          110 ALEALPGVGRKTANVVLNT  128 (211)
T ss_dssp             HHHHSTTCCHHHHHHHHHH
T ss_pred             HHHhCCCCChHHHHHHHHH
Confidence            7777777777777777665

>3huf_A DNA repair and telomere maintenance protein NBS1; NBS1, FHA domain, BRCT domain, phosphoprotein binding, phosp binding, DNA repair; HET: DNA TPO; 2.15A {Schizosaccharomyces pombe} PDB: 3hue_A* 3i0m_A* 3i0n_A*

Probab=80.29  E-value=2.9  Score=43.80  Aligned_cols=57  Identities=16%  Similarity=0.045  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc----HHHHHHcCCeEEeHHHHHHHHh
Q psy11422        623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK----LEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K----l~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      +.++.+.++.+|+++.+-.+..|++||.....+.|    .-.|.=.|.+|++.+.|.+++.
T Consensus       126 ~~~L~~~L~~LGik~v~~~~detTHlVm~krnT~KvTvK~L~ALI~gkPIV~~~Fl~al~~  186 (325)
T 3huf_A          126 LSQWASNLNLLGIPTGLRDSDATTHFVMNRQAGSSITVGTMYAFLKKTVIIDDSYLQYLST  186 (325)
T ss_dssp             HHHHHHHHHTTTCCEESSCCTTCCEEECCCCCSSCCCHHHHHHHHTTCEEECHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCEEEEccCCCEEEEEEeccccccchHHHHHHHHCCCcEecHHHHHHHHH
Confidence            67799999999999994458889999998655555    8888888999999999988874

---

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	687
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	2e-69
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	2e-67
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	2e-62
d1dgsa1	181	a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, do	8e-24
d1dgsa2	86	b.40.4.6 (A:315-400) NAD+-dependent DNA ligase {Th	1e-22
d1l7ba_	92	c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4	4e-18
d2a1jb1	78	a.60.2.5 (B:219-296) DNA excision repair protein E	8e-13
d1x2ia1	68	a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF201	9e-09
d2bgwa1	70	a.60.2.5 (A:160-229) DNA repair endonuclease XPF {	3e-08
d1kfta_	56	a.60.2.3 (A:) Excinuclease UvrC C-terminal domain	6e-07
d2a1ja1	62	a.60.2.5 (A:837-898) DNA repair endonuclease XPF {	7e-06

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Length = 312

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

 Score =  227 bits (579), Expect = 2e-69
 Identities = 129/309 (41%), Positives = 189/309 (61%), Gaps = 7/309 (2%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  EL++ L+R+   YY+ D P + D +YD+L+ EL  IEE+YPEL T DS TQ +G   
Sbjct: 8   RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPP 67

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
            E  + V H   MMSL N F + D+  F++R+  E        Y+ EL  DG+AV++RYE
Sbjct: 68  LEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQE---VGEAAYVCELAIDGLAVSVRYE 124

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            GY  Q +TRGDG  GE+IT N+  I  +PL L     P  LE R E  + K  F++LN+
Sbjct: 125 DGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK---EPVSLEARGEAFMPKASFLRLNE 181

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G + F NPRNAAAG LRQL+PK+  ++ L  F +G+ +   + + S HSE L++ 
Sbjct: 182 ERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIAS-HSEALDYL 240

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
           Q +G  +  E    + ++++I F  + + KR  LPYEIDG+V K++  + Q+ LG T+++
Sbjct: 241 QALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKS 300

Query: 317 PRFALAYKF 325
           PR+A+AYKF
Sbjct: 301 PRWAIAYKF 309

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} Length = 313

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

 Score =  222 bits (565), Expect = 2e-67
 Identities = 122/309 (39%), Positives = 180/309 (58%), Gaps = 6/309 (1%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R  EL+K+L++++  YY+ D P + D  YD+L  EL  IE ++P+L+T DS TQ VG   
Sbjct: 10  RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKV 69

Query: 77  GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
               +   H   M SL++GFS ED+  F++R+   +   K + Y  ELK DG+A++LRYE
Sbjct: 70  LSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIG--KPVAYCCELKIDGLAISLRYE 127

Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
            G   + +TRGDG +GENIT N+  +  +P        P  +EVR E  + K+ F+ LN+
Sbjct: 128 NGVFVRGATRGDGTVGENITENLRTVRSVP---MRLTEPISVEVRGECYMPKQSFVALNE 184

Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
            R   G   F NPRNAAAG LRQL+ KI   + L+ F + V +   M   +   E L   
Sbjct: 185 EREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKT-QFEALEEL 243

Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
             IG     E  +   ++++  + ++ + KR  LPYEIDG+V K+N  + Q +LGFT +A
Sbjct: 244 SAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKA 303

Query: 317 PRFALAYKF 325
           PR+A+AYKF
Sbjct: 304 PRWAIAYKF 312

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Length = 314

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

 Score =  208 bits (530), Expect = 2e-62
 Identities = 125/312 (40%), Positives = 182/312 (58%), Gaps = 10/312 (3%)

Query: 17  RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
           R+ EL+  +  HN  YY+  +P ISD +YD+LL ELK++EE++PE  + DS T+ VG   
Sbjct: 9   RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARP 68

Query: 77  GENS-KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
            E + + V H  +M SLDN F+ E+V+ F +R+    +      Y  E K DG++V L Y
Sbjct: 69  LEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLER--EAEAPSLYTVEHKVDGLSV-LYY 125

Query: 136 EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
           E G    ++  GDG +GE +T N+  I  IP    +K  P+ LEVR EV +  + F++LN
Sbjct: 126 EEG--VWSTGSGDGEVGEEVTQNLLTIPTIPR--RLKGVPDRLEVRGEVYMPIEAFLRLN 181

Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILH--FFAHGVGELRGMNMPSSHSELL 253
           +     G K F NPRNAAAG LRQ +P++   + L   F+A G+G     +   S  ELL
Sbjct: 182 EELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYELL 241

Query: 254 NWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
            W ++ G  +   Y    G   + E Y++   +R  LP+E DGVV K++ L+   +LG+T
Sbjct: 242 LWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYT 301

Query: 314 SRAPRFALAYKF 325
           +RAPRFALAYKF
Sbjct: 302 ARAPRFALAYKF 313

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Length = 181

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

 Score = 96.9 bits (240), Expect = 8e-24
 Identities = 61/182 (33%), Positives = 107/182 (58%), Gaps = 4/182 (2%)

Query: 413 KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEK 472
           + P  CP C  +++      + RC      C A+R   ++H++SRKAM+I GLG+K+IE+
Sbjct: 1   RWPEACPECGHRLVKEGK--VHRCPNP--LCPAKRFEAIRHYASRKAMDIEGLGEKLIER 56

Query: 473 LVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVG 532
           L+   +V    DLY +  ++LL L+R+  K A N+L  I++SK     R +YALG+  VG
Sbjct: 57  LLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVG 116

Query: 533 ETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
           E  A+ LA  F  ++ + +A+ E+L+ + ++G  T +A ++ +  P  R L+ +L++ G+
Sbjct: 117 EVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGV 176

Query: 593 YW 594
             
Sbjct: 177 SM 178

>d1dgsa2 b.40.4.6 (A:315-400) NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Length = 86

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

 Score = 90.3 bits (224), Expect = 1e-22
 Identities = 35/84 (41%), Positives = 56/84 (66%)

Query: 327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVV 386
           ++E  T++  +  Q+GRTG +TPV +L+PV I+G  ++R TLHNES I   +I+IGD V+
Sbjct: 1   AEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVL 60

Query: 387 VHRSGNVIPKITSSILSLRPNDSK 410
           VH++G VIP++   +   R    +
Sbjct: 61  VHKAGGVIPEVLRVLKERRTGKER 84

>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]} Length = 92

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: NAD+-dependent DNA ligase, domain 4
species: Thermus thermophilus [TaxId: 274]

 Score = 77.8 bits (192), Expect = 4e-18
 Identities = 30/80 (37%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 664
             LK   FV TG L +  R E   L+  LG KV + +S+ T+YLV G+ PG KLEKA  L
Sbjct: 6   EALKGLTFVITGEL-SRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARAL 64

Query: 665 NIKILDEKNFVKIVKGFSTE 684
            +  L E+   ++++  + +
Sbjct: 65  GVPTLTEEELYRLLEARTGK 84

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 8e-13
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 510 AIQ-KSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT 567
            +  K +    SR    L  ++ V +T ++ L   F +LE +  A+ E L   P +G   
Sbjct: 4   LLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQK 63

Query: 568 VKAFIKFINQPLHRL 582
            +     +++P  ++
Sbjct: 64  ARRLFDVLHEPFLKV 78

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 68

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 50.2 bits (120), Expect = 9e-09
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 516 LTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574
           LT   R    + G+ HV  T A+ L  +F ++E +F A+  +L+ +  IG    K   + 
Sbjct: 2   LTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRV 61

Query: 575 INQP 578
           I  P
Sbjct: 62  ITAP 65

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Length = 70

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 523 IYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578
           +Y L     +G  TA+ +   F +LE  F A++ ++  +  IG    +   K +  P
Sbjct: 12  LYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP 68

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 10/48 (20%), Positives = 18/48 (37%)

Query: 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574
            I  VG    + L  Y   L+ +  A+ E++  +P I     +     
Sbjct: 6   TIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWS 53

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (98), Expect = 7e-06
 Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLL 583
           L +  V     + L ++ KN+  +   ++++L +I    +   K    FI+     ++
Sbjct: 6   LKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSIL-GNAANAKQLYDFIHTSFAEVV 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	687
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	100.0
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	100.0
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	100.0
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	100.0
d1dgsa2	86	NAD+-dependent DNA ligase {Thermus filiformis [Tax	99.97
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	99.82
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	99.19
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	99.08
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	99.06
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	99.04
d1x9na3	220	DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId:	98.78
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	98.69
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	98.63
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	98.57
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	98.53
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	98.52
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	98.49
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	98.44
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	98.31
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	98.22
d1t15a2	102	Breast cancer associated protein, BRCA1 {Human (Ho	98.05
d1a0ia2	239	ATP-dependent DNA ligase, N-terminal domain {Bacte	97.95
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	97.93
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	97.83
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	97.72
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	97.64
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	97.56
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	97.54
d1fvia2	188	ATP-dependent DNA ligase, N-terminal domain {Chlor	97.4
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	97.27
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	97.13
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	96.94
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	96.88
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	96.79
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	96.73
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	96.63
d1p16a2	245	mRNA capping enzyme alpha subunit {Yeast (Candida	96.24
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	96.16
d1lb2b_	72	C-terminal domain of RNA polymerase alpha subunit	96.14
d1z3eb1	67	C-terminal domain of RNA polymerase alpha subunit	96.14
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	96.13
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.09
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	96.09
d1in1a_	88	DNA ligase III alpha {Human (Homo sapiens) [TaxId:	95.97
d1kzyc1	153	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	95.48
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	95.34
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	95.06
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	94.73
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	94.02
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	93.92
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	93.73
d2csba3	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	93.37
d1l0ba2	97	Breast cancer associated protein, BRCA1 {Rat (Ratt	93.24
d1xdna_	265	RNA editing ligase MP52 {Trypanosoma brucei [TaxId	92.72
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	92.64
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	91.7
d1ckma2	228	RNA guanylyltransferase (mRNA capping enzyme), N-t	91.65
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	91.0
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	90.7
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	90.68
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	89.98
d1u9la_	68	Transcription elongation protein NusA {Escherichia	89.9
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	89.34
d1u9la_	68	Transcription elongation protein NusA {Escherichia	88.54
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	87.93
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	87.85
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	87.03
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	85.89
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	85.8
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	85.27
d1zeta2	273	DNA polymerase iota {Human (Homo sapiens) [TaxId:	84.97
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	84.92
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	82.8
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	81.84
d1s68a_	233	RNA ligase 2, N-terminal domain {Bacteriophage T4	81.7
d1jx4a2	240	DinB homolog (DBH) {Archaeon Sulfolobus solfataric	81.24
d2q0zx1	176	Protein pro2281 {Human (Homo sapiens) [TaxId: 9606	80.9
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	80.39

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=1.9e-84  Score=689.24  Aligned_cols=311  Identities=41%  Similarity=0.689  Sum_probs=295.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11422         11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM   90 (687)
Q Consensus        11 ~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl   90 (687)
                      -.++++||++|+++|++||++||+.|+|+|||++||+|+++|+.||++||+|..++|||++||+.+...+.+++|+.||+
T Consensus         2 ~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~l~~~~s~~~~v~~~~~~~~~~~~h~~pml   81 (312)
T d1b04a_           2 RQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMM   81 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHHHHHHCGGGCCTTCGGGGTCCCCCSCCCEECCSSCCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCCcccccccccccccccccccccc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11422         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (687)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (687)
                      ||+|+++.+|+..|.+++.+..+   ...|+|||||||+|++|+|++|+|++|+|||||.+|+|||+|+++|++||+++.
T Consensus        82 Sl~~~~~~~~~~~~~~~~~~~~~---~~~~~v~~KlDG~si~l~Y~~G~l~~a~TRGdG~~GeDIT~~~~~i~~iP~~~~  158 (312)
T d1b04a_          82 SLANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK  158 (312)
T ss_dssp             CCCEECSTTHHHHHHHHHHHHHS---SCCEEEEEEESSEEEEEEEETTEEEEEEECTTSSCEEBCHHHHHTCTTSCSBCS
T ss_pred             ccccccchhhccchhhccccccc---ccceeeeeeeecceeeeeecccceEEEeecCCcchhhhHHHHHhhhcCCCCccC
Confidence            99999999999999999877654   468999999999999999999999999999999999999999999999999986


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHH
Q psy11422        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS  250 (687)
Q Consensus       171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~  250 (687)
                         .|..++||||+||++++|+++|+.+.+.|++.|+||||+|||+||+++|..+..|.|+|++|.++...... +.+|+
T Consensus       159 ---~~~~~~irGE~~~~~~~f~~~~~~~~~~~~~~f~NpRN~aAG~l~~k~~~~~~~~~l~~~~y~~~~~~~~~-~~~~~  234 (312)
T d1b04a_         159 ---EPVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHS  234 (312)
T ss_dssp             ---SCCCEEEEEEEECCHHHHHHHHHHHHHC--CCCSCHHHHHHHHHHSSCHHHHHHTCCEEEEEEETTTTTTT-CCBHH
T ss_pred             ---CCcccccccceeeecchhhhhhhhhhhccccccchhhHHhhcccccccchhhhhhhhhheeeecccccccc-chhHH
Confidence               47899999999999999999999999999999999999999999999999999999999999998755443 48999


Q ss_pred             HHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCc
Q psy11422        251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (687)
Q Consensus       251 e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (687)
                      +.|++|+.|||+++++...+.+++++.+|+++|.+.|..+||+|||||||+||..+|+.||+|+|+||||||||||+|
T Consensus       235 e~l~~L~~~gf~~~~~~~~~~~~~~v~~~~~~~~~~R~~l~Y~iDGIVikvn~~~~~~~lG~ts~~PrwAiA~Kfpae  312 (312)
T d1b04a_         235 EALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE  312 (312)
T ss_dssp             HHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHHSTTCSSCEEEEEEEECBHHHHHHHCCCSSSCTTEEEEECCCC
T ss_pred             HHHHHHHhcCcccccceEEECCHHHHHHHHHHHHhhhhcCCCCCCeEEEEEcCHHHHHHcCCcCCCCCceEEeCcCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999986

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

Probab=100.00  E-value=2.9e-84  Score=688.20  Aligned_cols=311  Identities=39%  Similarity=0.640  Sum_probs=297.4

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccc
Q psy11422         10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKM   89 (687)
Q Consensus        10 ~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pM   89 (687)
                      ++..++.|+++|+++|++||++||+.|+|+|||++||+|+++|++||++||+++.++|||++||+.+...|.+++|+.||
T Consensus         3 ~~~~~~~~~~~L~~~i~~~~~~Yy~~~~p~iSD~eYD~L~~~L~~le~~~p~~~~~~s~~~~vg~~~~~~~~~~~h~~pm   82 (313)
T d1ta8a_           3 TLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPM   82 (313)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCCCBCSSCCEEECSSCC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCcccccccccccccccccchhcc
Confidence            56778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccc
Q psy11422         90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL  169 (687)
Q Consensus        90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l  169 (687)
                      +||+|+++.+|+..|..++.+.++.  +..|+||||+||+|++|+|++|+|++|+|||||.+|+|||+|+++|++||.+|
T Consensus        83 ~sl~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~KiDG~si~l~Y~~G~l~~a~TRGdG~~GeDiT~~~~~i~~ip~~l  160 (313)
T d1ta8a_          83 YSLNDGFSKEDIFAFDERVRKAIGK--PVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRL  160 (313)
T ss_dssp             CCCCEECSHHHHHHHHHHHHHHHSS--CCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSBC
T ss_pred             cccccccchhhhhhhhhhhhhhccc--ccceeeeeecccceEEEEecCCcEEEeeecccchHHHHHHHhhhhhccccccc
Confidence            9999999999999999999887763  56899999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCH
Q psy11422        170 NIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH  249 (687)
Q Consensus       170 ~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~  249 (687)
                      +   .|..++||||+||++++|.++|+++.+++++.|+||||+|||+||++++..+..|.|+|++|.++...... ..+|
T Consensus       161 ~---~~~~~~iRGEl~~~~~~f~~~n~~~~~~~~~~f~N~RN~vaG~l~~k~~~~~~~~~l~f~~y~v~~~~~~~-~~~~  236 (313)
T d1ta8a_         161 T---EPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK-AKTQ  236 (313)
T ss_dssp             S---SCCCEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHTCSBHHHHHTSCCEEEEEEESCCTTCC-CSBH
T ss_pred             c---CCcceeeeeEEEEeccchhhhHHHHHHhcccccccchhhhcccchhcccchhhhccccceeeecceecccc-cchh
Confidence            7   37889999999999999999999999999999999999999999999999999999999999998754433 3789


Q ss_pred             HHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11422        250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (687)
Q Consensus       250 ~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (687)
                      .+.+.+|+.+||.++++...+.+++++++|+++|.+.|..+||+|||||||+||..+|+.||+|+|+||||||||||
T Consensus       237 ~~~~~~l~~~g~~~~~~~~~~~~~~ei~~~~~~~~~~R~~l~YeIDGIVikvn~~~~q~~lG~ts~~PrwAiA~KfP  313 (313)
T d1ta8a_         237 FEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP  313 (313)
T ss_dssp             HHHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHTGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEEECC
T ss_pred             HHHhhhhhhcCCcCCCCeEEeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEEeCHHHHHHcCCcCCCCCceEEecCC
Confidence            99999999999999998999999999999999999999999999999999999999999999999999999999998

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

Probab=100.00  E-value=1.8e-84  Score=689.72  Aligned_cols=308  Identities=40%  Similarity=0.602  Sum_probs=289.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccC-CCCcceecccccc
Q psy11422         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGG-ENSKYVHHTFKMM   90 (687)
Q Consensus        12 ~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~-~~~~kv~H~~pMl   90 (687)
                      .+++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||+|..++|||++||+.+. ..|.||+|++|||
T Consensus         4 ~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~le~~~p~l~~~~s~~~~vg~~~~~~~~~kv~h~~pMl   83 (314)
T d1dgsa3           4 EEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMY   83 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHHHTTSSGGGCCTTSGGGGCSSSCCCCCCCEEECSSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCcccccccccccccccccccceeee
Confidence            467889999999999999999999999999999999999999999999999999999999999875 5789999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11422         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (687)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (687)
                      ||+|+|+.+|+..|.+|+.+.+.  .+..|+|||||||+|+ |+|++|  ++|+|||||.+|+|||+|+++|++||++|+
T Consensus        84 SL~k~~~~~~~~~~~~r~~~~~~--~~~~~~ve~KlDG~Si-L~y~~G--v~~~TRGdG~~GeDiT~~~~~I~~iP~~l~  158 (314)
T d1dgsa3          84 SLDNAFTYEEVLAFEERLEREAE--APSLYTVEHKVDGLSV-LYYEEG--VWSTGSGDGEVGEEVTQNLLTIPTIPRRLK  158 (314)
T ss_dssp             CCCEECSHHHHHHHHHHTTSSSC--SCCEEEEEECCSCEEE-EEEETT--EEEEEECSSSEEEBCTGGGTSSTTSCSBCS
T ss_pred             ccccccchhhhhhhhhhhhcccc--ccchhhhhhccCcceE-EEecCC--EeEEeecCCceehhhHhhHhhhcCcchhcc
Confidence            99999999999999999876554  2467999999999999 999999  579999999999999999999999999997


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC--CCCCCC
Q psy11422        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMPSS  248 (687)
Q Consensus       171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~--~~~~~~  248 (687)
                      +  .|..++||||+||++++|+++|+++.+.++++|+||||+|||+||++++..++.|.|+|++|.++....  ...+.+
T Consensus       159 ~--~~~~l~IRGEl~i~~~~F~~~n~~~~~~~~~~f~NpRN~aaG~l~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  236 (314)
T d1dgsa3         159 G--VPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKS  236 (314)
T ss_dssp             S--CCSEEEEEEEEECCHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHSCSSHHHHHHSCCEEECCCBCTTTTTTSCCCCB
T ss_pred             C--CCccceeeeeEEeecchHHHHHHHHHHhcCCcccccchhhhhhhhcccchhhhhccccceeeeccccccccCCCccc
Confidence            4  689999999999999999999999999999999999999999999999999999999999998865432  123589


Q ss_pred             HHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11422        249 HSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (687)
Q Consensus       249 ~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (687)
                      |.+.+.+|..|||++++....+.+.+++.+++++|...|..+||+||||||||||..+|+.||+|||+||||||||||
T Consensus       237 ~~e~~~~l~~~g~~~~~~~~~~~~~e~l~~~~~~~~~~R~~l~y~iDGiVikvnd~~~q~~LG~ts~~PrwAiA~KfP  314 (314)
T d1dgsa3         237 QYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFP  314 (314)
T ss_dssp             HHHHHHHHHHTTCCCCSCEEEEEHHHHHHHHHHHHHHTTTTSSSCCCEEEEEESBTHHHHHSCBCSSCBSSEEEEECC
T ss_pred             HHHHHHhhhcccccCCcceEEECCHHHHHHHHHHHHHhhhcCCCCCCceEEEEeCHHHHHHhCcccCCCCceEEecCC
Confidence            999999999999999988888999999999999999999999999999999999999999999999999999999998

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=100.00  E-value=7.1e-49  Score=383.27  Aligned_cols=179  Identities=34%  Similarity=0.675  Sum_probs=173.3

Q ss_pred             CCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhh
Q psy11422        414 IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL  493 (687)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L  493 (687)
                      ||++||+||++|+++  +..+||+|+ . ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|+.++|
T Consensus         2 fP~~CP~C~s~l~~e--~~~~~C~n~-~-Cpaq~~~~l~hf~sr~amdI~GlG~~~i~~L~~~g~i~~~~Dly~L~~~~l   77 (181)
T d1dgsa1           2 WPEACPECGHRLVKE--GKVHRCPNP-L-CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDL   77 (181)
T ss_dssp             CCSBCTTTCCBCEEE--TTEEECCCT-T-CGGGHHHHHHHHHSTTSSCCTTCCHHHHHHHHHTTSCSSGGGGGGGCCHHH
T ss_pred             cCCCCCCCCCeeeec--CceeECCCC-C-CHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhcCCcchhhhhhhhhhHHH
Confidence            799999999999975  357899996 6 999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11422        494 LRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (687)
Q Consensus       494 ~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~  573 (687)
                      ..++|||+|+|+||+++|++||+.+|+|||+||||||||+.+|+.|+++|+++++|..|+.++|.+|+|||+++|++|.+
T Consensus        78 ~~l~~~g~ksa~nl~~~Ie~sk~~~l~r~l~aLGI~~vG~~~Ak~La~~f~sl~~l~~as~eeL~~I~GIG~~~A~si~~  157 (181)
T d1dgsa1          78 LGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILE  157 (181)
T ss_dssp             HTTSSCCSTTHHHHHHHHHHGGGCCHHHHHHHTTCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHHTSTTCCHHHHHHHHH
T ss_pred             hcccccchHHHHHHHHHHHhhcchhHHHHHHHHHhhhhhHHHHHHHHHHhhhhhhhhhhHHHHHhhcCCcCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcchhHHHHHHHHHhcCccccc
Q psy11422        574 FINQPLHRLLISQLRDVGIYWLN  596 (687)
Q Consensus       574 ff~~~~n~~~i~~L~~~Gv~~~~  596 (687)
                      ||+++.|+++|++|.+.||++..
T Consensus       158 ff~~~~n~~~i~~L~~~Gv~~e~  180 (181)
T d1dgsa1         158 TLKDPAFRDLVRRLKEAGVSMES  180 (181)
T ss_dssp             HHHCHHHHHHHHHHHHTTCCCBC
T ss_pred             HHCCHHHHHHHHHHHHcCCCccc
Confidence            99999999999999999998753

>d1dgsa2 b.40.4.6 (A:315-400) NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

Probab=99.97  E-value=1.2e-31  Score=227.25  Aligned_cols=85  Identities=41%  Similarity=0.696  Sum_probs=81.4

Q ss_pred             CceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCC
Q psy11422        327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP  406 (687)
Q Consensus       327 ~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~  406 (687)
                      +++++|+|++|+|||||||++||+|+|+||.|+|++|+||||||+++|+++||++||+|.|.|||||||+|++|+.+.|+
T Consensus         1 Ae~~~t~v~~I~~~vgrtG~itPva~lePV~l~G~~V~~atlhN~~~i~~~~i~~Gd~V~i~raGdVIP~I~~vi~~~r~   80 (86)
T d1dgsa2           1 AEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRT   80 (86)
T ss_dssp             CCCEEEEEEEEEEEECTTSBEEEEEEEEEEEETTEEEEEEECCSHHHHHHTTCBSSCEEEEEEETTTEEEEEEECGGGCC
T ss_pred             CCEEEEEEEEEEEecCCCcEEeEEEEEEEeeEcCceEeEEecCCHHHHhhcCCCcCceEEEEECCCCccceeEeecccCC
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999998887


Q ss_pred             CCCcc
Q psy11422        407 NDSKI  411 (687)
Q Consensus       407 ~~~~~  411 (687)
                      +.++|
T Consensus        81 ~~~~p   85 (86)
T d1dgsa2          81 GKERP   85 (86)
T ss_dssp             SCCCB
T ss_pred             CCCCc
Confidence            76544

>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: NAD+-dependent DNA ligase, domain 4
species: Thermus thermophilus [TaxId: 274]

Probab=99.82  E-value=3.8e-21  Score=166.01  Aligned_cols=80  Identities=38%  Similarity=0.573  Sum_probs=75.5

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhccc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS  682 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~~s  682 (687)
                      .++||+|++|||||+|+ ++|++++++|+++||+|+++||++|||||+|+++|+|++||+++||+||+|++|++||+..+
T Consensus         4 ~~~~l~G~~iv~TG~~~-~~R~e~~~~i~~~Gg~v~~sVs~~t~~LV~g~~~g~K~~kA~~~gI~IisE~~f~~~l~~~~   82 (92)
T d1l7ba_           4 GGEALKGLTFVITGELS-RPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEART   82 (92)
T ss_dssp             CCCSSTTCEEECSTTTT-SCHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHHH
T ss_pred             CCCCcCCCEEEEeCCcc-CCHHHHHHHHHHhCCEEcCccccceeEEEECCCCCcHHHHHHHcCCcEecHHHHHHHHHhCC
Confidence            46799999999999996 79999999999999999999999999999999999999999999999999999999998644


Q ss_pred             C
Q psy11422        683 T  683 (687)
Q Consensus       683 ~  683 (687)
                      +
T Consensus        83 ~   83 (92)
T d1l7ba_          83 G   83 (92)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=8.9e-12  Score=103.50  Aligned_cols=67  Identities=24%  Similarity=0.415  Sum_probs=62.7

Q ss_pred             HcccCCHHHHHHHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchh
Q psy11422        513 KSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (687)
Q Consensus       513 ~sk~~~l~r~L~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~  579 (687)
                      ++++..+.+++.+| +|||||+..|+.|+++|+|++++.+|+.++|.+++|||++.|++|++||++|.
T Consensus         8 ~~~~~~~~~~~~~L~~I~gIg~~~a~~L~~~F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~pf   75 (78)
T d2a1jb1           8 KLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPF   75 (78)
T ss_dssp             HHHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCS
T ss_pred             HHcCCcHHHHHHHhcCCCCcCHHHHHHHHHHhCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcCcc
Confidence            45566788999999 99999999999999999999999999999999999999999999999998874

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.08  E-value=6.4e-11  Score=96.15  Aligned_cols=55  Identities=25%  Similarity=0.493  Sum_probs=52.1

Q ss_pred             HHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11422        524 YAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (687)
Q Consensus       524 ~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~  578 (687)
                      +.| +|||||+++|+.|+++|++++.+.+|+.++|.+++|||+++|++|++||+.+
T Consensus        13 ~~L~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~~~   68 (70)
T d2bgwa1          13 YILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP   68 (70)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHcCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHhCc
Confidence            345 9999999999999999999999999999999999999999999999999875

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.06  E-value=9.9e-11  Score=94.46  Aligned_cols=55  Identities=29%  Similarity=0.485  Sum_probs=52.4

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhH
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n  580 (687)
                      .||||||+.+|+.|+++|++++++.+|+.++|.+++|||+++|++|++||+.+.+
T Consensus        13 ~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~~~~~   67 (68)
T d1x2ia1          13 EGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYI   67 (68)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCC
T ss_pred             cCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHhchhc
Confidence            4999999999999999999999999999999999999999999999999987753

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.04  E-value=5.5e-11  Score=92.26  Aligned_cols=51  Identities=20%  Similarity=0.325  Sum_probs=49.6

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      .|||||+++|++|+++|++++++.+|+.++|.+++|||+++|++|++||++
T Consensus         6 ~I~gVG~~~a~~L~~~F~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~l~N   56 (56)
T d1kfta_           6 TIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH   56 (56)
T ss_dssp             GCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHTC
T ss_pred             cCCCccHHHHHHHHHHhCCHHHHHHhhHHHHHhcCCCCHHHHHHHHHHHcC
Confidence            799999999999999999999999999999999999999999999999974

>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=2.4e-08  Score=97.81  Aligned_cols=159  Identities=16%  Similarity=0.177  Sum_probs=104.1

Q ss_pred             eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhcc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11422        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (687)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~  196 (687)
                      ..|++|+|+||+-|.+.+.+|.=+++.||    .|.|+|+....|.. ++. +... .+..+.+-||++.-..+.     
T Consensus        28 ~~~~~e~K~DG~R~~i~~~~~~~v~l~SR----~g~~~t~~~p~l~~~~~~-~~~~-~~~~~iLDGEl~~~d~~~-----   96 (220)
T d1x9na3          28 AAFTCEYKYDGQRAQIHALEGGEVKIFSR----NQEDNTGKYPDIISRIPK-IKLP-SVTSFILDTEAVAWDREK-----   96 (220)
T ss_dssp             SCEEEEEEESSEEEEEEECTTSCEEEECT----TSCBCTTTCHHHHHTSGG-GBCT-TCCCEEEEEEEEEECTTT-----
T ss_pred             CcEEEEEeECcEEEEEEEECCCEEEEEeC----CCccccccchhHHHHHHH-hhcC-CCcceeeeeeeEEecCCC-----
Confidence            47999999999999887644434789999    48999987765433 332 2211 234688999999754321     


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce-----Ee
Q psy11422        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS-----VL  270 (687)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~-----~~  270 (687)
                             . --.+.+..++..+...+......++.|++|++...++..+ -.+..+..+.|.++--+......     .+
T Consensus        97 -------~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~~~~~p~~eR~~~L~~~~~~~~~~~~~~~~~~~  168 (220)
T d1x9na3          97 -------K-QIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDT  168 (220)
T ss_dssp             -------C-SBCCHHHHTTSCSSCCCGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBTTTEEECCEECC
T ss_pred             -------C-ccchHHHHhhhhhcccchhhhccccceEEEEEEEECCcchhhhhHHHHHHHHHHHhccCCCeEEEEEeecc
Confidence                   1 1223344444444444444445679999999876554322 24689999999887655443222     35


Q ss_pred             CCHHHHHHHHHHHHHhhcCCCCccceEEEEE
Q psy11422        271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKI  301 (687)
Q Consensus       271 ~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv  301 (687)
                      .+.+++.++++.+.+.      -..|+|+|-
T Consensus       169 ~~~~~~~~~~~~~~~~------g~EGim~K~  193 (220)
T d1x9na3         169 KDIEQIAEFLEQSVKD------SCEGLMVKT  193 (220)
T ss_dssp             CCHHHHHHHHHHHHHT------SEEEEEEEE
T ss_pred             CCHHHHHHHHHHHHHC------CCceEEEec
Confidence            6889999988876543      247999995

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=5.4e-09  Score=82.52  Aligned_cols=53  Identities=19%  Similarity=0.334  Sum_probs=50.5

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchh
Q psy11422        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~  579 (687)
                      .+|||||++.++.|+++|+|+++|.+||.++|.++.| |++.|+.|++||+.+.
T Consensus         6 ~~iPGIg~~~~~~Ll~~f~Si~~l~~As~~eL~~v~G-~~~~A~~i~~f~~~~~   58 (62)
T d2a1ja1           6 LKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFIHTSF   58 (62)
T ss_dssp             HTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHCCC
T ss_pred             hcCCCCCHHHHHHHHHHhccHHHHHhCCHHHHHHCcC-cHHHHHHHHHHHhhhh
Confidence            6899999999999999999999999999999999999 9999999999998753

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=98.63  E-value=2.1e-08  Score=78.54  Aligned_cols=56  Identities=20%  Similarity=0.324  Sum_probs=51.8

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~  516 (687)
                      .+|||+||+++++|+++|+ .|+.+|..++.++|.+++|||++.|++|+++..+..+
T Consensus         2 ~~IpGIG~~~a~~L~~~G~-~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar~~~d   57 (60)
T d2i1qa1           2 TDLPGVGPSTAEKLVEAGY-IDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCD   57 (60)
T ss_dssp             TTSTTCCHHHHHHHHHHTC-CSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHccC-CCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHHHcC
Confidence            5899999999999999996 9999999999999999999999999999998776544

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.57  E-value=3.7e-08  Score=77.33  Aligned_cols=58  Identities=24%  Similarity=0.220  Sum_probs=52.9

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11422        457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK  515 (687)
Q Consensus       457 r~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk  515 (687)
                      |..++|+|+||+++++|+++|+ .|+.+|..++.++|.+++|||++.|++|+++..+.-
T Consensus         1 ~~L~~i~GIG~~~a~~L~~~g~-~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar~~~   58 (61)
T d1pzna1           1 RSIEDLPGVGPATAEKLREAGY-DTLEAIAVASPIELKEVAGISEGTALKIIQAARKAA   58 (61)
T ss_dssp             CCSSCCTTCCHHHHHHHHTTTC-CSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_pred             CccccCCCCCHHHHHHHHHhcC-CCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHHHc
Confidence            3568999999999999999986 899999999999999999999999999999876643

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.53  E-value=5.4e-08  Score=76.99  Aligned_cols=56  Identities=20%  Similarity=0.268  Sum_probs=52.3

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s  514 (687)
                      +.|+.+|+|++++++|+++|+ .|+.+|...+.++|.+++|||+++|++|+++..+.
T Consensus         4 ~~L~~~Gig~~~~~kL~~aG~-~Tve~ia~~t~~~L~~i~Gi~e~~a~KIi~~A~k~   59 (64)
T d1szpa1           4 EKLQVNGITMADVKKLRESGL-HTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARL   59 (64)
T ss_dssp             GGGCCTTCCHHHHHHHHTTSC-CSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHhHCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            468899999999999999996 89999999999999999999999999999998764

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.52  E-value=2.5e-08  Score=80.41  Aligned_cols=57  Identities=21%  Similarity=0.238  Sum_probs=52.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK  515 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk  515 (687)
                      +.|+++|+|++++++|+++|+ .|+.+|..++.++|++++||++++|++|++++++.-
T Consensus        11 ~~L~~~Gig~~~i~kL~~aG~-~Tv~~i~~at~~~L~~i~G~~e~~A~KIi~~a~k~~   67 (70)
T d1b22a_          11 SRLEQCGINANDVKKLEEAGF-HTVEAVAYAPKKELINIKGISEAKADKILAEAAKLV   67 (70)
T ss_dssp             HHHHHTTCSHHHHHHHHTTCC-SSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHHS
T ss_pred             HHHhhCCCCHHHHHHHHHcCc-chHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHHHHc
Confidence            457899999999999999996 999999999999999999999999999999987653

>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA-repair protein XRCC1
domain: DNA-repair protein XRCC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=1.2e-07  Score=80.31  Aligned_cols=76  Identities=13%  Similarity=0.320  Sum_probs=67.3

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHH--cCCeEEeHHHHHHHHhc
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIK--LNIKILDEKNFVKIVKG  680 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~--lgI~Ii~E~~f~~~l~~  680 (687)
                      +-|+|..|+++|.++..+|.+++++|..+||++...++++|+++|+....+.+.+.+..  .+++||+.+++.+.+..
T Consensus         4 d~F~g~~f~v~g~~~~~~~~~l~~~i~~~GG~v~~~~~~~~THvI~~~~~~~~~~~~~~~~~~i~iV~~~Wl~dc~~~   81 (96)
T d1cdza_           4 DFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEK   81 (96)
T ss_dssp             CTTTTCEEEECSCCCTHHHHHHHHHHHHTTCEECSSCSTTCSEEECSSCCCHHHHHHHTTCTTCEEECTHHHHHHHTT
T ss_pred             cccCCcEEEEeCCCCHHHHHHHHHHHHHhCCEEeccCCCCceEEEEccCCcceeeehhhhCCCCeEEEEhHHHHHHHc
Confidence            46899999999998877899999999999999999999999999999887766666654  48999999999998864

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=98.44  E-value=1.4e-07  Score=73.62  Aligned_cols=51  Identities=22%  Similarity=0.246  Sum_probs=47.5

Q ss_pred             cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      ..|||||++++++|.++ |+|++.+..|++++|.+++|||+++|++|++.++
T Consensus         2 ~~IpGIG~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar   53 (60)
T d2i1qa1           2 TDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGAR   53 (60)
T ss_dssp             TTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            36999999999999987 9999999999999999999999999999987654

>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA topoisomerase II binding protein 1, TopBP1
domain: DNA topoisomerase II binding protein 1, TopBP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=6.2e-07  Score=80.78  Aligned_cols=76  Identities=13%  Similarity=0.114  Sum_probs=65.5

Q ss_pred             CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccH--HHHHHcCCeEEeHHHHHHHHhc
Q psy11422        604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKL--EKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl--~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      ...|.|.+|+|+|. ....|+++..+|..+||++...+++++++||++...+.+.  ..|...+|+||+.+++.+.+..
T Consensus        38 ~~~f~G~~i~isGf-~~~~~~~l~~~i~~~GG~~~~~~~~~vTHvIv~~~~~~~~~~~~~~~~~i~iV~~~Wl~~c~~~  115 (132)
T d1wf6a_          38 EDLLDGCRIYLCGF-SGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWLLECFSK  115 (132)
T ss_dssp             TTTTTTCEEEEESC-CSHHHHHHHHHHHHTTCEEESSCCSSCCEEEESSCCSHHHHHHHHSCCCCCEEEHHHHHHHHHH
T ss_pred             hhhhCCeEEEEeeC-CCHHHHHHHHHHHHcCCEEecccCCCceEEEecCCCccHHHHHHHhcCCCCcCCHHHHHHHHHc
Confidence            34699999999994 5568999999999999999999999999999998777544  4566678999999999998754

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.22  E-value=4.6e-07  Score=70.90  Aligned_cols=52  Identities=23%  Similarity=0.298  Sum_probs=47.5

Q ss_pred             cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      ..|||||+++|++|.++ |+|++.|..|++++|.+++|||+++|+.|.+.+++
T Consensus         4 ~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar~   56 (61)
T d1pzna1           4 EDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARK   56 (61)
T ss_dssp             SCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            36999999999999974 89999999999999999999999999999887643

>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=3.4e-06  Score=71.37  Aligned_cols=75  Identities=11%  Similarity=0.045  Sum_probs=59.8

Q ss_pred             ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccc-----ccEEEEcC-C----CCccHHHHHHcCCeEEeHHHHH
Q psy11422        606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKN-----TNYLVKGQ-K----PGKKLEKAIKLNIKILDEKNFV  675 (687)
Q Consensus       606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~-----t~~LV~G~-~----~g~Kl~kA~~lgI~Ii~E~~f~  675 (687)
                      .|+|.+|||+|.++..+|++++.+|+.+||++...+...     ++.++++. .    .+.+...|...||+|++.++++
T Consensus         3 iF~g~~i~~~g~~~~~~~~~L~~li~~~GG~v~~~~~~~~~~~~~t~~~i~~~~~~~~~~~~~~~~~~~~i~iV~~~Wl~   82 (102)
T d1t15a2           3 IFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVL   82 (102)
T ss_dssp             TTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTCSSCEEEHHHHH
T ss_pred             CCCCcEEEEeCCCCCcCHHHHHHHHHHhCCEEeeccccccccccccchheecccccchhhHHHHHHHhCCCcEEeeHHHH
Confidence            689999999999888899999999999999998777542     23444443 1    2256667778899999999999


Q ss_pred             HHHhc
Q psy11422        676 KIVKG  680 (687)
Q Consensus       676 ~~l~~  680 (687)
                      +-+..
T Consensus        83 dsi~~   87 (102)
T d1t15a2          83 DSVAL   87 (102)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            98754

>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: ATP-dependent DNA ligase, N-terminal domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=97.95  E-value=3e-05  Score=75.59  Aligned_cols=176  Identities=13%  Similarity=0.037  Sum_probs=98.6

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhh------hhhhhccCCcccccCCCCceEEEEEEEEeehhhHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITT------NIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFI  192 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~------n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~  192 (687)
                      .+.+|+|+||+-+.+.+.++.-+...||    .|.++|+      ....+..+-..+.. ..|..+.+-||++....+|+
T Consensus        27 ~~~~E~K~DG~R~~~~~~~~~~~~~~SR----~g~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~vLDGEl~~~~~~f~  101 (239)
T d1a0ia2          27 YLIAEIKYDGVRGNICVDNTANSYWLSR----VSKTIPALEHLNGFDVRWKRLLNDDRC-FYKDGFMLDGELMVKGVDFN  101 (239)
T ss_dssp             SEEEEECCCSEEEEEEEETTSEEEEECT----TSCBCGGGGGGCEECHHHHHHHHSTTC-CCTTEEEEEEEEEESSSCTT
T ss_pred             CEEEEEeeceEEEEEEEECCeEEEEEec----CCCcccchhhhhhhhhhHHHHHHHHhh-cCCcceEEeeeEeeccCCcc
Confidence            5899999999999999988766677788    4555543      22222211111111 13667999999999999999


Q ss_pred             HHHHHHHHcCCCCC--CChhhhHHhHhhhcCcc--cccccccEEEEEeccccc----CCCC---CCCHHHHHHHHH----
Q psy11422        193 KLNKYRYHLGLKKF--TNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELR----GMNM---PSSHSELLNWYQ----  257 (687)
Q Consensus       193 ~~n~~~~~~g~~~f--~NpRN~aaG~lr~~~~~--~~~~r~l~f~~y~~~~~~----~~~~---~~~~~e~l~~L~----  257 (687)
                      .++..........-  ..+.+.....+++.+..  ....+++.|++|++...+    +...   .....+.++.|.    
T Consensus       102 ~~~~~v~~~~~~~~~~~~~f~~l~~r~~~~~~~~~~~~~~~l~~~vfD~l~l~~~~~~~~~~~~~~~~~~r~~~l~~~~~  181 (239)
T d1a0ia2         102 TGSGLLRTKWTDTKNQEFHEELFVEPIRKKDKVPFKLHTGHLHIKLYAILPLHIVESGEDCDVMTLLMQEHVKNMLPLLQ  181 (239)
T ss_dssp             THHHHHHCCSCCSSBSSCC--------CCCSCCCCCBCTTTEEEEEEEEEEHHHHHHCCCEEEEHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhcccccccccCCHHHHHhhhccCccchhhhhcccceEEEEEEeeccccccccchhhccccHHHHHHHHHHHHh
Confidence            88776554332221  22344444455554432  334567899999875321    1110   012333333332    


Q ss_pred             hc----CCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        258 KI----GLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       258 ~~----Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                      ..    .+..++ ...+.+.+++.++++...+.    .|  -|+|+|--+..+
T Consensus       182 ~~~~~~~~~~~~-~~~~~~~~el~~~~~~~~~~----g~--EGlmiK~~~s~Y  227 (239)
T d1a0ia2         182 EYFPEIEWQAAE-SYEVYDMVELQQLYEQKRAE----GH--EGLIVKDPMCIY  227 (239)
T ss_dssp             HHCTTSEEEECC-EEEESSHHHHHHHHHHHHTT----TC--CCEEEECTTCEE
T ss_pred             hcCCCccEEEee-eEecCCHHHHHHHHHHHHHC----CC--cEEEEeCCCCcc
Confidence            21    111222 33578899999998876422    33  599999765444

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.93  E-value=1.7e-06  Score=66.39  Aligned_cols=52  Identities=19%  Similarity=0.264  Sum_probs=47.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      .-+|||+|+++.++|++.-  .++.+|..++.++|.+++|+|++.|++|++.++
T Consensus         4 L~~I~gVG~~~a~~L~~~F--~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~l~   55 (56)
T d1kfta_           4 LETIEGVGPKRRQMLLKYM--GGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   55 (56)
T ss_dssp             GGGCTTCSSSHHHHHHHHH--SCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             cccCCCccHHHHHHHHHHh--CCHHHHHHhhHHHHHhcCCCCHHHHHHHHHHHc
Confidence            3479999999999999983  699999999999999999999999999999874

>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=1.5e-05  Score=69.10  Aligned_cols=69  Identities=13%  Similarity=-0.023  Sum_probs=60.5

Q ss_pred             eEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        610 KIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       610 ~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      .+|++||.-. -.++.++++++.+||++..+++.+|++||+++..+      .|+..|...|++|++.+++.+.+.
T Consensus         2 ~~i~~SGl~~-~e~~~l~~~i~~~Gg~~~~~~~~~~THlI~~~~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~   76 (109)
T d1t15a1           2 MSMVVSGLTP-EEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIK   76 (109)
T ss_dssp             CEEEEESCCH-HHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHH
T ss_pred             EEEEECCCCH-HHHHHHHHHHHHcCCEEEeEecCCccEEEEecCcchhhHhhHHHHHHHHCCCccccHHHHHHHHH
Confidence            4789999654 47889999999999999999999999999987543      478889999999999999999875

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.72  E-value=1.6e-05  Score=63.18  Aligned_cols=51  Identities=12%  Similarity=0.313  Sum_probs=47.7

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .|+|+|+++...|.+. + .|+.+|+.++.++|..+||+|++.|++|.+.+..
T Consensus        14 ~I~gIG~~~a~~L~~~-f-~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~~   64 (68)
T d1x2ia1          14 GLPHVSATLARRLLKH-F-GSVERVFTASVAELMKVEGIGEKIAKEIRRVITA   64 (68)
T ss_dssp             TSTTCCHHHHHHHHHH-H-CSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHS
T ss_pred             CCCCcCHHHHHHHHHH-c-CCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            6999999999999998 3 6999999999999999999999999999998864

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=97.64  E-value=2.2e-05  Score=74.26  Aligned_cols=69  Identities=19%  Similarity=0.348  Sum_probs=61.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCC
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIR  529 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp  529 (687)
                      +|+|+|+|+++...|.+.  ..++++|+.++.++|.+++|+|++.|+.|.+.+....+..+-.-|...|+.
T Consensus       109 aLGI~~vG~~~Ak~La~~--f~sl~~l~~as~eeL~~I~GIG~~~A~si~~ff~~~~n~~~i~~L~~~Gv~  177 (181)
T d1dgsa1         109 ALGLPGVGEVLARNLARR--FGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVS  177 (181)
T ss_dssp             HTTCSSCCHHHHHHHHHT--TSBHHHHTTCCHHHHHTSTTCCHHHHHHHHHHHHCHHHHHHHHHHHHTTCC
T ss_pred             HHHhhhhhHHHHHHHHHH--hhhhhhhhhhHHHHHhhcCCcCHHHHHHHHHHHCCHHHHHHHHHHHHcCCC
Confidence            799999999999999986  378999999999999999999999999999999887777777777777764

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.56  E-value=3.4e-05  Score=61.54  Aligned_cols=52  Identities=12%  Similarity=0.278  Sum_probs=47.9

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+|||+|+++...|+++-  .|+.+|...+.++|.+++|+|++.|+.|.+.++.
T Consensus        16 ~~IpgIG~~~a~~L~~~F--~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~~   67 (70)
T d2bgwa1          16 QSFPGIGRRTAERILERF--GSLERFFTASKAEISKVEGIGEKRAEEIKKILMT   67 (70)
T ss_dssp             HTSTTCCHHHHHHHHHHH--SSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHS
T ss_pred             cCCCCcCHHHHHHHHHHh--CCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHhC
Confidence            389999999999999973  6899999999999999999999999999998864

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=2.5e-05  Score=63.74  Aligned_cols=51  Identities=10%  Similarity=0.098  Sum_probs=47.8

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .|+|+|++++..|.+.-  .|+.+|+.++.++|..++|+|++.|++|++.+++
T Consensus        23 ~I~gIg~~~a~~L~~~F--~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~   73 (78)
T d2a1jb1          23 TVKSVNKTDSQTLLTTF--GSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   73 (78)
T ss_dssp             TSTTCCHHHHHHHHHHH--SSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS
T ss_pred             CCCCcCHHHHHHHHHHh--CCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcC
Confidence            79999999999999873  6999999999999999999999999999999864

>d1fvia2 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: ATP-dependent DNA ligase, N-terminal domain
species: Chlorella virus PBCV-1 [TaxId: 10506]

Probab=97.40  E-value=0.00037  Score=65.30  Aligned_cols=140  Identities=12%  Similarity=0.066  Sum_probs=82.1

Q ss_pred             eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~  198 (687)
                      ++++|||+||+-+.   -++   +..||    .|+++|....... ....     .+  ..+-||++.....|+.     
T Consensus        20 p~~~e~K~DG~R~~---~~~---~l~SR----~g~~~~~~~~~~~-~~~~-----~~--~~lDGEl~~~~~~~~~-----   76 (188)
T d1fvia2          20 PCLATPKIAGIRSV---KQT---QMLSR----TFKPIRNSVMNRL-LTEL-----LP--EGSDGEISIEGATFQD-----   76 (188)
T ss_dssp             SEEEEECCCSEEEE---ESS---SEECT----TSCBCSCHHHHHH-HHHH-----SC--TTEEEEEECTTSCHHH-----
T ss_pred             cEEEEeccccEeEE---eEE---EEEec----CCCccCCcChHHH-HhhC-----cc--ccccceeeccCCchhh-----
Confidence            57899999998874   244   46899    5788886643211 1000     11  2268999987777654     


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhc-------CCC----C-CCC
Q psy11422        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLS----I-CGE  266 (687)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------Gf~----~-~~~  266 (687)
                                    .+|.+++..+..  ...+.|++|++......   ....+.+..|+++       ...    . ...
T Consensus        77 --------------~~~~~~~~~~~~--~~~~~~~vfD~~~~~~~---~~~~~r~~~l~~~l~~~~~~~~~~~~~~~~~~  137 (188)
T d1fvia2          77 --------------TTSAVMTGHKMY--NAKFSYYWFDYVTDDPL---KKYIDRVEDMKNYITVHPHILEHAQVKIIPLI  137 (188)
T ss_dssp             --------------HHHHHHSCC------CCEEEEEEEECSSCTT---SCHHHHHHHHHHHHHHCGGGGGCSSEEEEECC
T ss_pred             --------------hHHHHhhccccc--ccccEEEEEEEecCccc---ccHHHHHHHHHHHHHhcccccccCceEEEeee
Confidence                          344555444332  33588999997754321   3455655555432       111    0 012


Q ss_pred             ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       267 ~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                      ...+++.+++.++++...+.    .|  .|+|+|--|..+
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~----G~--EGlmiK~~ds~Y  171 (188)
T d1fvia2         138 PVEINNITELLQYERDVLSK----GF--EGVMIRKPDGKY  171 (188)
T ss_dssp             CEEECSHHHHHHHHHHHHHT----TC--CSEEEECTTCCC
T ss_pred             eEecCCHHHHHHHHHHHHHC----CC--cEEEEECCCCcc
Confidence            34467899999988776422    23  899999655333

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.27  E-value=0.00011  Score=57.03  Aligned_cols=53  Identities=15%  Similarity=0.146  Sum_probs=48.0

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK  515 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk  515 (687)
                      ..|||+|++++..|.+.-  .|+.+|..++.++|.+++| |++.|++|++.++...
T Consensus         6 ~~iPGIg~~~~~~Ll~~f--~Si~~l~~As~~eL~~v~G-~~~~A~~i~~f~~~~~   58 (62)
T d2a1ja1           6 LKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSILG-NAANAKQLYDFIHTSF   58 (62)
T ss_dssp             HTSTTCCHHHHHHHHHHC--SSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHCCC
T ss_pred             hcCCCCCHHHHHHHHHHh--ccHHHHHhCCHHHHHHCcC-cHHHHHHHHHHHhhhh
Confidence            479999999999999754  7999999999999999999 9999999999997643

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.13  E-value=0.00024  Score=55.47  Aligned_cols=50  Identities=18%  Similarity=0.260  Sum_probs=45.9

Q ss_pred             HcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11422        525 ALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       525 aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      .|..+|||+..+++|.+. |.|++.+..++.++|.+++|||+..|++|.+.
T Consensus         5 ~L~~~Gig~~~~~kL~~aG~~Tve~ia~~t~~~L~~i~Gi~e~~a~KIi~~   55 (64)
T d1szpa1           5 KLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNE   55 (64)
T ss_dssp             GGCCTTCCHHHHHHHHTTSCCSHHHHHHSCSHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHhHCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHcCCCCHHHHHHHHHH
Confidence            467899999999999876 99999999999999999999999999999874

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=96.94  E-value=0.00083  Score=53.36  Aligned_cols=52  Identities=15%  Similarity=0.219  Sum_probs=41.5

Q ss_pred             HcCCCCCCHHHHHHHHhhcCChHHHHh----cCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11422        525 ALGIRHVGETTAKELANYFKNLECMFK----ATEEQLLNIPKIGSTTVKAFIKFINQ  577 (687)
Q Consensus       525 aLGIp~vG~~~Ak~La~~f~sld~l~~----As~eeL~~I~GIG~~~A~sI~~ff~~  577 (687)
                      -+.++|||+++|-.++..|+ .+++..    -+...|.++||||+++|+.|.--+++
T Consensus        11 Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~   66 (71)
T d1bvsa2          11 LLSVSGVGPRLAMATLAVHD-AAALRQALADSDVASLTRVPGIGRRGAERIVLELAD   66 (71)
T ss_dssp             HHTSSSCCHHHHHHHHHHSC-HHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHHHSSG
T ss_pred             HhccCCcCHHHHHHHHHhCC-HHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHHHHHH
Confidence            35899999999999888774 565544    47889999999999999998755443

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.88  E-value=0.00096  Score=53.24  Aligned_cols=52  Identities=13%  Similarity=0.181  Sum_probs=41.5

Q ss_pred             HHcCCCCCCHHHHHHHHhhcCChHH----HHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11422        524 YALGIRHVGETTAKELANYFKNLEC----MFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (687)
Q Consensus       524 ~aLGIp~vG~~~Ak~La~~f~sld~----l~~As~eeL~~I~GIG~~~A~sI~~ff~  576 (687)
                      .-+++.|||+++|-.++..+. .++    +.+.+.+.|.+++|||+++|+.|.--++
T Consensus        11 ~Li~V~GIGpk~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          11 LLLSVSGVGPKVALALLSALP-PRLLARALLEGDARLLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HHHSSSCCCHHHHHHHHHHSC-HHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HHhccCCcCHHHHHHHHHHcc-HHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            345899999999998887775 444    4455889999999999999999876554

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.79  E-value=0.00032  Score=55.72  Aligned_cols=53  Identities=21%  Similarity=0.286  Sum_probs=46.5

Q ss_pred             HHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        523 IYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       523 L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.-|.++|||+..+++|.+. |.|++.|..++.++|.+++||+++.|++|.+..
T Consensus        10 i~~L~~~Gig~~~i~kL~~aG~~Tv~~i~~at~~~L~~i~G~~e~~A~KIi~~a   63 (70)
T d1b22a_          10 ISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEA   63 (70)
T ss_dssp             HHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHH
T ss_pred             HHHHhhCCCCHHHHHHHHHcCcchHHHHHhCCHHHHHHcCCCCHHHHHHHHHHH
Confidence            33456689999999998865 899999999999999999999999999998754

>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=96.73  E-value=0.0013  Score=52.01  Aligned_cols=50  Identities=20%  Similarity=0.410  Sum_probs=46.0

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        463 IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      -+|+..+...|-.+| |.++.||..++.++|..++|||+|+.+.|.+.+++
T Consensus        13 L~LS~R~~N~L~~~g-I~tv~dL~~~s~~dLl~i~n~G~ksl~EI~~~L~~   62 (69)
T d1doqa_          13 LGLSTRVLHSLKEEG-IESVRALLALNLKDLKNIPGIGERSLEEIKEALEK   62 (69)
T ss_dssp             HTCCHHHHHHHHHTT-CCSHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHcC-CccHHHHHHCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            378999999999988 58999999999999999999999999999988865

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=96.63  E-value=0.0012  Score=53.29  Aligned_cols=49  Identities=18%  Similarity=0.254  Sum_probs=39.7

Q ss_pred             cCCCCCCHHHHHHHHhhcCChHHH----HhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        526 LGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       526 LGIp~vG~~~Ak~La~~f~sld~l----~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.+.|||+++|-.++..|. .+++    ..-+...|.+++|||+++|+.|.--+
T Consensus        12 i~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          12 IKTNGVGPKLALAILSGMS-AQQFVNAVEREEVGALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             HHSSSCCHHHHHHHHHHSC-HHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HccCCccHHHHHHHHHhCC-HHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHH
Confidence            4789999999998887774 4444    45588999999999999999987544

>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: mRNA capping enzyme alpha subunit
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=96.24  E-value=0.0098  Score=57.40  Aligned_cols=146  Identities=13%  Similarity=0.011  Sum_probs=76.7

Q ss_pred             eEEEEEccceeEEEEEEe---C-CEEEEEEecCCCCccchhhhhhhhhccCCccc-ccCCCCceEEEEEEEEeehhhHHH
Q psy11422        119 EYIAELKFDGIAVNLRYE---Y-GYLKQASTRGDGNIGENITTNIHIIHKIPLVL-NIKYPPELLEVRCEVLIYKKDFIK  193 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~---~-G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l-~~~~~~~~~evRGEi~~~~~~F~~  193 (687)
                      .|+|++|.||+-+.|.+-   + ..-+..++|.+...  .+. + ..+...+... .....-....+.||++..+..+. 
T Consensus        61 ~Y~v~eK~DG~R~lL~i~~~~~~~~~~~li~R~~~~~--~~~-~-~~~~~~~~~~~~~~~~~~~tilDGElv~~~~~~~-  135 (245)
T d1p16a2          61 DYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYY--FIP-N-IHFPLSVNETREKPTYHHGTLLDGELVLENRNVS-  135 (245)
T ss_dssp             CEEEEEEECSEEEEEEEEEETTTEEEEEEEETTCCEE--ECC-S-CCCCSCTTCCSSSCCCCSSEEEEEEEEEECCSSS-
T ss_pred             CEEEEECcCCeEEEEEEEEcCCCceEEEEEeCCCCeE--Ecc-c-cccccccccccccccccCCeeEEEEEEeecccCC-
Confidence            699999999999988662   1 23356789875422  111 1 1111111111 01112234679999997644321 


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCC-----------
Q psy11422        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL-----------  261 (687)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf-----------  261 (687)
                                                       .....|++|++....+... .....+.++.|..+=.           
T Consensus       136 ---------------------------------~~~~~~~ifDil~~~g~~l~~~~l~~R~~~l~~~i~~~~~~~~~~~~  182 (245)
T d1p16a2         136 ---------------------------------EPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNP  182 (245)
T ss_dssp             ---------------------------------CCEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHTHHHHHHHHHHCH
T ss_pred             ---------------------------------cceEEEEEeeehhhCCceeeeccHHHHHHHHHHHHHHhhhhhhhccc
Confidence                                             1235789999876555332 1356666666654310           


Q ss_pred             -----CCCCCceEeC---CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11422        262 -----SICGEYSVLS---GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (687)
Q Consensus       262 -----~~~~~~~~~~---~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (687)
                           ..........   ..+++...    .+....++|.+||+|++-.+..+
T Consensus       183 ~~~~~~~~~~~~~~k~~~~~~~~~~l----~~~~~~~~~~~DGLIf~p~~~pY  231 (245)
T d1p16a2         183 DIVNSPEFPFKVGFKTMLTSYHADDV----LSKMDKLFHASDGLIYTCAETPY  231 (245)
T ss_dssp             HHHSCTTSCCEEEECCCEEGGGTHHH----HTTGGGCSSCEEEEEEEESSSCC
T ss_pred             ccccchhhhhhhhhhhhhhHHHHHHH----HHHhhhcCCCCCeEEEEcCCCCE
Confidence                 0000000111   12223222    23456789999999999766444

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.16  E-value=0.0012  Score=52.71  Aligned_cols=52  Identities=23%  Similarity=0.279  Sum_probs=40.6

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHhc----CChhhhhcccCccHHHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ..++|.|+||+++-.+....   ++.+|..    =+...|.++||+|+|+|++|+-.++
T Consensus        11 ~Li~V~GIGpk~Al~iLs~~---~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          11 LLLSVSGVGPKVALALLSAL---PPRLLARALLEGDARLLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HHHSSSCCCHHHHHHHHHHS---CHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HHhccCCcCHHHHHHHHHHc---cHHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            36789999999999998743   4566665    2456788999999999999997764

>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]

Probab=96.14  E-value=0.0042  Score=49.28  Aligned_cols=53  Identities=15%  Similarity=0.097  Sum_probs=46.8

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ++--+|+..+...|-.+| |.++.||..+++++|..+++||.||.+.|.+.+++
T Consensus         8 I~~L~lS~R~~N~L~~~g-I~tvgdL~~~s~~dLl~~~n~G~KSl~EI~~~L~~   60 (72)
T d1lb2b_           8 VDDLELTVRSANCLKAEA-IHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   60 (72)
T ss_dssp             GGGGCCCHHHHHHHHHTT-CCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHhHcC-CcCHHHHHhCCHHHHHhCCCCcHhHHHHHHHHHHH
Confidence            344578899999999988 68999999999999999999999999999887765

>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Bacillus subtilis [TaxId: 1423]

Probab=96.14  E-value=0.0045  Score=48.41  Aligned_cols=53  Identities=11%  Similarity=0.222  Sum_probs=47.3

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      ++-=+|+..+...|-.+| |.++.||..+++++|..+++||+||.+.|.+.++.
T Consensus         9 I~~L~LS~R~~N~Lk~~~-I~tv~dL~~~s~~dLl~~~nfG~kSl~EIk~~L~~   61 (67)
T d1z3eb1           9 IEELDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   61 (67)
T ss_dssp             GGGSCCBHHHHHHHHHTT-CCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHcC-CcCHHHHHHCCHHHHHhCCCCchhhHHHHHHHHHH
Confidence            344588999999999888 68999999999999999999999999999888765

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=96.13  E-value=0.0014  Score=51.95  Aligned_cols=51  Identities=18%  Similarity=0.371  Sum_probs=40.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhc-CC---hhhhhcccCccHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      .+.|.|+|||++-.+...-   ++.+|.. ..   ...|..+||+|+|+|++|+-.++
T Consensus        11 Li~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk   65 (71)
T d1bvsa2          11 LLSVSGVGPRLAMATLAVH---DAAALRQALADSDVASLTRVPGIGRRGAERIVLELA   65 (71)
T ss_dssp             HHTSSSCCHHHHHHHHHHS---CHHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHHHSS
T ss_pred             HhccCCcCHHHHHHHHHhC---CHHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            6789999999999998643   6677776 33   45688999999999999986653

>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Achaeal helicase C-terminal domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.09  E-value=0.0011  Score=63.09  Aligned_cols=61  Identities=18%  Similarity=0.226  Sum_probs=45.2

Q ss_pred             HHHhhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcc-cCccHHHHHHH
Q psy11422        446 QRKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL-DRVSNKLANNI  507 (687)
Q Consensus       446 q~~~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~gfG~Ksa~~L  507 (687)
                      .+..||.|=|..   ..|.|+|+|++++.+||++| |+|+.||-....+.+..+ +|||+|.+++|
T Consensus       130 ~L~~Rl~~Gv~~ell~L~~i~gvgr~rAr~L~~~G-i~t~~dl~~a~~~~~~~~~~g~g~ki~~~i  194 (198)
T d2p6ra2         130 GLTERIKHGVKEELLELVRIRHIGRVRARKLYNAG-IRNAEDIVRHREKVASLIGRGIAERVVEGI  194 (198)
T ss_dssp             THHHHHHHTCCGGGHHHHTSTTCCHHHHHHHHTTT-CCSHHHHHHTHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHccCCHHHHhHhcCCCCCHHHHHHHHHcC-CCCHHHHHHccHhhHHHHhcchHHHHHHHh
Confidence            356677776655   35679999999999999976 699999998765544444 56666655554

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=96.09  E-value=0.0015  Score=52.84  Aligned_cols=52  Identities=15%  Similarity=0.343  Sum_probs=40.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhc----CChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+.|.|+|||++-.+....   ++.+|..    =+...|..+||+|+|+|++|+-.+..
T Consensus        11 Li~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~   66 (78)
T d1cuka2          11 LIKTNGVGPKLALAILSGM---SAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKD   66 (78)
T ss_dssp             HHHSSSCCHHHHHHHHHHS---CHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHccCCccHHHHHHHHHhC---CHHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHHHH
Confidence            6789999999999988643   5566665    23567889999999999999988764

>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: DNA ligase III alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.97  E-value=0.0029  Score=52.23  Aligned_cols=68  Identities=4%  Similarity=-0.003  Sum_probs=55.9

Q ss_pred             CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc-cccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11422        603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK-NTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  680 (687)
Q Consensus       603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk-~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~  680 (687)
                      -.+.|.|++|+|.|..+  +|++++.+|.++||.+.....+ .++++|+......        +++++..+++.+.++.
T Consensus        13 l~diF~G~~~~i~~~~p--~~~~L~r~i~a~GG~~~~~~~~~~vTHvI~~~~~~~--------~~~iV~p~Wi~dci~~   81 (88)
T d1in1a_          13 LLDIFTGVRLYLPPSTP--DFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKNP--------AAQQVSPEWIWACIRK   81 (88)
T ss_dssp             CCSSSTTCBCCCCTTST--THHHHHHHHHHHTCBCCCTTCCTTCCCEESCCTTCT--------TSCEECHHHHHHHHHH
T ss_pred             hhhHhCCeEEEECCCCC--CHHHHHHHHHHhCCEEeeeccCCCceEEEEcCCCCC--------CcEEEehHHHHHHHHc
Confidence            45689999999999663  7999999999999999877665 5999998754433        4689999999998864

>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.48  E-value=0.027  Score=50.99  Aligned_cols=60  Identities=10%  Similarity=0.061  Sum_probs=49.5

Q ss_pred             cCCHHHHHHHHHhcCCEEccccc------ccccEEEEcCCC-CccHHHHHHcCCeEEeHHHHHHHHh
Q psy11422        620 AFKRNEAIILIENLGGKVVNFIS------KNTNYLVKGQKP-GKKLEKAIKLNIKILDEKNFVKIVK  679 (687)
Q Consensus       620 ~~~R~e~~~~i~~~Gg~v~~sVs------k~t~~LV~G~~~-g~Kl~kA~~lgI~Ii~E~~f~~~l~  679 (687)
                      .+++......|++.||.+...+.      ..+.+||++... ..|+-.|..+|++||+.+++.+.+.
T Consensus        57 p~~~~~~~~~i~~~gg~v~~~~~~~~~~~~~~~~LIa~~~~RT~Kyl~Ala~g~piv~~~Wi~~c~~  123 (153)
T d1kzyc1          57 PFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCLLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCH  123 (153)
T ss_dssp             CCCHHHHHHHHHTTTCEECSSCCTTTTTTTCEEEEEESSCCCSHHHHHHHHHTCCEEETHHHHHHHH
T ss_pred             ccchhhhhhhhhhcCCeEeeccccccccccceEEEecCCCCchHHHHHHHccCCcEEcHHHHHHHHH
Confidence            35778889999999999988764      235578886643 4899999999999999999998875

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=95.34  E-value=0.0031  Score=49.09  Aligned_cols=57  Identities=25%  Similarity=0.439  Sum_probs=42.4

Q ss_pred             ChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcC
Q psy11422        481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI  560 (687)
Q Consensus       481 ~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I  560 (687)
                      ++-||-+++.++|..++|+|++.|.+|++.    +                          .|.        +.+||.++
T Consensus         7 ~~idiNtA~~~eL~~lpgig~~~A~~Iv~~----R--------------------------~f~--------s~edL~~v   48 (65)
T d2duya1           7 TPVSLNEASLEELMALPGIGPVLARRIVEG----R--------------------------PYA--------RVEDLLKV   48 (65)
T ss_dssp             CSEETTTCCHHHHTTSTTCCHHHHHHHHHT----C--------------------------CCS--------SGGGGGGS
T ss_pred             CCcccccCCHHHHHHCCCCCHHHHHHHHHc----C--------------------------CCC--------CHHHHHhC
Confidence            344677788888888888888888888853    1                          144        34778888


Q ss_pred             CCCCHHHHHHHHHHH
Q psy11422        561 PKIGSTTVKAFIKFI  575 (687)
Q Consensus       561 ~GIG~~~A~sI~~ff  575 (687)
                      +|||+.+.+.|..|+
T Consensus        49 ~gi~~~~~~~i~~~l   63 (65)
T d2duya1          49 KGIGPATLERLRPYL   63 (65)
T ss_dssp             TTCCHHHHHHHGGGE
T ss_pred             CCCCHHHHHHHHHHc
Confidence            899888888877665

>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.06  E-value=0.042  Score=46.24  Aligned_cols=74  Identities=9%  Similarity=0.016  Sum_probs=57.7

Q ss_pred             CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccc----------ccccccEEEEcCCC-CccHHHHHHcCCeEEeHHH
Q psy11422        605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNF----------ISKNTNYLVKGQKP-GKKLEKAIKLNIKILDEKN  673 (687)
Q Consensus       605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~s----------Vsk~t~~LV~G~~~-g~Kl~kA~~lgI~Ii~E~~  673 (687)
                      +||.|.+|.+.+....=-++-+..++...||.++..          --.+.|++|+-..- ..=++.|..+|||++|-++
T Consensus         1 npF~~l~vl~vs~~~~~F~e~Ws~IL~~~Ga~vV~~~~~~~~~sd~~~~~~DVvvTD~scp~~vl~~a~~~~ipvVS~EW   80 (106)
T d1kzyc2           1 NPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQEW   80 (106)
T ss_dssp             CTTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTTCCHHHHHHHHHHTCCEECHHH
T ss_pred             CCCcceEEEEEecccccHHHHHHHHHHhCCceEeeccccchhhccCccccccEEEeCCCCCHHHHHHHHHcCCcEeeHHH
Confidence            589999999988764312677888888899977432          12368888887664 4888999999999999999


Q ss_pred             HHHHH
Q psy11422        674 FVKIV  678 (687)
Q Consensus       674 f~~~l  678 (687)
                      .++-|
T Consensus        81 VIQsL   85 (106)
T d1kzyc2          81 VIQCL   85 (106)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99876

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=94.73  E-value=0.013  Score=49.14  Aligned_cols=56  Identities=20%  Similarity=0.321  Sum_probs=43.0

Q ss_pred             HHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCC
Q psy11422        483 VDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPK  562 (687)
Q Consensus       483 ~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~G  562 (687)
                      -||-+++.++|..+||+|++.|++|++      +               |         .|.        +.+||.+++|
T Consensus        19 idlN~As~~eL~~lpGIg~~~A~~Iv~------~---------------g---------pf~--------s~edL~~V~G   60 (98)
T d2axtu1          19 IDLNNTNIAAFIQYRGLYPTLAKLIVK------N---------------A---------PYE--------SVEDVLNIPG   60 (98)
T ss_dssp             EESSSSCGGGGTTSTTCTHHHHHHHHH------S---------------C---------CCS--------SGGGGGGCTT
T ss_pred             eecccccHHHHHHhhhhcHHHHHHHHH------c---------------C---------CcC--------CHHHHhhCCC
Confidence            366667778888888888888888872      1               1         255        3478899999


Q ss_pred             CCHHHHHHHHHHHc
Q psy11422        563 IGSTTVKAFIKFIN  576 (687)
Q Consensus       563 IG~~~A~sI~~ff~  576 (687)
                      ||+++.+.|+.|+.
T Consensus        61 Ig~~~~e~lk~yl~   74 (98)
T d2axtu1          61 LTERQKQILRENLE   74 (98)
T ss_dssp             CCTTHHHHHHHHGG
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999988874

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.02  E-value=0.019  Score=47.40  Aligned_cols=59  Identities=22%  Similarity=0.389  Sum_probs=39.2

Q ss_pred             HHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCC
Q psy11422        484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKI  563 (687)
Q Consensus       484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GI  563 (687)
                      ||-+++.++|..+||+|++.|++|++..++-  -                        .|.        +.++|..++||
T Consensus        28 diN~As~~~L~~lpGig~~~A~~Iv~~R~~~--G------------------------~f~--------s~edL~~v~gi   73 (90)
T d3bzka1          28 DVNTASAALLARISGLNSTLAQNIVAHRDAN--G------------------------AFR--------TRDELKKVSRL   73 (90)
T ss_dssp             ETTTCCHHHHTTSTTCCHHHHHHHHHHHHHH--C------------------------SCS--------SSGGGGGSTTC
T ss_pred             ehhhCCHHHHhHCCCCCHHHHHHHHHHHHHc--C------------------------CCC--------CHHHHhhCCCC
Confidence            5666777888888888888888887754321  1                        233        23566677777


Q ss_pred             CHHHHHHHHHHHc
Q psy11422        564 GSTTVKAFIKFIN  576 (687)
Q Consensus       564 G~~~A~sI~~ff~  576 (687)
                      |+++-+++..|+.
T Consensus        74 ~~k~~e~i~~~l~   86 (90)
T d3bzka1          74 GEKTFEQAAGFLR   86 (90)
T ss_dssp             CHHHHHHHHTTEE
T ss_pred             CHHHHHHhcCCEe
Confidence            7777777766654

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=93.92  E-value=0.0084  Score=50.28  Aligned_cols=49  Identities=8%  Similarity=0.154  Sum_probs=40.3

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11422        457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (687)
Q Consensus       457 r~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~  513 (687)
                      .+.+.++|+||++++++++.|-.+++        ++|.+++|+|+++.++|-..++.
T Consensus        27 ~eL~~lpGIg~~~A~~Iv~~gpf~s~--------edL~~V~GIg~~~~e~lk~yl~~   75 (98)
T d2axtu1          27 AAFIQYRGLYPTLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLEH   75 (98)
T ss_dssp             GGGTTSTTCTHHHHHHHHHSCCCSSG--------GGGGGCTTCCTTHHHHHHHHGGG
T ss_pred             HHHHHhhhhcHHHHHHHHHcCCcCCH--------HHHhhCCCCCHHHHHHHHHHHhc
Confidence            45667999999999999999876665        56677899999999988776654

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.73  E-value=0.024  Score=46.80  Aligned_cols=29  Identities=24%  Similarity=0.127  Sum_probs=19.6

Q ss_pred             HHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        484 DLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      ||-+++.++|..+||+|++.|++|++.-+
T Consensus        26 ~iNtAs~~eL~~lpgig~~~A~~II~yR~   54 (91)
T d2edua1          26 LLNEGSARDLRSLQRIGPKKAQLIVGWRE   54 (91)
T ss_dssp             HHHHSCHHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             ccccCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            55566777777777777777777776543

>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Topoisomerase V repeat domain
domain: Topoisomerase V
species: Methanopyrus kandleri [TaxId: 2320]

Probab=93.37  E-value=0.067  Score=37.62  Aligned_cols=43  Identities=26%  Similarity=0.382  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHhhcCChHHHHhc----CHHHHhcCCCCCHHHHHHH
Q psy11422        529 RHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGSTTVKAF  571 (687)
Q Consensus       529 p~vG~~~Ak~La~~f~sld~l~~A----s~eeL~~I~GIG~~~A~sI  571 (687)
                      .|+|.++|++|+..|++.+.+.+.    ..+.|.++.|+|+.+..++
T Consensus         8 egvgrktaerllrafgnpervkqlarefeieklasvegvgervlrsl   54 (55)
T d2csba3           8 EGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSL   54 (55)
T ss_dssp             TTCCHHHHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHH
T ss_pred             ccccHhHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcchHHHHHHhc
Confidence            466666776666667766665543    4688999999999876654

>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein, BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.24  E-value=0.14  Score=42.17  Aligned_cols=75  Identities=5%  Similarity=-0.013  Sum_probs=51.4

Q ss_pred             cCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccc------ccEEEEcCCCC----ccHHHHHHcCCeEEeHHHHHH
Q psy11422        607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKN------TNYLVKGQKPG----KKLEKAIKLNIKILDEKNFVK  676 (687)
Q Consensus       607 l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~------t~~LV~G~~~g----~Kl~kA~~lgI~Ii~E~~f~~  676 (687)
                      |+|..||+-|-|..|++++++.+++-.||.|+++.+.-      +-++|+-..+-    .=-.-|+...+++++-++.++
T Consensus         2 f~~~~icc~gpFt~mt~d~Le~mv~lCGAsVvk~~~~l~~~~~~~~viVvqpda~t~~~~~~~i~~~~~~~vVtreWvLD   81 (97)
T d1l0ba2           2 FEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCKGRLVMWDWVLD   81 (97)
T ss_dssp             CTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC-------------------CEEETHHHHH
T ss_pred             CCCceEEEEccccCCCHHHHHHHHHHcCceeecChhhcCCCCCCeeEEEEcCCccccccccHHHHHhccccEEehhHhhh
Confidence            67899999999999999999999999999999987542      33566654321    111334556899999999999


Q ss_pred             HHhcc
Q psy11422        677 IVKGF  681 (687)
Q Consensus       677 ~l~~~  681 (687)
                      -+..+
T Consensus        82 SIA~Y   86 (97)
T d1l0ba2          82 SISVY   86 (97)
T ss_dssp             HHHTT
T ss_pred             hhhhe
Confidence            88765

>d1xdna_ d.142.2.4 (A:) RNA editing ligase MP52 {Trypanosoma brucei [TaxId: 5691]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: RNA ligase
domain: RNA editing ligase MP52
species: Trypanosoma brucei [TaxId: 5691]

Probab=92.72  E-value=0.14  Score=49.70  Aligned_cols=178  Identities=17%  Similarity=0.144  Sum_probs=100.1

Q ss_pred             cccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEe---CCEEEEEEecCCCCccch----------
Q psy11422         88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGEN----------  154 (687)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeD----------  154 (687)
                      +..||+|.+ +.-    ++++.+. +. ..-.|+++.||||.-.++++.   +|..++-+.| +|...++          
T Consensus         6 ~Y~~ien~~-~~~----i~~~k~~-gl-~~~ewVa~EKIHGaNFsii~~~~~dg~~V~~aKR-~~~l~~~e~Ffgy~~i~   77 (265)
T d1xdna_           6 PYIEIDLPS-ESR----IQSLHKS-GL-AAQEWVACEKVHGTNFGIYLINQGDHEVVRFAKR-SGIMDPNENFFGYHILI   77 (265)
T ss_dssp             CCCCCCCCC-HHH----HHHHHHT-TG-GGSCEEEEEECCSEEEEEEEEEETTEEEEEEEET-TEECCTTCCCTTGGGGH
T ss_pred             cchhccCch-HHH----HHHHHhc-Cc-ccceEEEEEeecCccEEEEEeecCCCcEEEEeec-ccccCCcccccchhhHH
Confidence            456888865 222    4444331 11 134799999999999999872   6788888888 4544332          


Q ss_pred             --hhhhhhhhccCCc---ccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccc
Q psy11422        155 --ITTNIHIIHKIPL---VLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKI  229 (687)
Q Consensus       155 --vT~n~~~i~~iP~---~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~  229 (687)
                        .+..++.+..+=.   .++   -...+.|-||+|=-.=.+-..+... ....-.--+|||. ||---|++|-+--...
T Consensus        78 ~~l~~~~~~l~~~l~~~~~v~---~~~~~vvyGELfGg~Y~hp~v~~~~-~~~~~~~g~~~~~-~~~~iQk~~~v~Y~p~  152 (265)
T d1xdna_          78 DEFTAQIRILNDLLKQKYGLS---RVGRLVLNGELFGAKYKHPLVPKSE-KWCTLPNGKKFPI-AGVQIQREPFPQYSPE  152 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCS---CCSEEEEEEEEEEEECCCTTSCCCC-CEEECTTSCEEEG-GGCCSCCCSSCCCEEE
T ss_pred             HHHHHHHHHHHHHHHhhhccC---CccEEEEEEEecccccCCCcccccc-cccccccCccccc-cceeeccccccccCCC
Confidence              3444444332110   011   1346999999986211111000000 0000112347774 4444467754434446


Q ss_pred             cEEEEEecccccCCC----CCCCHHHHHHHHHh-cCCCCCCCceEeCCHHHHHHH
Q psy11422        230 LHFFAHGVGELRGMN----MPSSHSELLNWYQK-IGLSICGEYSVLSGVNKLIEF  279 (687)
Q Consensus       230 l~f~~y~~~~~~~~~----~~~~~~e~l~~L~~-~Gf~~~~~~~~~~~~~ei~~~  279 (687)
                      |+|+||++....+..    ...++-+.++...+ .||+..+. ....+++++.+|
T Consensus       153 l~FyAFDI~~~~~~~~~~~~fl~~d~~~e~~~~~~gl~yap~-L~rGt~~e~~~~  206 (265)
T d1xdna_         153 LHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARA-LVRGTLDECLAF  206 (265)
T ss_dssp             EEEEEEEEEEESSCCGGGEEECCHHHHHHHHHTSTTCEECCC-SEEESHHHHHTC
T ss_pred             ccEEEEEEEeccCCCcceeeeccHHHHHHHHhhccCccccch-hhcccHHHHhcC
Confidence            999999996543311    01456677777776 49998874 345678887765

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.04  Score=41.39  Aligned_cols=26  Identities=23%  Similarity=0.279  Sum_probs=24.3

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYK  487 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (687)
                      +|-|+||+++++|+++| ++|++||-.
T Consensus        12 ~I~GvGp~~A~~l~~~G-i~ti~dLr~   37 (57)
T d2bcqa2          12 NIWGAGTKTAQMWYQQG-FRSLEDIRS   37 (57)
T ss_dssp             TSTTCCHHHHHHHHHTT-CCSHHHHHH
T ss_pred             ccccccHHHHHHHHHhC-CCCHHHHHh
Confidence            79999999999999998 699999975

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.70  E-value=0.061  Score=40.36  Aligned_cols=27  Identities=30%  Similarity=0.464  Sum_probs=24.2

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (687)
                      ++|-|+||+++++|++.| ++|++||-.
T Consensus        10 ~~I~GvGp~~A~~l~~~G-i~ti~dLr~   36 (57)
T d2fmpa2          10 TRVSGIGPSAARKFVDEG-IKTLEDLRK   36 (57)
T ss_dssp             TTSTTCCHHHHHHHHHTT-CCSHHHHHT
T ss_pred             hccccccHHHHHHHHHhC-CCCHHHHHh
Confidence            479999999999999997 599999964

>d1ckma2 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain
species: Chlorella virus PBCV-1 [TaxId: 10506]

Probab=91.65  E-value=0.29  Score=46.29  Aligned_cols=146  Identities=16%  Similarity=0.146  Sum_probs=78.4

Q ss_pred             eEEEEEccceeEEEEEEe--CC-EEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHH
Q psy11422        119 EYIAELKFDGIAVNLRYE--YG-YLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN  195 (687)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~--~G-~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n  195 (687)
                      .|+|++|.||+-..|...  +| .-+..++|-.-    ..+...   ..+|..+     .....+-||++.....     
T Consensus        66 ~Y~vseK~DG~R~ll~~~~~~~~~~~~li~r~~~----~~~~~~---~~~~~~~-----~~~ti~DGEli~~~~~-----  128 (228)
T d1ckma2          66 KYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMT----VYLLPF---KNIPRVL-----FQGSIFDGELCVDIVE-----  128 (228)
T ss_dssp             CEEEEEEECSEEEEEEEEEETTEEEEEEECTTCC----EEECCC---SCCCTTG-----GGCEEEEEEEEEETTT-----
T ss_pred             CeEEEEeecCEEEEEEEEecCCceEEEEEeCCCc----eEEccc---ccCchhh-----cCCceEeEEEEeeccc-----
Confidence            699999999999877432  33 23556777422    111111   1233332     2246788998864311     


Q ss_pred             HHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcC--CCCC--C-----
Q psy11422        196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIG--LSIC--G-----  265 (687)
Q Consensus       196 ~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~G--f~~~--~-----  265 (687)
                                                      ....|.+|++....+... .....++++.|+++=  +...  .     
T Consensus       129 --------------------------------~~~~f~ifD~l~~~g~~~~~~pf~~Rl~~L~~~l~~~~~~~~~~~~i~  176 (228)
T d1ckma2         129 --------------------------------KKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILR  176 (228)
T ss_dssp             --------------------------------TEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHHTTCCCCTTSSSEEE
T ss_pred             --------------------------------ccceEEEeeEEEEcCcchhcCChHHHHHHHHHHHhhhhccccCceeEE
Confidence                                            123477777655444321 245677777776531  1110  0     


Q ss_pred             --CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11422        266 --EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (687)
Q Consensus       266 --~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (687)
                        ........+.+.+.++     ...++|.+||+|++=.+..+      +..  ||.-.||+-
T Consensus       177 ~k~~~~~~~~~~l~~~~~-----~~~~~y~~DGLIf~p~~~pY------~~G--r~~~~~KWK  226 (228)
T d1ckma2         177 YKEWIPLEHPTIIKDHLK-----KANAIYHTDGLIIMSVDEPV------IYG--RNFNLFKLK  226 (228)
T ss_dssp             ECCCEETTCHHHHHHHHH-----HHHHHSCEEEEEEEESSSCC------CCE--EEEEEEEEC
T ss_pred             eeeeeehhhHHHHHHHHh-----hhccCCCCceEEEEeCCCCE------eCC--CCCCeEEeC
Confidence              1112335555555443     23468999999999655333      222  676677763

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.00  E-value=0.055  Score=41.07  Aligned_cols=27  Identities=22%  Similarity=0.315  Sum_probs=24.7

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11422        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (687)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (687)
                      ++|-|+||+++++|++.| ++|++||..
T Consensus        11 ~~I~GvGp~~A~~l~~~G-i~ti~dL~~   37 (60)
T d1jmsa3          11 TSVFGVGLKTAEKWFRMG-FRTLSKIQS   37 (60)
T ss_dssp             HTSTTCCHHHHHHHHHTT-CCSHHHHHH
T ss_pred             hccccccHHHHHHHHHhC-CCCHHHHHh
Confidence            479999999999999998 699999984

>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Thymine-DNA glycosylase
species: Archaeon Methanobacterium thermoformicicum [TaxId: 145262]

Probab=90.70  E-value=0.27  Score=46.55  Aligned_cols=76  Identities=17%  Similarity=0.259  Sum_probs=45.4

Q ss_pred             HHHHHHCCCCCChHHHhcCChhhhhc-cc--CccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCCh
Q psy11422        470 IEKLVNANIVVTAVDLYKINFKNLLR-LD--RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL  546 (687)
Q Consensus       470 i~~L~~~g~I~~i~DL~~L~~~~L~~-l~--gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sl  546 (687)
                      ..+|++.-  .++++|..+..++|.+ +.  ||-...|.+|.+.                         |+.|.+.|++ 
T Consensus        55 ~~~l~~~~--pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~-------------------------a~~i~~~~~g-  106 (217)
T d1keaa_          55 YDKFFVKY--KCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKEL-------------------------ARVVINDYGG-  106 (217)
T ss_dssp             HHHHHHHC--CSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHH-------------------------HHHHHHHHTT-
T ss_pred             HHHHHHhc--ccHHHHHHhhHHHHHHHHHHHHhhhHHHHHHHHH-------------------------HHHHHhhccC-
Confidence            34444432  4777777776655542 23  3335566655543                         3334444432 


Q ss_pred             HHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        547 ECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       547 d~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                        ..-.+.++|.++||||+++|..|..|-
T Consensus       107 --~~p~~~~~L~~LpGVG~kTA~~il~~~  133 (217)
T d1keaa_         107 --RVPRNRKAILDLPGVGKYTCAAVMCLA  133 (217)
T ss_dssp             --SCCSCHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             --CcchhhHHHHHHHhhhhhhhHHHHHHh
Confidence              122357899999999999999998874

>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

Probab=90.68  E-value=0.42  Score=45.13  Aligned_cols=70  Identities=20%  Similarity=0.287  Sum_probs=44.0

Q ss_pred             ChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH-hcCHHH
Q psy11422        481 TAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF-KATEEQ  556 (687)
Q Consensus       481 ~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~-~As~ee  556 (687)
                      |+++|..++.++|.++   -||...+|..|.+-                         |+.+.+.|..+..+. ..+.++
T Consensus        67 t~~~la~a~~eel~~~ir~~G~~~~KA~~i~~~-------------------------a~~i~~~~~~~~~~~~~~~~~~  121 (217)
T d1pu6a_          67 NLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDL-------------------------SGNILKDFQSFENFKQEVTREW  121 (217)
T ss_dssp             HHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHH-------------------------HHHHHHHHSSHHHHHHHCCHHH
T ss_pred             CHHHHHCCCHHHHHHHHHHCCCcHHHHHHHHHH-------------------------HHHHHHhhhhcccCCcHHHHHH
Confidence            6777888887776542   36766777766542                         223333444443332 235678


Q ss_pred             HhcCCCCCHHHHHHHHHHH
Q psy11422        557 LLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       557 L~~I~GIG~~~A~sI~~ff  575 (687)
                      |.+++|||+++|..+..|.
T Consensus       122 L~~lpGIG~kTA~~vl~~~  140 (217)
T d1pu6a_         122 LLDQKGIGKESADAILCYA  140 (217)
T ss_dssp             HHTSTTCCHHHHHHHHHHT
T ss_pred             HHHHhhhhhHHHHHHHHHH
Confidence            8888888888888877654

>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Achaeal helicase C-terminal domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.98  E-value=0.09  Score=49.38  Aligned_cols=51  Identities=25%  Similarity=0.360  Sum_probs=38.4

Q ss_pred             HHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcC-CCCCHHHHHHHH
Q psy11422        522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNI-PKIGSTTVKAFI  572 (687)
Q Consensus       522 ~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I-~GIG~~~A~sI~  572 (687)
                      +|.-+.|||||.++|+.|.+. |.|++.|..++.+.+..+ +|+|+++.++|.
T Consensus       143 ll~L~~i~gvgr~rAr~L~~~Gi~t~~dl~~a~~~~~~~~~~g~g~ki~~~i~  195 (198)
T d2p6ra2         143 LLELVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVASLIGRGIAERVVEGIS  195 (198)
T ss_dssp             GHHHHTSTTCCHHHHHHHHTTTCCSHHHHHHTHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHhHhcCCCCCHHHHHHHHHcCCCCHHHHHHccHhhHHHHhcchHHHHHHHhc
Confidence            444569999999999999864 789999998876555544 677777766653

>d1u9la_ a.60.4.2 (A:) Transcription elongation protein NusA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: NusA extra C-terminal domains
domain: Transcription elongation protein NusA
species: Escherichia coli [TaxId: 562]

Probab=89.90  E-value=0.47  Score=36.54  Aligned_cols=53  Identities=28%  Similarity=0.300  Sum_probs=44.9

Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11422        519 FSRFIYALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       519 l~r~L~aLGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      +..|+.+|++.   +..|..|.. .|.|++.+..++.++|.+|.|+-+.+|+.+++-
T Consensus         5 ~~~F~~~LdVD---e~lA~lLv~EGF~siEeIAyv~~~eL~~IegfDee~a~eL~~R   58 (68)
T d1u9la_           5 IDTFTKYLDID---EDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRER   58 (68)
T ss_dssp             HHHHHHHHTCC---HHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCc---HHHHHHHHHhccCcHHHHhcCCHHHHHHhcccCHHHHHHHHHH
Confidence            35678888876   567887764 599999999999999999999999999988763

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.34  E-value=0.21  Score=40.92  Aligned_cols=45  Identities=18%  Similarity=0.271  Sum_probs=36.2

Q ss_pred             cccccCCCCHHHHHHHHH----CCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11422        458 KAMNIIGLGKKMIEKLVN----ANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (687)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~----~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~  510 (687)
                      +.+.++|+|++++.++++    .|..+++        ++|..++|||++..++|.+.
T Consensus        34 eL~~lpgig~~~A~~II~yR~~~G~f~sl--------edL~~V~Gi~~k~~eki~k~   82 (91)
T d2edua1          34 DLRSLQRIGPKKAQLIVGWRELHGPFSQV--------EDLERVEGITGKQMESFLKA   82 (91)
T ss_dssp             HHHHSTTCCHHHHHHHHHHHHHHCCCSSG--------GGGGGSTTCCHHHHHHHHHH
T ss_pred             HHhhCCCCCHHHHHHHHHHHHHcCCCCCH--------HHHhcCCCCCHHHHHHHHHc
Confidence            455689999999999996    4666665        55677899999999999875

>d1u9la_ a.60.4.2 (A:) Transcription elongation protein NusA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: NusA extra C-terminal domains
domain: Transcription elongation protein NusA
species: Escherichia coli [TaxId: 562]

Probab=88.54  E-value=0.41  Score=36.90  Aligned_cols=56  Identities=16%  Similarity=0.275  Sum_probs=46.9

Q ss_pred             hhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        450 GLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       450 ~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      .+..|+.  .|||+   +...+.|+++|+ +|+.+|-....++|..++||-+..|+.|.+.-
T Consensus         4 ~~~~F~~--~LdVD---e~lA~lLv~EGF-~siEeIAyv~~~eL~~IegfDee~a~eL~~RA   59 (68)
T d1u9la_           4 AIDTFTK--YLDID---EDFATVLVEEGF-STLEELAYVPMKELLEIEGLDEPTVEALRERA   59 (68)
T ss_dssp             HHHHHHH--HHTCC---HHHHHHHHHTTC-CCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHH--HcCCc---HHHHHHHHHhcc-CcHHHHhcCCHHHHHHhcccCHHHHHHHHHHH
Confidence            3455663  56655   889999999998 89999999999999999999999998887653

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.93  E-value=0.14  Score=42.93  Aligned_cols=25  Identities=20%  Similarity=0.348  Sum_probs=23.2

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFK  551 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~  551 (687)
                      ||||||+++|-.|.+.|++++++..
T Consensus        20 GV~GIG~ktA~kli~~~gsle~i~~   44 (105)
T d1rxwa1          20 GVKGVGVKKALNYIKTYGDIFRALK   44 (105)
T ss_dssp             CCTTCCHHHHHHHHHHHSSHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHhCCHHHHHH
Confidence            8999999999999999999998864

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=87.85  E-value=0.15  Score=42.92  Aligned_cols=26  Identities=15%  Similarity=0.341  Sum_probs=23.3

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKA  552 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~A  552 (687)
                      |+||||+++|..|.+.|+|++.+...
T Consensus        23 GV~GiG~KtA~kli~~~gsle~i~~~   48 (105)
T d1xo1a1          23 GVEGIGAKRGYNIIREFGNVLDIIDQ   48 (105)
T ss_dssp             CCTTCCHHHHHHHHHHHCSHHHHHHH
T ss_pred             CcCCcCHHHHHHHHHHcchhHHHHHh
Confidence            88999999999999999999888753

>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=87.03  E-value=0.77  Score=43.01  Aligned_cols=78  Identities=17%  Similarity=0.261  Sum_probs=41.6

Q ss_pred             HHHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhc
Q psy11422        467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (687)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f  543 (687)
                      .+...+|++..  .++.++..+..+++..+   -||....|.+|+...+                         .|.+.|
T Consensus        49 ~~~~~~l~~~~--pt~~~la~~~~~e~~~~i~~~g~y~~ka~~l~~~a~-------------------------~i~~~~  101 (214)
T d1orna_          49 NKVTKRLFEKY--RTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCA-------------------------MLIDKY  101 (214)
T ss_dssp             HHHHHHHHHHC--CSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHH-------------------------HHHHHS
T ss_pred             HHHHhhhhccc--CchhhhhhccHHHhhhhhhhhhhhhHHHHHHHHHhh-------------------------hHHHHh
Confidence            34445555543  47778877765443222   3555556666554432                         222333


Q ss_pred             CChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11422        544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (687)
Q Consensus       544 ~sld~l~~As~eeL~~I~GIG~~~A~sI~~f  574 (687)
                      +.   -.-.+.++|.++||||+++|..|..|
T Consensus       102 ~g---~vp~~~~~L~~LpGVG~kTA~~il~~  129 (214)
T d1orna_         102 NG---EVPRDRDELMKLPGVGRKTANVVVSV  129 (214)
T ss_dssp             TT---SCCSCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             CC---CCCCCHHHHHhCcCcccchHHHHHHH
Confidence            21   01124566777777777777777665

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=85.89  E-value=0.17  Score=42.54  Aligned_cols=25  Identities=24%  Similarity=0.258  Sum_probs=22.9

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFK  551 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~  551 (687)
                      ||||||+++|-.|.+.|++++.+..
T Consensus        21 GV~GIGpktA~klIk~~g~ie~l~~   45 (108)
T d1a77a1          21 GVKGIGFKRAYELVRSGVAKDVLKK   45 (108)
T ss_dssp             CSTTCCHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHcCCHHHHHH
Confidence            8999999999999999999988764

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=85.80  E-value=0.47  Score=36.13  Aligned_cols=43  Identities=14%  Similarity=0.320  Sum_probs=34.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11422        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL  509 (687)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~  509 (687)
                      .+.++|+|++++.++++..-..        +.++|..++|+|++..++|..
T Consensus        19 L~~lpgig~~~A~~Iv~~R~f~--------s~edL~~v~gi~~~~~~~i~~   61 (65)
T d2duya1          19 LMALPGIGPVLARRIVEGRPYA--------RVEDLLKVKGIGPATLERLRP   61 (65)
T ss_dssp             HTTSTTCCHHHHHHHHHTCCCS--------SGGGGGGSTTCCHHHHHHHGG
T ss_pred             HHHCCCCCHHHHHHHHHcCCCC--------CHHHHHhCCCCCHHHHHHHHH
Confidence            4568999999999999976322        357888899999999888754

>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=85.27  E-value=0.56  Score=43.97  Aligned_cols=78  Identities=17%  Similarity=0.210  Sum_probs=41.2

Q ss_pred             HHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC
Q psy11422        468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK  544 (687)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~  544 (687)
                      +..++|++..  .++.++..++.++|.++   -||-...|.+|.+..                         +.|.+.|+
T Consensus        49 ~~~~~l~~~~--~t~~~la~a~~~~l~~~i~~~G~y~~Ka~~l~~~a-------------------------~~i~~~~~  101 (211)
T d2abka_          49 KATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTC-------------------------RILLEQHN  101 (211)
T ss_dssp             HHHHHHTTTC--CSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHH-------------------------HHHHHHTT
T ss_pred             HHHHHHHHhc--cChHHHHhhhHhHhHHHHHHhhhhhhHHHHHHHHH-------------------------HHHHHHhc
Confidence            3445555443  47777777665544322   244455665555433                         22333333


Q ss_pred             ChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        545 NLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       545 sld~l~~As~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      .   ..-.+.++|.++||||+++|..|..|-
T Consensus       102 g---~~p~~~~~L~~LpGVG~~TA~~Il~~a  129 (211)
T d2abka_         102 G---EVPEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             T---SCCSCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             C---chhHHHHHHHHHHhhchHHHHHHHHHH
Confidence            2   112245667777777777777776653

>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase iota
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.97  E-value=0.34  Score=47.18  Aligned_cols=48  Identities=23%  Similarity=0.187  Sum_probs=41.1

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11422        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (687)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I  511 (687)
                      +|+|+|+++.++|-..| |.|+.||..+..+.|.+.  ||.+.+..|++..
T Consensus       212 ~l~GiG~~~~~~L~~~G-I~ti~dl~~~~~~~L~~~--fG~~~g~~l~~~a  259 (273)
T d1zeta2         212 EIPGIGYKTAKCLEALG-INSVRDLQTFSPKILEKE--LGISVAQRIQKLS  259 (273)
T ss_dssp             GSTTCCHHHHHHHHTTT-CCSHHHHHHSCHHHHHHH--HHHHHHHHHHHHH
T ss_pred             HhcCCCHHHHHHHHHhC-CCcHHHHhcCCHHHHHHH--HCHHHHHHHHHHH
Confidence            79999999999997766 799999999999999886  8988887776543

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.92  E-value=0.27  Score=43.10  Aligned_cols=26  Identities=27%  Similarity=0.438  Sum_probs=24.2

Q ss_pred             CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11422        527 GIRHVGETTAKELANYFKNLECMFKA  552 (687)
Q Consensus       527 GIp~vG~~~Ak~La~~f~sld~l~~A  552 (687)
                      ||||||+++|..|...|++++.+...
T Consensus        20 gv~gIG~ktA~kli~~~~~le~i~~~   45 (140)
T d1ul1x1          20 SIRGIGPKRAVDLIQKHKSIEEIVRR   45 (140)
T ss_dssp             CCTTCCHHHHHHHHHHSSSHHHHHTT
T ss_pred             CCCCccHHHHHHHHHHhCCHHHHHHH
Confidence            89999999999999999999998765

>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 8-oxoguanine glycosylase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.80  E-value=1.5  Score=40.10  Aligned_cols=70  Identities=11%  Similarity=0.138  Sum_probs=43.3

Q ss_pred             CChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCC---hHHHHhcC---
Q psy11422        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKAT---  553 (687)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~s---ld~l~~As---  553 (687)
                      .++.+|-.++.+++...-|++.| |..|....                         +.+.+.+..   ++.+...+   
T Consensus        47 P~~~~la~~~~e~~l~~~~~~~r-a~~i~~~a-------------------------~~i~~~~~~~~~l~~l~~~~~~~  100 (190)
T d2noha1          47 PSLQALAGPEVEAHLRKLGLGYR-ARYVSASA-------------------------RAILEEQGGLAWLQQLRESSYEE  100 (190)
T ss_dssp             CCHHHHHSTTHHHHHHHTTCTTH-HHHHHHHH-------------------------HHHHHTSCSHHHHHHTTTSCHHH
T ss_pred             CCHHHHHHcchHHHHHhcchHHH-HHHHHHHH-------------------------HHHHHhcccccCHHHhcCCCcHH
Confidence            47777877777777666677754 55555432                         222222222   22333333   


Q ss_pred             -HHHHhcCCCCCHHHHHHHHHHH
Q psy11422        554 -EEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       554 -~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                       .++|.+++|||+.+|+.+.-|-
T Consensus       101 ~~~~L~~l~GIG~wTA~~il~~~  123 (190)
T d2noha1         101 AHKALCILPGVGTQVADCICLMA  123 (190)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCchHHHHHHHHHHH
Confidence             3578999999999999887764

>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Escherichia coli [TaxId: 562]

Probab=81.84  E-value=1.7  Score=40.83  Aligned_cols=23  Identities=26%  Similarity=0.472  Sum_probs=17.8

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHH
Q psy11422        553 TEEQLLNIPKIGSTTVKAFIKFI  575 (687)
Q Consensus       553 s~eeL~~I~GIG~~~A~sI~~ff  575 (687)
                      +.++|.+++|||+++|..|..|-
T Consensus       107 ~~~~L~~LpGVG~kTA~~il~~a  129 (224)
T d1kg2a_         107 TFEEVAALPGVGRSTAGAILSLS  129 (224)
T ss_dssp             SHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhhhHHHHHHh
Confidence            56778888888888888887653

>d1s68a_ d.142.2.4 (A:) RNA ligase 2, N-terminal domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: RNA ligase
domain: RNA ligase 2, N-terminal domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=81.70  E-value=1.1  Score=42.02  Aligned_cols=52  Identities=21%  Similarity=0.309  Sum_probs=36.9

Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecC
Q psy11422         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRG  147 (687)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRG  147 (687)
                      ..|++|.+...    +++++... + .....|++|.|+||-.+++.+.+|++ ++.||+
T Consensus         5 y~~~~~~~~~~----~~~~~~~~-~-~~~~~~vveEKlDG~n~~l~~~~~~~-~~~SR~   56 (233)
T d1s68a_           5 YSSLENHYNSK----FIEKLYSL-G-LTGGEWVAREKIHGTNFSLIIERDKV-TCAKRT   56 (233)
T ss_dssp             CCCCEETTCHH----HHHHHHHH-T-CSCSCEEEEECCCSEEEEEEEESSCE-EEEETT
T ss_pred             cccccchHHHH----HHHhhhhh-c-cCCCeEEEEEeECCccEEEEEECCEE-EEEecC
Confidence            34677777653    34444321 1 12458999999999999999988875 789996

>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DinB homolog (DBH)
species: Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]

Probab=81.24  E-value=0.5  Score=45.08  Aligned_cols=61  Identities=20%  Similarity=0.299  Sum_probs=46.0

Q ss_pred             HHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11422        444 IAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (687)
Q Consensus       444 ~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~  510 (687)
                      |....+.|.++-   .=+++|+|+++.++|-..| |.|+.||..+..+.|...  ||.+.+..|++.
T Consensus       168 ~~~~~~~L~~lp---l~~l~GiG~~~~~~L~~~G-i~t~gdl~~~~~~~L~~~--fG~~~g~~l~~~  228 (240)
T d1jx4a2         168 DEEVKRLIRELD---IADVPGIGNITAEKLKKLG-INKLVDTLSIEFDKLKGM--IGEAKAKYLISL  228 (240)
T ss_dssp             HHHHHHHHHHSB---GGGSTTCCHHHHHHHHTTT-CCBGGGGGSSCHHHHHHH--HCHHHHHHHHHH
T ss_pred             cccccccccccc---hhhcCCCCHHHHHHHHHhC-CCcHHHHHcCCHHHHHHH--HCHHHHHHHHHH
Confidence            333444444432   4479999999999997766 689999999999999875  898777776654

>d2q0zx1 a.289.1.1 (X:33-208) Protein pro2281 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Sec63 N-terminal domain
domain: Protein pro2281
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.90  E-value=1.1  Score=40.36  Aligned_cols=56  Identities=7%  Similarity=0.092  Sum_probs=47.6

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11422        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (687)
Q Consensus       456 sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie  512 (687)
                      +-..+.+|++|+..+.+|.+.| +.++.||.+++.+++..+-|++++....+.+.+.
T Consensus       118 ~~~L~Qlp~~~~~~~~kl~~~~-i~sl~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~  173 (176)
T d2q0zx1         118 DSYLKQLPHFTSEHIKRCTDKG-VESVFDIMEMEDEERNALLQLTDSQIADVARFCN  173 (176)
T ss_dssp             SCGGGGSTTCCHHHHHHHHHTT-CCSHHHHHHSCHHHHHHHHCCCHHHHHHHHHHHT
T ss_pred             CCCccCCCcCCHHHHHHHHHCC-CCCHHHHHhCCHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3357899999999999998887 5899999999998888888899988887777653

>d1pvma3 g.41.13.1 (A:143-178) Hypothetical protein Ta0289 C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Hypothetical protein Ta0289 C-terminal domain
family: Hypothetical protein Ta0289 C-terminal domain
domain: Hypothetical protein Ta0289 C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=80.39  E-value=0.74  Score=29.65  Aligned_cols=26  Identities=27%  Similarity=0.729  Sum_probs=17.1

Q ss_pred             CCCCCCCcce-e--e-cCc-eeEEecCCCCCCH
Q psy11422        417 ICPICNSKII-Y--I-ESN-LIARCSGSWIECI  444 (687)
Q Consensus       417 ~CP~C~~~l~-~--~-~~~-~~~~C~n~~~~C~  444 (687)
                      -||.||-.+. -  . .|+ ..+||+|+ . |.
T Consensus         3 lcpkcgvgvl~pvy~~kgeikvfrcsnp-a-cd   33 (36)
T d1pvma3           3 LCPKCGVGVLEPVYNEKGEIKVFRCSNP-A-CD   33 (36)
T ss_dssp             BCTTTSSSBEEEEECTTSCEEEEEESCT-T-CC
T ss_pred             cCCccCceEEEEeecCCCcEEEEEcCCC-c-cc
Confidence            5999997532 1  1 222 66899996 5 84