Psyllid ID: psy11423

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Local Sequence Feature Prediction

Residue Number Marker
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Protein Sequence
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccEEEEEEccccccEEEEEEcccEEEEEcccccccccccccccccccccccccccccccccEEEEccEEEccHHHHHHHHHHHHHccccccccccccccccccccccHHHHcccccEEEEEccccccccccccHHHHHHHHHHcccccccccEEEccHHHHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHcccccccHHHHcccccccccEEEEEEEEEEccccccccccEEEEEEEEccEEEcccccccHHHHHHcccccccEEEEEEcccccccccEEcccccccccccccccccccccccccccccccEEEEccccccccHHHHHcHHHHcccccccccccccHHHHHHHHHccccccccccccccHHHHcccccccHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHcccHHHHHcccHHHHHcccccHHHHHHHHHHHHccHHHHHHHHHHHHcccccccccccccccccccccccccEEEEcccccccHHHHHHccccEEcHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHHHHHHHHHHccccccccccccccccccHHHccccEcccccccccccccHHHHHHHHHHHHHHccccccEEEEEEEcccEEEEEEEEEccEEEEEEEcccccccccHHHccccHcccccEccccccccEEEEEcEEEccHHHHHHHHHHHHHcccccccccHHHHHccHHcccccEEcccccEEEEEEEEEcccccccccHHHHHHHHHHccccccHHHHHcccHHHHHHHHHHHHHHHccccccccEEEEEEccHHHHHHHccccccccEEEEEccccHHHHEEEEcEEEEEcccccEcccEEEcEEEEEEEEEcccccccHHHHHHcccEEccEEEEEEcccccHHHHHHHHHHcccccccEEcccccccccccEEEccccEEEEEcccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHcHHHHHHHHHHHHHHHcccHHHHHHHHccHHHHHHHHHHHHHHHccHHHHHHccHHHHHHccccHHHHHHHHHHHHHcHHHHHHHHHHHHcccccHHHHHHcccEEEEEccccccEEEEcccccHHHHHHHHcccEEEcHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
msfhakkkinfsklSFRVTELKKELHRHNIayylydnpiisdnkYDQLLFELKKIEEKYpelltkdsltqhvglvggenskyVHHTFKmmsldngfsdedVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGylkqastrgdgnigenittnihiihkiplvlnikyppeLLEVRCEVLIYKKDFIKLNKYRYhlglkkftnprnaAAGILRqlnpkinknKILHFFAHGvgelrgmnmpsshSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKInikrfnlpyeidgVVYKINCLStqkklgftsraPRFALAYKFLSKEALTKIKAINIQigrtgiitpvallkpvlidgititratlhneseiyrkniqigDTVVVHrsgnvipkITSSilslrpndskifkipnicpicnskiIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQllnipkigSTTVKAFIKFINQPLHRLLISQLRDVGIYwlnnpntkggkvVNFISKNTNYlvkgqkpgkKLEKAIKLNIKILDEKNFVKIVKgfstetki
Flexible Loop (DISEMBL)
msfhakkkinfsklsfRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLkqastrgdgniGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLglkkftnprnAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLStqkklgftsrAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITratlhneseiyrkniqigdtvvvHRSGNVIPKitssilslrpndskifkipnICPICNSKIIYIESNLIARCSGSWIECIAQRKaglqhfssrKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAiqksklttFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNpntkggkvVNFISKNTNylvkgqkpgkklEKAIKLnikildeknfvkivkgfstetki
Low Complexity Region (SEG)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDgnigenittnihiihkiPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Disordered region (IsUnstruct)
********INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF******
Disordered Region (DISOPRED)
****************RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL*************ISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF******
Disordered Region (DISEMBL)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
Disordered Region (DISPRO)
********INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSFHAKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTETKI
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	655	2.2.26 [Sep-21-2011]
A6SZQ8	692	DNA ligase OS=Janthinobac	yes	N/A	0.975	0.923	0.493	0.0
A4G4R4	696	DNA ligase OS=Herminiimon	yes	N/A	0.972	0.915	0.491	0.0
Q470D2	711	DNA ligase OS=Cupriavidus	yes	N/A	0.960	0.884	0.452	0.0
B2JID1	683	DNA ligase OS=Burkholderi	yes	N/A	0.974	0.934	0.458	0.0
A4JF81	691	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.920	0.450	0.0
A9AIK9	691	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.920	0.447	0.0
Q2SX03	691	DNA ligase OS=Burkholderi	yes	N/A	0.966	0.916	0.448	1e-180
B2T5K0	688	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.924	0.457	1e-180
Q13XB0	688	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.924	0.454	1e-180
A0K8E8	691	DNA ligase OS=Burkholderi	yes	N/A	0.970	0.920	0.447	1e-180

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

 Score =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/671 (49%), Positives = 454/671 (67%), Gaps = 32/671 (4%)

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 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL-----NNP--- 598
           E + +A+EEQLL +  IG    ++   F++ PL+  LI QL+  G+ W      N P   
Sbjct: 558 EALLQASEEQLLEVADIGPVVAQSIRSFLSDPLNMELIEQLQAAGVRWPEHVVENKPKPF 617

Query: 599 -----------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIK 635
                                     GGKV   +SK T+Y+V G   G KL KA +L I 
Sbjct: 618 AGKTFVLTGTLPTLSRDQAAEKIEAAGGKVAGSVSKKTSYVVAGADAGSKLAKAEELGIT 677

Query: 636 ILDEKNFVKIV 646
           ILDE   ++++
Sbjct: 678 ILDESALLQLL 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 =  706 bits (1823), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/668 (49%), Positives = 447/668 (66%), Gaps = 31/668 (4%)

Query: 10  NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLT 69
           + S  S R   L+ EL+RHN AYY+ DNPI+ D +YDQL  EL+ +E  +PELL  DS T
Sbjct: 23  DASDPSARAAWLRSELNRHNYAYYVLDNPIVPDAEYDQLFRELQALEASHPELLVFDSPT 82

Query: 70  QHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGI 129
           Q VG +       V H+  M+SL NGF DEDV+ F+KR++  L   + +EY  ELKFDG+
Sbjct: 83  QRVGALALTAFPPVTHSVPMLSLGNGFEDEDVLAFDKRVSEGLNSREEVEYATELKFDGL 142

Query: 130 AVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK 189
           A+NLRYE G L QA+TRGDG  GEN+T NI  +  IPL L+   PP++L+VR EV++YK 
Sbjct: 143 AINLRYEDGVLVQAATRGDGATGENVTANIRTVRAIPLRLHTNNPPKVLDVRGEVMMYKA 202

Query: 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
           D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FF++G+G L G +MP+SH
Sbjct: 203 DLAKLNARQRDAGAKEFANPRNAAAGSLRQLDSRITAQRSLRFFSYGIGLLEGADMPASH 262

Query: 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
           S LL+WY ++G+ +C E +V+ GV  L+EFYK  + KR  LPYEIDGVVYK+N +  Q +
Sbjct: 263 SALLDWYAELGIPVCSERAVVRGVQGLLEFYKATSEKRPQLPYEIDGVVYKVNRVDQQLQ 322

Query: 310 LGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLH 369
           LGF SRAPRFA+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+T ATLH
Sbjct: 323 LGFVSRAPRFAIAHKFPAEEALTTVQDIEVQVGRTGAITPVARLAPVLVGGVTVTNATLH 382

Query: 370 NESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIE 429
           NE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP  ++ F +P+ CP+C S I+ +E
Sbjct: 383 NEDEVRRKDIQIGDTVIVRRAGDVIPEVVAFVPERRPASARPFIMPSSCPVCGSPIVRLE 442

Query: 430 SNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489
              IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA DLYK+ 
Sbjct: 443 DEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAADLYKLG 502

Query: 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM 549
           F+ L  LDR+++K A N+L A++KSK TT +RFIYALGIRHVGE TAKELA +F NL+ +
Sbjct: 503 FRALAELDRMADKSAQNVLDALEKSKRTTLARFIYALGIRHVGEATAKELARHFGNLDAL 562

Query: 550 FKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL-----NNP------ 598
            +A+ EQLL +  IG     +   F    ++  LI QLR  G+ W      N P      
Sbjct: 563 LQASPEQLLEVADIGPVVAASITAFFTDAMNIELIEQLRAAGVTWPEHVVENRPRPLAGK 622

Query: 599 --------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 638
                                  GGKV   +SK T+Y+V G + G KL KA +L + ILD
Sbjct: 623 TFVLTGTLPTLSRDAAAEKIEAAGGKVAGSVSKKTSYVVAGAEAGSKLAKAEELGVTILD 682

Query: 639 EKNFVKIV 646
           E   ++++
Sbjct: 683 ETGLLQLL 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 =  642 bits (1657), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 306/676 (45%), Positives = 429/676 (63%), Gaps = 47/676 (6%)

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 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN------ 597
             L+ +  A E  LL +  +G    ++ + F  +P +  +I QLR  G++W  +      
Sbjct: 565 GKLDGLMVADEAALLEVNDVGPVVAQSIVNFFGEPHNVEVIEQLRAAGVHWPESEPVARA 624

Query: 598 ---------------PN-----------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIK 631
                          P+             G KV   +SK T+Y+V G + G KL+KA  
Sbjct: 625 PAPLAGKTFVLTGTLPSLSREAAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLDKAEA 684

Query: 632 LNIKILDEKNFVKIVK 647
           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 =  638 bits (1646), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 309/674 (45%), Positives = 437/674 (64%), Gaps = 36/674 (5%)

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-IYWLNNP------------ 598
           AT E+LL +  +G    +A  +F  +  +R +I QLR  G + W   P            
Sbjct: 550 ATVEELLEVNDVGPIVAEAIHQFFAEEHNRTVIEQLRAPGKVTWAEGPPAPKAPQGVLAG 609

Query: 599 ---------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKIL 637
                                   G KV   +SK T+Y+V G + G KL KA +L I +L
Sbjct: 610 KTVVLTGTLPNMGRDEAKELLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKAEELGIPVL 669

Query: 638 DEKNFVKIVKGFST 651
           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 =  637 bits (1642), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 306/679 (45%), Positives = 435/679 (64%), Gaps = 43/679 (6%)

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-IYWLNNP---- 598
            +L+ +  A+ E+LL +  +G    ++  +F  +  +R +I QLR  G + W   P    
Sbjct: 550 GSLDPIMDASIEELLEVNDVGPIVAESIHQFFAEEHNRTVIDQLRAPGKVTWPEGPPAPK 609

Query: 599 -----------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKA 629
                                           G KV   +SK T+Y+V G + G KL KA
Sbjct: 610 APQGVLAGKTVVLTGTLPTLTRDAAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKA 669

Query: 630 IKLNIKILDEKNFVKIVKG 648
            +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|A9AIK9|DNLJ_BURM1 DNA ligase OS=Burkholderia multivorans (strain ATCC 17616 / 249) GN=ligA PE=3 SV=1

 Score =  634 bits (1635), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 304/679 (44%), Positives = 434/679 (63%), Gaps = 43/679 (6%)

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-IYWLNNP---- 598
            +L+ +  AT ++LL +  +G    ++  +F  +  +R +I QLR  G + W   P    
Sbjct: 550 GSLDPIMNATIDELLEVNDVGPIVAESIHQFFAEEHNRTVIEQLRAPGKVTWPEGPPAPK 609

Query: 599 -----------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKA 629
                                           G KV   +SK T+Y++ G + G KL KA
Sbjct: 610 APQGVLAGKTVVLTGTLPNLTRDDAKEMLEAAGAKVAGSVSKKTDYVIAGAEAGSKLAKA 669

Query: 630 IKLNIKILDEKNFVKIVKG 648
             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 =  634 bits (1634), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 303/676 (44%), Positives = 436/676 (64%), Gaps = 43/676 (6%)

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-IYWLNNP--------- 598
           +  A+ ++LL +  +G    ++  +F  +  +R +I QLR  G + W   P         
Sbjct: 555 IMDASIDELLEVNDVGPIVAESIHQFFAEAHNRTVIEQLRAKGKVTWPEGPPAPRAPQGV 614

Query: 599 ------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNI 634
                                      G KV   +SK T+Y+V G   G KL KA +L I
Sbjct: 615 LAGKTVVLTGTLPTLTREAAKEMLEAAGAKVAGSVSKKTDYVVAGADAGSKLAKAEELGI 674

Query: 635 KILDEKNFVKIVKGFS 650
            +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|B2T5K0|DNLJ_BURPP DNA ligase OS=Burkholderia phytofirmans (strain DSM 17436 / PsJN) GN=ligA PE=3 SV=1

 Score =  633 bits (1633), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 309/676 (45%), Positives = 432/676 (63%), Gaps = 40/676 (5%)

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-IYWLNNP------- 598
           + +  A+ E LL +  +G    ++  +F  +  +R +I QLR  G + W   P       
Sbjct: 551 DPIMDASVEALLEVNDVGPVVAESIHQFFAEEHNRTVIEQLRAPGKVTWPEGPPAPKAPQ 610

Query: 599 --------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 632
                                        G KV   +SK T+YLV G   G KL KA +L
Sbjct: 611 GVLAGKTVVLTGTLPSLAREEAKEMLEAAGAKVAGSVSKKTDYLVAGADAGSKLAKAEEL 670

Query: 633 NIKILDEKNFVKIVKG 648
            + +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|Q13XB0|DNLJ_BURXL DNA ligase OS=Burkholderia xenovorans (strain LB400) GN=ligA PE=3 SV=1

 Score =  633 bits (1632), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 307/676 (45%), Positives = 436/676 (64%), Gaps = 40/676 (5%)

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-IYWLNNP------- 598
           + +  A+ E LL +  +G    ++  +F  +  +R +I QLR  G + W   P       
Sbjct: 551 DPIMDASVEALLEVNDVGPVVAESIHQFFAEEHNRTVIEQLRAPGRVTWPEGPPAPKAPQ 610

Query: 599 --------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL 632
                                        G KV   +SK T+Y+V G + G KL KA +L
Sbjct: 611 GVLAGKTVVLTGTLPSLAREEAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKAEEL 670

Query: 633 NIKILDEKNFVKIVKG 648
            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|A0K8E8|DNLJ_BURCH DNA ligase OS=Burkholderia cenocepacia (strain HI2424) GN=ligA PE=3 SV=1

 Score =  632 bits (1631), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 304/679 (44%), Positives = 435/679 (64%), Gaps = 43/679 (6%)

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

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

Query: 124 LKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCE 183
           LKFDG+A++LRYE G   QA+TRGDG  GE++T N+  I  IPL L  K+ P +L+VR E
Sbjct: 131 LKFDGLAISLRYEQGVFVQAATRGDGTTGEDVTENVRTIRSIPLKLKGKHVPAVLDVRGE 190

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

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

Query: 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI 363
              Q++LGF SRAPRFALA+KF ++EALTK+ AI++Q+GRTG ITPVA L+PV + G T+
Sbjct: 311 RDEQERLGFVSRAPRFALAHKFPAQEALTKLVAIDVQVGRTGAITPVARLEPVFVGGATV 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 TNATLHNEDEVRRKDIRIGDTVIVRRAGDVIPEVVGALLDRRPADAAEFVMPTECPVCGS 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++ +++K+K TT +RFIY LGIRHVGE+TAK+LA +F
Sbjct: 490 DLFNLGFATLAELDRFAEKSAQNLIDSLEKAKHTTLARFIYGLGIRHVGESTAKDLAKHF 549

Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVG-IYWLNNP---- 598
            +L  +  A+ E+LL +  +G    ++  +F  +  +R +I QLR  G + W   P    
Sbjct: 550 GSLTPIMDASIEELLEVNDVGPIVAESLHQFFAEEHNRTVIEQLRAPGKVTWPEGPPAPK 609

Query: 599 -----------------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKA 629
                                           G KV   +SK T+Y+V G + G KL KA
Sbjct: 610 APQGVLAGKTVVLTGTLPNLTRDAAKEMLEAAGAKVAGSVSKKTDYVVAGAEAGSKLAKA 669

Query: 630 IKLNIKILDEKNFVKIVKG 648
            +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 cenocepacia (strain HI2424) (taxid: 331272)

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	655
399017276	705	DNA ligase, NAD-dependent [Herbaspirillu	0.975	0.906	0.5	0.0
152981161	692	DNA ligase [Janthinobacterium sp. Marsei	0.975	0.923	0.493	0.0
134094553	696	DNA ligase [Herminiimonas arsenicoxydans	0.972	0.915	0.491	0.0
340786485	694	DNA ligase [Collimonas fungivorans Ter33	0.963	0.909	0.499	0.0
300311482	688	NAD-dependent DNA ligase [Herbaspirillum	0.955	0.909	0.492	0.0
409405979	686	NAD-dependent DNA ligase [Herbaspirillum	0.964	0.921	0.486	0.0
398834963	682	DNA ligase, NAD-dependent [Herbaspirillu	0.964	0.926	0.477	0.0
237745525	685	DNA ligase [Oxalobacter formigenes HOxBL	0.961	0.919	0.483	0.0
329912476	679	DNA ligase [Oxalobacteraceae bacterium I	0.948	0.914	0.474	0.0
237747723	685	DNA ligase [Oxalobacter formigenes OXCC1	0.972	0.929	0.475	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 =  719 bits (1855), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 336/672 (50%), Positives = 450/672 (66%), Gaps = 33/672 (4%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN----------------- 599
           LL +  IG    ++ I F    L+  L++QLR  GI+W                      
Sbjct: 558 LLEVADIGPVVARSLISFFADGLNVELVNQLRAAGIHWTEGAGIDIPAKTLAGKIFVLTG 617

Query: 600 ---------------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 644
                            GGKV   +SK T+Y+V G + G KL KA +L I ILDE+  V 
Sbjct: 618 TLPTMSRDDAAQMIEAAGGKVSGSVSKKTSYVVAGAEAGSKLAKAEELGIAILDEEALVA 677

Query: 645 IVK-GFSTETKI 655
           +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|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 =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/671 (49%), Positives = 454/671 (67%), Gaps = 32/671 (4%)

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 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL-----NNP--- 598
           E + +A+EEQLL +  IG    ++   F++ PL+  LI QL+  G+ W      N P   
Sbjct: 558 EALLQASEEQLLEVADIGPVVAQSIRSFLSDPLNMELIEQLQAAGVRWPEHVVENKPKPF 617

Query: 599 -----------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIK 635
                                     GGKV   +SK T+Y+V G   G KL KA +L I 
Sbjct: 618 AGKTFVLTGTLPTLSRDQAAEKIEAAGGKVAGSVSKKTSYVVAGADAGSKLAKAEELGIT 677

Query: 636 ILDEKNFVKIV 646
           ILDE   ++++
Sbjct: 678 ILDESALLQLL 688

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

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 =  706 bits (1823), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/668 (49%), Positives = 447/668 (66%), Gaps = 31/668 (4%)

Query: 10  NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLT 69
           + S  S R   L+ EL+RHN AYY+ DNPI+ D +YDQL  EL+ +E  +PELL  DS T
Sbjct: 23  DASDPSARAAWLRSELNRHNYAYYVLDNPIVPDAEYDQLFRELQALEASHPELLVFDSPT 82

Query: 70  QHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGI 129
           Q VG +       V H+  M+SL NGF DEDV+ F+KR++  L   + +EY  ELKFDG+
Sbjct: 83  QRVGALALTAFPPVTHSVPMLSLGNGFEDEDVLAFDKRVSEGLNSREEVEYATELKFDGL 142

Query: 130 AVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK 189
           A+NLRYE G L QA+TRGDG  GEN+T NI  +  IPL L+   PP++L+VR EV++YK 
Sbjct: 143 AINLRYEDGVLVQAATRGDGATGENVTANIRTVRAIPLRLHTNNPPKVLDVRGEVMMYKA 202

Query: 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
           D  KLN  +   G K+F NPRNAAAG LRQL+ +I   + L FF++G+G L G +MP+SH
Sbjct: 203 DLAKLNARQRDAGAKEFANPRNAAAGSLRQLDSRITAQRSLRFFSYGIGLLEGADMPASH 262

Query: 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
           S LL+WY ++G+ +C E +V+ GV  L+EFYK  + KR  LPYEIDGVVYK+N +  Q +
Sbjct: 263 SALLDWYAELGIPVCSERAVVRGVQGLLEFYKATSEKRPQLPYEIDGVVYKVNRVDQQLQ 322

Query: 310 LGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLH 369
           LGF SRAPRFA+A+KF ++EALT ++ I +Q+GRTG ITPVA L PVL+ G+T+T ATLH
Sbjct: 323 LGFVSRAPRFAIAHKFPAEEALTTVQDIEVQVGRTGAITPVARLAPVLVGGVTVTNATLH 382

Query: 370 NESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIE 429
           NE E+ RK+IQIGDTV+V R+G+VIP++ + +   RP  ++ F +P+ CP+C S I+ +E
Sbjct: 383 NEDEVRRKDIQIGDTVIVRRAGDVIPEVVAFVPERRPASARPFIMPSSCPVCGSPIVRLE 442

Query: 430 SNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489
              IARCSG W++C AQRK GL HF SR+AM++ GLG +++E+LV+ +I+ TA DLYK+ 
Sbjct: 443 DEAIARCSGGWVKCAAQRKGGLLHFVSRRAMDVEGLGDQLVEQLVDKHIITTAADLYKLG 502

Query: 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM 549
           F+ L  LDR+++K A N+L A++KSK TT +RFIYALGIRHVGE TAKELA +F NL+ +
Sbjct: 503 FRALAELDRMADKSAQNVLDALEKSKRTTLARFIYALGIRHVGEATAKELARHFGNLDAL 562

Query: 550 FKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL-----NNP------ 598
            +A+ EQLL +  IG     +   F    ++  LI QLR  G+ W      N P      
Sbjct: 563 LQASPEQLLEVADIGPVVAASITAFFTDAMNIELIEQLRAAGVTWPEHVVENRPRPLAGK 622

Query: 599 --------------------NTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILD 638
                                  GGKV   +SK T+Y+V G + G KL KA +L + ILD
Sbjct: 623 TFVLTGTLPTLSRDAAAEKIEAAGGKVAGSVSKKTSYVVAGAEAGSKLAKAEELGVTILD 682

Query: 639 EKNFVKIV 646
           E   ++++
Sbjct: 683 ETGLLQLL 690

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

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 =  705 bits (1820), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 332/665 (49%), Positives = 450/665 (67%), Gaps = 34/665 (5%)

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 EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN----------------- 597
           EQLL +  IG    ++ + F   PL+R L+ QLR  GI+W  N                 
Sbjct: 563 EQLLEVADIGPVVARSLLAFFADPLNRELVEQLRAAGIHWPENLPAAGGSKFLLGKTFVL 622

Query: 598 ----PN-----------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
               P              GGKV   +SK T+Y+V G + G KL KA +LNI ILDE   
Sbjct: 623 TGSLPTLTRDAAAAMIEAAGGKVTGSVSKKTSYVVAGAEAGSKLTKAEELNIPILDEDGL 682

Query: 643 VKIVK 647
             +++
Sbjct: 683 RTLLE 687

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

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 =  695 bits (1793), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/658 (49%), Positives = 440/658 (66%), Gaps = 32/658 (4%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN------------------- 597
           LL +  +G     +   F +  L+  L+ QLR VG++W  +                   
Sbjct: 561 LLEVADVGPVVATSIRSFFDDALNVELVEQLRAVGVHWPESAGVEAAAKHLAGKTFVLTG 620

Query: 598 --PN-----------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
             PN             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|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 =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/664 (48%), Positives = 442/664 (66%), Gaps = 32/664 (4%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN------------------- 597
           LL +  IG     +   F N P++  L+ QLR VG++W  +                   
Sbjct: 557 LLEVADIGPVVASSIRAFFNDPINVELVEQLRAVGVHWPESEGVDAGAKHLAGKTFVLTG 616

Query: 598 --PN-----------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 644
             PN             GGKV   +SK T+Y+V G + G KL KA +L + ILDE     
Sbjct: 617 TLPNLSRDDASQMIEAAGGKVSGSVSKKTSYVVAGAEAGSKLAKAEELGVAILDEDALKA 676

Query: 645 IVKG 648
           +  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 =  676 bits (1744), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/664 (47%), Positives = 435/664 (65%), Gaps = 32/664 (4%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN------------------- 597
           LL +  IG     +   F +   +  L+ QLR VG+ W  +                   
Sbjct: 557 LLEVADIGPVVAASIRAFFDDAQNVELVEQLRAVGLEWSEDAGSDSQPKHLAGKTFVLTG 616

Query: 598 --PN-----------TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 644
             PN             GGKV   +SK T+Y+V G + G KL +A +L + ILDE     
Sbjct: 617 TLPNLSRDQASQMIEAAGGKVAGSVSKKTSYVVAGAEAGSKLARAEELGLAILDEDALKA 676

Query: 645 IVKG 648
           +  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 =  675 bits (1741), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/664 (48%), Positives = 451/664 (67%), Gaps = 34/664 (5%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
           LL +  IG     +  +F +   +R LI +L++ G++W      +               
Sbjct: 557 LLEVDDIGPVVALSIRQFFDDVRNRELIGKLQNDGVHWPERAMKEKPPALPLQDRKFVLT 616

Query: 602 ------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFV 643
                             GGKV N +SK T+Y++ G +PG KL KA +L I+ILDE+ FV
Sbjct: 617 GTLSSLTREAAAEIIRNLGGKVSNSVSKKTDYVLAGSEPGSKLAKAQELGIRILDEEAFV 676

Query: 644 KIVK 647
           ++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 =  671 bits (1730), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 310/653 (47%), Positives = 432/653 (66%), Gaps = 32/653 (4%)

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 TVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK------------------------- 601
              + ++F   PL+  L+ QLR  G++W  +   +                         
Sbjct: 562 VACSILEFFADPLNVELVEQLRAAGVHWTEHAGRQVVSLPQSGKTFVLTGTLPTLGRDEA 621

Query: 602 -------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK 647
                  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 =  661 bits (1705), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/671 (47%), Positives = 457/671 (68%), Gaps = 34/671 (5%)

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 FKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW-----------LNNP 598
            +A+EEQLL +  IG     +  +F +   +  L+ +L  VG++W           L   
Sbjct: 550 RQASEEQLLEVADIGPIVAASIKQFFSDERNLALVDKLLGVGLHWPEHEMKEKPEELPFQ 609

Query: 599 NTK----------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKI 636
           N K                      GGKV + +S+NT+Y++ G +PG KL KA +L +++
Sbjct: 610 NKKFVLTGTLPSLTRDAAAEIIRNLGGKVSSSVSRNTDYVLAGSEPGSKLAKAEELGVRV 669

Query: 637 LDEKNFVKIVK 647
           +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	655
TIGR_CMR|CBU_0542	673	CBU_0542 "DNA ligase, NAD-depe	0.888	0.864	0.416	8.1e-140
UNIPROTKB|P15042	671	ligA [Escherichia coli K-12 (t	0.880	0.859	0.418	2.7e-128
UNIPROTKB|Q9KTD1	669	ligA "DNA ligase" [Vibrio chol	0.888	0.869	0.420	1.7e-126
TIGR_CMR|VC_0971	669	VC_0971 "DNA ligase" [Vibrio c	0.888	0.869	0.420	1.7e-126
TIGR_CMR|SO_2896	689	SO_2896 "DNA ligase, NAD-depen	0.868	0.825	0.403	8.2e-123
TIGR_CMR|CHY_1100	664	CHY_1100 "DNA ligase, NAD-depe	0.870	0.858	0.397	3.6e-112
TIGR_CMR|GSU_0890	670	GSU_0890 "DNA ligase, NAD-depe	0.929	0.908	0.396	9.7e-112
TIGR_CMR|DET_0596	677	DET_0596 "DNA ligase, NAD-depe	0.868	0.840	0.362	1.1e-103
TIGR_CMR|BA_0306	669	BA_0306 "DNA ligase, NAD-depen	0.883	0.865	0.368	8.8e-102
UNIPROTKB|P63973	691	ligA "DNA ligase" [Mycobacteri	0.862	0.817	0.361	3.3e-98

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

 Score = 1263 (449.7 bits), Expect = 8.1e-140, Sum P(2) = 8.1e-140
 Identities = 243/583 (41%), Positives = 373/583 (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 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594
             A+ E L  I  IG    +    F +Q  +  LI++L  +G++W
Sbjct:   547 ASIETLQEIRDIGPVAAENIHAFFHQKNNAELINKLIHLGVHW 589

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 = 1190 (424.0 bits), Expect = 2.7e-128, Sum P(2) = 2.7e-128
 Identities = 242/578 (41%), Positives = 357/578 (61%)

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

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 = 1167 (415.9 bits), Expect = 1.7e-126, Sum P(2) = 1.7e-126
 Identities = 245/583 (42%), Positives = 359/583 (61%)

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 594
             A+ EQ + +P +G         F  Q  ++ +I++L + GI W
Sbjct:   541 ASLEQFIEVPDVGVVVASHLQAFFAQDRNQQVINELLEQGITW 583

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 = 1167 (415.9 bits), Expect = 1.7e-126, Sum P(2) = 1.7e-126
 Identities = 245/583 (42%), Positives = 359/583 (61%)

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 594
             A+ EQ + +P +G         F  Q  ++ +I++L + GI W
Sbjct:   541 ASLEQFIEVPDVGVVVASHLQAFFAQDRNQQVINELLEQGITW 583

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 = 1136 (405.0 bits), Expect = 8.2e-123, Sum P(2) = 8.2e-123
 Identities = 233/577 (40%), Positives = 353/577 (61%)

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-LISQLRDVGIYW 594
              +  IG    +    F  QP H L +I  L   G+ W
Sbjct:   566 EVEDIGEVVAQHVAHFFAQP-HNLEVIDALIAAGVNW 601

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 = 1107 (394.7 bits), Expect = 3.6e-112, P = 3.6e-112
 Identities = 229/576 (39%), Positives = 349/576 (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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
             ++ IP +G     +   F  Q  +  LI +L+  G+
Sbjct:   543 IMAIPSVGPKMAASIKAFFAQKENLELIEKLKAAGV 578

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 = 1103 (393.3 bits), Expect = 9.7e-112, P = 9.7e-112
 Identities = 244/616 (39%), Positives = 360/616 (58%)

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 EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTN 614
             E+LL+I ++G    ++ I F     +R  I ++   G+         GG+        T 
Sbjct:   546 EELLSIREVGPQVARSIITFFRNEGNRETIRRMFKAGVRPTAEEKKVGGRFTGKTFVFTG 605

Query:   615 YLVKGQKPG--KKLEK 628
              L +  +P   K +EK
Sbjct:   606 ALTRFSRPEAQKMVEK 621

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 = 963 (344.1 bits), Expect = 1.1e-103, Sum P(2) = 1.1e-103
 Identities = 213/587 (36%), Positives = 334/587 (56%)

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 LECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
             +  +  A  ++L  IP IG+    +   + ++  +  +I +L   G+
Sbjct:   542 IWALAGAGLDELQTIPDIGAKIASSIKAYFSEEKNIAVIRRLETAGV 588

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 = 1009 (360.2 bits), Expect = 8.8e-102, P = 8.8e-102
 Identities = 218/592 (36%), Positives = 349/592 (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-NQPLHRLLISQLRDVGIYWLNNPNTKGGKVVN 607
             L  I +IG    ++ + +  N+ +  LL  Q ++ G+    N   KG K+ +
Sbjct:   542 LKAINEIGEKMAQSVVAYFDNEDVLELL-QQFKEYGV----NMTYKGIKIAD 588

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 = 874 (312.7 bits), Expect = 3.3e-98, Sum P(2) = 3.3e-98
 Identities = 212/586 (36%), Positives = 322/586 (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 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
             + +  A+ +QL  +  +G T   A  ++     HR ++ + R  G+
Sbjct:   553 DAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGV 598

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	0.4456	0.9526	0.8801	yes	N/A
B6J878	DNLJ_COXB1	6, ., 5, ., 1, ., 2	0.4095	0.9648	0.9390	yes	N/A
B1XTU0	DNLJ_POLNS	6, ., 5, ., 1, ., 2	0.4482	0.9679	0.9448	yes	N/A
B1YSH2	DNLJ_BURA4	6, ., 5, ., 1, ., 2	0.4514	0.9694	0.9189	yes	N/A
B4ECN6	DNLJ_BURCJ	6, ., 5, ., 1, ., 2	0.4477	0.9709	0.9204	yes	N/A
B2T5K0	DNLJ_BURPP	6, ., 5, ., 1, ., 2	0.4571	0.9709	0.9244	yes	N/A
Q604U8	DNLJ_METCA	6, ., 5, ., 1, ., 2	0.4240	0.9541	0.9286	yes	N/A
Q1LNG5	DNLJ_RALME	6, ., 5, ., 1, ., 2	0.4359	0.9587	0.8710	yes	N/A
B8GTL0	DNLJ_THISH	6, ., 5, ., 1, ., 2	0.4086	0.9664	0.9377	yes	N/A
B2JID1	DNLJ_BURP8	6, ., 5, ., 1, ., 2	0.4584	0.9740	0.9341	yes	N/A
B3PGQ8	DNLJ_CELJU	6, ., 5, ., 1, ., 2	0.4050	0.9709	0.9352	yes	N/A
Q62JB9	DNLJ_BURMA	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
A1K713	DNLJ_AZOSB	6, ., 5, ., 1, ., 2	0.4195	0.9480	0.8961	yes	N/A
Q470D2	DNLJ_CUPPJ	6, ., 5, ., 1, ., 2	0.4526	0.9603	0.8846	yes	N/A
Q2SX03	DNLJ_BURTA	6, ., 5, ., 1, ., 2	0.4482	0.9664	0.9160	yes	N/A
Q13XB0	DNLJ_BURXL	6, ., 5, ., 1, ., 2	0.4541	0.9709	0.9244	yes	N/A
A0K8E8	DNLJ_BURCH	6, ., 5, ., 1, ., 2	0.4477	0.9709	0.9204	yes	N/A
A9II69	DNLJ_BORPD	6, ., 5, ., 1, ., 2	0.4026	0.9526	0.8952	yes	N/A
A2SB66	DNLJ_BURM9	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
A9NC33	DNLJ_COXBR	6, ., 5, ., 1, ., 2	0.4099	0.9694	0.9477	yes	N/A
B6J1C6	DNLJ_COXB2	6, ., 5, ., 1, ., 2	0.4084	0.9694	0.9379	yes	N/A
Q1BHI7	DNLJ_BURCA	6, ., 5, ., 1, ., 2	0.4477	0.9709	0.9204	yes	N/A
C1D4R5	DNLJ_LARHH	6, ., 5, ., 1, ., 2	0.4133	0.9480	0.8973	yes	N/A
Q82TW6	DNLJ_NITEU	6, ., 5, ., 1, ., 2	0.4115	0.9648	0.9280	yes	N/A
Q63T07	DNLJ_BURPS	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
Q12AD4	DNLJ_POLSJ	6, ., 5, ., 1, ., 2	0.4250	0.9679	0.8980	yes	N/A
Q7WCJ7	DNLJ_BORBR	6, ., 5, ., 1, ., 2	0.4134	0.9496	0.8936	yes	N/A
A4SYV5	DNLJ_POLSQ	6, ., 5, ., 1, ., 2	0.4452	0.9679	0.9448	yes	N/A
A3NWN7	DNLJ_BURP0	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
A1V575	DNLJ_BURMS	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
Q83DZ6	DNLJ_COXBU	6, ., 5, ., 1, ., 2	0.4095	0.9648	0.9390	yes	N/A
Q7VRX7	DNLJ_BORPE	6, ., 5, ., 1, ., 2	0.4149	0.9496	0.8936	yes	N/A
Q7W0T4	DNLJ_BORPA	6, ., 5, ., 1, ., 2	0.4120	0.9496	0.8936	yes	N/A
B1JUF5	DNLJ_BURCC	6, ., 5, ., 1, ., 2	0.4477	0.9709	0.9204	yes	N/A
Q0KA11	DNLJ_CUPNH	6, ., 5, ., 1, ., 2	0.4500	0.9526	0.8801	yes	N/A
A4G4R4	DNLJ_HERAR	6, ., 5, ., 1, ., 2	0.4910	0.9725	0.9152	yes	N/A
A3NAV3	DNLJ_BURP6	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
Q0BE10	DNLJ_BURCM	6, ., 5, ., 1, ., 2	0.4514	0.9694	0.9189	yes	N/A
Q39F38	DNLJ_BURS3	6, ., 5, ., 1, ., 2	0.4506	0.9709	0.9204	yes	N/A
Q5NYU3	DNLJ_AROAE	6, ., 5, ., 1, ., 2	0.4083	0.9603	0.9236	yes	N/A
Q2KUU5	DNLJ_BORA1	6, ., 5, ., 1, ., 2	0.4096	0.9526	0.8978	yes	N/A
A4JF81	DNLJ_BURVG	6, ., 5, ., 1, ., 2	0.4506	0.9709	0.9204	yes	N/A
A9AIK9	DNLJ_BURM1	6, ., 5, ., 1, ., 2	0.4477	0.9709	0.9204	yes	N/A
Q47FA0	DNLJ_DECAR	6, ., 5, ., 1, ., 2	0.4149	0.9603	0.9209	yes	N/A
Q1H1G6	DNLJ_METFK	6, ., 5, ., 1, ., 2	0.4123	0.9664	0.9134	yes	N/A
A9KCS0	DNLJ_COXBN	6, ., 5, ., 1, ., 2	0.4069	0.9694	0.9477	yes	N/A
Q21WC8	DNLJ_RHOFD	6, ., 5, ., 1, ., 2	0.4065	0.9633	0.9144	yes	N/A
Q3JR23	DNLJ_BURP1	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
A3MKU9	DNLJ_BURM7	6, ., 5, ., 1, ., 2	0.4508	0.9740	0.9232	yes	N/A
A6SZQ8	DNLJ_JANMA	6, ., 5, ., 1, ., 2	0.4932	0.9755	0.9234	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	655
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-174
PRK14351	689	PRK14351, ligA, NAD-dependent DNA ligase LigA; Pro	1e-153
cd00114	307	cd00114, LIGANc, NAD+ dependent DNA ligase adenyla	1e-119
pfam01653	314	pfam01653, DNA_ligase_aden, NAD-dependent DNA liga	1e-106
PRK14350	669	PRK14350, ligA, NAD-dependent DNA ligase LigA; Pro	6e-86
pfam03120	82	pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase	1e-33
PRK08097	562	PRK08097, ligB, NAD-dependent DNA ligase LigB; Rev	7e-21
pfam12826	64	pfam12826, HHH_2, Helix-hairpin-helix motif	1e-18
COG5275	276	COG5275, COG5275, BRCT domain type II [General fun	8e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	0.002

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

 Score =  763 bits (1974), Expect = 0.0
 Identities = 285/660 (43%), Positives = 414/660 (62%), Gaps = 31/660 (4%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
           L  +  +G    ++ ++F     +R LI +L + G+                        
Sbjct: 545 LAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQ 604

Query: 602 -------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
                        G KV   +SK T+ +V G+  G KL KA +L I++LDE+ F++++  
Sbjct: 605 LSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664

Length = 665

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

 Score =  697 bits (1800), Expect = 0.0
 Identities = 283/663 (42%), Positives = 408/663 (61%), Gaps = 37/663 (5%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
           L +IP IG    ++ I+F     +R LI +L   G+ W                      
Sbjct: 545 LASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTG 604

Query: 602 -----------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 644
                            G KV   +SK T+Y+V G+  G KL KA +L +KI+DE+ F+ 
Sbjct: 605 TLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLA 664

Query: 645 IVK 647
           ++ 
Sbjct: 665 LLG 667

Length = 667

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

 Score =  650 bits (1678), Expect = 0.0
 Identities = 278/657 (42%), Positives = 402/657 (61%), Gaps = 40/657 (6%)

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 PKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW-------------------------- 594
             +G    ++ + F + P +R LI +L ++G+                            
Sbjct: 536 EGVGPKVAESIVNFFHDPNNRQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGT 595

Query: 595 LNNPNTK---------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
           L+  +           GGKV + +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 =  502 bits (1295), Expect = e-174
 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 =  458 bits (1181), Expect = e-153
 Identities = 222/662 (33%), Positives = 359/662 (54%), Gaps = 54/662 (8%)

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 QLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN---------------- 599
            L  +  +G T  +   +F +   +R +I  L D G+    +P                 
Sbjct: 561 ALRAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGV----DPQPAESEGGDALDGLTFV 616

Query: 600 ------------------TKGGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEK 640
                               GG     +S NT+YLV G+ PG+ K + A   ++  LDE+
Sbjct: 617 FTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEE 676

Query: 641 NF 642
            F
Sbjct: 677 EF 678

Length = 689

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

 Score =  356 bits (915), Expect = e-119
 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 (830), Expect = e-106
 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 =  282 bits (723), Expect = 6e-86
 Identities = 206/685 (30%), Positives = 339/685 (49%), Gaps = 71/685 (10%)

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---EQLLNIPKIGSTTVKAFIKFINQPL-------------------- 579
           F  +  + +  E    +LL I  IG       I+  N  +                    
Sbjct: 526 FDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSI 585

Query: 580 -----HRLLISQ-----------LRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG 623
                +  L  +            R V I  L     KG      ++K  ++L+ G+K G
Sbjct: 586 NIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTK---KGAIFNTCVTKYLDFLLVGEKAG 642

Query: 624 KKLEKAIKLNIKIL---DEKNFVKI 645
            KL+KA  L IKI+   D K++V +
Sbjct: 643 LKLKKANNLGIKIMSLFDIKSYVDL 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 = 96.5 bits (241), Expect = 7e-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 = 1e-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 = 44.7 bits (105), Expect = 8e-05
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGFSTE 652
           GG+V    S  T +LV G   G  K+EK  +L IK +DE+ F  ++K     
Sbjct: 184 GGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDTPAA 235

Length = 276

>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	655
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
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	99.63
cd07894	342	Adenylation_RNA_ligase Adenylation domain of RNA c	99.17
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	98.77
cd07896	174	Adenylation_kDNA_ligase_like Adenylation domain of	98.76
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	98.74
PRK09125	282	DNA ligase; Provisional	98.7
cd07898	201	Adenylation_DNA_ligase Adenylation domain of ATP-d	98.61
PRK06195	309	DNA polymerase III subunit epsilon; Validated	98.51
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	98.43
cd07901	207	Adenylation_DNA_ligase_Arch_LigB Adenylation domai	98.43
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	98.41
PF01068	202	DNA_ligase_A_M: ATP dependent DNA ligase domain; I	98.38
PRK03180	508	ligB ATP-dependent DNA ligase; Reviewed	98.38
TIGR02779	298	NHEJ_ligase_lig DNA polymerase LigD, ligase domain	98.36
cd07906	190	Adenylation_DNA_ligase_LigD_LigC Adenylation domai	98.35
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.34
PRK07636	275	ligB ATP-dependent DNA ligase; Reviewed	98.32
cd07900	219	Adenylation_DNA_ligase_I_Euk Adenylation domain of	98.27
TIGR00574	514	dnl1 DNA ligase I, ATP-dependent (dnl1). All prote	98.19
cd06846	182	Adenylation_DNA_ligase_like Adenylation domain of	98.19
COG5275	276	BRCT domain type II [General function prediction o	98.18
PRK08224	350	ligC ATP-dependent DNA ligase; Reviewed	98.18
cd07903	225	Adenylation_DNA_ligase_IV Adenylation domain of DN	98.15
cd07897	207	Adenylation_DNA_ligase_Bac1 Adenylation domain of	98.15
COG1793	444	CDC9 ATP-dependent DNA ligase [DNA replication, re	98.14
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	98.07
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	98.04
cd07905	194	Adenylation_DNA_ligase_LigC Adenylation domain of	98.04
KOG2841|consensus	254		98.02
PHA00454	315	ATP-dependent DNA ligase	97.99
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	97.98
PRK09247	539	ATP-dependent DNA ligase; Validated	97.97
cd08039	235	Adenylation_DNA_ligase_Fungal Adenylation domain o	97.95
PHA02587	488	30 DNA ligase; Provisional	97.95
PRK12766	232	50S ribosomal protein L32e; Provisional	97.94
cd07902	213	Adenylation_DNA_ligase_III Adenylation domain of D	97.92
PRK09633	610	ligD ATP-dependent DNA ligase; Reviewed	97.89
PRK01109	590	ATP-dependent DNA ligase; Provisional	97.89
PRK09632	764	ATP-dependent DNA ligase; Reviewed	97.84
PRK08609	570	hypothetical protein; Provisional	97.84
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	97.83
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	97.66
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	97.61
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	97.56
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	97.55
cd07895	215	Adenylation_mRNA_capping Adenylation domain of GTP	97.5
PRK05972	860	ligD ATP-dependent DNA ligase; Reviewed	97.49
PLN03113	744	DNA ligase 1; Provisional	97.49
PRK14973	936	DNA topoisomerase I; Provisional	97.49
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.46
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	97.43
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	97.42
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	97.4
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	97.32
PRK13482	352	DNA integrity scanning protein DisA; Provisional	97.26
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	97.23
PRK12766	232	50S ribosomal protein L32e; Provisional	97.18
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.18
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	97.08
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	97.07
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	97.05
TIGR01209	374	RNA ligase, Pab1020 family. Members of this family	97.04
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	96.95
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	96.84
PRK00254	720	ski2-like helicase; Provisional	96.83
PRK08609	570	hypothetical protein; Provisional	96.79
PRK14973	936	DNA topoisomerase I; Provisional	96.77
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	96.76
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	96.71
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	96.7
PRK13766	773	Hef nuclease; Provisional	96.66
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	96.57
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	96.54
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	96.46
PF03118	66	RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha	96.44
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.37
COG1423	382	ATP-dependent DNA ligase, homolog of eukaryotic li	96.36
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	96.35
TIGR01259	120	comE comEA protein. This model describes the ComEA	96.35
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	96.32
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	96.21
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	96.14
PRK05601	377	DNA polymerase III subunit epsilon; Validated	96.14
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	95.97
PRK07758	95	hypothetical protein; Provisional	95.95
TIGR02307	325	RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of t	95.84
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	95.76
PRK00254	720	ski2-like helicase; Provisional	95.7
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	95.65
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	95.61
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	95.57
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	95.43
TIGR01259	120	comE comEA protein. This model describes the ComEA	95.39
PRK02362	737	ski2-like helicase; Provisional	95.36
PRK02515	132	psbU photosystem II complex extrinsic protein prec	94.94
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	94.92
PHA02142	366	putative RNA ligase	94.81
TIGR02236	310	recomb_radA DNA repair and recombination protein R	94.59
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.47
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	94.46
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	94.46
PRK01172	674	ski2-like helicase; Provisional	94.41
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	94.29
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	94.24
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	94.2
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	94.01
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	94.0
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	93.99
PF09414	186	RNA_ligase: RNA ligase; InterPro: IPR021122 This e	93.92
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	93.91
PRK02515	132	psbU photosystem II complex extrinsic protein prec	93.9
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	93.88
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	93.84
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.82
PRK00024	224	hypothetical protein; Reviewed	93.81
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	93.8
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	93.77
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	93.74
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	93.68
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	93.67
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	93.56
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.37
COG1623	349	Predicted nucleic-acid-binding protein (contains t	93.32
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	93.31
TIGR00608	218	radc DNA repair protein radc. This family is based	93.25
COG2003	224	RadC DNA repair proteins [DNA replication, recombi	93.11
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	92.73
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	92.44
PF14490	94	HHH_4: Helix-hairpin-helix containing domain; PDB:	92.42
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	92.34
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	92.3
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	92.21
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	92.11
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	92.01
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	91.72
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	91.7
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	91.68
KOG0967|consensus	714		91.56
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	91.42
PRK01172	674	ski2-like helicase; Provisional	91.26
PRK10702	211	endonuclease III; Provisional	91.22
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	91.14
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	91.08
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	90.42
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	90.17
smart00292	80	BRCT breast cancer carboxy-terminal domain.	90.03
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	89.68
PRK09482	256	flap endonuclease-like protein; Provisional	88.98
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	88.82
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	88.14
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	87.97
PTZ00035	337	Rad51 protein; Provisional	87.47
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	87.33
smart00475	259	53EXOc 5'-3' exonuclease.	87.31
PF01367	101	5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold	87.0
PRK00420	112	hypothetical protein; Validated	86.5
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	86.49
PRK13482	352	DNA integrity scanning protein DisA; Provisional	86.47
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	86.37
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	86.02
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	85.63
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	85.12
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	84.85
COG2231	215	Uncharacterized protein related to Endonuclease II	84.82
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	84.78
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	84.28
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	84.24
PRK14976	281	5'-3' exonuclease; Provisional	84.04
KOG2534|consensus	353		84.01
TIGR02776	552	NHEJ_ligase_prk DNA ligase D. Members of this prot	83.93
TIGR01083	191	nth endonuclease III. This equivalog model identif	83.9
PF01331	192	mRNA_cap_enzyme: mRNA capping enzyme, catalytic do	83.68
PRK02362	737	ski2-like helicase; Provisional	83.61
PRK13766	773	Hef nuclease; Provisional	83.52
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	83.45
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	82.87
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	82.42
COG5241	224	RAD10 Nucleotide excision repair endonuclease NEF1	82.0
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	81.93
PRK07758	95	hypothetical protein; Provisional	81.9
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	81.82
TIGR03491	457	RecB family nuclease, putative, TM0106 family. Mem	81.64
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	80.86
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	80.81
PRK10736	374	hypothetical protein; Provisional	80.73
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	80.66
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	80.17
PF09151	36	DUF1936: Domain of unknown function (DUF1936); Int	80.01

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

Probab=100.00  E-value=1.1e-193  Score=1593.49  Aligned_cols=633  Identities=45%  Similarity=0.733  Sum_probs=613.8

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccc
Q psy11423         10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKM   89 (655)
Q Consensus        10 ~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pM   89 (655)
                      ++.++++++++|+++|++|+++||++|+|.|||++||+|+++|++||.+||++.++|||||+||+.+..+|.+|+|.+||
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             cCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccc
Q psy11423         90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL  169 (655)
Q Consensus        90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l  169 (655)
                      |||+|+||++||.+|++|+.+.++.  +..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|
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             ccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCH
Q psy11423        170 NIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH  249 (655)
Q Consensus       170 ~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~  249 (655)
                      ++  +|..+||||||||++++|+++|+++++.|+++|+||||+|||+|||+||++++.|+|.||+|+|+...+...+.||
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  6999999999999999999999999999999999999999999999999999999999999999875532336899


Q ss_pred             HHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcce
Q psy11423        250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (655)
Q Consensus       250 ~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (655)
                      +|.|++|++|||+|+++...|.|.+||.+||++|.+.|++|||+|||+|||+||+++|+.||+|+|+||||||||||+++
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             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (655)
Q Consensus       330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (655)
                      +.|+|++|+|||||||+|||||+|+||.|+|+||+||||||.++|+++||+|||+|.|+|||||||+|++|+.+.|++++
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             ccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCC
Q psy11423        410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN  489 (655)
Q Consensus       410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  489 (655)
                      .+|.+|++||+|||+|++.++++.+||+|++. ||+|.+++|+||+||+||||+|||+|+|++|+++++|++++|||+|+
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            99999999999999999999999999999767 99999999999999999999999999999999999999999999999


Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK  569 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~  569 (655)
                      .++|..|+|||+|+++||+++|++||+.+|+|||+||||||||+++|+.|+++|+|+++|..|+.++|..++|||+++|.
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             HHHHHhcChhHHHHHHHHHHcCcccccCC--------------------------------CCCCCeEecccccCccEEE
Q psy11423        570 AFIKFINQPLHRLLISQLRDVGIYWLNNP--------------------------------NTKGGKVVNFISKNTNYLV  617 (655)
Q Consensus       570 ~I~~~f~~~~n~~li~~L~~~Gi~~~~~~--------------------------------~~~G~~v~~sVsk~t~ylv  617 (655)
                      +|.+||++++|++++++|.+.|+.+....                                .++||+|++||||||||||
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            99999999999999999999998653310                                1889999999999999999


Q ss_pred             ecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        618 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       618 ~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      +|+++|||++||++|||+||+|++|++++.
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=3e-179  Score=1523.72  Aligned_cols=634  Identities=45%  Similarity=0.734  Sum_probs=605.9

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11423         11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM   90 (655)
Q Consensus        11 ~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl   90 (655)
                      +..++++|++|+++|++||++||+.|+|+|||++||+|+++|++||++||++..++|||++||+.+..+|.||+|++|||
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            45567889999999999999999999999999999999999999999999999999999999999988999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccc
Q psy11423         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (655)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (655)
                      ||+|+|+.+||.+|++++.+.++. .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+
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            999999999999999999877652 2457999999999999999999999999999999999999999999999999996


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEeccccc-CCCCCCCH
Q psy11423        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELR-GMNMPSSH  249 (655)
Q Consensus       171 ~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~-~~~~~~~~  249 (655)
                      . ..|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|...+ +.. +.+|
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 212 4799


Q ss_pred             HHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcce
Q psy11423        250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE  329 (655)
Q Consensus       250 ~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~  329 (655)
                      ++.|++|++|||+|+++...+.+++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++
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             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (655)
Q Consensus       330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (655)
                      ++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.
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            99999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             ccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCC
Q psy11423        410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN  489 (655)
Q Consensus       410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~  489 (655)
                      .+|.+|++||+||++|++.++++.+||+|..+ ||+|++++|.||+||+||||+||||++|++||++|+|++++|||+|+
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            89999999999999999988899999999756 99999999999999999999999999999999999999999999999


Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK  569 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~  569 (655)
                      .++|..|+|||+|+++||+++|+.+|+.+|+|||+||||||||+++|++|+++|+|+++|..|+.++|.+++|||+++|+
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             HHHHHhcChhHHHHHHHHHHcCcccccC------C----------------------CCCCCeEecccccCccEEEecCC
Q psy11423        570 AFIKFINQPLHRLLISQLRDVGIYWLNN------P----------------------NTKGGKVVNFISKNTNYLVKGQK  621 (655)
Q Consensus       570 ~I~~~f~~~~n~~li~~L~~~Gi~~~~~------~----------------------~~~G~~v~~sVsk~t~ylv~g~~  621 (655)
                      +|++||+++.|+++++.|.+.|+.+...      .                      ..+|++|++|||++|||||||+.
T Consensus       558 sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~  637 (665)
T PRK07956        558 SIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEA  637 (665)
T ss_pred             HHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCC
Confidence            9999999999999999999988864310      0                      18999999999999999999999


Q ss_pred             CCchHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423        622 PGKKLEKAIKLNIKILDEKNFVKIVKG  648 (655)
Q Consensus       622 ~g~K~~kA~~lgi~ii~e~~f~~~l~~  648 (655)
                      +|+|++||+++||+||+|++|.+||++
T Consensus       638 ~gsK~~kA~~lgI~ii~E~~f~~~l~~  664 (665)
T PRK07956        638 AGSKLAKAQELGIEVLDEEEFLRLLGE  664 (665)
T ss_pred             CChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence            999999999999999999999999864

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=100.00  E-value=9.5e-177  Score=1496.37  Aligned_cols=621  Identities=31%  Similarity=0.501  Sum_probs=584.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCC
Q psy11423         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSL   92 (655)
Q Consensus        13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL   92 (655)
                      +++++|++|+++|++||++||++++|+|||++||+|+++|++||++||++.+++|||++||+.+...|.||+|++|||||
T Consensus         4 ~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~lE~~~p~~~~~~Spt~~Vg~~~~~~f~kv~H~~pMlSL   83 (669)
T PRK14350          4 DIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLKFGSDLLNDFKEVEHSFPILSL   83 (669)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCccCCccccccCCceecCCccccc
Confidence            44678999999999999999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             CCCCChHHHHHHHHHHHHhhcc-CCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423         93 DNGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (655)
Q Consensus        93 ~k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (655)
                      +|+|+.+||.+|++|+...+.. ..+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus        84 ~k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~~  163 (669)
T PRK14350         84 DKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDE  163 (669)
T ss_pred             cccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcCC
Confidence            9999999999999999732210 113579999999999999999999999999999999999999999999999999963


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (655)
Q Consensus       172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e  251 (655)
                         |..+|||||+||++++|+++|+++    .++|+||||+|||+|||+||.+++.|+|+||+|+|...+. . ..+|++
T Consensus       164 ---~~~levRGEv~m~~~~F~~lN~~~----~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~-~-~~t~~e  234 (669)
T PRK14350        164 ---KVELVLRGEIYITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL-E-LKTNHD  234 (669)
T ss_pred             ---CceEEEEEEEEeeHHHHHHHHHhh----hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC-C-CCCHHH
Confidence               678999999999999999999876    3689999999999999999999999999999999964332 1 369999


Q ss_pred             HHHHHHhCCCCCCCCceeeCC---HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        252 LLNWYQKIGLSICGEYSVLSG---VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       252 ~l~~L~~~GF~~~~~~~~~~~---~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                      .|++|++|||+++++...+++   .+++++|+++|.+.|+.+||+|||+|||+|++.+|+.||+|+|+||||||||||++
T Consensus       235 ~l~~L~~~GF~v~~~~~~~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~  314 (669)
T PRK14350        235 AFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL  314 (669)
T ss_pred             HHHHHHHCCCCCCcceEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc
Confidence            999999999999998888876   99999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCC
Q psy11423        329 EALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPND  408 (655)
Q Consensus       329 ~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~  408 (655)
                      +++|+|++|+|||||||+|||||+|+||+|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++.
T Consensus       315 ~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~  394 (669)
T PRK14350        315 SGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF  394 (669)
T ss_pred             eeEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             CccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcC
Q psy11423        409 SKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKI  488 (655)
Q Consensus       409 ~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L  488 (655)
                         |.+|++||+||++|++  +++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|
T Consensus       395 ---~~~P~~CP~C~s~l~~--~~~~~~C~n~-~-C~aq~~~~i~hf~sr~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L  467 (669)
T PRK14350        395 ---FKIPDNCPSCKTALIK--EGAHLFCVNN-H-CPSVIVERIKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTF  467 (669)
T ss_pred             ---CCCCCCCCCCCCEeee--CCEEEEECCC-C-CHHHHHhhhheeccCCcccccCcCHHHHHHHHHcCCcCCHHHHhhC
Confidence               8899999999999986  4699999996 6 9999999999999999999999999999999999999999999999


Q ss_pred             ChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHH-HhCCCHHHHHh------cCHHHHhcCC
Q psy11423        489 NFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA-NYFKNLECMFK------ATEEQLLNIP  561 (655)
Q Consensus       489 ~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~-~~fgsl~~l~~------as~eeL~~i~  561 (655)
                      +.++|++++|||+|+++||+++|+.||+.+|+|||+|||||+||+.+|+.|+ ++|++++++.+      ++.++|.+|+
T Consensus       468 ~~~~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~  547 (669)
T PRK14350        468 NFDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIK  547 (669)
T ss_pred             CHHHHhhccCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCC
Confidence            9999999999999999999999999999999999999999999999999999 89999999986      5889999999


Q ss_pred             CCCHHHHHHHHHHhcChhHHHHHHHHHHcCccccc------C-C--------------------------CCCCCeEecc
Q psy11423        562 KIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLN------N-P--------------------------NTKGGKVVNF  608 (655)
Q Consensus       562 GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~------~-~--------------------------~~~G~~v~~s  608 (655)
                      |||+++|++|++||+++.|+++++.|.+.|+.+..      . .                          +++||+|++|
T Consensus       548 giG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ss  627 (669)
T PRK14350        548 GIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTC  627 (669)
T ss_pred             CccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEecc
Confidence            99999999999999999999999999988875320      0 0                          1899999999


Q ss_pred             cccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423        609 ISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF  649 (655)
Q Consensus       609 Vsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~~~  649 (655)
                      ||++|||||+|+++|+|++||++|||+||+|++|.+||+.+
T Consensus       628 VSkktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l~~~  668 (669)
T PRK14350        628 VTKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYVDLD  668 (669)
T ss_pred             ccCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHhcCC
Confidence            99999999999999999999999999999999999999743

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=100.00  E-value=1.4e-176  Score=1500.59  Aligned_cols=617  Identities=45%  Similarity=0.744  Sum_probs=591.6

Q ss_pred             HHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHH
Q psy11423         21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDED  100 (655)
Q Consensus        21 L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~e  100 (655)
                      |+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.++|.||+|++|||||+|+|+.+|
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            67899999999999999999999999999999999999999999999999999999899999999999999999999999


Q ss_pred             HHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEE
Q psy11423        101 VIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEV  180 (655)
Q Consensus       101 l~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~ev  180 (655)
                      |.+|++++.+.++  .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++.+.|..+||
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            9999999987765  13579999999999999999999999999999999999999999999999999974335889999


Q ss_pred             EEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCC
Q psy11423        181 RCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG  260 (655)
Q Consensus       181 RGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~G  260 (655)
                      |||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|...++.. +.+|++.|++|++||
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            9999999999999999999999999999999999999999999999999999999996433222 379999999999999


Q ss_pred             CCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEe
Q psy11423        261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ  340 (655)
Q Consensus       261 F~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q  340 (655)
                      |+|+++...+++++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|++|+||
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             ecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCC
Q psy11423        341 IGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPI  420 (655)
Q Consensus       341 vGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~  420 (655)
                      |||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.++|.+|++||+
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            99999999999999999999999999999999999999999999999999999999999999999988889999999999


Q ss_pred             CCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCc
Q psy11423        421 CNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS  500 (655)
Q Consensus       421 C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG  500 (655)
                      ||++|++.++++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++||++|+|++++|||+|+.++|..|+|||
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            9999999888999999995 6 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhH
Q psy11423        501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (655)
Q Consensus       501 ~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n  580 (655)
                      +|+++||+++|+.+|..+|+|||.+|||||||+++|++|+++|+|+++|..|+.++|.+++|||+++|++|++||+++.|
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             HHHHHHHHHcCcccc---c----C--C--------------------------CCCCCeEecccccCccEEEecCCCCch
Q psy11423        581 RLLISQLRDVGIYWL---N----N--P--------------------------NTKGGKVVNFISKNTNYLVKGQKPGKK  625 (655)
Q Consensus       581 ~~li~~L~~~Gi~~~---~----~--~--------------------------~~~G~~v~~sVsk~t~ylv~g~~~g~K  625 (655)
                      +++|+.|.+.|+.+.   .    .  .                          .++||+|.+|||++|||||+|+.+|+|
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            999999999888642   0    1  0                          189999999999999999999999999


Q ss_pred             HHHHHHcCCeeeCHHHH
Q psy11423        626 LEKAIKLNIKILDEKNF  642 (655)
Q Consensus       626 ~~kA~~lgi~ii~e~~f  642 (655)
                      ++||+++||+||+|++|
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=1.3e-175  Score=1493.13  Aligned_cols=633  Identities=34%  Similarity=0.590  Sum_probs=601.9

Q ss_pred             cCCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecc
Q psy11423          7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHT   86 (655)
Q Consensus         7 ~~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~   86 (655)
                      ...+.+..+++|++|+++|++||++||++++|+|||++||+|+++|++||++| ++.+++|||++||+.+..+|.||+|+
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            45566777789999999999999999999999999999999999999999999 89999999999999999999999999


Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC
Q psy11423         87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP  166 (655)
Q Consensus        87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP  166 (655)
                      +|||||+|+|+.+|+.+|++|+.+.++   ...|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||
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             cccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC
Q psy11423        167 LVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP  246 (655)
Q Consensus       167 ~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~  246 (655)
                      ++|+. .+|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|...++ . +
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 2688999999999999999999999999999999999999999999999999999999999999965432 2 4


Q ss_pred             CCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       247 ~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                      .+|++.|++|++|||+++++...|++++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||
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             cceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCC
Q psy11423        327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP  406 (655)
Q Consensus       327 ~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~  406 (655)
                      +++++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+
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            99999999999999999999999999999999999999999999999999999999999999999999999999997654


Q ss_pred             CCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHh
Q psy11423        407 NDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY  486 (655)
Q Consensus       407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~  486 (655)
                      +.   |.+|++||+||++|++  +++.++|+|... ||+|++++|.||+||++|||+|||+++|++|+++|+|++++|||
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   8899999999999986  467889999756 99999999999999999999999999999999999999999999


Q ss_pred             cCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHH
Q psy11423        487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST  566 (655)
Q Consensus       487 ~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~  566 (655)
                      +|+.++|..|+|||+|+++||+++|++||+.+|+|||+||||||||+++|++|+++|+++++|..|+.++|.+++|||++
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             HHHHHHHHhcChhHHHHHHHHHHcCcccccC------C------------------------CCCCCeEecccccCccEE
Q psy11423        567 TVKAFIKFINQPLHRLLISQLRDVGIYWLNN------P------------------------NTKGGKVVNFISKNTNYL  616 (655)
Q Consensus       567 ~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~------~------------------------~~~G~~v~~sVsk~t~yl  616 (655)
                      +|++|++||++++|+++++.|.+.|+.+...      .                        .++||+|.+|||++||||
T Consensus       572 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~L  651 (689)
T PRK14351        572 VAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYL  651 (689)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHhcccccccccccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEE
Confidence            9999999999999999999999988864210      0                        189999999999999999


Q ss_pred             EecCCCC-chHHHHHHcCCeeeCHHHHHHHHhcccCC
Q psy11423        617 VKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGFSTE  652 (655)
Q Consensus       617 v~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~~~~~  652 (655)
                      |+|+.+| ||++||+++||+||+|++|.+||++.+..
T Consensus       652 v~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~~~~~  688 (689)
T PRK14351        652 VVGENPGQSKRDDAEANDVPTLDEEEFEELLAERGVA  688 (689)
T ss_pred             EEcCCCChhHHHHHHHCCCeEecHHHHHHHHHhcCCC
Confidence            9999999 99999999999999999999999876654

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=100.00  E-value=2.1e-153  Score=1276.39  Aligned_cols=533  Identities=21%  Similarity=0.317  Sum_probs=502.8

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccc
Q psy11423          8 KINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTF   87 (655)
Q Consensus         8 ~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~   87 (655)
                      ..+...++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++.+++|||++||+       ||+|++
T Consensus        24 ~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~p~~~~~~spt~~vg~-------kv~H~~   96 (562)
T PRK08097         24 DWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVPLPPLNG-------KVLHPV   96 (562)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcCcCCCCCCCCCCCC-------ceECCC
Confidence            3466778889999999999999999999999999999999999999999999999999999999986       899999


Q ss_pred             cccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCc
Q psy11423         88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPL  167 (655)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~  167 (655)
                      |||||+|+||.+||.+|++++.         .|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||+
T Consensus        97 PMlSL~k~~s~eel~~w~~~~~---------~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~  167 (562)
T PRK08097         97 AHTGVKKLADKQALARWMAGRS---------DLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQ  167 (562)
T ss_pred             CcccccccCCHHHHHHHHhhcc---------ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccch
Confidence            9999999999999999998852         5999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCC
Q psy11423        168 VLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPS  247 (655)
Q Consensus       168 ~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~  247 (655)
                      +|+.  .|..+|||||+||++++|++.+     .|   |+||||+|||+|||+||+++ .|+|+||+|++..  +   +.
T Consensus       168 ~l~~--~~~~levRGEv~m~~~~F~~~~-----~g---~aNPRN~AAGsLr~~d~~~~-~r~L~~f~y~~~~--~---~~  231 (562)
T PRK08097        168 QLPG--ALANLVLQGELFLRREGHIQQQ-----MG---GINARAKVAGLMMRKDPSPT-LNQIGVFVWAWPD--G---PA  231 (562)
T ss_pred             hhcC--CCCeEEEEEEEEEeHHHHHHHh-----cC---cCCchHHHhHHHhhcCcHhh-hccceEEEEECCC--C---CC
Confidence            9974  4778999999999999998632     22   89999999999999999999 8999999999842  2   47


Q ss_pred             CHHHHHHHHHhCCCCCCC-CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        248 SHSELLNWYQKIGLSICG-EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       248 ~~~e~l~~L~~~GF~~~~-~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                      +|++.|++|++|||++++ +...+.+.+++.+|+++|.  |..+||+|||+|||+||+.+|+  |+|+|+||||||||||
T Consensus       232 t~~e~l~~L~~~GF~v~~~~~~~~~~~~~i~~~~~~~~--r~~l~y~iDGiViKvn~~~~~~--~~ts~~PrWAiAyKf~  307 (562)
T PRK08097        232 SMPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY--RAPLPFVTDGVVVRQAKEPPGR--YWQPGQGEWAVAWKYP  307 (562)
T ss_pred             CHHHHHHHHHHCCCCcCccceEeeCCHHHHHHHHHHHh--hccCCCCCCcEEEEecCHHHHh--hccCCCCCceEEEcCC
Confidence            999999999999999996 7778999999999999886  9999999999999999999998  7899999999999999


Q ss_pred             cceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCC
Q psy11423        327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP  406 (655)
Q Consensus       327 ~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~  406 (655)
                      +++++|+|++|+|||||||++||||+|+||+|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.  |+
T Consensus       308 ~~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~GttVsrATLhN~~~i~~~~I~iGD~V~V~raGdVIP~I~~vv~--~~  385 (562)
T PRK08097        308 PVQQVAEVRAVQFAVGRTGKITVVLELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVVW--RG  385 (562)
T ss_pred             CcEEEEEEEEEEEecCCCceeeEEEEEEEEEeCCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCCCcceeeeec--cc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998  55


Q ss_pred             CCCccccCCCCCCCCCCcceeecCceeEEecC-CCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHH
Q psy11423        407 NDSKIFKIPNICPICNSKIIYIESNLIARCSG-SWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDL  485 (655)
Q Consensus       407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n-~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL  485 (655)
                      +.+.++.+|+.           ++++.+||+| ... ||+|++++|.|||||+||||+|||+++|++|+++|+|++++||
T Consensus       386 ~~~~~~~~P~~-----------~~~~~~~C~n~~~~-Cpaq~~~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Di  453 (562)
T PRK08097        386 AERTKPTPPDA-----------DRFHSLSCFRASPG-CQEQFLARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSW  453 (562)
T ss_pred             ccCCCCcCCCC-----------CCceEEEeCCCCCC-CHHHHHHHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHH
Confidence            55556777764           2457899998 556 9999999999999999999999999999999999999999999


Q ss_pred             hcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCH
Q psy11423        486 YKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGS  565 (655)
Q Consensus       486 ~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~  565 (655)
                      |+|+.++|++++|||+|+++||+++|++||+.+|+|||+|||||+||+.+|+.   +|+++++|.+++.++|.+|+|||+
T Consensus       454 y~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~  530 (562)
T PRK08097        454 LALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGE  530 (562)
T ss_pred             hcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchH
Confidence            99999999999999999999999999999999999999999999999988876   899999999999999999999999


Q ss_pred             HHHHHHHHHhcChhHHHHHHHHHHcCcc
Q psy11423        566 TTVKAFIKFINQPLHRLLISQLRDVGIY  593 (655)
Q Consensus       566 ~~A~~I~~~f~~~~n~~li~~L~~~Gi~  593 (655)
                      ++|++|++||++++|+++++.|.+.|++
T Consensus       531 ~~a~si~~~f~~~~~~~~i~~L~~~gv~  558 (562)
T PRK08097        531 GRARQLIAFLQHPEVKALADWLAAQGIT  558 (562)
T ss_pred             HHHHHHHHHHcCHHHHHHHHHHHHcCCC
Confidence            9999999999999999999999998875

>smart00532 LIGANc Ligase N family

Probab=100.00  E-value=7.5e-138  Score=1131.69  Aligned_cols=440  Identities=47%  Similarity=0.758  Sum_probs=420.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCC
Q psy11423         15 SFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDN   94 (655)
Q Consensus        15 ~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k   94 (655)
                      +++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+.++|.||+|++|||||+|
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            46799999999999999999999999999999999999999999999999999999999999899999999999999999


Q ss_pred             CCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCC
Q psy11423         95 GFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYP  174 (655)
Q Consensus        95 ~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~  174 (655)
                      +|+.+||.+|++++.+.++  .+..|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+. +.
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            9999999999999987665  24689999999999999999999999999999999999999999999999999974 25


Q ss_pred             CceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHH
Q psy11423        175 PELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN  254 (655)
Q Consensus       175 p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~  254 (655)
                      |..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++...++.....+|++.|+
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 psy11423        255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI  334 (655)
Q Consensus       255 ~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v  334 (655)
                      +|++|||+|+++...+.+++++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|
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             EEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccC
Q psy11423        335 KAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKI  414 (655)
Q Consensus       335 ~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~  414 (655)
                      ++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++++.+|.+
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            99999999999999999999999999999999999999999999999999999999999999999999999888889999


Q ss_pred             CCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccc
Q psy11423        415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKA  459 (655)
Q Consensus       415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~  459 (655)
                      |++||+||++|++.++++.+||+|. . ||+|++++|.||+||+|
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=5.8e-95  Score=762.49  Aligned_cols=306  Identities=47%  Similarity=0.768  Sum_probs=292.6

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCC
Q psy11423         17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGF   96 (655)
Q Consensus        17 ~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~   96 (655)
                      +|++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.+.|.||+|++|||||+|+|
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            68999999999999999999999999999999999999999999999999999999999988999999999999999999


Q ss_pred             ChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCc
Q psy11423         97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPE  176 (655)
Q Consensus        97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~  176 (655)
                      +.+||.+|++++.+.++  .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.  .|.
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             eEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHH
Q psy11423        177 LLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY  256 (655)
Q Consensus       177 ~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L  256 (655)
                      .+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..++.. +.+|++.|++|
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            99999999999999999999999999999999999999999999999999999999999997543322 47999999999


Q ss_pred             HhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCc
Q psy11423        257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (655)
Q Consensus       257 ~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (655)
                      ++|||+|+++...|.+++++++|+++|.+.|..+||+|||+|||+|++.+|+.||.|+|+||||||||||+
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=2.5e-94  Score=760.75  Aligned_cols=313  Identities=44%  Similarity=0.689  Sum_probs=270.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcc-cCCCCcceeccccccC
Q psy11423         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTFKMMS   91 (655)
Q Consensus        13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~pMlS   91 (655)
                      ++++++++|+++|++||++||+.|+|+|||++||+|+++|++||++||++.+++|||++||+. +.+.|.+|+|++||||
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            357899999999999999999999999999999999999999999999999999999999954 4566999999999999


Q ss_pred             CCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (655)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (655)
                      |+|+|+.+||.+|++++.+.++.. ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|.+||++|+.
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            999999999999999999888742 2269999999999999999999999999999999999999999999999999985


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (655)
Q Consensus       172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e  251 (655)
                      .  |+.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|..+++...+.+|++
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  79999999999999999999999999999999999999999999999999999999999999997654223589999


Q ss_pred             HHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       252 ~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                      .|++|++|||+|+++...+.+.++|++++++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||++
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=1.5e-31  Score=227.09  Aligned_cols=82  Identities=51%  Similarity=0.764  Sum_probs=70.7

Q ss_pred             eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423        330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS  409 (655)
Q Consensus       330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~  409 (655)
                      ++|+|++|+|||||||++||||+|+||.|+|++|+||||||+++|+++||++||+|.|+|||||||+|++|++++|++++
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            47999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cc
Q psy11423        410 KI  411 (655)
Q Consensus       410 ~~  411 (655)
                      +|
T Consensus        81 ~p   82 (82)
T PF03120_consen   81 QP   82 (82)
T ss_dssp             BB
T ss_pred             CC
Confidence            54

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.

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

Probab=99.63  E-value=4.5e-16  Score=127.57  Aligned_cols=64  Identities=45%  Similarity=0.719  Sum_probs=55.4

Q ss_pred             HHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHH
Q psy11423        521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI  584 (655)
Q Consensus       521 r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li  584 (655)
                      |||+||||||||+++|+.|+++|+|+++|.+|+.++|.+++|||+++|++|++||+++.|+++|
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            7999999999999999999999999999999999999999999999999999999999999875

>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins

Probab=99.17  E-value=3.7e-10  Score=121.47  Aligned_cols=144  Identities=22%  Similarity=0.195  Sum_probs=109.3

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~  198 (655)
                      .|+||+|+||.++.+.|.+|+ +.|.||| |..++++|++++.+  +|..+.. ..| .+.+.||++++...|..     
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  5776642 234 49999999998755421     


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCCCCCc--eeeCCHHHH
Q psy11423        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEY--SVLSGVNKL  276 (655)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~~~~~--~~~~~~~ev  276 (655)
                          .   .             .|.   .+++.||+|++...++. ...++.+..++|.++||+.++..  ..+.+.+++
T Consensus       118 ----~---~-------------~~~---~~~v~F~vFDI~~~~~~-~~lp~~eR~~lLe~lg~~~v~~~~~~~~~d~~~l  173 (342)
T cd07894         118 ----G---S-------------YPE---VEDVGFFVFDIRKKNTG-RPLPVEERRELLEKYGLPTVRLFGEFTADEIEEL  173 (342)
T ss_pred             ----c---c-------------Ccc---ccccEEEEEeeEEcCCC-CCCCHHHHHHHHHhcCCCCcceEEEEecCCHHHH
Confidence                0   0             111   26899999999864322 23678999999999999877642  234567788


Q ss_pred             HHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423        277 IEFYKKINIKRFNLPYEIDGVVYKINC  303 (655)
Q Consensus       277 ~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (655)
                      .++++.+.+.-      --|||+|--+
T Consensus       174 ~~~l~~~~~~G------~EGVVlK~~~  194 (342)
T cd07894         174 KEIIRELDKEG------REGVVLKDPD  194 (342)
T ss_pred             HHHHHHHHHCC------CceEEEeccc
Confidence            88887764322      5799998765

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.

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=98.77  E-value=5.4e-09  Score=111.64  Aligned_cols=49  Identities=20%  Similarity=0.332  Sum_probs=47.1

Q ss_pred             CCCCeEecccccCccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKG  648 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~~  648 (655)
                      ++|++|.+|||++|||||||+++|  ||++||+++||+||+|++|++||..
T Consensus       257 ~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll~~  307 (313)
T PRK06063        257 HAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLRA  307 (313)
T ss_pred             HcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHHHh
Confidence            899999999999999999999988  9999999999999999999999953

>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins

Probab=98.76  E-value=5e-08  Score=95.34  Aligned_cols=139  Identities=16%  Similarity=0.239  Sum_probs=94.6

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~  198 (655)
                      .|++|+|+||+.+.+   +|.  ++.||+    |+++|.......         .+|. +.+.||+++....|+.+    
T Consensus        17 ~~~~e~K~DG~R~~~---~~~--~~~SR~----g~~~t~~~~~~~---------~l~~-~ilDGElv~~~~~f~~l----   73 (174)
T cd07896          17 GYLVSEKLDGVRAYW---DGK--QLLSRS----GKPIAAPAWFTA---------GLPP-FPLDGELWIGRGQFEQT----   73 (174)
T ss_pred             HeeechhhceEEEEE---ecc--EEEecC----CcCCCCCHHHHh---------hCCC-CccCceEEcCCCCHHHH----
Confidence            689999999999854   454  889996    999997522111         1343 78999999987777665    


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhC-------CCCCCCCceeeC
Q psy11423        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLSICGEYSVLS  271 (655)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------GF~~~~~~~~~~  271 (655)
                                     +|.++++++......++.|++|++...     ..+..+..+.|.++       .|.+++ ...+.
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                           344444444333446799999999872     24555655555332       233333 23567


Q ss_pred             CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       272 ~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                      +.+++.++++...+.      ..+|+|+|-.|..++
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      579999999887774

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

>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=8.3e-09  Score=83.45  Aligned_cols=56  Identities=29%  Similarity=0.361  Sum_probs=52.2

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .+..++|+|+|++++.+|++.| +.|+.||+.++.++|..++|||+++|++|+++++
T Consensus         4 ~~~L~~I~Gig~~~a~~L~~~G-~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~   59 (60)
T PF14520_consen    4 FDDLLSIPGIGPKRAEKLYEAG-IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR   59 (60)
T ss_dssp             HHHHHTSTTCHHHHHHHHHHTT-CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred             HHhhccCCCCCHHHHHHHHhcC-CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence            3467899999999999999998 6999999999999999999999999999999875

...

>PRK09125 DNA ligase; Provisional

Probab=98.70  E-value=1.2e-06  Score=92.39  Aligned_cols=198  Identities=17%  Similarity=0.179  Sum_probs=124.5

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR  198 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~  198 (655)
                      .|++|+|+||+-+.   .+|  +++.||    .|+|+|+--        .+.. .+| .+.+-||+++...+|+.+....
T Consensus        44 ~~~~E~K~DG~R~~---~~~--v~l~SR----~g~~it~p~--------~~~~-~~~-~~vLDGElv~~~~~F~~l~~r~  104 (282)
T PRK09125         44 GYLVSEKLDGVRAY---WDG--KQLLTR----QGNPIAAPA--------WFTA-GFP-PFPLDGELWAGRGQFEAISSIV  104 (282)
T ss_pred             hEEEEeeeeeEeEE---ECC--eEEEcC----CCCcCCCch--------hHHh-cCC-CccEeEEEEeCCCCHHHHHHHH
Confidence            69999999999994   366  589999    788998721        1111 134 5789999999989998775532


Q ss_pred             HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCC-CCC-----ceeeCC
Q psy11423        199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSI-CGE-----YSVLSG  272 (655)
Q Consensus       199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~-~~~-----~~~~~~  272 (655)
                                         +++++......++.|++|++...+     .+..+..+.|+++==+. .+.     ...+.+
T Consensus       105 -------------------~~k~~~~~~~~~v~~~vFDll~~~-----gpl~eRr~~L~~li~~~~~~~i~~~~~~~~~~  160 (282)
T PRK09125        105 -------------------RDKTPDDAAWRKVRFMVFDLPDAP-----GDFEERLAVLKKLLAKLPSPYIKIIEQIRVRS  160 (282)
T ss_pred             -------------------ccCCcchhhhcccEEEEEEcCCCC-----CCHHHHHHHHHHHHhhCCCCcEEEEeEEEcCC
Confidence                               222222122347999999997643     25566666666541111 111     223568


Q ss_pred             HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-cceeeeEE
Q psy11423        273 VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPVA  351 (655)
Q Consensus       273 ~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~itPvA  351 (655)
                      .+++.++++.+.+      -...|+|+|--|..+.  -|   ++..| +=+| +....+..|.++.|..|| +|.+.-..
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            8899998887653      2368999997776654  24   45567 4444 335578899999998874 45443221


Q ss_pred             EEEEEEECCEEEEEeeCCCHHHHH
Q psy11423        352 LLKPVLIDGITITRATLHNESEIY  375 (655)
Q Consensus       352 ~lePV~l~G~tVsratLhN~~~i~  375 (655)
                      .-   .-+|.+++=+|....+.-+
T Consensus       228 v~---~~~g~~~~VgsG~t~~~r~  248 (282)
T PRK09125        228 VE---TPDGREFKIGSGFSDAERE  248 (282)
T ss_pred             EE---eCCCCEEEeCCCCCHHHhc
Confidence            11   1256555445666666544

>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases

Probab=98.61  E-value=1.2e-06  Score=87.60  Aligned_cols=166  Identities=16%  Similarity=0.155  Sum_probs=105.9

Q ss_pred             CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh----hHH
Q psy11423        117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFI  192 (655)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~----~F~  192 (655)
                      ...|++|+|+||.-+.+.+..|. +++.||    -|.|+|+....+...   +.  ..|..+.+-||++.-..    .|.
T Consensus        20 ~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~i~~~---~~--~~~~~~vLDGElv~~~~~~~~~f~   89 (201)
T cd07898          20 PAAAWVEDKYDGIRAQVHKDGGR-VEIFSR----SLEDITDQFPELAAA---AK--ALPHEFILDGEILAWDDNRGLPFS   89 (201)
T ss_pred             CCeEEEEEeeceEEEEEEEeCCE-EEEEcC----CChhchhhhhhHHHH---HH--hCCCCEEEEEEEEEEeCCCCCcHH
Confidence            35799999999999998776554 699999    467898755433221   11  13567899999986432    365


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc----
Q psy11423        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY----  267 (655)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~----  267 (655)
                      .+.....   .      |+..      ..  .....++.|++|++....+.++ ..+..+..+.|+++.-+.+...    
T Consensus        90 ~~~~~~~---~------~~~~------~~--~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~  152 (201)
T cd07898          90 ELFKRLG---R------KFRD------KF--LDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP  152 (201)
T ss_pred             HHHHHhc---c------cccc------hh--hhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee
Confidence            5433210   0      0000      00  1123469999999986544332 2578899999999865543332    


Q ss_pred             -eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423        268 -SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (655)
Q Consensus       268 -~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (655)
                       ..+++.+++.++++.+.+      -..+|+|+|--+..+.  .|  .++..|
T Consensus       153 ~~~~~~~~~~~~~~~~~~~------~g~EGim~K~~~s~Y~--~g--~Rs~~w  195 (201)
T cd07898         153 ALPVESAEELEAAFARARA------RGNEGLMLKDPDSPYE--PG--RRGLAW  195 (201)
T ss_pred             eEEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCcC--CC--CcCCCc
Confidence             235688888888776654      3369999999876553  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

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=98.51  E-value=9.1e-08  Score=102.14  Aligned_cols=49  Identities=43%  Similarity=0.636  Sum_probs=45.7

Q ss_pred             CCCCeEecccccCccEEEecC---------CCCchHHHHHHc-----CCeeeCHHHHHHHHhc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQ---------KPGKKLEKAIKL-----NIKILDEKNFVKIVKG  648 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~---------~~g~K~~kA~~l-----gi~ii~e~~f~~~l~~  648 (655)
                      .+||+|.+|||++|||||+|+         .+|+|++||++|     ||+||+|++|.+||..
T Consensus       246 ~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~ii~E~~f~~l~~~  308 (309)
T PRK06195        246 RLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEFLQKCKE  308 (309)
T ss_pred             HhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEEecHHHHHHHHhh
Confidence            899999999999999999995         457999999999     9999999999999863

>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=98.43  E-value=1e-07  Score=65.19  Aligned_cols=28  Identities=36%  Similarity=0.816  Sum_probs=19.2

Q ss_pred             CCCCCCCcceeecCceeEEecCCCcCCHH
Q psy11423        417 ICPICNSKIIYIESNLIARCSGSWIECIA  445 (655)
Q Consensus       417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~  445 (655)
                      +||+||++|++.++++.+||+|++. |||
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            6999999999999999999999767 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.

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

Probab=98.43  E-value=3.3e-06  Score=85.02  Aligned_cols=156  Identities=20%  Similarity=0.130  Sum_probs=103.6

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCC-ceEEEEEEEEeehh-----hH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPP-ELLEVRCEVLIYKK-----DF  191 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p-~~~evRGEv~~~~~-----~F  191 (655)
                      ..|++|+|+||.-+.+.+.+| =+++.||+    |.|+|+.+..+...-..+    .+ ..+.+-||+++...     +|
T Consensus        25 ~~~~~E~K~DG~R~~~~~~~~-~v~~~SR~----~~~~t~~~pel~~~~~~~----~~~~~~iLDGElv~~~~~g~~~~F   95 (207)
T cd07901          25 GEAAVEYKYDGIRVQIHKDGD-EVRIFSRR----LEDITNALPEVVEAVREL----VKAEDAILDGEAVAYDPDGRPLPF   95 (207)
T ss_pred             CcEEEEEeEcceeEEEEEeCC-EEEEEeCC----CccccchhhHHHHHHHhc----CCCCCEEEeCEEEEECCCCCccCH
Confidence            479999999999999877655 47999996    899999876654321112    12 46899999998762     57


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCC--C
Q psy11423        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--E  266 (655)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~--~  266 (655)
                      +.+-...                   ++...  ......++.|++|++....+.++ .....+..+.|.++.-+...  .
T Consensus        96 ~~l~~r~-------------------~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~~~i~~  156 (207)
T cd07901          96 QETLRRF-------------------RRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPETEAILL  156 (207)
T ss_pred             HHHHHHh-------------------ccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcCCcEEE
Confidence            6543321                   11110  01123579999999986554332 24788888899887654311  0


Q ss_pred             --ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       267 --~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                        ...+.+.+++.++++.+.+.      ...|+|+|--+..+.
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~  193 (207)
T cd07901         157 APRIVTDDPEEAEEFFEEALEA------GHEGVMVKSLDSPYQ  193 (207)
T ss_pred             EEEEecCCHHHHHHHHHHHHHc------CCceEEEeCCCCCcC
Confidence              12356788999988877543      368999998775543

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

>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=98.41  E-value=6.9e-07  Score=72.21  Aligned_cols=55  Identities=33%  Similarity=0.421  Sum_probs=50.5

Q ss_pred             HHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       522 ~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      |...+.|||||++++++|.+. |.+++.|..++.++|.+++|||+++|++|++.++
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            444568999999999999999 9999999999999999999999999999998764

...

>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=98.38  E-value=5.3e-06  Score=82.49  Aligned_cols=158  Identities=17%  Similarity=0.192  Sum_probs=101.4

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc-cCCcccccCCCCceEEEEEEEEe------ehhh
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH-KIPLVLNIKYPPELLEVRCEVLI------YKKD  190 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~-~iP~~l~~~~~p~~~evRGEv~~------~~~~  190 (655)
                      ..|++|+|+||+-+.+.+.+|. +++.||    .|.++|+....+. .+...+..  -+..+.+-||+++      +...
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    6889998544331 12222211  1236999999999      3344


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC--
Q psy11423        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE--  266 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~--  266 (655)
                      |.                   ..++.+++.+... ....++.|++|++...++..+ ..+..+..+.|.++--.....  
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 114579999999986544221 247888888888765111121  


Q ss_pred             ---ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        267 ---YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       267 ---~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                         ...+.+.+++.++++.+.+..      -.|+|+|--+..+.
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~g------~EG~v~K~~~~~Y~  190 (202)
T PF01068_consen  153 IVESYVVNSKEELEELFEEAIDQG------FEGLVLKDPDSPYE  190 (202)
T ss_dssp             EEEEEEESSHHHHHHHHHHHHHTT------SSEEEEEETTSSC-
T ss_pred             EeeeecCCCHHHHHHHHHHHHHcC------CceEEEECCCCccC
Confidence               234678999999988775433      58999998665443

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 ....

>PRK03180 ligB ATP-dependent DNA ligase; Reviewed

Probab=98.38  E-value=1.7e-05  Score=90.10  Aligned_cols=216  Identities=17%  Similarity=0.108  Sum_probs=137.3

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh-----hHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFIK  193 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~-----~F~~  193 (655)
                      .|++|+|+||.-+.+...+|. ++..||+    |+|+|+....+......++    ...+.+-||++.-..     .|+.
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 7999995    8999988765543222221    246889999998653     5654


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-CCCcee
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-CGEYSV  269 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~-~~~~~~  269 (655)
                      +-..                   ++++.+  ......++.|++|++...++.++ ..+..+..+.|.++--+. ......
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            4221                   111111  01123579999999987655443 257788888888763211 111234


Q ss_pred             eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeec-Ccceee
Q psy11423        270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIG-RTGIIT  348 (655)
Q Consensus       270 ~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvG-RTG~it  348 (655)
                      +.+.+++.++++...+.      ..-|+|+|--+..++  .|.  +...| +-+|- .......|.+..|.-| |+|.++
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            67889999988876432      468999998775553  232  23445 45663 5677888999888888 566654


Q ss_pred             e--EEEEEEEEECCE--EEEEe-eCCCHHHHHh
Q psy11423        349 P--VALLKPVLIDGI--TITRA-TLHNESEIYR  376 (655)
Q Consensus       349 P--vA~lePV~l~G~--tVsra-tLhN~~~i~~  376 (655)
                      .  +|..+|-  +|.  +|.++ |.++-+++++
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  2433331  244  45555 6677755554

>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain

Probab=98.36  E-value=2.1e-05  Score=83.72  Aligned_cols=209  Identities=19%  Similarity=0.189  Sum_probs=131.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~  193 (655)
                      ..|++|+|+||.-+.+...+| -++..||    .|+|+|+....+...-..++    ...+.+-||+++-    ..+|+.
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 5799999    79999987654433322221    2368999999983    456766


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC-c-e--
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-Y-S--  268 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~-~-~--  268 (655)
                      +-..                   ++...     ..++.|++|++...++.++ .....+..+.|+++-=+.... . .  
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     1579999999987655433 246778888887762111111 1 1  


Q ss_pred             eeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceee
Q psy11423        269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIIT  348 (655)
Q Consensus       269 ~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~it  348 (655)
                      ...+.+++.++++...+.      ...|||+|--|..++.  |   +++.| +-+| +....+..|.+.....||.|.+.
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            235677888887766532      3689999998866542  3   36778 4555 33456778888888877665544


Q ss_pred             eE--EEEEEEEECCE--EEEEe-eCCCHHHHHh
Q psy11423        349 PV--ALLKPVLIDGI--TITRA-TLHNESEIYR  376 (655)
Q Consensus       349 Pv--A~lePV~l~G~--tVsra-tLhN~~~i~~  376 (655)
                      ..  +..++    |.  .|-++ |..+.+..++
T Consensus       206 slll~~~~~----~~l~~vg~vgsG~s~~~~~~  234 (298)
T TIGR02779       206 ALLLGVYEG----GGLRYVGRVGTGFSEAELAT  234 (298)
T ss_pred             eEEEEEECC----CeEEEEeEecCCCCHHHHHH
Confidence            33  22222    32  34454 6777776665

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=98.35  E-value=6.1e-06  Score=81.89  Aligned_cols=163  Identities=17%  Similarity=0.192  Sum_probs=101.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~----~~F~~  193 (655)
                      ..|++|+|+||.-+.+.+.+| -+++.||    .|+++|+....|...=..+    .+..+.+-||+++-.    ..|..
T Consensus        16 ~~~~~e~K~DG~R~~i~~~~~-~v~~~SR----~g~~~t~~~p~l~~~~~~~----~~~~~iLDGElv~~~~~~~~~F~~   86 (190)
T cd07906          16 EDWLYEIKWDGYRALARVDGG-RVRLYSR----NGLDWTARFPELAEALAAL----PVRDAVLDGEIVVLDEGGRPDFQA   86 (190)
T ss_pred             CCeEEEEeEceEEEEEEEECC-EEEEEcC----CCCcchhhhHHHHHHHHhc----CCCCEEEEeEEEEECCCCCCCHHH
Confidence            369999999999999988666 5799999    6888887554433211111    134688999999843    35654


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG  272 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~~~~  272 (655)
                      +-.                   ..++.+ .......+.|++|++...++..+ ..+..+..+.|.++.-+..+...++..
T Consensus        87 l~~-------------------~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~  146 (190)
T cd07906          87 LQN-------------------RLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEH  146 (190)
T ss_pred             HHH-------------------hhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECce
Confidence            321                   111111 12234579999999976544332 257889999999987665343333332


Q ss_pred             H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423        273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (655)
Q Consensus       273 ~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (655)
                      . .+..++++++.+      -..+|+|+|--+..+.  .|.  +++.|
T Consensus       147 ~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~--~g~--rs~~w  184 (190)
T cd07906         147 FEGGGAALFAAACE------LGLEGIVAKRADSPYR--SGR--RSRDW  184 (190)
T ss_pred             EcCCHHHHHHHHHH------cCCcEEEEecCCCCcC--CCC--CCCcc
Confidence            2 222455554432      2469999999886554  233  34667

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.34  E-value=5.9e-07  Score=106.05  Aligned_cols=125  Identities=20%  Similarity=0.334  Sum_probs=103.6

Q ss_pred             hHHHHHhCCCCccHHHHHHHHHhCCC--HHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc-ChhHHHHHHHHHHcCccccc
Q psy11423        520 SRFIYALGIRHVGETTAKELANYFKN--LECMFKATEEQLLNIPKIGSTTVKAFIKFIN-QPLHRLLISQLRDVGIYWLN  596 (655)
Q Consensus       520 ~r~L~algIpgIG~~~Ak~L~~~fgs--l~~l~~as~eeL~~i~GIG~~~A~~I~~~f~-~~~n~~li~~L~~~Gi~~~~  596 (655)
                      .+||..-.|||||+++|++|.++||.  ++.|.+ +++.|..|+|||++.++.|.+-+. ....++++.+|...|++...
T Consensus        81 ~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~-~~~~L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~gi~~~~  159 (720)
T TIGR01448        81 VAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDD-DPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKL  159 (720)
T ss_pred             HHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHh-CHHHHhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcCCCHHH
Confidence            47777667999999999999999993  444544 588999999999999999998554 45578899999999997544


Q ss_pred             CC---CCCCCeEecccccCccEEEecCCCC---chHHH-HHHcCCeeeCHHHHHHHH
Q psy11423        597 NP---NTKGGKVVNFISKNTNYLVKGQKPG---KKLEK-AIKLNIKILDEKNFVKIV  646 (655)
Q Consensus       597 ~~---~~~G~~v~~sVsk~t~ylv~g~~~g---~K~~k-A~~lgi~ii~e~~f~~~l  646 (655)
                      ..   ..+|......|..|| |.++.+..|   .++|+ |+++|++..++..+...+
T Consensus       160 a~ki~~~yg~~~~~~i~~nP-Y~L~~~i~gigF~~aD~iA~~~g~~~~d~~Ri~a~i  215 (720)
T TIGR01448       160 AQRIYKFYQADTLDRVEKDP-YLLAEDVKGIGFLTADQLAQALGIALNDPRRITAGL  215 (720)
T ss_pred             HHHHHHHHhHHHHHHHHhCc-hhhhhhcCCCCHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            33   478999999999999 999876554   89999 999999999999877654

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.

>PRK07636 ligB ATP-dependent DNA ligase; Reviewed

Probab=98.32  E-value=8.2e-05  Score=78.31  Aligned_cols=205  Identities=18%  Similarity=0.213  Sum_probs=128.4

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~----~~F~~  193 (655)
                      ..|++|+|+||.-+.+.-.+| -+++.||    .|.|+|+....+-..       ..|..+.+-||++...    .+|+.
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            479999999999997754455 4799999    688999876544321       1345689999999843    46766


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG  272 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~~~~  272 (655)
                      +-...                   ++..+  ....++.|++|++...++.++ ..+..+..+.|+++.-+. +....+..
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            53210                   11111  124579999999987655433 247889999999886543 33333332


Q ss_pred             -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeEE
Q psy11423        273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA  351 (655)
Q Consensus       273 -~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPvA  351 (655)
                       .++..++++...+      -...|||+|--|..++    ...++..| +-.| ..+..+..|.+.  ..|..|.+  ++
T Consensus       144 ~~~~~~~~~~~~~~------~g~EGiV~K~~ds~Y~----~g~Rs~~W-lKiK-~~~~~e~vV~G~--~~~~~g~l--lg  207 (275)
T PRK07636        144 IEGHGTAYFELVEE------RELEGIVIKKANSPYE----INKRSDNW-LKVI-NYQYTDVLITGY--RKEEFGLL--LS  207 (275)
T ss_pred             ccccHHHHHHHHHH------cCCcEEEEeCCCCCCC----CCCCCCCe-EEEe-cCCeEEEEEEEE--ecCCCcEE--EE
Confidence             2355566655532      2356999999887664    12345678 6666 345566777666  34445533  44


Q ss_pred             EEEEEEECCEEEEEeeCCCHHHHHhc
Q psy11423        352 LLKPVLIDGITITRATLHNESEIYRK  377 (655)
Q Consensus       352 ~lePV~l~G~tVsratLhN~~~i~~~  377 (655)
                      ..     +|..|-++.-...+..+++
T Consensus       208 ~~-----~g~~~G~vgt~~~~~~~~l  228 (275)
T PRK07636        208 YL-----DGRSAGIMEFMPYDARKKF  228 (275)
T ss_pred             ec-----CCeEEEEECCCCHHHHHHH
Confidence            32     5667777643555555544

>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I

Probab=98.27  E-value=2.5e-05  Score=79.45  Aligned_cols=159  Identities=17%  Similarity=0.172  Sum_probs=103.7

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccC-CcccccCCCCceEEEEEEEEeehh------h
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLNIKYPPELLEVRCEVLIYKK------D  190 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~~~~~p~~~evRGEv~~~~~------~  190 (655)
                      ..|++|+|+||.-+.+.+.+|.-++..||    .|+|+|+....+... ...+..  -+..+.+-||+++-..      .
T Consensus        31 ~~~~~E~K~DG~R~~~h~~~~~~v~l~SR----~g~~~t~~~pel~~~~~~~~~~--~~~~~iLDGElv~~~~~~g~~~~  104 (219)
T cd07900          31 KEFTCEYKYDGERAQIHLLEDGKVKIFSR----NLENNTEKYPDIVAVLPKSLKP--SVKSFILDSEIVAYDRETGKILP  104 (219)
T ss_pred             CeEEEEEeecceEEEEEEcCCCeEEEECC----CCccccchhhHHHHHHHHHhcc--cCccEEEeeEEEEEEcCCCCCcC
Confidence            47999999999999999976334799999    589999887655432 222210  1456899999987543      4


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc--
Q psy11423        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY--  267 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~--  267 (655)
                      |+.+-..                   .+...+......++.|++|++...++..+ ..+..+..+.|.++-=+.+...  
T Consensus       105 F~~l~~r-------------------~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~  165 (219)
T cd07900         105 FQVLSTR-------------------KRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQF  165 (219)
T ss_pred             hHHHhhh-------------------cccccccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCCCeEEE
Confidence            5443211                   01111111234679999999987655443 2477788888887632222111  


Q ss_pred             ---eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC--hhhh
Q psy11423        268 ---SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC--LSTQ  307 (655)
Q Consensus       268 ---~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~--~~~~  307 (655)
                         ..+.+.+++.++++.+.+.      ..-|||+|--+  ..++
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~~~s~Y~  204 (219)
T cd07900         166 ATSKDSEDTEEIQEFLEEAVKN------NCEGLMVKTLDSDATYE  204 (219)
T ss_pred             EEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCccC
Confidence               2356788999988877543      46899999877  5553

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

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

Probab=98.19  E-value=7.4e-05  Score=85.32  Aligned_cols=218  Identities=18%  Similarity=0.175  Sum_probs=134.5

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc-cc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII-HK-IPLVLNIKYPPELLEVRCEVLIYKK------D  190 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i-~~-iP~~l~~~~~p~~~evRGEv~~~~~------~  190 (655)
                      .|++|+|+||.-+.+.+.+|. ++..||    .|+|+|+....+ .. +...++.   .....+-||++.-..      .
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            799999999999999875554 799999    688999766443 21 1111210   125789999997643      4


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcC-cccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc-
Q psy11423        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLN-PKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY-  267 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d-~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~-  267 (655)
                      |+.+-...                   ++.+ .......++.||+|++...++.++ ..+..+..+.|.++-=+.+... 
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            55432210                   1101 011134579999999987555332 2578888888988643333222 


Q ss_pred             ----eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC-------cceeeEEEEE
Q psy11423        268 ----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA  336 (655)
Q Consensus       268 ----~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~  336 (655)
                          ..+.+.+++.++++...+.      ...|+|+|--+..++  .|  .+++.|   +|+-       .......|.+
T Consensus       321 ~~~~~~~~~~e~~~~~~~~~~~~------g~EGlv~K~~ds~Y~--~G--~Rs~~W---lK~K~~y~~~~~~~~D~vvig  387 (514)
T TIGR00574       321 IAEMKITSNVEELEKFLNEAISE------GCEGLMLKDLKSIYE--PG--KRGWLW---LKFKPEYLEGMGDTLDLVVIG  387 (514)
T ss_pred             EEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCccc--CC--CCCCcc---eeCchhhcccccCceeEEEEe
Confidence                2346888999988766543      368999998776554  23  345667   4554       3566778888


Q ss_pred             EEEeecC-cceeeeEE--EEEEEEECCE--EEEEe-eCCCHHHHHhcC
Q psy11423        337 INIQIGR-TGIITPVA--LLKPVLIDGI--TITRA-TLHNESEIYRKN  378 (655)
Q Consensus       337 I~~qvGR-TG~itPvA--~lePV~l~G~--tVsra-tLhN~~~i~~~~  378 (655)
                      ..+.-|| .|.++...  ..++-  .|.  +|.++ |.+..+.++++.
T Consensus       388 ~~~g~gk~~g~~~~~l~g~~d~~--~~~~~~v~kvgsG~sd~~l~~l~  433 (514)
T TIGR00574       388 AYYGKGKRTGMYGSFLLACYDPE--SEEFKTITKVGTGFTDADLQELG  433 (514)
T ss_pred             eEecCCccCCceeEEEEEEEcCC--CCeEEEEEEECCCCCHHHHHHHH
Confidence            8888774 45444332  22220  021  45444 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).

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

Probab=98.19  E-value=1.8e-05  Score=77.76  Aligned_cols=150  Identities=17%  Similarity=0.152  Sum_probs=96.7

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~  197 (655)
                      ..|++|+|.||.-+.+.+.+|. +.+.||    .|+++|.-...+..  ..+.  ..+....+-||+++....+      
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            5799999999999999887665 789999    67788875433321  0111  1244689999999865433      


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCC--Cce-----e
Q psy11423        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--EYS-----V  269 (655)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~--~~~-----~  269 (655)
                                                  ....+.|++|++...++.++ ..+..+.++.|+++-=....  ...     .
T Consensus        84 ----------------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~~  135 (182)
T cd06846          84 ----------------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLEN  135 (182)
T ss_pred             ----------------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEeec
Confidence                                        12369999999987554332 24778888888775422210  011     1


Q ss_pred             eC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423        270 LS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (655)
Q Consensus       270 ~~-~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (655)
                      +. ..+++.+++++.      .....||+|+|--+..+.   |...+.+.|
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            12 222366666544      346789999999887664   445566666

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

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

Probab=98.18  E-value=1.5e-06  Score=85.71  Aligned_cols=50  Identities=38%  Similarity=0.618  Sum_probs=47.9

Q ss_pred             CCCCeEecccccCccEEEecCCCC-chHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF  649 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~~  649 (655)
                      .|||+|..+.|.+|+|||.|+++| +|++|+++|+|+.|+|++|..||..-
T Consensus       182 ~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~  232 (276)
T COG5275         182 VYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDT  232 (276)
T ss_pred             HhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHHHHhcC
Confidence            899999999999999999999999 99999999999999999999999643

>PRK08224 ligC ATP-dependent DNA ligase; Reviewed

Probab=98.18  E-value=7e-05  Score=81.37  Aligned_cols=215  Identities=14%  Similarity=0.129  Sum_probs=131.3

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh---hhHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK---KDFIKLN  195 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~---~~F~~~n  195 (655)
                      .|.+|+|+||.-+.+.+.+|. ++..||    .|.|+|+....|...-..+    .|..+.+-||++.-.   .+|+.+.
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            699999999999988776555 799999    7999998776654322222    255789999999865   3788774


Q ss_pred             HHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCcee---eC
Q psy11423        196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSV---LS  271 (655)
Q Consensus       196 ~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~---~~  271 (655)
                      ....   .    ++.+     .+++    ....++.|++|++...++.++ .....+..+.|+++ |...+..++   +.
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    0100     1111    123479999999987655443 24677888888877 333222222   33


Q ss_pred             CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeE-
Q psy11423        272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV-  350 (655)
Q Consensus       272 ~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPv-  350 (655)
                      +.++..++++...      .-...|||+|--|..++  -|..+    | +-+| +....+..|.+..+.-|+ |.+.-. 
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-FKVK-HERTADCVVAGYRYHKSG-PVVGSLL  223 (350)
T ss_pred             CHHHHHHHHHHHH------hCCCcEEEEeCCCCCcC--CCCcC----E-EEEc-cCCcEEEEEEEEEcCCCC-CccccEE
Confidence            4567777776553      23468999999887664  23322    7 4555 345567778887776655 332221 


Q ss_pred             -EEEEEEEECCE--EEEEeeCCCHHHHHhc
Q psy11423        351 -ALLKPVLIDGI--TITRATLHNESEIYRK  377 (655)
Q Consensus       351 -A~lePV~l~G~--tVsratLhN~~~i~~~  377 (655)
                       +..++   +|.  .|-+++..+.+..+++
T Consensus       224 lg~~d~---~g~l~~vG~v~Gf~~~~~~~L  250 (350)
T PRK08224        224 LGLYDD---DGQLHHVGVTSAFPMARRREL  250 (350)
T ss_pred             EEEECC---CCcEEEEEEECCCCHHHHHHH
Confidence             21121   242  4556666666666543

>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV

Probab=98.15  E-value=0.00012  Score=74.51  Aligned_cols=168  Identities=18%  Similarity=0.148  Sum_probs=104.4

Q ss_pred             CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC---ccccc--CCCCceEEEEEEEEeehh--
Q psy11423        117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP---LVLNI--KYPPELLEVRCEVLIYKK--  189 (655)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP---~~l~~--~~~p~~~evRGEv~~~~~--  189 (655)
                      ...|++|+|+||.-+.+.+.+|. +++.||    .|.|+|+....+...-   ..|..  ...+..+.+-||+++-..  
T Consensus        32 ~~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~  106 (225)
T cd07903          32 GKPFYIETKLDGERIQLHKDGNE-FKYFSR----NGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKET  106 (225)
T ss_pred             CCeEEEEEeeCceEEEEEecCCE-EEEEeC----CCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCc
Confidence            35799999999999999887664 799999    6889997654332210   01100  012457899999997432  


Q ss_pred             ----hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCC
Q psy11423        190 ----DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC  264 (655)
Q Consensus       190 ----~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~  264 (655)
                          .|..+               ++.++  ++.   .......+.|++|++...++.++ .....+..+.|.++--+..
T Consensus       107 ~~~~~f~~l---------------~~~~~--~~~---~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~~  166 (225)
T cd07903         107 KRFLPFGTL---------------KDVAK--LRE---VEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIP  166 (225)
T ss_pred             CeeccchHH---------------HHHHh--hcc---cccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCCC
Confidence                34332               11111  110   01123568999999986554332 2477888888888743322


Q ss_pred             CCc-----eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423        265 GEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF  319 (655)
Q Consensus       265 ~~~-----~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw  319 (655)
                      ...     ..+.+.+++.++++.+.+.      ...|+|+|--+..+..  |  .++..|
T Consensus       167 ~~i~~~~~~~~~~~~~~~~~~~~~~~~------g~EGlv~K~~~s~Y~~--g--~Rs~~w  216 (225)
T cd07903         167 GRLEVVKRTEASTKEEIEEALNEAIDN------REEGIVVKDLDSKYKP--G--KRGGGW  216 (225)
T ss_pred             CeEEEEEEEeCCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcc--C--CcCCCc
Confidence            211     2345778999988877643      3799999998866542  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

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

Probab=98.15  E-value=4.2e-05  Score=77.11  Aligned_cols=157  Identities=17%  Similarity=0.104  Sum_probs=101.1

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~----~F~~  193 (655)
                      -.|++|+|+||.-+.+.. +|.=++..||    .|+|+|+....+...-.     ..|..+.+-||+++-..    +|+.
T Consensus        24 ~~~~~E~K~DG~R~~~~~-~~~~v~l~SR----~g~~~t~~~p~l~~~~~-----~l~~~~iLDGElv~~~~~~~~~F~~   93 (207)
T cd07897          24 SDWQAEWKWDGIRGQLIR-RGGEVFLWSR----GEELITGSFPELLAAAE-----ALPDGTVLDGELLVWRDGRPLPFND   93 (207)
T ss_pred             ccEEEEEeEceEEEEEEE-cCCEEEEEeC----CCCcccccchHHHHHHH-----hCCCCeEEEeEEEEecCCCccCHHH
Confidence            369999999999998765 4445799999    56789876654432211     13557899999998654    7876


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCC-CC-----
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GE-----  266 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~-~~-----  266 (655)
                      +.....   .      ++ +...       .....++.|++|++....+.++. ....+..+.|.++--+.. ..     
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            643211   0      01 0011       11235799999999876553321 357778888877622221 11     


Q ss_pred             ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       267 ~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                      ...+.+.+++.++++...+.      ...|||+|--+..++
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~  191 (207)
T cd07897         157 LIAFADWEELAALRAQSRER------GAEGLMLKRRDSPYL  191 (207)
T ss_pred             eEecCCHHHHHHHHHHHHHc------CCeEEEEeCCCCCcC
Confidence            22356788999988866532      358999999886654

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.

>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]

Probab=98.14  E-value=0.00019  Score=80.42  Aligned_cols=215  Identities=19%  Similarity=0.211  Sum_probs=138.4

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhh-hcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIH-IIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~-~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~  193 (655)
                      .|.+|+|+||.-+.+...+|. ++.+||    .|+|||+... .+..+=..++    +....+-||+++-    ..+|+.
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            699999999999999998885 799999    7999998876 3333322232    3468999999995    568887


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhC--C---CCCCC
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI--G---LSICG  265 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~--G---F~~~~  265 (655)
                      +....                   +++.+  ......++.||+|++...++.++. ....+..+.|.++  +   |...+
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  111334799999999987766543 2455666666553  1   33333


Q ss_pred             CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcc
Q psy11423        266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTG  345 (655)
Q Consensus       266 ~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG  345 (655)
                      ... +.+.++...+++...      ...+.|||+|--|..++.    ..+.-.| +-+| +.++..-.|.+..++-|+-+
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            333 377888888876543      346899999965555541    1122233 3444 33778899999999998765


Q ss_pred             eeeeEEEEEEEEECCE-----EEEEeeCCCHHHHHh
Q psy11423        346 IITPVALLKPVLIDGI-----TITRATLHNESEIYR  376 (655)
Q Consensus       346 ~itPvA~lePV~l~G~-----tVsratLhN~~~i~~  376 (655)
                        ..=+-+-.+.-++.     .++=.|...-++.++
T Consensus       333 --~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~  366 (444)
T COG1793         333 --LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEE  366 (444)
T ss_pred             --ccceEEEEEEcCCCceEEEEecccCCCCHHHHHH
Confidence              44455556666664     333345555444433

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=98.07  E-value=1.2e-05  Score=80.19  Aligned_cols=69  Identities=17%  Similarity=0.256  Sum_probs=57.4

Q ss_pred             hCCCCccHHHHHHHHHhCCC---HHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh----------------HHHHHHH
Q psy11423        526 LGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL----------------HRLLISQ  586 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgs---l~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~----------------n~~li~~  586 (655)
                      +.|||||+++|++|+++|+.   .+++.+++.++|.++||||+++|+.|+..|+...                ..+++..
T Consensus        76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~a  155 (192)
T PRK00116         76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSA  155 (192)
T ss_pred             hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHH
Confidence            47999999999999999997   6778888999999999999999999998776432                3456666


Q ss_pred             HHHcCccc
Q psy11423        587 LRDVGIYW  594 (655)
Q Consensus       587 L~~~Gi~~  594 (655)
                      |...|++.
T Consensus       156 L~~LG~~~  163 (192)
T PRK00116        156 LVALGYKP  163 (192)
T ss_pred             HHHcCCCH
Confidence            77777653

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=98.04  E-value=2.1e-06  Score=90.00  Aligned_cols=59  Identities=20%  Similarity=0.205  Sum_probs=54.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      ..|.++|+|||++..||+++.|++.++|-. +....+..|+|||+|++++|++++.....
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            378999999999999999999999999998 78899999999999999999999987544

>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases

Probab=98.04  E-value=6.1e-05  Score=75.12  Aligned_cols=159  Identities=15%  Similarity=0.105  Sum_probs=98.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee---hhhHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY---KKDFIKL  194 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~---~~~F~~~  194 (655)
                      ..|++|+|+||.-+.+.+.+|. ++..||    .|+|+|+....+...-..+    .|..+.+-||+++-   ..+|+.+
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    7889998654433211111    35578999999984   3467665


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCCCCc---eee
Q psy11423        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEY---SVL  270 (655)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~~~~---~~~  270 (655)
                      -...   +.+..   +      .    +......++.|++|++...++.++. ....+..+.|.++-=+..+..   ..+
T Consensus        87 ~~r~---~~~~~---~------~----~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~  150 (194)
T cd07905          87 QQRI---HPAAS---R------V----RRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPAT  150 (194)
T ss_pred             HHHh---ccccc---c------h----hhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECCcc
Confidence            3321   11000   0      0    1112356799999999875544322 467777777776521111111   223


Q ss_pred             CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       271 ~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                      .+.+++.++++...+      -..-|||+|--+..++
T Consensus       151 ~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~  181 (194)
T cd07905         151 TDRAEAREWLEEFEG------AGLEGVVAKRLDGPYR  181 (194)
T ss_pred             CCHHHHHHHHHHHHH------CCCceEEEeCCCCCcC
Confidence            566778887776543      2357999998776553

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

>KOG2841|consensus

Probab=98.02  E-value=4.3e-06  Score=83.86  Aligned_cols=60  Identities=32%  Similarity=0.450  Sum_probs=54.9

Q ss_pred             hHHHHHh-CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423        520 SRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (655)
Q Consensus       520 ~r~L~al-gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~  579 (655)
                      .+++..| .||||++.-|..|+.+|||+..|.+||.++|.+++|+|+..|++|++||+.|.
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            3455555 79999999999999999999999999999999999999999999999999764

>PHA00454 ATP-dependent DNA ligase

Probab=97.99  E-value=0.0016  Score=69.91  Aligned_cols=240  Identities=19%  Similarity=0.143  Sum_probs=134.0

Q ss_pred             ccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc--
Q psy11423         85 HTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII--  162 (655)
Q Consensus        85 H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i--  162 (655)
                      |+.||+-.+  ||+..+.+=.+++    |     .|++|+|+||.-+.+...+|.=+++.||.    |.+++.-+...  
T Consensus         5 ~~~~~~~~~--~~~~~i~~~~~~~----g-----~~~~E~K~DG~R~~~~~~~~~~v~l~SR~----g~~~p~l~~~~~~   69 (315)
T PHA00454          5 KTNPFRAVD--FNESAIEKALEKA----G-----YLIADVKYDGVRGNIVVDNTADHGWLSRE----GKTIPALEHLNGF   69 (315)
T ss_pred             cCCcccccc--CCHHHHHHHHHhC----C-----cEEEEEccceEEEEEEEcCCCeEEEEeCC----CCcccchhhhhhh
Confidence            566664333  4554444333332    2     69999999999999887666447999994    34554422111  


Q ss_pred             -ccCCccccc--CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcC--cccccccceEEEEEec
Q psy11423        163 -HKIPLVLNI--KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLN--PKINKNKILHFFAHGV  237 (655)
Q Consensus       163 -~~iP~~l~~--~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d--~~~~~~r~L~f~~y~~  237 (655)
                       ..++..+..  ...|..+.+-||++....+|+.+.                   |.|+++.  +......++.|++|++
T Consensus        70 ~~~~~~~~~~~~~~l~~~~vLDGElv~~~~~f~~~~-------------------~~l~~k~~~~~~~~~~~v~~~vFDl  130 (315)
T PHA00454         70 DRRWAKLLNDDRCIFPDGFMLDGELMVKGVDFNTGS-------------------GLLRRKWKVLFELHLKKLHVVVYDV  130 (315)
T ss_pred             hhhhhhhhhhhhhcCCCCeEEEEEEEecCCCHHHHH-------------------HHhccCccchhhhccCceEEEEEEe
Confidence             011222211  013457899999999766676543                   3333332  1222346899999999


Q ss_pred             ccccCC----CC----CCCHHHHHHHHHhC----C---CCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11423        238 GELRGM----NM----PSSHSELLNWYQKI----G---LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN  302 (655)
Q Consensus       238 ~~~~~~----~~----~~~~~e~l~~L~~~----G---F~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~  302 (655)
                      ...++.    ++    .....+.-+.|.++    +   +..++ ...+.+.+++.++++...+      -...|||+|--
T Consensus       131 l~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~  203 (315)
T PHA00454        131 TPLDVLESGEDYDVMSLLMYEHVRAMVPLLMEYFPEIDWFLSE-SYEVYDMESLQELYEKKRA------EGHEGLVVKDP  203 (315)
T ss_pred             eEeccccCCccccccccccHHHHHHHHHHHHhhCCCcceEeec-eEEcCCHHHHHHHHHHHHh------CCCceEEEeCC
Confidence            865421    11    12344444445433    1   22222 2245678899998876642      34689999988


Q ss_pred             ChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-c--ceeeeEEEEEEEEECCEEEEEeeCCCHHHHHh
Q psy11423        303 CLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-T--GIITPVALLKPVLIDGITITRATLHNESEIYR  376 (655)
Q Consensus       303 ~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-T--G~itPvA~lePV~l~G~tVsratLhN~~~i~~  376 (655)
                      +..++  -|..   ..|- -+| +....+..|.+..+-.|+ .  |.+.  +-+--. =+|. ...+|..+.+..++
T Consensus       204 ds~Y~--~Grr---~~~~-K~K-~~~~~d~vIvG~~~g~g~~~~~g~~~--~~~~~~-~~g~-l~~gtGfs~~~~~~  269 (315)
T PHA00454        204 SLIYR--RGKK---SGWW-KMK-PECEADGTIVGVVWGTPGLANEGKVI--GFRVLL-EDGR-VVNATGISRALMEE  269 (315)
T ss_pred             CCCCC--CCCc---cCcE-EEc-ccCceeEEEEEEEECCCCccCCceEE--EEEEEe-CCCc-EEEccCCCHHHHHH
Confidence            76654  2332   2362 444 334678888888887742 3  3332  211101 1343 33477777766654

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=97.98  E-value=8.5e-06  Score=93.31  Aligned_cols=51  Identities=22%  Similarity=0.335  Sum_probs=49.8

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      +|||||+++.++|+++|||+++|..||.+||.+++||++++|+.|+++|+.
T Consensus       518 ~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~  568 (574)
T PRK14670        518 KIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK  568 (574)
T ss_pred             cCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999999964

>PRK09247 ATP-dependent DNA ligase; Validated

Probab=97.97  E-value=0.00044  Score=79.36  Aligned_cols=219  Identities=16%  Similarity=0.140  Sum_probs=137.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh------hhH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KDF  191 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~------~~F  191 (655)
                      ..|++|+|.||.-+.+...+|. ++..||    -|+|+|+....|...-..     .|..+.+-||++.-.      ..|
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    578999877665443222     355689999998754      466


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-----
Q psy11423        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-----  263 (655)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~-----  263 (655)
                      +.+...                   ++++..  ......++.|++|++....+.++ .....+..+.|+++ |..     
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            655432                   111111  11123579999999987655443 24677888888765 221     


Q ss_pred             ---CCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEe
Q psy11423        264 ---CGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ  340 (655)
Q Consensus       264 ---~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q  340 (655)
                         ++ ...+.+.+++.++++...+      -...|+|+|--+..++  .|..  ...| +=+|-........|.+..|-
T Consensus       355 i~~~~-~~~~~~~~e~~~~~~~a~~------~g~EGlm~K~~~s~Y~--~Grr--~~~W-lK~K~~~~t~DlVvig~~~G  422 (539)
T PRK09247        355 LDLSP-LVPFSDWDELAALRAAARE------RGVEGLMLKRRDSPYL--VGRK--KGPW-WKWKRDPLTIDAVLMYAQRG  422 (539)
T ss_pred             EEecC-ceecCCHHHHHHHHHHHHH------CCCceEEEecCCCCcC--CCCC--cchh-hcccCCCCcEEEEEEEeecC
Confidence               12 2335678899998876543      3479999998775543  2322  2223 23443334667777777776


Q ss_pred             ecC-cceeee--EEEEEEEEECC--EEEEEe-eCCCHHHHHhcC
Q psy11423        341 IGR-TGIITP--VALLKPVLIDG--ITITRA-TLHNESEIYRKN  378 (655)
Q Consensus       341 vGR-TG~itP--vA~lePV~l~G--~tVsra-tLhN~~~i~~~~  378 (655)
                      .|| +|.++.  +|..+|=.=.+  ++|-++ |.++.++++++.
T Consensus       423 ~Gkr~g~~~~~lla~~~~~~~~~~~~~v~kvgsGftd~~l~~l~  466 (539)
T PRK09247        423 HGRRASLYTDYTFGVWDGPEGGRQLVPFAKAYSGLTDEEIKQLD  466 (539)
T ss_pred             CCCcCCccccEEEEEEcCCCCceeEEEEEEECCCCCHHHHHHHH
Confidence            665 465654  56655421001  256666 889988887763

>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins

Probab=97.95  E-value=0.0002  Score=73.67  Aligned_cols=170  Identities=16%  Similarity=0.140  Sum_probs=103.1

Q ss_pred             CceEEEEEecceeEEEEEEe---CCEEeEEEecCCCCccchhhhhhhhcccC-Ccccc----cCCCCceEEEEEEEEeeh
Q psy11423        117 NIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLN----IKYPPELLEVRCEVLIYK  188 (655)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~----~~~~p~~~evRGEv~~~~  188 (655)
                      ...|++|+|.||.-+.+.+.   +|.-++..||    -|+|+|+....+..+ ...+.    ....+..+.+-||+++-.
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            34699999999999999875   2445899999    789999865443211 11110    000135799999996532


Q ss_pred             ------hhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCC
Q psy11423        189 ------KDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL  261 (655)
Q Consensus       189 ------~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF  261 (655)
                            ..|+.+....         ..++.....  ..++......++.|++|++....+.++ ..+..+..+.|.++--
T Consensus        97 ~~~g~~~~F~~L~~~~---------~~~~~~~~~--~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~  165 (235)
T cd08039          97 DRQGKIDPFHKIRKHV---------ERSGSFIGT--DNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVH  165 (235)
T ss_pred             CCCCccCCHHHHHhhc---------ccccchhcc--ccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcc
Confidence                  3787763210         111111000  111122234679999999987554433 2578888888988743


Q ss_pred             CCCCCce-----ee-----CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        262 SICGEYS-----VL-----SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       262 ~~~~~~~-----~~-----~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                      +++....     .+     .+.+++.++++...+.      ..-|||+|--+..+.
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            3332211     11     2677888888765432      357999999886654

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

>PHA02587 30 DNA ligase; Provisional

Probab=97.95  E-value=0.00075  Score=76.58  Aligned_cols=235  Identities=14%  Similarity=0.110  Sum_probs=130.8

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc----cCCcccccCCCCceEEEEEEEEeehhh----
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH----KIPLVLNIKYPPELLEVRCEVLIYKKD----  190 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~----~iP~~l~~~~~p~~~evRGEv~~~~~~----  190 (655)
                      .|++|+|.||.-+.+...+|. ++..||    .|+|+|. ...|.    .+...+..  .|..+.+-||++.-..+    
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            699999999999999887665 799999    5778764 22221    11122211  24578999999976321    


Q ss_pred             HHHHHHHHHHcCCCCCC---ChhhhHHhHhh---hcCcccccccceEEEEEecccc----cCCCCCCCHHHHHHHHHhC-
Q psy11423        191 FIKLNKYRYHLGLKKFT---NPRNAAAGILR---QLNPKINKNKILHFFAHGVGEL----RGMNMPSSHSELLNWYQKI-  259 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~---NpRN~aaG~lr---~~d~~~~~~r~L~f~~y~~~~~----~~~~~~~~~~e~l~~L~~~-  259 (655)
                      |- ++--..+.+.+.|.   -.|..-.|..+   +.........++.|++|++...    .+........+..+.|.++ 
T Consensus       225 ~~-~~f~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~  303 (488)
T PHA02587        225 NG-LSFLFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMF  303 (488)
T ss_pred             cc-chhhcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHH
Confidence            00 00000000000000   01221122211   1111123456799999999731    1111125677777777665 


Q ss_pred             ---CCCCCCC--ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEE
Q psy11423        260 ---GLSICGE--YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI  334 (655)
Q Consensus       260 ---GF~~~~~--~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v  334 (655)
                         +.+....  ...+.+.+++.+++++..+      -...|+|+|--+..++  -|   +...| +=+| +.......|
T Consensus       304 ~~~~~~~i~l~~~~~~~~~ee~~~~~~~a~~------~G~EGimlK~~ds~Y~--~G---Rs~~W-lKiK-~~~~~dlvV  370 (488)
T PHA02587        304 EDCGYDRVELIENQVVNNLEEAKEIYKRYVD------QGLEGIILKNTDGLWE--DG---RSKDQ-IKFK-EVIDIDLEI  370 (488)
T ss_pred             hhcCCCcEEEEeeEEcCCHHHHHHHHHHHHh------CCCCeEEEECCCCCCC--CC---CCCCc-EEec-CCCceEEEE
Confidence               2111111  1236788999998876643      2468999998776654  24   22235 5566 345578889


Q ss_pred             EEEEEeecCcceeeeEEEEEEEEECCEEEEE-eeCCCHHHHHhcC
Q psy11423        335 KAINIQIGRTGIITPVALLKPVLIDGITITR-ATLHNESEIYRKN  378 (655)
Q Consensus       335 ~~I~~qvGRTG~itPvA~lePV~l~G~tVsr-atLhN~~~i~~~~  378 (655)
                      .++.++-+|.|.+.-...-   .-+|.++-+ .|.+.-+.+++++
T Consensus       371 vG~~~~~k~~~~~gs~ll~---~~~g~~~~~vgsGftd~~~~~l~  412 (488)
T PHA02587        371 VGVYEHKKDPNKVGGFTLE---SACGKITVNTGSGLTDTTHRKKD  412 (488)
T ss_pred             EeEEeCCCCCCceeEEEEE---ecCCcEEEEECCCCChHHhhhhc
Confidence            9999987777665432211   114544434 4788888877653

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=97.94  E-value=1.4e-05  Score=80.88  Aligned_cols=51  Identities=22%  Similarity=0.302  Sum_probs=49.5

Q ss_pred             CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      .|||||++++++|+++ |+|++.|..|+.++|.+++|||.++|+.|+++|+.
T Consensus         7 ~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~   58 (232)
T PRK12766          7 DISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG   58 (232)
T ss_pred             cCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence            7899999999999999 99999999999999999999999999999999974

>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III

Probab=97.92  E-value=0.00018  Score=72.83  Aligned_cols=157  Identities=15%  Similarity=0.148  Sum_probs=96.0

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhh-hhhccc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~  196 (655)
                      .|++|+|+||.-+.+.+.+|. +++.||+    |.|+|.. +..+.. ++..+.   ....+.+-||+++-...      
T Consensus        35 ~~~~E~K~DG~R~~i~~~~~~-v~l~SR~----g~~~t~~~~~~~~~~~~~~~~---~~~~~iLDGEiv~~d~~------  100 (213)
T cd07902          35 GMYAEIKYDGERVQVHKQGDN-FKFFSRS----LKPVLPHKVAHFKDYIPKAFP---HGHSMILDSEVLLVDTK------  100 (213)
T ss_pred             ceEEEeccCCEEEEEEEcCCE-EEEEcCC----CcccccchhHHHHHHHHHhcc---cccceeeeeEEEEEECC------
Confidence            599999999999988776554 7999995    8888853 322211 232222   13368999999984321      


Q ss_pred             HHHHcCCC-CCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC-----cee
Q psy11423        197 YRYHLGLK-KFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-----YSV  269 (655)
Q Consensus       197 ~~~~~g~~-~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~-----~~~  269 (655)
                          .|.+ .|..    .....+.    .....++.|++|++....+.++ .....+..+.|.++--+.+..     ...
T Consensus       101 ----~g~~~~F~~----l~~~~~~----~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~~~~~~~~~  168 (213)
T cd07902         101 ----TGKPLPFGT----LGIHKKS----AFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIMLSEMKF  168 (213)
T ss_pred             ----CCcccccch----hhhhhcc----ccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCeEEEEEEEE
Confidence                1111 1211    1000010    0123469999999987555332 246778888888763222221     123


Q ss_pred             eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423        270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ  307 (655)
Q Consensus       270 ~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~  307 (655)
                      +.+.+++.++++.+.+.      ...|+|+|--+..++
T Consensus       169 ~~~~~~l~~~~~~~~~~------g~EGvV~K~~~s~Y~  200 (213)
T cd07902         169 VKKADDLSAMIARVIKE------GLEGLVLKDLKSVYE  200 (213)
T ss_pred             cCCHHHHHHHHHHHHHC------CCCeEEEeCCCCCcc
Confidence            56888999988877532      368999999886654

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

>PRK09633 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.89  E-value=0.0005  Score=79.71  Aligned_cols=217  Identities=16%  Similarity=0.176  Sum_probs=128.3

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccC----CcccccCCCCceEEEEEEEEee----hh
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI----PLVLNIKYPPELLEVRCEVLIY----KK  189 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i----P~~l~~~~~p~~~evRGEv~~~----~~  189 (655)
                      -.|++|.|+||.-+.+.+.+|. ++..||    -|+|+|+....|...    +..++.   ...+.+-||++.-    ..
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 899999    789999876654332    222211   1147899999984    46


Q ss_pred             hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhC----CCCCC
Q psy11423        190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI----GLSIC  264 (655)
Q Consensus       190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~----GF~~~  264 (655)
                      +|+.+......      .++.+     +.+    .....++.|++|++....+.++. .+..+..+.|+++    +.+..
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            78776432110      11111     111    12345799999999876654432 4677777777665    21100


Q ss_pred             ------CCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEE
Q psy11423        265 ------GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAIN  338 (655)
Q Consensus       265 ------~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~  338 (655)
                            .....+.+.+++.++++...+      ....|||+|--+..++.    ..++..| +-+|. ....+..|.+..
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                  134456677788888776543      23599999988865531    2244556 34453 345566666654


Q ss_pred             EeecCcceeeeEEEEEEEEECCE--EEEEe-eCCCHHHHHhc
Q psy11423        339 IQIGRTGIITPVALLKPVLIDGI--TITRA-TLHNESEIYRK  377 (655)
Q Consensus       339 ~qvGRTG~itPvA~lePV~l~G~--tVsra-tLhN~~~i~~~  377 (655)
                      +  | .|.+. ++..    -+|.  .|-++ |..+.+..+++
T Consensus       221 ~--~-~g~~l-lgv~----~~g~l~~vGkvgtGft~~~~~~L  254 (610)
T PRK09633        221 P--S-NGYFT-GSVY----KDGQLTEVGSVKHGMEDEERQTL  254 (610)
T ss_pred             c--C-CceEE-EEEe----cCCeEEEEEEecCCCCHHHHHHH
Confidence            4  3 34321 2222    2454  34443 56666555443

>PRK01109 ATP-dependent DNA ligase; Provisional

Probab=97.89  E-value=0.00035  Score=81.07  Aligned_cols=216  Identities=17%  Similarity=0.149  Sum_probs=134.6

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC-cccccCCCCceEEEEEEEEeehh------hH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP-LVLNIKYPPELLEVRCEVLIYKK------DF  191 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP-~~l~~~~~p~~~evRGEv~~~~~------~F  191 (655)
                      .|++|.|.||.-+.+.+.+|. ++..||    -|+|+|+....|...- ..+.    +..+.+-||++.-..      .|
T Consensus       249 ~~~~E~K~DG~R~qih~~~~~-v~l~SR----~~~d~T~~~pel~~~~~~~~~----~~~~ILDGElv~~d~~~g~~~~F  319 (590)
T PRK01109        249 EALVEYKYDGERAQIHKKGDK-VKIFSR----RLENITHQYPDVVEYAKEAIK----AEEAIVEGEIVAVDPETGEMRPF  319 (590)
T ss_pred             CeEEEecCCceEEEEEEcCCE-EEEEeC----CchhhccccchHHHHHHHhcC----ccceEEeeeEEEEECCCCcccCh
Confidence            589999999999998876664 799999    4999998876654322 1231    346899999987541      46


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc---
Q psy11423        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY---  267 (655)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~---  267 (655)
                      +.+-..    .       |......       .....++.|++|++...++.++ ..+..+..+.|.++- ...+..   
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            654221    0       1100000       1124579999999987665443 247788888888763 222221   


Q ss_pred             --eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCC-------cceeeEEEEE
Q psy11423        268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA  336 (655)
Q Consensus       268 --~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~  336 (655)
                        ....+.+++.++++...+.      ..-|||+|--  +..++  -|  .+...|   +|+-       .+.....|.+
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              2356788999988766543      3689999997  65543  13  355677   5554       3456667888


Q ss_pred             EEEeecC-cceeeeE--EEEEEEEECCE--EEEEe-eCCCHHHHHhc
Q psy11423        337 INIQIGR-TGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYRK  377 (655)
Q Consensus       337 I~~qvGR-TG~itPv--A~lePV~l~G~--tVsra-tLhN~~~i~~~  377 (655)
                      ..|--|| +|.+...  |..+|  =+|.  +|.++ |..+.+.++++
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            7777665 5554432  22222  1232  44454 77887777665

>PRK09632 ATP-dependent DNA ligase; Reviewed

Probab=97.84  E-value=0.00089  Score=79.14  Aligned_cols=208  Identities=17%  Similarity=0.163  Sum_probs=126.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~  193 (655)
                      -.|++|.|+||.-+.+.+.+|. ++..||    .|.|+|+....|..+...+.    ...+.+-||+++-    ..+|+.
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    79999998766554444442    2368999999983    346765


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYSVLSG  272 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~~~~~~~~~  272 (655)
                      +...                           ....++.|++|++...++.++. ....+..+.|+++- ...+...+...
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                           0124699999999876665432 46778888887763 21111122111


Q ss_pred             -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-cceeeeE
Q psy11423        273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPV  350 (655)
Q Consensus       273 -~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~itPv  350 (655)
                       ..++.++++...+      -..-|||+|--+..++  -|  .++..| +-+| +....+..|.+..+.-|| .|.+.-.
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-IKDK-HWRTQEVVIGGWRPGEGGRSSGIGSL  667 (764)
T ss_pred             ecccHHHHHHHHHH------cCCcEEEEeCCCCCCC--CC--CcCCCe-EEEe-cCCceEEEEEEEEcCCCCcCCceeeE
Confidence             1234455554432      2468999999886654  12  224445 3445 234456677777776663 4444333


Q ss_pred             --EEEEEEEECC-EEEEEe-eCCCHHHHHhc
Q psy11423        351 --ALLKPVLIDG-ITITRA-TLHNESEIYRK  377 (655)
Q Consensus       351 --A~lePV~l~G-~tVsra-tLhN~~~i~~~  377 (655)
                        +..+.   +| ..|-++ |..+.+..+++
T Consensus       668 LlGv~d~---~~L~yvGkVGTGftd~~l~~L  695 (764)
T PRK09632        668 LLGIPDP---GGLRYVGRVGTGFTERELASL  695 (764)
T ss_pred             EEEEEcC---CeeEEEEEEeCCCCHHHHHHH
Confidence              22222   12 345566 77888777664

>PRK08609 hypothetical protein; Provisional

Probab=97.84  E-value=7.3e-06  Score=94.44  Aligned_cols=59  Identities=25%  Similarity=0.245  Sum_probs=53.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      ..+.|+|+|||++.+||+...|+|++||.. +..++|..++|||+|++++|+++|+..+.
T Consensus        89 ~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~  148 (570)
T PRK08609         89 PLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGK  148 (570)
T ss_pred             HHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhc
Confidence            357899999999999999888999999998 67889999999999999999999987543

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=97.83  E-value=2.2e-05  Score=89.90  Aligned_cols=49  Identities=24%  Similarity=0.407  Sum_probs=48.0

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +|||||+++.++|+++|||+++|..||.+||.++ ||++++|+.|+++|+
T Consensus       518 ~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~  566 (567)
T PRK14667        518 KIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS  566 (567)
T ss_pred             cCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence            8999999999999999999999999999999999 999999999999985

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=97.66  E-value=7.3e-05  Score=86.57  Aligned_cols=51  Identities=24%  Similarity=0.393  Sum_probs=49.8

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      +|||||++++++|+++|+|++.+..|+.++|.+++|||+++|++|.+||++
T Consensus       547 ~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~  597 (598)
T PRK00558        547 DIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK  597 (598)
T ss_pred             hCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence            999999999999999999999999999999999999999999999999975

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

Probab=97.61  E-value=9.2e-05  Score=60.76  Aligned_cols=57  Identities=21%  Similarity=0.255  Sum_probs=44.4

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT  517 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~  517 (655)
                      +|+|+|+|+++.+.|.++=  .+++.|...+.++|..+||+|++.|++|.+-++..++.
T Consensus         5 aLGI~~VG~~~ak~L~~~f--~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~   61 (64)
T PF12826_consen    5 ALGIPGVGEKTAKLLAKHF--GSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENR   61 (64)
T ss_dssp             HCTSTT--HHHHHHHHHCC--SCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHH
T ss_pred             eCCCCCccHHHHHHHHHHc--CCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhh
Confidence            6999999999999998754  58999999999999999999999999999988776543

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=97.56  E-value=0.00012  Score=84.78  Aligned_cols=50  Identities=32%  Similarity=0.426  Sum_probs=48.3

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      +|||||++++++|+++|||+++|..||.++|.++  ||+++|+.|+++|+.+
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  9999999999999864

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=97.55  E-value=0.00015  Score=74.71  Aligned_cols=54  Identities=24%  Similarity=0.449  Sum_probs=51.4

Q ss_pred             HhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        525 ALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       525 algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      -..|||||...|++|+++|+|+..+..|+.++|..+.|||++.|..|+.||..+
T Consensus       184 l~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~  237 (254)
T COG1948         184 LESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTE  237 (254)
T ss_pred             HHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhch
Confidence            348999999999999999999999999999999999999999999999999765

>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes

Probab=97.50  E-value=0.0012  Score=66.78  Aligned_cols=156  Identities=20%  Similarity=0.174  Sum_probs=97.6

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~  197 (655)
                      ..|++|+|.||+-+.+...+..-+.+.||+    |+++|.....+..+.. ..  ..+....+-||++.....       
T Consensus        41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~----~~~~~~~~~~~~~~~~-~~--~~~~~~ilDGElv~~~~~-------  106 (215)
T cd07895          41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRK----NDVFKVPGLFFPRRKN-LE--PHHQGTLLDGELVIDKVP-------  106 (215)
T ss_pred             CCeEEEEeEcCeEEEEEEecCCcEEEEeCC----CCeEEeccccCCCccc-cc--ccccCeeeEEEEEEEcCC-------
Confidence            479999999999998866541457999996    5567665544321101 11  123467899999965321       


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC----------
Q psy11423        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE----------  266 (655)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~----------  266 (655)
                          +                        ..++.|++|++....+.++ .....+.++.|.++-......          
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                        2368999999987655433 246778888887764332110          


Q ss_pred             ----ceeeC---CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11423        267 ----YSVLS---GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK  324 (655)
Q Consensus       267 ----~~~~~---~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K  324 (655)
                          .....   ..+++.+..+.+   +..++...||+|+|-.+..+.-  |   +.+.| +=||
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   3467899999999999977642  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.

>PRK05972 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.49  E-value=0.0013  Score=78.70  Aligned_cols=179  Identities=18%  Similarity=0.145  Sum_probs=112.2

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIKL  194 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~~  194 (655)
                      .|++|.|+||.-+.+.+.+|. ++..||    .|+|+|+....|...-..+.    .....+-|||++-    ..+|+.+
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    68899988765543322221    2357899999983    4577765


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCC-CCCceeeCC
Q psy11423        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYSVLSG  272 (655)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~-~~~~~~~~~  272 (655)
                      ....                   +..     ...++.|++|++...++.++. ....+..+.|+++-=+. .+..++...
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     123689999999887665432 46788888888763111 122333332


Q ss_pred             H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC
Q psy11423        273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR  343 (655)
Q Consensus       273 ~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR  343 (655)
                      + .+..++++...+      -...|||+|--|..++-  |   ++..| +=+|.- ...+..|-+....-|+
T Consensus       377 ~~~~g~~ll~~a~~------~GlEGIVaKr~dS~Y~~--G---Rs~~W-lKiK~~-~~~E~VIgGy~~~~Gk  435 (860)
T PRK05972        377 FDAGGDAVLASACR------LGLEGVIGKRADSPYVS--G---RSEDW-IKLKCR-ARQEFVIGGYTDPKGS  435 (860)
T ss_pred             ecchHHHHHHHHHH------cCCceEEEeCCCCCCCC--C---CCCCc-EEEecC-CCceEEEEEEeCCCCc
Confidence            2 234455554432      33689999998877652  3   45556 344432 3345666666665554

>PLN03113 DNA ligase 1; Provisional

Probab=97.49  E-value=0.0033  Score=74.44  Aligned_cols=221  Identities=16%  Similarity=0.152  Sum_probs=130.7

Q ss_pred             ceEEEEEecceeEEEEEEe-CCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh------hh
Q psy11423        118 IEYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KD  190 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~------~~  190 (655)
                      ..|+||.|.||.-+.+.|. +|. ++..||    -|+|+|+....+-..-..+... ....+.+-||++.-.      -.
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            4799999999999999985 665 799999    6899998876543321122100 124689999999753      35


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCC-CCCce
Q psy11423        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYS  268 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~-~~~~~  268 (655)
                      |+.+-..           .|..+.  +      .....++.||+|++....|.++. .+..+..+.|.++ |.. +....
T Consensus       465 Fq~Lq~R-----------~rk~~~--~------~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~-~~~~~~~i~  524 (744)
T PLN03113        465 FQILSTR-----------ARKNVV--M------SDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYES-FEEDPGFFQ  524 (744)
T ss_pred             HHHHHhh-----------hccccc--h------hccccceEEEEEeccccCccChhcCCHHHHHHHHHHH-hccCCCcEE
Confidence            7655331           011000  0      01135799999999876665432 4677888888775 432 22222


Q ss_pred             e-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCCc-----ceeeEEEEE
Q psy11423        269 V-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKA  336 (655)
Q Consensus       269 ~-----~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~  336 (655)
                      +     ..+.+++.+|++...+      ...-|||+|--  +..++    ...+...| +=+|-..     ......|.+
T Consensus       525 ~~~~~~~~~~ee~~~~~~~ai~------~g~EGlmvK~l~~dS~Y~----pGkRs~~W-lKlK~dy~~~~~dtlDlVvIG  593 (744)
T PLN03113        525 FATAITSNDLEEIQKFLDAAVD------ASCEGLIIKTLNKDATYE----PSKRSNNW-LKLKKDYMESIGDSLDLVPIA  593 (744)
T ss_pred             EeeeeccCCHHHHHHHHHHHHH------cCCceEEEeccCCCCCcc----CCCCCCCe-EEEechhhccccccccEEEEE
Confidence            2     3568899998876643      34789999972  22222    12344556 2344221     244555566


Q ss_pred             EEEeec-CcceeeeE--EEEEEEEECC--EEEEEe-eCCCHHHHHhc
Q psy11423        337 INIQIG-RTGIITPV--ALLKPVLIDG--ITITRA-TLHNESEIYRK  377 (655)
Q Consensus       337 I~~qvG-RTG~itPv--A~lePV~l~G--~tVsra-tLhN~~~i~~~  377 (655)
                      -.|--| |+|.++..  |..+|-  +|  .+|-++ |.+.-++++++
T Consensus       594 a~~G~GkR~g~~g~fLla~yd~~--~~~~~~v~KvgTGfsd~~l~~l  638 (744)
T PLN03113        594 AFHGRGKRTGVYGAFLLACYDSN--KEEFQSICKIGTGFSEAVLEER  638 (744)
T ss_pred             EEeCCCCcCCccceEEEEEEcCC--CCEEEEeeEECCCCCHHHHHHH
Confidence            666555 56655543  344442  12  244455 77777776653

>PRK14973 DNA topoisomerase I; Provisional

Probab=97.49  E-value=0.00052  Score=83.05  Aligned_cols=127  Identities=16%  Similarity=0.141  Sum_probs=102.2

Q ss_pred             Hhhccccc----cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh--cccch--
Q psy11423        448 KAGLQHFS----SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS--KLTTF--  519 (655)
Q Consensus       448 ~~~i~~F~----sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s--k~~~l--  519 (655)
                      .+++.-|+    -...|.++|+-+.++++||+.|+ +++.|+-....+.|+.++|+.+-.+.++.......  +..+-  
T Consensus       789 ~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~-~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  867 (936)
T PRK14973        789 AASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGF-DTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGRPVPEKI  867 (936)
T ss_pred             HHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcC-CCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcCCCchhh
Confidence            34555555    34489999999999999999996 99999999999999999999999998886655422  11110  


Q ss_pred             -------hHHHHHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        520 -------SRFIYALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       520 -------~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                             .+. ..+.|+|+|+++..+|.. -+.+.+.|.+++.++|....||+.+.+..++.+..
T Consensus       868 ~~~~~~~~~~-el~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~  931 (936)
T PRK14973        868 SKAAFERGRA-ELLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK  931 (936)
T ss_pred             hhhhhcccch-hhhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence                   011 035799999999988776 47789999999999999999999999999988764

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.46  E-value=0.00042  Score=82.20  Aligned_cols=121  Identities=17%  Similarity=0.224  Sum_probs=89.2

Q ss_pred             hhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc-cchhHHHHHhC
Q psy11423        449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL-TTFSRFIYALG  527 (655)
Q Consensus       449 ~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~-~~l~r~L~alg  527 (655)
                      ..|..|.|- . .|+|+||++++++++.-....+.-|.+ ..+.|..++|+|+|.++.|.++++..+. ..+..||..+|
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            344445442 2 599999999999999877555544433 4678999999999999999999987653 44556777767


Q ss_pred             CCCccHHHHHHHHHhCCC--HHHHHhcCHHHHh-cCCCCCHHHHHHHHHHhc
Q psy11423        528 IRHVGETTAKELANYFKN--LECMFKATEEQLL-NIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       528 IpgIG~~~Ak~L~~~fgs--l~~l~~as~eeL~-~i~GIG~~~A~~I~~~f~  576 (655)
                      |+   ...|.+|.++||+  ++.|. .++=.|. .++|||-++|.+|...+.
T Consensus       155 i~---~~~a~ki~~~yg~~~~~~i~-~nPY~L~~~i~gigF~~aD~iA~~~g  202 (720)
T TIGR01448       155 IG---IKLAQRIYKFYQADTLDRVE-KDPYLLAEDVKGIGFLTADQLAQALG  202 (720)
T ss_pred             CC---HHHHHHHHHHHhHHHHHHHH-hCchhhhhhcCCCCHHHHHHHHHHcC
Confidence            65   7899999999984  23333 3443455 699999999999987653

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.

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=97.43  E-value=0.00023  Score=82.65  Aligned_cols=50  Identities=30%  Similarity=0.450  Sum_probs=48.7

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .|||||++++++|+++|||+++|..|+.++|.+++|||+++|+.|+++|+
T Consensus       641 ~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~  690 (694)
T PRK14666        641 RVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK  690 (694)
T ss_pred             hCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999985

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=97.42  E-value=0.0002  Score=82.83  Aligned_cols=50  Identities=20%  Similarity=0.291  Sum_probs=47.6

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .|||||++++++|+++|||+++|..||.++|.+++||+.++|+.|+.--.
T Consensus       612 ~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~  661 (691)
T PRK14672        612 RLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAAT  661 (691)
T ss_pred             cCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhh
Confidence            89999999999999999999999999999999999999999999987543

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=97.40  E-value=0.00024  Score=82.51  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=47.4

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .+|||||+++++.|+++|+|++.|..|+.++|.++  ||+++|++|.+||+
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            49999999999999999999999999999999999  99999999999986

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=97.32  E-value=0.00029  Score=80.90  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=46.5

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +|||||+++.++|+++|||++.|..||.+||.++ ||+.++|+.|+++|
T Consensus       534 ~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~  581 (581)
T COG0322         534 DIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL  581 (581)
T ss_pred             cCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence            8999999999999999999999999999999999 99999999998864

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=97.26  E-value=0.00046  Score=74.25  Aligned_cols=51  Identities=20%  Similarity=0.304  Sum_probs=48.1

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      .||++++..|++|.++|||+..+.+|+.++|.+++|||++.|..|.+.+..
T Consensus       291 ~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R  341 (352)
T PRK13482        291 KIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR  341 (352)
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence            799999999999999999999999999999999999999999998877653

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=97.23  E-value=0.00084  Score=67.06  Aligned_cols=57  Identities=16%  Similarity=0.261  Sum_probs=44.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCh-HHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      ..++|+|+|||++.++++.-....+ ..+..-+.+.|.++||+|+|+|++|+..+...
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            3678999999999999986533322 22334567889999999999999999998753

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=97.18  E-value=0.00056  Score=69.39  Aligned_cols=54  Identities=24%  Similarity=0.316  Sum_probs=50.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ...+|+|+|++++.+|++.|+ .|+.+|-..+.++|.+++|+|++.|++|++.+.
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

>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=97.18  E-value=0.00061  Score=47.47  Aligned_cols=30  Identities=33%  Similarity=0.667  Sum_probs=26.3

Q ss_pred             CHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        545 NLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       545 sl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      +++.+..++.++|.++||||+++|+.|.+|
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            467788999999999999999999999876

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 ....

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=97.08  E-value=0.00074  Score=77.89  Aligned_cols=49  Identities=27%  Similarity=0.415  Sum_probs=47.3

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .|||||++++++|+++|||++++..|+.++|.++||+|+++|+.|.+++
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            8999999999999999999999999999999999999999999998764

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=97.07  E-value=0.00053  Score=81.36  Aligned_cols=50  Identities=24%  Similarity=0.372  Sum_probs=46.0

Q ss_pred             CCCCeEecccccCccEEEecCC---CC-chHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQK---PG-KKLEKAIKLNIKILDEKNFVKIVKGF  649 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~---~g-~K~~kA~~lgi~ii~e~~f~~~l~~~  649 (655)
                      .+||+++++|+++|++|++|+.   +| +|+++|+++||+|++|++|.+++...
T Consensus       214 ~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~i~~~  267 (815)
T PLN03122        214 KHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDSIEKQ  267 (815)
T ss_pred             HcCCEEccccccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHHHhcC
Confidence            7899999999999999888876   66 89999999999999999999999754

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

Probab=97.05  E-value=0.00064  Score=55.08  Aligned_cols=41  Identities=29%  Similarity=0.396  Sum_probs=35.2

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHH
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEK  640 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~  640 (655)
                      .+||.+...+++++++|||++..|.|.++|++.||||++.+
T Consensus        22 ~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~   62 (63)
T PF12738_consen   22 ALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPD   62 (63)
T ss_dssp             CTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHH
T ss_pred             HCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCC
Confidence            88999999999999999998888899999999999999875

>TIGR01209 RNA ligase, Pab1020 family

Probab=97.04  E-value=0.011  Score=64.30  Aligned_cols=168  Identities=24%  Similarity=0.205  Sum_probs=98.0

Q ss_pred             eccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc
Q psy11423         84 HHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH  163 (655)
Q Consensus        84 ~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~  163 (655)
                      +|-..++.|+..            +.+.+.   ...+++|.|+||-.+.+..-+|++ .|.||| |.+=-==|+.++..-
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            566788888875            222222   235999999999999998889985 899999 332110112333332


Q ss_pred             cCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCC
Q psy11423        164 KIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM  243 (655)
Q Consensus       164 ~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~  243 (655)
                      +  ..+-. +.| ++.+-||++=+..-               |+           ..+... ...+..||+|++-+.+..
T Consensus       123 ~--~~~~~-d~p-~l~LcGE~iGpenp---------------Y~-----------~hs~~y-~~l~~~FfvFDI~d~~t~  171 (374)
T TIGR01209       123 D--LEFFD-DNP-DLVLCGEMAGPENP---------------YT-----------PEYYPE-VKEDLGFFLFDIREGKTN  171 (374)
T ss_pred             h--HHhhc-cCC-CeEEEEEEcCCCCC---------------Cc-----------ccCccc-cCCCceEEEEEEEECCCC
Confidence            2  23322 133 58899998733111               10           000111 122689999998643222


Q ss_pred             CCCCCHHHHHHHHHhCCCCCCCCceeeCCHHHHH-HHHHHHHHhhcCCCCccceEEEEECCh
Q psy11423        244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLI-EFYKKINIKRFNLPYEIDGVVYKINCL  304 (655)
Q Consensus       244 ~~~~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~-~~~~~~~~~r~~l~y~iDGiVikv~~~  304 (655)
                      . +-+..+..+++..+||+.++....+ +.+++. +..+.+.+.-...   --|||+|-.+-
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 4688899999999999988754343 334433 3332222211111   47999997653

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.

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.95  E-value=0.003  Score=63.21  Aligned_cols=90  Identities=14%  Similarity=0.212  Sum_probs=63.1

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHH----HhcCHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l----~~as~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-++++|||+++|..++..|+ .+.+    ..-+.+.|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vpGIGk  118 (194)
T PRK14605         54 REDALSLFGFATTEELSLFE--------------TLIDVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIPGIGK  118 (194)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhCCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence            46667777998776654442              234899999999999999987 5543    4457889999999999


Q ss_pred             HHHHHHHHHhcCh---------------hHHHHHHHHHHcCccc
Q psy11423        566 TTVKAFIKFINQP---------------LHRLLISQLRDVGIYW  594 (655)
Q Consensus       566 ~~A~~I~~~f~~~---------------~n~~li~~L~~~Gi~~  594 (655)
                      ++|++|+--+.+.               ...+++..|...|++.
T Consensus       119 KtAerIilELk~Ki~~~~~~~~~~~~~~~~~e~~~aL~~LGy~~  162 (194)
T PRK14605        119 KTASRIVLELKDKIAKNWEAGVLSQVTEANSDILATLTALGYSS  162 (194)
T ss_pred             HHHHHHHHHHHHHHHhhhhccccccccchHHHHHHHHHHcCCCH
Confidence            9999955322211               2234566666667653

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.84  E-value=0.0041  Score=62.19  Aligned_cols=72  Identities=15%  Similarity=0.166  Sum_probs=54.6

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. +++|..|    +...|.++||||+
T Consensus        53 rED~~~LYGF~t~~Er~lF~--------------~LisVsGIGPK~ALaILs~~~-~~el~~aI~~~D~~~L~~vpGIGk  117 (196)
T PRK13901         53 REDELKLFGFLNSSEREVFE--------------ELIGVDGIGPRAALRVLSGIK-YNEFRDAIDREDIELISKVKGIGN  117 (196)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence            46666777898776654442              224889999999999999874 6655554    7889999999999


Q ss_pred             HHHHHHHHHhc
Q psy11423        566 TTVKAFIKFIN  576 (655)
Q Consensus       566 ~~A~~I~~~f~  576 (655)
                      |+|++|+--+.
T Consensus       118 KtAeRIIlELk  128 (196)
T PRK13901        118 KMAGKIFLKLR  128 (196)
T ss_pred             HHHHHHHHHHH
Confidence            99999875443

>PRK00254 ski2-like helicase; Provisional

Probab=96.83  E-value=0.0026  Score=75.64  Aligned_cols=54  Identities=24%  Similarity=0.456  Sum_probs=50.6

Q ss_pred             HhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        525 ALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       525 algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      -..|||+|++++++|.++ |+|+++|..|+.++|.+++|||+++|++|+++++..
T Consensus       647 L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~  701 (720)
T PRK00254        647 LMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE  701 (720)
T ss_pred             hhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence            348999999999999999 999999999999999999999999999999998743

>PRK08609 hypothetical protein; Provisional

Probab=96.79  E-value=0.0027  Score=73.43  Aligned_cols=84  Identities=13%  Similarity=0.185  Sum_probs=65.6

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccch--------hHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhcCH-HHHhc
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELANY--FKNLECMFKATE-EQLLN  559 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l--------~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~as~-eeL~~  559 (655)
                      ++|..+||+|++.|++|-+-++.-+-..+        ..++.-+.|||||++++++|-+.  +.|+++|..+.. ..+..
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            37899999999999998887764222111        24555569999999999999875  568999998754 35889


Q ss_pred             CCCCCHHHHHHHHHH
Q psy11423        560 IPKIGSTTVKAFIKF  574 (655)
Q Consensus       560 i~GIG~~~A~~I~~~  574 (655)
                      ++|+|+++.++|..-
T Consensus       128 ~~gfg~k~~~~il~~  142 (570)
T PRK08609        128 LAGFGKKTEEKILEA  142 (570)
T ss_pred             ccCcchhHHHHHHHH
Confidence            999999999998653

>PRK14973 DNA topoisomerase I; Provisional

Probab=96.77  E-value=0.013  Score=71.26  Aligned_cols=149  Identities=13%  Similarity=0.243  Sum_probs=106.4

Q ss_pred             CCCCCCCCCcceee--cC--ceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCCh
Q psy11423        415 PNICPICNSKIIYI--ES--NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF  490 (655)
Q Consensus       415 P~~CP~C~~~l~~~--~~--~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~  490 (655)
                      ...||.||.+++..  .|  +-++-|  + . |.....      ..+.+-+++|+|+++.++|-.++ +.++.++-..+.
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            46799999964433  22  336667  3 3 743221      33367789999999999999888 588899988888


Q ss_pred             hhhccccCCcHHHHHHHHHHHHH-----hcccchhHHHHHhCCCCccHHHHHHHHH----hCCCHHHHHhcCHHHHhcCC
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELAN----YFKNLECMFKATEEQLLNIP  561 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~-----sk~~~l~r~L~algIpgIG~~~Ak~L~~----~fgsl~~l~~as~eeL~~i~  561 (655)
                      +++..--+.+.+.++++...-+.     .+...+.+|+...-.|.=|...|+.+..    -..++.+|..|++..|..- 
T Consensus       704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  782 (936)
T PRK14973        704 EALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKFVRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKKA-  782 (936)
T ss_pred             hHhhhhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccHHHHHHHHHhcCcchHHHHhhCCHHHHHHc-
Confidence            88887666777777777664332     2234577888888888888887764433    4567888999988877764 


Q ss_pred             CCCHHHHHHHHHHh
Q psy11423        562 KIGSTTVKAFIKFI  575 (655)
Q Consensus       562 GIG~~~A~~I~~~f  575 (655)
                      |+++.-+.++.++-
T Consensus       783 ~~sE~~~~~~~~~a  796 (936)
T PRK14973        783 GLSEAEAASLLAEA  796 (936)
T ss_pred             CCCHHHHHHHHHHH
Confidence            88888887777655

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.76  E-value=0.0049  Score=61.40  Aligned_cols=90  Identities=17%  Similarity=0.194  Sum_probs=64.4

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. ++++..|    +...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~AL~iLs~~~-~~el~~aI~~~D~~~L~~vpGIGk  118 (188)
T PRK14606         54 SQDGITLYGFSNERKKELFL--------------SLTKVSRLGPKTALKIISNED-AETLVTMIASQDVEGLSKLPGISK  118 (188)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhccCCccHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence            56677777898776554432              224789999999999998874 6655554    7889999999999


Q ss_pred             HHHHHHHHHhcCh----------hHHHHHHHHHHcCccc
Q psy11423        566 TTVKAFIKFINQP----------LHRLLISQLRDVGIYW  594 (655)
Q Consensus       566 ~~A~~I~~~f~~~----------~n~~li~~L~~~Gi~~  594 (655)
                      ++|++|+--+.+.          ...+.++.|...|.+.
T Consensus       119 KtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~  157 (188)
T PRK14606        119 KTAERIVMELKDEFESAGIKDMRIYHESLEALVSLGYPE  157 (188)
T ss_pred             HHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCH
Confidence            9999988644432          1234566677777653

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=96.71  E-value=0.003  Score=63.05  Aligned_cols=69  Identities=16%  Similarity=0.178  Sum_probs=51.6

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .+|-..|=||..+....+.              ..-+++||||+++|..|+..+. ++++..|    +...|.++||||+
T Consensus        53 red~~~LyGF~~~~Er~lF--------------~~L~~V~GIGpK~Al~iL~~~~-~~el~~aI~~~d~~~L~~ipGiGk  117 (191)
T TIGR00084        53 REDAELLFGFNTLEERELF--------------KELIKVNGVGPKLALAILSNMS-PEEFVYAIETEEVKALVKIPGVGK  117 (191)
T ss_pred             ecCCceeeCCCCHHHHHHH--------------HHHhCCCCCCHHHHHHHHhcCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence            4566667788877554443              3335899999999999988875 6555544    5688999999999


Q ss_pred             HHHHHHHH
Q psy11423        566 TTVKAFIK  573 (655)
Q Consensus       566 ~~A~~I~~  573 (655)
                      ++|++|.-
T Consensus       118 KtAerIil  125 (191)
T TIGR00084       118 KTAERLLL  125 (191)
T ss_pred             HHHHHHHH
Confidence            99999973

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.

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.70  E-value=0.0061  Score=60.42  Aligned_cols=90  Identities=19%  Similarity=0.278  Sum_probs=64.4

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. .+++..|    +...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF~--------------~Li~VsGIGpK~Al~ILs~~~-~~el~~aI~~~D~~~L~~vpGIGk  118 (183)
T PRK14601         54 KEDSNKLYGFLDKDEQKMFE--------------MLLKVNGIGANTAMAVCSSLD-VNSFYKALSLGDESVLKKVPGIGP  118 (183)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhccCCccHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence            46677777898775544432              224789999999999998875 6666554    7788999999999


Q ss_pred             HHHHHHHHHhcCh---------hHHHHHHHHHHcCccc
Q psy11423        566 TTVKAFIKFINQP---------LHRLLISQLRDVGIYW  594 (655)
Q Consensus       566 ~~A~~I~~~f~~~---------~n~~li~~L~~~Gi~~  594 (655)
                      |+|++|+--+.+.         ...+.++.|.+.|.+.
T Consensus       119 KtAeRIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~~  156 (183)
T PRK14601        119 KSAKRIIAELSDAKTKLENVSDDKSEALAALLTLGFKQ  156 (183)
T ss_pred             HHHHHHHHHHHHHhhccCCCCccHHHHHHHHHHcCCCH
Confidence            9999987544332         1235666677777653

>PRK13766 Hef nuclease; Provisional

Probab=96.66  E-value=0.0025  Score=76.34  Aligned_cols=54  Identities=26%  Similarity=0.451  Sum_probs=51.1

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~  579 (655)
                      .+|||||++++++|+++|++++.+..++.++|..++|+|++.|+.|.+||+.+.
T Consensus       718 ~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~  771 (773)
T PRK13766        718 ESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSEY  771 (773)
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhh
Confidence            389999999999999999999999999999999999999999999999998653

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.57  E-value=0.0081  Score=60.19  Aligned_cols=73  Identities=19%  Similarity=0.228  Sum_probs=54.2

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. +++|..|    +...|.++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~iLs~~~-~~el~~aI~~~D~~~L~kvpGIGk  118 (195)
T PRK14604         54 REDALTLYGFSTPAQRQLFE--------------LLIGVSGVGPKAALNLLSSGT-PDELQLAIAGGDVARLARVPGIGK  118 (195)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence            46666777888776654432              224789999999999998864 6555544    7788999999999


Q ss_pred             HHHHHHHHHhcC
Q psy11423        566 TTVKAFIKFINQ  577 (655)
Q Consensus       566 ~~A~~I~~~f~~  577 (655)
                      ++|++|+--+++
T Consensus       119 KtAerIilELk~  130 (195)
T PRK14604        119 KTAERIVLELKG  130 (195)
T ss_pred             HHHHHHHHHHHH
Confidence            999998765543

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=96.54  E-value=0.002  Score=64.34  Aligned_cols=52  Identities=21%  Similarity=0.429  Sum_probs=43.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-CCh---hhhccccCCcHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INF---KNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~---~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ..++|+|+|||++..+..   +-++.+|.. +..   +.|.++||||+|+|++|+-.+.
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            478999999999999955   347888887 444   7799999999999999994443

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.

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.46  E-value=0.0084  Score=59.63  Aligned_cols=70  Identities=20%  Similarity=0.248  Sum_probs=47.8

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .+|-..|=||..+....+..              .-+++.|||+++|-.++..+. ++++..|    +...| ++||||+
T Consensus        54 rEd~~~LyGF~~~~Er~lF~--------------~LisV~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L-~vpGIGk  117 (186)
T PRK14600         54 RDNVTQLYGFLNREEQDCLR--------------MLVKVSGVNYKTAMSILSKLT-PEQLFSAIVNEDKAAL-KVNGIGE  117 (186)
T ss_pred             ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHccCC-HHHHHHHHHcCCHhhe-ECCCCcH
Confidence            45555666787665544332              224778888888888888774 5555443    66778 8888888


Q ss_pred             HHHHHHHHHh
Q psy11423        566 TTVKAFIKFI  575 (655)
Q Consensus       566 ~~A~~I~~~f  575 (655)
                      ++|++|+--+
T Consensus       118 KtAerIilEL  127 (186)
T PRK14600        118 KLINRIITEL  127 (186)
T ss_pred             HHHHHHHHHH
Confidence            8888887543

>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=96.44  E-value=0.0048  Score=51.00  Aligned_cols=51  Identities=24%  Similarity=0.297  Sum_probs=43.0

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      +-=||...+...|-..| |.++.||..++.++|..++|||+|+.+.|.+.++
T Consensus        15 ~~L~LS~Ra~n~L~~~~-I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~   65 (66)
T PF03118_consen   15 EDLGLSVRAYNCLKRAG-IHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK   65 (66)
T ss_dssp             GGSTSBHHHHHHHHCTT---BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHhC-CcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence            34478899999998877 6999999999999999999999999999988775

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 ....

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.37  E-value=0.005  Score=73.69  Aligned_cols=51  Identities=20%  Similarity=0.353  Sum_probs=48.2

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCC-HHHHHHHHHHhcCh
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIG-STTVKAFIKFINQP  578 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG-~~~A~~I~~~f~~~  578 (655)
                      +.|||||++.|++|+.+|+|+.+|.+++.++|..+  +| ++.|+.|++||+.+
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            39999999999999999999999999999999996  77 99999999999865

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit

>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]

Probab=96.36  E-value=0.083  Score=56.53  Aligned_cols=168  Identities=21%  Similarity=0.167  Sum_probs=111.4

Q ss_pred             eeccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc
Q psy11423         83 VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII  162 (655)
Q Consensus        83 v~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i  162 (655)
                      .+|-..|+-|+.+     +++|.       +   -..++||.|+||-.+.+.=-+|. +-|+||| |.+====|+.++.+
T Consensus        68 fPkI~R~llL~p~-----ik~~F-------~---~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~l  130 (382)
T COG1423          68 FPKIRRALLLEPT-----IKKHF-------G---RGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRDL  130 (382)
T ss_pred             Cchhheeeccchh-----hHhhc-------C---CCcEEEEEeccCceEEEEEECCE-EEEEecC-ceecCchhHHHHhh
Confidence            3677788888875     44443       2   13799999999999999888887 5899998 66555557777654


Q ss_pred             ccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC
Q psy11423        163 HKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG  242 (655)
Q Consensus       163 ~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~  242 (655)
                        +|+.+-. ++| .+.+-||++=+                   .||=  +    . .++-  ...++.||.|++..-..
T Consensus       131 --~~~eff~-d~p-~lvlcgEmvG~-------------------enPY--v----~-~~~y--~~e~v~fFvFDire~~t  178 (382)
T COG1423         131 --IDLEFFD-DYP-DLVLCGEMVGP-------------------ENPY--V----P-GPYY--EKEDVGFFVFDIREKNT  178 (382)
T ss_pred             --cchhhHh-hCC-CcEEEEEeccC-------------------CCCC--C----C-CCCC--ccCCceEEEEEEEecCC
Confidence              5666654 355 57899998733                   2331  1    1 1111  23579999999976322


Q ss_pred             CCCCCCHHHHHHHHHhCCCCCCCCceee--CCH-HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423        243 MNMPSSHSELLNWYQKIGLSICGEYSVL--SGV-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (655)
Q Consensus       243 ~~~~~~~~e~l~~L~~~GF~~~~~~~~~--~~~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (655)
                      . .+-++.+.++.+.+.||+.+..--..  +.. ++|.+.++++.+..      --|||+|-.|-..
T Consensus       179 g-r~Lp~eer~~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~keG------REGVV~Kdpdm~~  238 (382)
T COG1423         179 G-RPLPVEERLELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNKEG------REGVVMKDPDMRV  238 (382)
T ss_pred             C-CCCCHHHHHHHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhhcC------CcceEecCccccc
Confidence            2 25789999999999999877532222  122 45555556554432      3799999887543

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.35  E-value=0.0075  Score=60.82  Aligned_cols=73  Identities=16%  Similarity=0.200  Sum_probs=55.9

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHH----hcCHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~----~as~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. .++|.    +-+...|.++||||+
T Consensus        55 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~ipGIGk  119 (203)
T PRK14602         55 REDALELFGFATWDERQTFI--------------VLISISKVGAKTALAILSQFR-PDDLRRLVAEEDVAALTRVSGIGK  119 (203)
T ss_pred             ecCcceeeCCCCHHHHHHHH--------------HHhCCCCcCHHHHHHHHhhCC-HHHHHHHHHhCCHHHHhcCCCcCH
Confidence            56777788998776654432              224889999999999999875 55444    448899999999999


Q ss_pred             HHHHHHHHHhcC
Q psy11423        566 TTVKAFIKFINQ  577 (655)
Q Consensus       566 ~~A~~I~~~f~~  577 (655)
                      |+|++|+--+++
T Consensus       120 KtAerIilELkd  131 (203)
T PRK14602        120 KTAQHIFLELKY  131 (203)
T ss_pred             HHHHHHHHHHHH
Confidence            999999865543

>TIGR01259 comE comEA protein

Probab=96.35  E-value=0.0031  Score=58.34  Aligned_cols=24  Identities=13%  Similarity=0.396  Sum_probs=19.6

Q ss_pred             cCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        552 ATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       552 as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      ++.++|.+++|||+++++.|..|+
T Consensus        95 ~s~eeL~~V~GIg~k~~~~i~~~l  118 (120)
T TIGR01259        95 KSVDDLTKVSGIGEKSLEKLKDYA  118 (120)
T ss_pred             CCHHHHHcCCCCCHHHHHHHHhce
Confidence            466888888899998888888775

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=96.32  E-value=0.0063  Score=50.44  Aligned_cols=43  Identities=28%  Similarity=0.519  Sum_probs=29.3

Q ss_pred             CCCccHHHHHHHHHh---CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        528 IRHVGETTAKELANY---FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       528 IpgIG~~~Ak~L~~~---fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +||+|++.|++|.++   ++.+.     +.++|.+++|||+++++.|..|+
T Consensus        22 ipgig~~~a~~Il~~R~~~g~~~-----s~~dL~~v~gi~~~~~~~i~~~~   67 (69)
T TIGR00426        22 MNGVGLKKAEAIVSYREEYGPFK-----TVEDLKQVPGIGNSLVEKNLAVI   67 (69)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCcC-----CHHHHHcCCCCCHHHHHHHHhhc
Confidence            555555555555554   44332     67788888888888888888775

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.

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=96.21  E-value=0.0072  Score=70.95  Aligned_cols=83  Identities=23%  Similarity=0.354  Sum_probs=57.2

Q ss_pred             cccccCCCCHHHHHHHHHcCC---CCChHHHhcCChhhhccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~---I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI  531 (655)
                      +.+.++|+|+|++++|++.--   -.....++     ..+.+||+|++.|..|++.+   +.-++.+...+   ..|+||
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            567899999999999987421   11112221     24578999999999998864   33333333332   379999


Q ss_pred             cHHHHHHHHHhCCCHHH
Q psy11423        532 GETTAKELANYFKNLEC  548 (655)
Q Consensus       532 G~~~Ak~L~~~fgsl~~  548 (655)
                      |+++|+.|.+.|.+...
T Consensus       539 G~~~A~~I~~ff~~~~~  555 (652)
T TIGR00575       539 GPKVAESIVNFFHDPNN  555 (652)
T ss_pred             CHHHHHHHHHHHhhhhH
Confidence            99999999999976443

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.

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.14  E-value=0.01  Score=59.60  Aligned_cols=73  Identities=14%  Similarity=0.154  Sum_probs=54.4

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHh----cCHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK----ATEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~----as~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+++.|||+++|-.++..+. ++.+..    -+...|.++||||+
T Consensus        53 rEd~~~LyGF~~~~Er~lF~--------------~L~~V~GIGpK~AL~iLs~~~-~~~l~~aI~~~D~~~L~kvpGIGk  117 (197)
T PRK14603         53 REDALSLYGFPDEDSLELFE--------------LLLGVSGVGPKLALALLSALP-PALLARALLEGDARLLTSASGVGK  117 (197)
T ss_pred             ccCCceeeCcCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence            45666777888776544432              224789999999999999875 555544    47889999999999


Q ss_pred             HHHHHHHHHhcC
Q psy11423        566 TTVKAFIKFINQ  577 (655)
Q Consensus       566 ~~A~~I~~~f~~  577 (655)
                      |+|++|+--+.+
T Consensus       118 KtAerIilELkd  129 (197)
T PRK14603        118 KLAERIALELKG  129 (197)
T ss_pred             HHHHHHHHHHHH
Confidence            999999865544

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=96.14  E-value=0.0043  Score=67.39  Aligned_cols=48  Identities=21%  Similarity=0.252  Sum_probs=45.0

Q ss_pred             CCCCeEecccccCccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+|..++.+||..|++|||.+...  +|+..|+.+|||++++++|+.++.
T Consensus       319 ~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~~gipl~~d~~fl~~~~  368 (377)
T PRK05601        319 RAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQRKGIPLLSDVAFLAAVE  368 (377)
T ss_pred             HccchhhhccccceeEEEeCCCCCccchhhhhhhcCCCccCHHHHHHHHH
Confidence            788999999999999999998754  999999999999999999999985

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=95.97  E-value=0.019  Score=53.21  Aligned_cols=83  Identities=22%  Similarity=0.182  Sum_probs=61.7

Q ss_pred             CCCCHHHHHHHHHcCCCCChHHHhcCChh-----hhccccCCcHHHHHHHHHHHHHhcccchhHHHHHh-CCCCccHHHH
Q psy11423        463 IGLGKKMIEKLVNANIVVTAVDLYKINFK-----NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTA  536 (655)
Q Consensus       463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~-----~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~al-gIpgIG~~~A  536 (655)
                      ||+|++...+|-+.| |.|..||+.....     .|+.--|+..+...++..             ++.| -|||||+.-|
T Consensus         1 pgi~~~~~~~L~~~G-I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~-------------~AdL~ri~gi~~~~a   66 (122)
T PF14229_consen    1 PGIGPKEAAKLKAAG-IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVN-------------QADLMRIPGIGPQYA   66 (122)
T ss_pred             CCCCHHHHHHHHHcC-CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHh-------------HHHhhhcCCCCHHHH
Confidence            799999999997777 7999999996532     255555566554444332             1222 6899999999


Q ss_pred             HHHHH-hCCCHHHHHhcCHHHHhc
Q psy11423        537 KELAN-YFKNLECMFKATEEQLLN  559 (655)
Q Consensus       537 k~L~~-~fgsl~~l~~as~eeL~~  559 (655)
                      ..|.. .+.|+++|..+++++|.+
T Consensus        67 ~LL~~AGv~Tv~~LA~~~p~~L~~   90 (122)
T PF14229_consen   67 ELLEHAGVDTVEELAQRNPQNLHQ   90 (122)
T ss_pred             HHHHHhCcCcHHHHHhCCHHHHHH
Confidence            98876 588999999999887764

>PRK07758 hypothetical protein; Provisional

Probab=95.95  E-value=0.016  Score=50.99  Aligned_cols=51  Identities=18%  Similarity=0.177  Sum_probs=46.3

Q ss_pred             cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .++|+-...+.|..+| |.++.||..+++++|+++.|||+|+.+.|.+.+.+
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            4578888899999998 69999999999999999999999999999988865

>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family

Probab=95.84  E-value=0.045  Score=58.78  Aligned_cols=128  Identities=16%  Similarity=0.135  Sum_probs=80.3

Q ss_pred             CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhh---------hhhhhcccCCcccccCC--CCceEEEEEEEE
Q psy11423        117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENIT---------TNIHIIHKIPLVLNIKY--PPELLEVRCEVL  185 (655)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT---------~n~~~i~~iP~~l~~~~--~p~~~evRGEv~  185 (655)
                      ...|+++.|+||.-.+++|.+|.-++..+| +|..++|-.         +....+..+...|....  -...+.|-||++
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            358999999999999999988834677788 566665421         11112222333331110  135799999999


Q ss_pred             eehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC--CCCCCCHHHHHHHHHhCC-CC
Q psy11423        186 IYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMPSSHSELLNWYQKIG-LS  262 (655)
Q Consensus       186 ~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~--~~~~~~~~e~l~~L~~~G-F~  262 (655)
                      =+                 .+.+|.+              .. .+.|++|++.....  ..+ -+.-+.++.+...| |+
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            33                 2344544              12 47999999955421  112 45556777888886 98


Q ss_pred             CCCCceeeCCHHHHHHH
Q psy11423        263 ICGEYSVLSGVNKLIEF  279 (655)
Q Consensus       263 ~~~~~~~~~~~~ev~~~  279 (655)
                      .++. ....++++++++
T Consensus       150 ~ap~-L~rGt~~e~l~~  165 (325)
T TIGR02307       150 YAPL-LGRGTLDELLAF  165 (325)
T ss_pred             cchh-hcccCHHHHHhc
Confidence            7763 344678888876

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.

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=95.76  E-value=0.014  Score=68.66  Aligned_cols=82  Identities=18%  Similarity=0.326  Sum_probs=56.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI  531 (655)
                      +.+.++|+|+|++++|+++-     ..--...-+++   +.++|+|++.|..|++.+   +.-++.+...+   ..|+||
T Consensus       480 ~L~~l~gfG~Ksa~~ll~~I-----e~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI  551 (665)
T PRK07956        480 DLLGLEGFGEKSAQNLLDAI-----EKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEEL---AAVEGV  551 (665)
T ss_pred             HHhcCcCcchHHHHHHHHHH-----HHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHH---hccCCc
Confidence            46689999999999998732     21112222232   367999999999888754   34334444443   378999


Q ss_pred             cHHHHHHHHHhCCCHH
Q psy11423        532 GETTAKELANYFKNLE  547 (655)
Q Consensus       532 G~~~Ak~L~~~fgsl~  547 (655)
                      |+++|+.|.+.|.+.+
T Consensus       552 G~~~A~sI~~ff~~~~  567 (665)
T PRK07956        552 GEVVAQSIVEFFAVEE  567 (665)
T ss_pred             CHHHHHHHHHHHhhhh
Confidence            9999999999987543

>PRK00254 ski2-like helicase; Provisional

Probab=95.70  E-value=0.013  Score=69.78  Aligned_cols=53  Identities=21%  Similarity=0.343  Sum_probs=49.6

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .+.|||+|++++.+|+++|+ .|+.||..++.++|.+++|+|+|.|++|.+.+.
T Consensus       647 L~~ipgig~~~~~~l~~~g~-~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~  699 (720)
T PRK00254        647 LMRLPMIGRKRARALYNAGF-RSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG  699 (720)
T ss_pred             hhcCCCCCHHHHHHHHHccC-CCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence            44799999999999999995 999999999999999999999999999999876

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=95.65  E-value=0.017  Score=68.16  Aligned_cols=92  Identities=17%  Similarity=0.224  Sum_probs=58.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI  531 (655)
                      +...++|+|+|++++|+++---+     -...-+++   +.+||+|++.|.+|++.+   +.-++.+...+   ..|+||
T Consensus       497 ~L~~l~g~g~Ksa~~Ll~~Ie~s-----k~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL---~~i~GI  568 (689)
T PRK14351        497 DLAELEGWGETSAENLLAELEAS-----REPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEAL---RAVDDV  568 (689)
T ss_pred             HHhcCcCcchhHHHHHHHHHHHH-----ccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH---hccCCc
Confidence            45578999999999988742111     01112222   457899999999998754   33333343333   368999


Q ss_pred             cHHHHHHHHHhCCCHHHHHhcCHHHHhc
Q psy11423        532 GETTAKELANYFKNLECMFKATEEQLLN  559 (655)
Q Consensus       532 G~~~Ak~L~~~fgsl~~l~~as~eeL~~  559 (655)
                      |+++|+.|.+.|.+.+....  .++|.+
T Consensus       569 G~k~A~sI~~ff~~~~n~~~--i~~L~~  594 (689)
T PRK14351        569 GPTVAEEIREFFDSERNRAV--IDDLLD  594 (689)
T ss_pred             CHHHHHHHHHHHhhhHHHHH--HHHHHh
Confidence            99999999988876554332  344544

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.61  E-value=0.034  Score=55.71  Aligned_cols=51  Identities=25%  Similarity=0.375  Sum_probs=40.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .+.|+|+|||++..+....   ++.+|.. +   +.+.|.++||+|+|+|++|+-.+.
T Consensus        75 Li~V~GIGpK~Al~ILs~~---~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk  129 (194)
T PRK14605         75 LIDVSGIGPKLGLAMLSAM---NAEALASAIISGNAELLSTIPGIGKKTASRIVLELK  129 (194)
T ss_pred             HhCCCCCCHHHHHHHHHhC---CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence            6789999999999999865   4556544 2   356788999999999999886664

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=95.57  E-value=0.024  Score=56.95  Aligned_cols=73  Identities=15%  Similarity=0.191  Sum_probs=51.2

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS  565 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~  565 (655)
                      .||-..|=||..+....+..              .-+.+.|||+++|-.++..+. ++.|.+|    +...|.++||||+
T Consensus        54 REd~~~LyGF~~~~ER~lF~--------------~LisVnGIGpK~ALaiLs~~~-~~~l~~aI~~~d~~~L~k~PGIGk  118 (201)
T COG0632          54 REDAHLLYGFLTEEERELFR--------------LLISVNGIGPKLALAILSNLD-PEELAQAIANEDVKALSKIPGIGK  118 (201)
T ss_pred             hhhHHHHcCCCCHHHHHHHH--------------HHHccCCccHHHHHHHHcCCC-HHHHHHHHHhcChHhhhcCCCCCH
Confidence            34445555787665544432              233678999999988888764 6666554    6788999999999


Q ss_pred             HHHHHHHHHhcC
Q psy11423        566 TTVKAFIKFINQ  577 (655)
Q Consensus       566 ~~A~~I~~~f~~  577 (655)
                      |+|++|+--+.+
T Consensus       119 KtAerivleLk~  130 (201)
T COG0632         119 KTAERIVLELKG  130 (201)
T ss_pred             HHHHHHHHHHhh
Confidence            999998765543

>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=95.43  E-value=0.025  Score=46.72  Aligned_cols=47  Identities=30%  Similarity=0.367  Sum_probs=42.3

Q ss_pred             CCCCeEecccccCccEEEecCC--CCchHHHHHHcCCeeeCHHHHHHHH
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQK--PGKKLEKAIKLNIKILDEKNFVKIV  646 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~--~g~K~~kA~~lgi~ii~e~~f~~~l  646 (655)
                      .+||++...+++.++++|++..  ...|...|...|++|++++-+.+.|
T Consensus        30 ~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci   78 (78)
T PF00533_consen   30 KHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI   78 (78)
T ss_dssp             HTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred             HcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence            8899999999999999999988  4588888999999999999887653

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 ....

>TIGR01259 comE comEA protein

Probab=95.39  E-value=0.024  Score=52.45  Aligned_cols=61  Identities=18%  Similarity=0.250  Sum_probs=46.1

Q ss_pred             ChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423        481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (655)
Q Consensus       481 ~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f  543 (655)
                      .+-||-+++.++|..+||+|++.|++|++..+.  +.++..+-.-..++|||++++.+|...+
T Consensus        58 ~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f~s~eeL~~V~GIg~k~~~~i~~~l  118 (120)
T TIGR01259        58 AAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGAFKSVDDLTKVSGIGEKSLEKLKDYA  118 (120)
T ss_pred             CCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCcCCHHHHHcCCCCCHHHHHHHHhce
Confidence            455788888999999999999999999998875  2233333233478999999988886643

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=95.36  E-value=0.015  Score=69.39  Aligned_cols=53  Identities=25%  Similarity=0.395  Sum_probs=48.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..+.|||+|++++.+|++.| |+|+.||..++.++|..+  ||+|.|++|++++..
T Consensus       653 ~L~~ip~i~~~~a~~l~~~g-i~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~~  705 (737)
T PRK02362        653 DLVGLRGVGRVRARRLYNAG-IESRADLRAADKSVVLAI--LGEKIAENILEQAGR  705 (737)
T ss_pred             HHhCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhCc
Confidence            46789999999999999966 799999999999999999  999999999999863

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=94.94  E-value=0.031  Score=52.06  Aligned_cols=41  Identities=15%  Similarity=0.268  Sum_probs=22.5

Q ss_pred             CCCccHHHHHHHHHh--CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        528 IRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       528 IpgIG~~~Ak~L~~~--fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +||||++.|++|.++  |.        +.|||.+++|||++..+.+..+.+
T Consensus        66 lpGigP~~A~~IV~nGpf~--------sveDL~~V~GIgekqk~~l~k~~~  108 (132)
T PRK02515         66 FPGMYPTLAGKIVKNAPYD--------SVEDVLNLPGLSERQKELLEANLD  108 (132)
T ss_pred             CCCCCHHHHHHHHHCCCCC--------CHHHHHcCCCCCHHHHHHHHHhhc
Confidence            455555555555532  33        345666666777666666555543

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=94.92  E-value=0.025  Score=65.00  Aligned_cols=92  Identities=17%  Similarity=0.115  Sum_probs=54.8

Q ss_pred             cccccCCCCHHHHHHHHHcCC---CCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGET  534 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~---I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~  534 (655)
                      +.+.++|+|+|.++.|+++=-   =..+.-++.     =+.++++|++.+..-...|+.-.+.+...+   ..|+|||+.
T Consensus       460 ~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~-----aLGI~~vG~~~ak~~~~~i~~l~~a~~e~l---~~i~gIG~~  531 (562)
T PRK08097        460 QLANTPGIGKARAEQLWHQFNLARQQPFSRWLK-----ALGIPLPQAALNALDDRSWQQLLSRSEQQW---QQLPGIGEG  531 (562)
T ss_pred             HHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHH-----HcCCccHHHHHHHHhcCCHHHHHcCCHHHH---hcCCCchHH
Confidence            677899999999999987411   011111111     134677888766553333444333333332   278899999


Q ss_pred             HHHHHHHhCCCHHHHHhcCHHHHhc
Q psy11423        535 TAKELANYFKNLECMFKATEEQLLN  559 (655)
Q Consensus       535 ~Ak~L~~~fgsl~~l~~as~eeL~~  559 (655)
                      +|..|.+.|.+-+....  .++|.+
T Consensus       532 ~a~si~~~f~~~~~~~~--i~~L~~  554 (562)
T PRK08097        532 RARQLIAFLQHPEVKAL--ADWLAA  554 (562)
T ss_pred             HHHHHHHHHcCHHHHHH--HHHHHH
Confidence            99999888876543322  345555

>PHA02142 putative RNA ligase

Probab=94.81  E-value=0.48  Score=51.79  Aligned_cols=147  Identities=17%  Similarity=0.202  Sum_probs=80.8

Q ss_pred             CceEEEEEecceeEEEEEEe--CCEEeE--------EEecCCCCccc---hhh-----hh-----hhhcccCCcccccCC
Q psy11423        117 NIEYIAELKFDGIAVNLRYE--YGYLKQ--------ASTRGDGNIGE---NIT-----TN-----IHIIHKIPLVLNIKY  173 (655)
Q Consensus       117 ~~~~~~e~KiDGlsi~l~Y~--~G~l~~--------a~TRGdG~~Ge---DvT-----~n-----~~~i~~iP~~l~~~~  173 (655)
                      ...|.++.|+||.|+++.|.  .+.+-.        |.+..+|..|-   +..     .|     +.. .+||..|..  
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  121111        11122222211   111     11     112 236667753  


Q ss_pred             CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHH
Q psy11423        174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL  253 (655)
Q Consensus       174 ~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l  253 (655)
                      ++..+.|.||+|=+                           |.  |.+.--  ...-+|++|++-.-+...+ -+..+..
T Consensus       245 ~~~~iaIqGEl~Gp---------------------------~I--Q~N~~~--~~~~~F~vF~v~~i~~~~y-l~~~e~~  292 (366)
T PHA02142        245 LGMSVAIQGELMGP---------------------------GI--QKNREN--FDKYRIFAFRAWFIDEQRF-ATDEEFQ  292 (366)
T ss_pred             hCCcEEEEEEEecc---------------------------cc--cCcccc--CCCCceEEEEEEEecccee-CCHHHHH
Confidence            45679999999931                           11  111111  1123789998832222223 5778888


Q ss_pred             HHHHhCCCCCCCCc------eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11423        254 NWYQKIGLSICGEY------SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN  302 (655)
Q Consensus       254 ~~L~~~GF~~~~~~------~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~  302 (655)
                      ++++++|++.++..      ...++++|++++-.    ...-.+-.--|+|+|--
T Consensus       293 ~~~~~~gl~~VPvL~~~~~~~~~~s~eE~L~~A~----~p~~~~~~~EGiViKp~  343 (366)
T PHA02142        293 DLCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD----IPSINHKIAEGVVYKSV  343 (366)
T ss_pred             HHHHHcCCceeeeecccccccccCCHHHHHhhcC----CCcccccccceEEEeec
Confidence            89999999876532      12237888888642    11111122579999763

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=94.59  E-value=0.17  Score=53.91  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=46.5

Q ss_pred             CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .|||||++++++|.+. |.+++.|..++.++|.++.|+++..|+.|++...
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            5899999999999998 9999999999999999999999999999987664

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.47  E-value=0.063  Score=57.63  Aligned_cols=55  Identities=22%  Similarity=0.215  Sum_probs=49.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ....++|+|++++++|.+.|+ .++.||+.++.++|.++.|++++.++.|++....
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 8999999999999999999999999999987754

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

Probab=94.46  E-value=0.089  Score=41.64  Aligned_cols=47  Identities=38%  Similarity=0.538  Sum_probs=41.1

Q ss_pred             CCCCeEecccccCccEEEecCCCCc-hHHHHHHcCCeeeCHHHHHHHH
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEKNFVKIV  646 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~-K~~kA~~lgi~ii~e~~f~~~l  646 (655)
                      .+||++..+++..++++|+++.... +...|...|++|++++-+.+.+
T Consensus        24 ~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~   71 (72)
T cd00027          24 KLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL   71 (72)
T ss_pred             HcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHh
Confidence            7899999999999999999988774 4778999999999999887654

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.

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=94.46  E-value=0.18  Score=49.64  Aligned_cols=81  Identities=16%  Similarity=0.296  Sum_probs=54.0

Q ss_pred             HHHHHcCCCCChHHHhcCChhhhcccc-------CCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423        471 EKLVNANIVVTAVDLYKINFKNLLRLD-------RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (655)
Q Consensus       471 ~~L~~~g~I~~i~DL~~L~~~~L~~l~-------GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f  543 (655)
                      ..|++..+..++.+|..++.++|..+=       ||-..+|.+|.+.                         |+.|.+.|
T Consensus        41 ~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~-------------------------a~~iie~y   95 (177)
T TIGR03252        41 HKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQAL-------------------------AQYVVDTY   95 (177)
T ss_pred             HHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHH-------------------------HHHHHHHh
Confidence            477654444689999888876665441       6666666666543                         33444444


Q ss_pred             C-CHHHHHhc----C---HHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        544 K-NLECMFKA----T---EEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       544 g-sl~~l~~a----s---~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      + +++.|...    +   .++|.++||||+++|.-+..+|.
T Consensus        96 ~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~  136 (177)
T TIGR03252        96 DGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLG  136 (177)
T ss_pred             CCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            3 45566541    1   36899999999999999988875

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).

>PRK01172 ski2-like helicase; Provisional

Probab=94.41  E-value=0.052  Score=64.23  Aligned_cols=62  Identities=18%  Similarity=0.180  Sum_probs=53.5

Q ss_pred             hccccccc---cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        450 GLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       450 ~i~~F~sk---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ||.|=+..   ..+.|||+|..++.+|+++| ++|+.||-.++.+++..+.|+|++.+++|+++..
T Consensus       602 rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g-~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~  666 (674)
T PRK01172        602 RIKEGIREDLIDLVLIPKVGRVRARRLYDAG-FKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM  666 (674)
T ss_pred             HHHcCCCHHHHhhcCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence            45554443   35679999999999999999 5999999999999999999999999999999854

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=94.29  E-value=0.11  Score=55.36  Aligned_cols=93  Identities=16%  Similarity=0.165  Sum_probs=63.1

Q ss_pred             CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh---------cccchhHHHHHhCCCCccHHHHHHHHHhC--CCHHH
Q psy11423        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS---------KLTTFSRFIYALGIRHVGETTAKELANYF--KNLEC  548 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s---------k~~~l~r~L~algIpgIG~~~Ak~L~~~f--gsl~~  548 (655)
                      .++++++..  +.+..|+|+|+..|++|-+-++.-         +..|. -++.-|.+||+|++.-..|.+.+  .+++.
T Consensus        44 e~~~ei~e~--~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~-gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~  120 (326)
T COG1796          44 EDLEEIEER--GRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPE-GLEPLLKVPGLGPKKIVSLYKELGIKDLEE  120 (326)
T ss_pred             cchHHHHhh--cccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCc-chHHHhhCCCCCcHHHHHHHHHHCcccHHH
Confidence            344455442  257788999988888877665431         12332 35556688999998877777765  46777


Q ss_pred             HHhcCH-HHHhcCCCCCHHHHHHHHHHh
Q psy11423        549 MFKATE-EQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       549 l~~as~-eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      |..|-. -.+..++|+|++.+..|..+.
T Consensus       121 l~~a~~~~~~~~l~GfG~kse~~il~~i  148 (326)
T COG1796         121 LQEALENGKIRGLRGFGKKSEAKILENI  148 (326)
T ss_pred             HHHHHHhCCccccCCccchhHHHHHHHH
Confidence            776533 357889999998888888743

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=94.24  E-value=0.065  Score=61.99  Aligned_cols=57  Identities=21%  Similarity=0.253  Sum_probs=50.9

Q ss_pred             cccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       454 F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +-| ...+|||+||++..+|++.=  .|+.+|...+.++|.+++|++++.|++|++.+.+
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            445 46799999999999999874  4899999999999999999999999999998865

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=94.20  E-value=0.18  Score=51.46  Aligned_cols=81  Identities=23%  Similarity=0.322  Sum_probs=49.4

Q ss_pred             HHHHHHHcCCC-----CChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHH
Q psy11423        469 MIEKLVNANIV-----VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA  540 (655)
Q Consensus       469 ~i~~L~~~g~I-----~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~  540 (655)
                      .+..|.+.+..     .++.+|..++.++|.++   -||-..+|..|.+-.                         +.+.
T Consensus        51 a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la-------------------------~~i~  105 (218)
T PRK13913         51 SLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLS-------------------------ENIL  105 (218)
T ss_pred             HHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHH-------------------------HHHH
Confidence            33456555432     38999999988887766   477776676665432                         2222


Q ss_pred             HhCCCHHHHHh-cCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        541 NYFKNLECMFK-ATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       541 ~~fgsl~~l~~-as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      +.|++++.+.. .+.++|.+++|||+++|..|.-|
T Consensus       106 ~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLly  140 (218)
T PRK13913        106 KDFGSFENFKQEVTREWLLDQKGIGKESADAILCY  140 (218)
T ss_pred             HHcCCchhccCchHHHHHHcCCCccHHHHHHHHHH
Confidence            33333332221 23467888888888888887764

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.01  E-value=0.048  Score=54.69  Aligned_cols=53  Identities=25%  Similarity=0.395  Sum_probs=42.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..+.|.|+|||++-.+....   ++.+|.. +   +...|..+||+|+|+|++|+-.++.
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   6777776 2   2456889999999999999977753

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.00  E-value=0.053  Score=54.74  Aligned_cols=52  Identities=21%  Similarity=0.354  Sum_probs=42.6

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|.|+|||++-.+....   ++.+|.. +   +...|..+||+|+|+|++|+-.++.
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            6789999999999998864   6777776 2   3466889999999999999977754

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=93.99  E-value=0.069  Score=62.58  Aligned_cols=54  Identities=9%  Similarity=0.056  Sum_probs=49.1

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ...+|+|+|++++.+|++.=  .|+.+|...+.++|.+++|+|++.|++|++.++.
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            47799999999999999973  4999999999999999999999999999998864

>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain

Probab=93.92  E-value=0.044  Score=53.94  Aligned_cols=155  Identities=16%  Similarity=0.150  Sum_probs=75.1

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCC---------CCc-cch-hhhhhhhcccCCcccc---cCCCCceEEEEEEE
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGD---------GNI-GEN-ITTNIHIIHKIPLVLN---IKYPPELLEVRCEV  184 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGd---------G~~-GeD-vT~n~~~i~~iP~~l~---~~~~p~~~evRGEv  184 (655)
                      +|+++.|+||-++++.+.++.-++..+|..         |.. +.+ .+..+..+. ....+.   ....+..+.|.||+
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            589999999999999886554345555543         111 111 111111111 111111   00136789999999


Q ss_pred             EeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCC---CCCCCHHHHHHHHHhCCC
Q psy11423        185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM---NMPSSHSELLNWYQKIGL  261 (655)
Q Consensus       185 ~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~---~~~~~~~e~l~~L~~~GF  261 (655)
                      +=.+..              --.|.=        +      ...+..|++|+|......   .+ .+..+...++..+||
T Consensus        81 ~G~~~~--------------Iq~~~~--------~------~~~~~~F~~Fdi~~~~~~~~~~~-l~~~~~~~~~~~~gl  131 (186)
T PF09414_consen   81 VGAKPS--------------IQKNRY--------Q------LDPPKDFYVFDIYDIDEQGEIRY-LSWDEVREFAEELGL  131 (186)
T ss_dssp             ECEECT--------------TCSS------------------ECCCEEEEEEEEEEETCCGEEE--HHHHHHHHHCCCT-
T ss_pred             eeeccc--------------cccccc--------c------cCCCceEEEEEEEEcCCCCeeEE-CCHHHHHHHHHHCCC
Confidence            953210              001100        0      012589999999765322   12 356677788889999


Q ss_pred             CCCCCceeeCCHHHHHHHHHHHHHh-hcCCCCccceEEEEECCh
Q psy11423        262 SICGEYSVLSGVNKLIEFYKKINIK-RFNLPYEIDGVVYKINCL  304 (655)
Q Consensus       262 ~~~~~~~~~~~~~ev~~~~~~~~~~-r~~l~y~iDGiVikv~~~  304 (655)
                      +++|... ...+.+...+-...... .....=.-=|+|+|..+.
T Consensus       132 ~~VPvl~-~g~~~~~~~~~~~~~~~~~~~~~~~~EGiVik~~~~  174 (186)
T PF09414_consen  132 KTVPVLY-RGTFTELDDLDDLFESGKPSGEGNIREGIVIKPEDE  174 (186)
T ss_dssp             EES-ECE-EECHHHHCTS-CCGBBTTS-STT-B--EEEEEETTT
T ss_pred             CEeCEEE-EEccchhhhhhHHHhhcccCCCCCccCEEEEEEeEe
Confidence            9887432 22444443321110000 111123346999999875

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.

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.91  E-value=0.052  Score=54.12  Aligned_cols=52  Identities=25%  Similarity=0.384  Sum_probs=42.3

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|.|+|||++-.+....   ++.+|.. +.   ...|..+||+|+|+|++|+-.+..
T Consensus        75 Li~V~GIGpK~AL~iLs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkd  130 (188)
T PRK14606         75 LTKVSRLGPKTALKIISNE---DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKD  130 (188)
T ss_pred             HhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            6789999999999998754   6777776 32   456889999999999999977754

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=93.90  E-value=0.11  Score=48.51  Aligned_cols=57  Identities=14%  Similarity=0.205  Sum_probs=44.3

Q ss_pred             ChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423        481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (655)
Q Consensus       481 ~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f  543 (655)
                      ..-||-+.+..+|.++||+|++.|++|++      +-++..+=.-+.+||||++..+.+.+..
T Consensus        51 ~kIdiN~A~~~el~~lpGigP~~A~~IV~------nGpf~sveDL~~V~GIgekqk~~l~k~~  107 (132)
T PRK02515         51 EKIDLNNSSVRAFRQFPGMYPTLAGKIVK------NAPYDSVEDVLNLPGLSERQKELLEANL  107 (132)
T ss_pred             CcccCCccCHHHHHHCCCCCHHHHHHHHH------CCCCCCHHHHHcCCCCCHHHHHHHHHhh
Confidence            44577788888999999999999999993      6677666666789999998766555543

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.88  E-value=0.053  Score=54.48  Aligned_cols=53  Identities=25%  Similarity=0.337  Sum_probs=42.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..+.|.|+|||++-.+....   ++.+|.. +   +...|.++||+|+|+|++|+-.+..
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   6777776 2   3456889999999999999977753

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.84  E-value=0.056  Score=54.15  Aligned_cols=52  Identities=15%  Similarity=0.377  Sum_probs=42.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|.|+|||++-.+....   ++.+|.. .   +...|..+||+|+|+|++|+-.+..
T Consensus        74 LisVsGIGPK~ALaILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkd  129 (196)
T PRK13901         74 LIGVDGIGPRAALRVLSGI---KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRG  129 (196)
T ss_pred             HhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            6789999999999998754   6777776 3   2456889999999999999977753

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.82  E-value=0.11  Score=55.57  Aligned_cols=51  Identities=25%  Similarity=0.263  Sum_probs=47.5

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .|+|+|++++++|.+.|+ .++.||..++.++|..+.|++++.++.|++...
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.

>PRK00024 hypothetical protein; Reviewed

Probab=93.81  E-value=0.13  Score=52.74  Aligned_cols=55  Identities=22%  Similarity=0.318  Sum_probs=45.4

Q ss_pred             HHHHHhCCCCccH-HHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        521 RFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       521 r~L~algIpgIG~-~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+|...|+|+-.. ..|++|+++|+++.++..++.++|.+++|||+..|..|..-+
T Consensus        31 a~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~   86 (224)
T PRK00024         31 AILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL   86 (224)
T ss_pred             HHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence            4445568887543 378899999999999999999999999999999998876643

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.80  E-value=0.053  Score=53.98  Aligned_cols=51  Identities=22%  Similarity=0.351  Sum_probs=40.6

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.+.|+|||++-.+....   ++.+|.. +.   ...| ++||+|+|+|++|+-.++.
T Consensus        75 LisV~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~  129 (186)
T PRK14600         75 LVKVSGVNYKTAMSILSKL---TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQY  129 (186)
T ss_pred             HhCcCCcCHHHHHHHHccC---CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence            6789999999999998754   6777776 32   3457 8999999999999977753

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=93.77  E-value=0.2  Score=38.36  Aligned_cols=47  Identities=17%  Similarity=0.325  Sum_probs=42.2

Q ss_pred             CCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        465 LGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       465 LG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      +.+..+.+|+++| +.++.||-.+..++|..++|+++..+++|+....
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            4578899999999 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.

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=93.74  E-value=0.15  Score=54.67  Aligned_cols=62  Identities=26%  Similarity=0.365  Sum_probs=42.8

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccch--------hHHHHHhCCCCccHHHHHHHHH-hCCCHHHHHhc
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELAN-YFKNLECMFKA  552 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l--------~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~~a  552 (655)
                      .++..+||+|++.+++|.+-++.-+-..+        .-++.-++|||||+++|+++.+ .+.|+++|..+
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            35688899999998888877664222112        2234445899999999998884 35678877765

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

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=93.68  E-value=0.049  Score=58.36  Aligned_cols=48  Identities=29%  Similarity=0.319  Sum_probs=40.3

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      ..++|+|+||+++.+|| +..|+|++||...-          |.|+.++++.+|+..+.
T Consensus        86 ~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~----------g~k~~~~i~~gl~~~~~  133 (307)
T cd00141          86 LLLRVPGVGPKTARKLY-ELGIRTLEDLRKAA----------GAKLEQNILIGLEYYED  133 (307)
T ss_pred             HHHcCCCCCHHHHHHHH-HcCCCCHHHHHHHh----------ccccHHHHHHHHHHHHH
Confidence            45789999999999999 56689999999732          88999999999986543

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

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.67  E-value=0.062  Score=53.35  Aligned_cols=52  Identities=15%  Similarity=0.298  Sum_probs=42.4

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|.|+|||++-.+....   ++.+|.. +.   ...|.++||+|+|+|++|+-.+..
T Consensus        75 Li~VsGIGpK~Al~ILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkd  130 (183)
T PRK14601         75 LLKVNGIGANTAMAVCSSL---DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSD  130 (183)
T ss_pred             HhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            6789999999999998754   7778887 33   456888999999999999977753

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=93.56  E-value=0.13  Score=42.55  Aligned_cols=58  Identities=16%  Similarity=0.159  Sum_probs=40.0

Q ss_pred             HHHhcCChhhhcc-ccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423        483 VDLYKINFKNLLR-LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY  542 (655)
Q Consensus       483 ~DL~~L~~~~L~~-l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~  542 (655)
                      -||-++..+.|.. ++|+|++.|++|++......  ++..+-.-..++|+|++++++|...
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            4566667778888 88999998888888776432  2222222246888888888887764

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.37  E-value=0.37  Score=51.69  Aligned_cols=50  Identities=24%  Similarity=0.372  Sum_probs=46.1

Q ss_pred             CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .+||||++++++|.+. |.+++.|..++.++|.++.|++++.|+.+++..+
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            6899999999999987 9999999999999999999999999999987654

>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]

Probab=93.32  E-value=0.099  Score=54.66  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=46.1

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .||.+-......|...|++++.|..||.++|.+++|||+..|..|.+-++
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            78888888899999999999999999999999999999999999987653

>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=93.31  E-value=0.1  Score=36.42  Aligned_cols=27  Identities=30%  Similarity=0.386  Sum_probs=20.3

Q ss_pred             HHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423        483 VDLYKINFKNLLRLDRVSNKLANNILL  509 (655)
Q Consensus       483 ~DL~~L~~~~L~~l~GfG~Ksa~nll~  509 (655)
                      ..+...+.++|.++||+|+|+|+.|+.
T Consensus         3 ~g~~pas~eeL~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen    3 DGLIPASIEELMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred             CCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence            345566788899999999999988764

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 ....

>TIGR00608 radc DNA repair protein radc

Probab=93.25  E-value=0.19  Score=51.38  Aligned_cols=55  Identities=22%  Similarity=0.338  Sum_probs=45.4

Q ss_pred             HHHHHhCCCCc-c-HHHHHHHHHhC---CCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        521 RFIYALGIRHV-G-ETTAKELANYF---KNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       521 r~L~algIpgI-G-~~~Ak~L~~~f---gsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+|...|.|+- . ...|+.|+++|   +++..+..++.++|.+++|||+..|..|..-+
T Consensus        21 ailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~   80 (218)
T TIGR00608        21 AIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV   80 (218)
T ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHH
Confidence            44555688875 2 24788999999   99999999999999999999999998887643

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]

Probab=93.11  E-value=0.31  Score=49.65  Aligned_cols=57  Identities=23%  Similarity=0.260  Sum_probs=45.8

Q ss_pred             chhHHHHHhCCCCccH-HHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        518 TFSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       518 ~l~r~L~algIpgIG~-~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      .|-.++..-|+||--. ..|+.|+++||++..+..|+.++|+.++|+|...|-++..-
T Consensus        28 ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~   85 (224)
T COG2003          28 ELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAA   85 (224)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHH
Confidence            3445555668886543 35689999999999999999999999999999888887664

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=92.73  E-value=0.065  Score=43.99  Aligned_cols=30  Identities=23%  Similarity=0.231  Sum_probs=21.1

Q ss_pred             HHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        484 DLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       484 DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ||-+++.++|..+||+|++.|++|++.-++
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            556677888999999999999888876543

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=92.44  E-value=0.2  Score=59.16  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=54.2

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccchhHHH-----HHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHh---cCCC
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFI-----YALGIRHVGETTAKELANYFKNLECMFKATEEQLL---NIPK  562 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L-----~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~---~i~G  562 (655)
                      .+-+.++|+|++.++.|++.=   .-.....+.     .-+.++|+|++.|+.|.+.+   +.=+..+.+.+.   .||+
T Consensus       436 r~aldI~GlG~~~i~~L~~~G---~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~I---e~sk~~~l~r~l~ALGI~~  509 (669)
T PRK14350        436 KKCMNIVGLSDKTIEFLFEKK---FISSEIDLYTFNFDRLINLKGFKDKRINNLKRSI---EASKKRPFSKLLLSMGIKD  509 (669)
T ss_pred             CCcccccCcCHHHHHHHHHcC---CcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHH---HHHhCCCHHHHHHHcCCCc
Confidence            345788999999999988631   111111111     11257999999999888754   333444555443   3899


Q ss_pred             CCHHHHHHHH-HHhcC
Q psy11423        563 IGSTTVKAFI-KFINQ  577 (655)
Q Consensus       563 IG~~~A~~I~-~~f~~  577 (655)
                      ||+..|+.|. .+|.+
T Consensus       510 vG~~~ak~La~~~f~~  525 (669)
T PRK14350        510 LGENTILLLINNNLNS  525 (669)
T ss_pred             hhHHHHHHHHHHhhCC
Confidence            9999999999 78865

>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A

Probab=92.42  E-value=0.02  Score=50.54  Aligned_cols=69  Identities=22%  Similarity=0.282  Sum_probs=45.4

Q ss_pred             ChhHHHHHHHHHHcCcccccCC---CCCCCeEecccccCccEEEecCCCC---chHHH-HHHcCCeeeCHHHHHHHH
Q psy11423        577 QPLHRLLISQLRDVGIYWLNNP---NTKGGKVVNFISKNTNYLVKGQKPG---KKLEK-AIKLNIKILDEKNFVKIV  646 (655)
Q Consensus       577 ~~~n~~li~~L~~~Gi~~~~~~---~~~G~~v~~sVsk~t~ylv~g~~~g---~K~~k-A~~lgi~ii~e~~f~~~l  646 (655)
                      +...++++.+|...|++.....   ..+|......|.+|| |.++++..|   .++|+ |+++|++..++.-....+
T Consensus         5 ~~~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nP-Y~L~~~i~gi~F~~aD~iA~~~g~~~~d~~Ri~A~i   80 (94)
T PF14490_consen    5 NRGLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENP-YRLIEDIDGIGFKTADKIALKLGIEPDDPRRIRAAI   80 (94)
T ss_dssp             ----HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-S-TCCCB-SSSSBHHHHHHHHHTTT--TT-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHCh-HHHHHHccCCCHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            3445667777888888754333   477888888999999 999997665   89999 999999999999877654

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=92.34  E-value=0.19  Score=58.83  Aligned_cols=60  Identities=15%  Similarity=0.088  Sum_probs=53.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchh
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~  520 (655)
                      .-+|+|+|+++..+|++.=  .|+.+|...+.++|.+++|++.+.|++|+.+-..+-..|..
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            5699999999999999864  48999999999999999999999999999998777666653

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=92.30  E-value=0.2  Score=48.18  Aligned_cols=23  Identities=22%  Similarity=0.492  Sum_probs=15.8

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        553 TEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       553 s~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +.+||..++|||+++.+.+..++
T Consensus       125 sv~dL~~v~GiG~~~~ekl~~~i  147 (149)
T COG1555         125 SVDDLAKVKGIGPKTLEKLKDYI  147 (149)
T ss_pred             cHHHHHhccCCCHHHHHHHHhhc
Confidence            45667777777777777776654

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

Probab=92.21  E-value=0.14  Score=59.41  Aligned_cols=88  Identities=20%  Similarity=0.310  Sum_probs=57.1

Q ss_pred             cccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHHHH---hcccchhHHHHH
Q psy11423        452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAIQK---SKLTTFSRFIYA  525 (655)
Q Consensus       452 ~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I~~---sk~~~l~r~L~a  525 (655)
                      -++-..+.+.++++|+|.+++|+++-     ..=-+....++   +.++.+|++.|..|...+..   -...++..+   
T Consensus       474 y~Lt~~~l~~l~~~~~ks~~nLl~aI-----e~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l---  545 (667)
T COG0272         474 YTLTEEDLLSLEGFGEKSAENLLNAI-----EKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEEL---  545 (667)
T ss_pred             HhCCHHHHhhccchhhhHHHHHHHHH-----HHhccCCHHHHHHHcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHH---
Confidence            34445678899999999999998631     11111112222   45678999999888776543   222333222   


Q ss_pred             hCCCCccHHHHHHHHHhCCCHH
Q psy11423        526 LGIRHVGETTAKELANYFKNLE  547 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~  547 (655)
                      ..|||||+..|+.|.+.|....
T Consensus       546 ~~i~giG~~vA~si~~ff~~~~  567 (667)
T COG0272         546 ASIPGIGEVVARSIIEFFANEE  567 (667)
T ss_pred             hhccchhHHHHHHHHHHHcCHH
Confidence            2699999999999999887543

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=92.11  E-value=0.13  Score=59.79  Aligned_cols=30  Identities=37%  Similarity=0.534  Sum_probs=28.5

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHH
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQ  556 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~ee  556 (655)
                      +|||||+++.++|+++|||+++|..||.++
T Consensus       545 ~I~GIG~kr~~~LL~~Fgs~~~i~~As~ee  574 (574)
T TIGR00194       545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE  574 (574)
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCccC
Confidence            999999999999999999999999999764

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.

>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

Probab=92.01  E-value=0.54  Score=47.71  Aligned_cols=76  Identities=21%  Similarity=0.139  Sum_probs=41.7

Q ss_pred             HHHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcc---cchhHHHH-HhCCCCccHHHHHHH
Q psy11423        467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKL---TTFSRFIY-ALGIRHVGETTAKEL  539 (655)
Q Consensus       467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~---~~l~r~L~-algIpgIG~~~Ak~L  539 (655)
                      .+....|++.-  .+++|+..+..++|..+   =||-..+|.||++--+.-..   -....-+. -+.+||||.++|...
T Consensus        48 n~at~~Lf~~~--~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvV  125 (211)
T COG0177          48 NKATPALFKRY--PTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVV  125 (211)
T ss_pred             HHHHHHHHHHc--CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHHHHH
Confidence            44556666654  49999999887655433   47888888877654332111   11111111 225566666666544


Q ss_pred             HHh-CC
Q psy11423        540 ANY-FK  544 (655)
Q Consensus       540 ~~~-fg  544 (655)
                      +.. ||
T Consensus       126 L~~a~g  131 (211)
T COG0177         126 LSFAFG  131 (211)
T ss_pred             HHhhcC
Confidence            443 44

>smart00483 POLXc DNA polymerase X family

Probab=91.72  E-value=0.3  Score=53.02  Aligned_cols=63  Identities=22%  Similarity=0.231  Sum_probs=46.4

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcc--------cch-hHHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcC
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKL--------TTF-SRFIYALGIRHVGETTAKELANY-FKNLECMFKAT  553 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~--------~~l-~r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as  553 (655)
                      ++|.++||+|++.|++|.+=++.-+-        .+. .-++.-+.|||||+++|+++.+. +.|+++|..+-
T Consensus        48 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~  120 (334)
T smart00483       48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNK  120 (334)
T ss_pred             HHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence            47889999999999999887764221        111 23455559999999999999882 45888887763

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=91.70  E-value=0.15  Score=51.34  Aligned_cols=18  Identities=33%  Similarity=0.447  Sum_probs=9.6

Q ss_pred             hccccCCcHHHHHHHHHH
Q psy11423        493 LLRLDRVSNKLANNILLA  510 (655)
Q Consensus       493 L~~l~GfG~Ksa~nll~~  510 (655)
                      |.++.|+|+|+|=+|+..
T Consensus        75 LisVnGIGpK~ALaiLs~   92 (201)
T COG0632          75 LISVNGIGPKLALAILSN   92 (201)
T ss_pred             HHccCCccHHHHHHHHcC
Confidence            445555555555555544

>smart00483 POLXc DNA polymerase X family

Probab=91.68  E-value=0.55  Score=50.97  Aligned_cols=57  Identities=11%  Similarity=0.170  Sum_probs=41.1

Q ss_pred             cchhHHHHHhCCCCccHHHHHHHHHh--CCCHH-HHHhc------CHHHHhcCCCCCHHHHHHHHH
Q psy11423        517 TTFSRFIYALGIRHVGETTAKELANY--FKNLE-CMFKA------TEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       517 ~~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~-~l~~a------s~eeL~~i~GIG~~~A~~I~~  573 (655)
                      .++..+-....|||||++.|++|.+-  -|++. .+...      ...+|.+|+|||+++|..+++
T Consensus        42 ~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~  107 (334)
T smart00483       42 FPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR  107 (334)
T ss_pred             CCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence            34444434558999999999988763  36655 22221      246899999999999999988

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>KOG0967|consensus

Probab=91.56  E-value=2.4  Score=49.00  Aligned_cols=180  Identities=17%  Similarity=0.230  Sum_probs=109.1

Q ss_pred             cccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEE-eCCEEeEEEecCCCCccchhhhhhhhccc
Q psy11423         86 TFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK  164 (655)
Q Consensus        86 ~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~  164 (655)
                      ..|||.  |  .-..+.+.++|++       ...|+||+|.||=-..+.+ ++|. +...+|    .+|+.|....-|-.
T Consensus       344 lKPMLA--k--pTK~i~evl~rf~-------~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi~~  407 (714)
T KOG0967|consen  344 LKPMLA--K--PTKGIQEVLERFQ-------DKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDIIE  407 (714)
T ss_pred             Ccchhc--C--cchhHHHHHHHhh-------CceeEEEeecCceeeeeEEccCCc-EEEEec----ccccccccCccHHH
Confidence            359975  2  2235666777764       4579999999999999986 6776 689999    78999987765433


Q ss_pred             -CCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccceEEEEEecccccC
Q psy11423        165 -IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRG  242 (655)
Q Consensus       165 -iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~~r~L~f~~y~~~~~~~  242 (655)
                       +++....  --..+.+-||++--..+    |.     --.+|.     +.-+=++++-.. ...-..+.|+|++....+
T Consensus       408 ~~~~~~kp--~v~sFIlD~EvVA~Dr~----~~-----~IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~ng  471 (714)
T KOG0967|consen  408 VISKLKKP--SVKSFILDCEVVAWDRE----KG-----KILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLNG  471 (714)
T ss_pred             HHHHhhCC--ccceeEEeeeEEEEecc----CC-----ccCchh-----hhhhhhccccchhhceEEEEEEEEeeeeeCC
Confidence             2322221  01468999999854332    10     112333     111112222211 112257888898877654


Q ss_pred             CCCC-CCHHHHHHHHHhCCCCCCCCcee-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423        243 MNMP-SSHSELLNWYQKIGLSICGEYSV-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC  303 (655)
Q Consensus       243 ~~~~-~~~~e~l~~L~~~GF~~~~~~~~-----~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (655)
                      ..+. ..-.+.-+.|.+-+=.++.+.++     +.+++++.+|.++..      +--.-|+-||.=+
T Consensus       472 ~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv------~~~cEGlMvKtLd  532 (714)
T KOG0967|consen  472 ESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESV------QNSCEGLMVKTLD  532 (714)
T ss_pred             hhhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhh------ccCcceeEEEeec
Confidence            3322 45566677777764444444444     357899999987643      3346799998865

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=91.42  E-value=0.3  Score=56.60  Aligned_cols=51  Identities=18%  Similarity=0.189  Sum_probs=46.3

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      ...+|+|+||++..+|++.=  .|+.+|...+.++|.++ |++++.|++|++.+
T Consensus       515 ~Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l  565 (567)
T PRK14667        515 ILDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKL-GIPPSVKQEVKKYL  565 (567)
T ss_pred             ccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence            35689999999999999875  59999999999999999 99999999998865

>PRK01172 ski2-like helicase; Provisional

Probab=91.26  E-value=0.74  Score=54.58  Aligned_cols=55  Identities=22%  Similarity=0.311  Sum_probs=48.8

Q ss_pred             HHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       521 r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      ..+.-+.|||+|..+|++|.+. +.|+.+|..++.+++.+|.|+|++.|++|++..
T Consensus       610 ~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~  665 (674)
T PRK01172        610 DLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA  665 (674)
T ss_pred             HHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence            4444458999999999999874 899999999999999999999999999998874

>PRK10702 endonuclease III; Provisional

Probab=91.22  E-value=0.72  Score=46.86  Aligned_cols=43  Identities=16%  Similarity=0.192  Sum_probs=30.0

Q ss_pred             HHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423        468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ  512 (655)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~  512 (655)
                      +....|+...  .++++|..+..++|..+   -||-...|.+|++..+
T Consensus        49 ~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~   94 (211)
T PRK10702         49 KATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCR   94 (211)
T ss_pred             HHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3445666543  58999999998888753   3676778887776554

>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=91.14  E-value=0.19  Score=39.67  Aligned_cols=26  Identities=35%  Similarity=0.360  Sum_probs=20.2

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHh
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLY  486 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~  486 (655)
                      ++|-|+||++++++++.|+ +|++||-
T Consensus         5 ~~I~GVG~~tA~~w~~~G~-rtl~Dl~   30 (52)
T PF10391_consen    5 TGIWGVGPKTARKWYAKGI-RTLEDLR   30 (52)
T ss_dssp             HTSTT--HHHHHHHHHTT---SHHHHH
T ss_pred             hhcccccHHHHHHHHHhCC-CCHHHHh
Confidence            5799999999999999885 9999995

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 ....

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=91.08  E-value=0.21  Score=42.33  Aligned_cols=26  Identities=27%  Similarity=0.488  Sum_probs=24.4

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      ||||||+++|.+|+..|++++.+..+
T Consensus        26 gv~giG~k~A~~ll~~~~~~~~~~~~   51 (75)
T cd00080          26 GVPGIGPKTALKLLKEYGSLENLLEN   51 (75)
T ss_pred             CCCcccHHHHHHHHHHhCCHHHHHHH
Confidence            89999999999999999999998875

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.

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=90.42  E-value=0.34  Score=56.66  Aligned_cols=52  Identities=23%  Similarity=0.297  Sum_probs=46.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ...|+|+|++++.+|++.=  .|+.+|+..+.++|.+++|+|++.|++|.+.+.
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            4689999999999999865  589999999999999999999999999988764

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=90.17  E-value=0.43  Score=45.87  Aligned_cols=56  Identities=18%  Similarity=0.245  Sum_probs=34.4

Q ss_pred             HhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423        485 LYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY  542 (655)
Q Consensus       485 L~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~  542 (655)
                      |-+.+.++|..|||+|+|+|+.|++.-++.-  +|..+=.-..++|||+++-+++...
T Consensus        91 iNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G--~f~sv~dL~~v~GiG~~~~ekl~~~  146 (149)
T COG1555          91 INTASAEELQALPGIGPKKAQAIIDYREENG--PFKSVDDLAKVKGIGPKTLEKLKDY  146 (149)
T ss_pred             ccccCHHHHHHCCCCCHHHHHHHHHHHHHcC--CCCcHHHHHhccCCCHHHHHHHHhh
Confidence            4445567777777788777777777665532  3333333336777777776665543

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=90.03  E-value=0.57  Score=37.80  Aligned_cols=48  Identities=33%  Similarity=0.451  Sum_probs=41.0

Q ss_pred             CCCCeEeccccc-CccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISK-NTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk-~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||.+...++. +++++|+++...  .+...|...+++|++++-+.+.+.
T Consensus        28 ~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~   78 (80)
T smart00292       28 ALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLK   78 (80)
T ss_pred             HcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHH
Confidence            789999999998 888999988765  335778999999999999988775

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=89.68  E-value=0.4  Score=55.76  Aligned_cols=50  Identities=16%  Similarity=0.196  Sum_probs=45.3

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      ...|+|+|++++.+|++.=  .|+.+++..+.++|..+||+|++.|+.|.+.
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            4489999999999999975  5999999999999999999999999988754

>PRK09482 flap endonuclease-like protein; Provisional

Probab=88.98  E-value=0.49  Score=49.50  Aligned_cols=26  Identities=35%  Similarity=0.709  Sum_probs=24.2

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      |+||||+++|.+|++.|+|++.|...
T Consensus       186 GVpGIG~KtA~~LL~~~gsle~i~~~  211 (256)
T PRK09482        186 GVAGIGPKSAAELLNQFRSLENIYES  211 (256)
T ss_pred             CCCCcChHHHHHHHHHhCCHHHHHHh
Confidence            89999999999999999999999854

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=88.82  E-value=0.25  Score=46.18  Aligned_cols=23  Identities=17%  Similarity=0.541  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11423        414 IPNICPICNSKIIYIESNLIARCSG  438 (655)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (655)
                      +-.|||.||.||.+.+|  ..||++
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            34699999999998655  669988

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=88.14  E-value=0.85  Score=49.12  Aligned_cols=53  Identities=23%  Similarity=0.233  Sum_probs=47.9

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      .=.|||+.++++|-++|+ .|+.|+...+..+|..+.|+++..+++|+++..+.
T Consensus         5 ~~~g~~~~~~~~L~~~g~-~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~   57 (313)
T TIGR02238         5 QAHGINAADIKKLKSAGI-CTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI   57 (313)
T ss_pred             hcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence            346799999999999995 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.

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=87.97  E-value=1.6  Score=33.37  Aligned_cols=43  Identities=26%  Similarity=0.289  Sum_probs=35.7

Q ss_pred             cHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        532 GETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       532 G~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      .+..+.+|.+ .|.+++.+..++.++|..++|+++..+..|+.-
T Consensus         2 ~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~   45 (50)
T TIGR01954         2 DEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR   45 (50)
T ss_pred             CHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence            3456666665 599999999999999999999999988888653

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.

>PTZ00035 Rad51 protein; Provisional

Probab=87.47  E-value=0.94  Score=49.25  Aligned_cols=54  Identities=24%  Similarity=0.239  Sum_probs=48.3

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      +.=+||++..+++|-++|+ .|+.||...+..+|..+.|+++..|++|++...+.
T Consensus        26 l~~~g~~~~~~~kL~~~g~-~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~   79 (337)
T PTZ00035         26 LQSAGINAADIKKLKEAGI-CTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL   79 (337)
T ss_pred             HhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence            4448999999999999985 89999999999999999999999999999877653

>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes

Probab=87.33  E-value=0.7  Score=47.79  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=24.2

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      ||||||+++|.+|++.|+|++++...
T Consensus       187 Gv~GiG~ktA~~Ll~~~gsle~i~~~  212 (240)
T cd00008         187 GVPGIGEKTAAKLLKEYGSLEGILEN  212 (240)
T ss_pred             CCCccCHHHHHHHHHHhCCHHHHHHh
Confidence            89999999999999999999999864

They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

>smart00475 53EXOc 5'-3' exonuclease

Probab=87.31  E-value=0.62  Score=48.80  Aligned_cols=26  Identities=35%  Similarity=0.583  Sum_probs=24.1

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      |+||||+++|.+|++.|+|++.+...
T Consensus       190 GV~GIG~KtA~~Ll~~ygsle~i~~~  215 (259)
T smart00475      190 GVPGIGEKTAAKLLKEFGSLENILEN  215 (259)
T ss_pred             CCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence            88999999999999999999999764

>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases

Probab=87.00  E-value=0.042  Score=49.32  Aligned_cols=25  Identities=28%  Similarity=0.507  Sum_probs=21.8

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFK  551 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~  551 (655)
                      |+||||+++|.+|+++|||+++|..
T Consensus        22 GV~GIG~KtA~~LL~~ygsle~i~~   46 (101)
T PF01367_consen   22 GVPGIGPKTAAKLLQEYGSLENILA   46 (101)
T ss_dssp             --TTSTCHCCCCCHHHHTSCHCCCC
T ss_pred             CCCCCCHHHHHHHHHHcCCHHHHHH
Confidence            8999999999999999999998876

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.

>PRK00420 hypothetical protein; Validated

Probab=86.50  E-value=0.45  Score=43.48  Aligned_cols=24  Identities=17%  Similarity=0.534  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11423        414 IPNICPICNSKIIYIESNLIARCSG  438 (655)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (655)
                      +..+||.||++|.+..+ ...+|++
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            45899999999997433 3678987

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=86.49  E-value=1.1  Score=48.18  Aligned_cols=51  Identities=20%  Similarity=0.181  Sum_probs=45.6

Q ss_pred             cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      -=+|.-.+..-|-.+| |.++.||..++.++|.++++||+||.+.|.+.+++
T Consensus       253 ~L~LS~R~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~  303 (310)
T PRK05182        253 ELELSVRSYNCLKRAG-INTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE  303 (310)
T ss_pred             HhccchHHHHHHHHcC-CcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence            3477888888888887 79999999999999999999999999999998876

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=86.47  E-value=1.2  Score=48.44  Aligned_cols=54  Identities=19%  Similarity=0.168  Sum_probs=46.5

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      .||++++..++.|+++=.  ++..+++.+.++|...+|+|++.|..|.+.+.+.+.
T Consensus       291 ~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e  344 (352)
T PRK13482        291 KIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAE  344 (352)
T ss_pred             cCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHH
Confidence            489999999999998753  889999999999999999999999998888766543

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=86.37  E-value=1.2  Score=48.57  Aligned_cols=54  Identities=26%  Similarity=0.249  Sum_probs=48.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .|.=.||++.++++|-++|+ .|+.||...+..+|..+.|+++..+++|++...+
T Consensus        33 ~l~~~g~~~~~~~kL~~~g~-~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~   86 (344)
T PLN03187         33 KLISQGINAGDVKKLQDAGI-YTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEK   86 (344)
T ss_pred             HHhhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            34447899999999999995 8999999999999999999999999999987654

>smart00478 ENDO3c endonuclease III

Probab=86.02  E-value=3  Score=39.35  Aligned_cols=41  Identities=20%  Similarity=0.113  Sum_probs=26.0

Q ss_pred             HHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHH
Q psy11423        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAI  511 (655)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I  511 (655)
                      .+.+|.+.-  .++.+|..++.++|..+   =||....++.|.+..
T Consensus        13 ~~~~l~~~~--~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a   56 (149)
T smart00478       13 ATERLFEKF--PTPEDLAAADEEELEELIRPLGFYRRKAKYLIELA   56 (149)
T ss_pred             HHHHHHHHC--CCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            334444432  38888888888777332   177777887777543

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=85.63  E-value=0.64  Score=38.10  Aligned_cols=28  Identities=29%  Similarity=0.546  Sum_probs=20.0

Q ss_pred             HHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        549 MFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       549 l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      |..|+.++|.++||||+..|++|++|-.
T Consensus         8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~   35 (65)
T PF12836_consen    8 INTASAEELQALPGIGPKQAKAIVEYRE   35 (65)
T ss_dssp             TTTS-HHHHHTSTT--HHHHHHHHHHHH
T ss_pred             CccCCHHHHHHcCCCCHHHHHHHHHHHH
Confidence            4567888888888888888888888753

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=85.12  E-value=2.9  Score=44.20  Aligned_cols=78  Identities=18%  Similarity=0.138  Sum_probs=48.2

Q ss_pred             HHHHHHcCCCCChHHHhcCChhhhc----cccCCcHHHHHHHHHHHHHhcc---cchhHHHHH-hCCCCccHHHHHHHHH
Q psy11423        470 IEKLVNANIVVTAVDLYKINFKNLL----RLDRVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELAN  541 (655)
Q Consensus       470 i~~L~~~g~I~~i~DL~~L~~~~L~----~l~GfG~Ksa~nll~~I~~sk~---~~l~r~L~a-lgIpgIG~~~Ak~L~~  541 (655)
                      ..+|++.  ..++.+|..++.++|.    .+ ||- ..|.+|.+..+.-..   ..+..-... +.+||||+++|..++.
T Consensus        48 ~~rl~~~--fpt~~~La~a~~eeL~~~~~~l-G~y-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~  123 (275)
T TIGR01084        48 FERFLER--FPTVQALANAPQDEVLKLWEGL-GYY-ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILS  123 (275)
T ss_pred             HHHHHHh--CCCHHHHHCcCHHHHHHHHHHC-CcH-HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHH
Confidence            3444443  2689999999998884    44 665 457788776653221   112222333 3899999999987775


Q ss_pred             -hCCCHHHHHh
Q psy11423        542 -YFKNLECMFK  551 (655)
Q Consensus       542 -~fgsl~~l~~  551 (655)
                       .|+-...+.+
T Consensus       124 ~a~~~~~~~vD  134 (275)
T TIGR01084       124 FALNKPYPILD  134 (275)
T ss_pred             HHCCCCCCcch
Confidence             4664443333

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.

>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

Probab=84.85  E-value=2.3  Score=40.49  Aligned_cols=80  Identities=21%  Similarity=0.206  Sum_probs=40.4

Q ss_pred             HHHHHHHcCCCCChHHHhcCChhhhccccCCc---HHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423        469 MIEKLVNANIVVTAVDLYKINFKNLLRLDRVS---NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (655)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG---~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs  545 (655)
                      .+.+|.+... -++++|..++.++|..+ +.+   ..+|+.|.+..+                         .+.+.+.+
T Consensus        21 ~~~~l~~~~g-pt~~~l~~~~~~~l~~~-~~~~G~~~kA~~i~~~a~-------------------------~~~~~~~~   73 (158)
T cd00056          21 AYERLFERYG-PTPEALAAADEEELREL-IRSLGYRRKAKYLKELAR-------------------------AIVEGFGG   73 (158)
T ss_pred             HHHHHHHHhC-CCHHHHHCCCHHHHHHH-HHhcChHHHHHHHHHHHH-------------------------HHHHHcCC
Confidence            3344444432 57788887777777664 222   345554444332                         22222222


Q ss_pred             HHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        546 LECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       546 l~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      ...=.....++|.+++|||+++|+.+.-|.
T Consensus        74 ~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~  103 (158)
T cd00056          74 LVLDDPDAREELLALPGVGRKTANVVLLFA  103 (158)
T ss_pred             ccCCCcccHHHHHcCCCCCHHHHHHHHHHH
Confidence            111001124567777777777777766543

>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]

Probab=84.82  E-value=4.2  Score=40.99  Aligned_cols=115  Identities=19%  Similarity=0.297  Sum_probs=58.6

Q ss_pred             HHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHH----------HHHHHHhcccchhHHHHHhCCCCccHH
Q psy11423        468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNI----------LLAIQKSKLTTFSRFIYALGIRHVGET  534 (655)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nl----------l~~I~~sk~~~l~r~L~algIpgIG~~  534 (655)
                      +-++.|-.++. -++..|..++.++|+.+   -||=..+|..|          ..+++..+...++.+|  |+|.|||+.
T Consensus        50 kAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R~~L--L~iKGIG~E  126 (215)
T COG2231          50 KALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREEL--LSIKGIGKE  126 (215)
T ss_pred             HHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHHHHH--HccCCcchh
Confidence            33455555553 45777777776666554   56666555555          2222222222222232  367777777


Q ss_pred             HHHHHHHh-CCCHHHHHhc-CHHHHhcCCCCCHHHHHHHHHHhcC--hhHHHHHH
Q psy11423        535 TAKELANY-FKNLECMFKA-TEEQLLNIPKIGSTTVKAFIKFINQ--PLHRLLIS  585 (655)
Q Consensus       535 ~Ak~L~~~-fgsl~~l~~a-s~eeL~~i~GIG~~~A~~I~~~f~~--~~n~~li~  585 (655)
                      +|..|+-. |.-...+..+ +.--|..+-++-.+.-++|.++|..  +++..+.+
T Consensus       127 TaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~~~~lyq  181 (215)
T COG2231         127 TADSILLYALDRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPENLRLYQ  181 (215)
T ss_pred             hHHHHHHHHhcCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchhHHHHHH
Confidence            77666543 4333333332 2333555555555556667766652  44444333

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=84.78  E-value=1.5  Score=47.00  Aligned_cols=53  Identities=17%  Similarity=0.201  Sum_probs=45.6

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ++-=+|.-.+..-|-.+| |.++.||..++.++|+.+++||+||.+.|.+.+++
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            344467777888888877 69999999999999999999999999999988865

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.

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=84.28  E-value=0.78  Score=30.65  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=11.2

Q ss_pred             hhccccCCcHHHHHHHHH
Q psy11423        492 NLLRLDRVSNKLANNILL  509 (655)
Q Consensus       492 ~L~~l~GfG~Ksa~nll~  509 (655)
                      +|..++|+|+|+|++|++
T Consensus         2 ~L~~i~GiG~k~A~~il~   19 (26)
T smart00278        2 ELLKVPGIGPKTAEKILE   19 (26)
T ss_pred             hhhhCCCCCHHHHHHHHH
Confidence            455666666666666664

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=84.24  E-value=1.1  Score=52.48  Aligned_cols=56  Identities=16%  Similarity=0.238  Sum_probs=48.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT  517 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~  517 (655)
                      ...+|+|+|+++..+|++.=  .|+.+|...+.++|.++  +|+|.|++|++.+...-..
T Consensus       553 ~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~~~~  608 (624)
T PRK14669        553 ELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAV--VGRAAAEAIIAHFTTEEAA  608 (624)
T ss_pred             HHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence            36699999999999999864  58999999999999998  9999999999988754443

>PRK14976 5'-3' exonuclease; Provisional

Probab=84.04  E-value=0.86  Score=48.32  Aligned_cols=25  Identities=32%  Similarity=0.667  Sum_probs=23.6

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFK  551 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~  551 (655)
                      |+||||+++|..|++.|+|++.+..
T Consensus       195 GVpGIG~KtA~~LL~~~gsle~i~~  219 (281)
T PRK14976        195 GVKGIGPKTAIKLLNKYGNIENIYE  219 (281)
T ss_pred             CCCcccHHHHHHHHHHcCCHHHHHH
Confidence            8999999999999999999999875

>KOG2534|consensus

Probab=84.01  E-value=2  Score=45.90  Aligned_cols=70  Identities=19%  Similarity=0.144  Sum_probs=47.5

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhc--------ccchhHHH-HHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhc
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSK--------LTTFSRFI-YALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLN  559 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk--------~~~l~r~L-~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~  559 (655)
                      .+++..|||+|+|.|++|.+=++.-.        +-+....| +=-.|-|||.++|++--. -|.|++.+. -+.+.|..
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            57788899999999988877665322        11222222 223899999999987654 588998888 44555554


Q ss_pred             C
Q psy11423        560 I  560 (655)
Q Consensus       560 i  560 (655)
                      -
T Consensus       134 q  134 (353)
T KOG2534|consen  134 Q  134 (353)
T ss_pred             H
Confidence            3

>TIGR02776 NHEJ_ligase_prk DNA ligase D

Probab=83.93  E-value=15  Score=42.64  Aligned_cols=178  Identities=15%  Similarity=0.094  Sum_probs=98.1

Q ss_pred             ccchhhhhhhhcccCCcccccCCCCceEEEEEEEEe----ehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccccc
Q psy11423        151 IGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI----YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINK  226 (655)
Q Consensus       151 ~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~----~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~  226 (655)
                      .|+|+|+....|-..-..+.    ...+.+-||+++    ...+|+.+...                   ++.     ..
T Consensus         3 ng~d~T~~fPel~~~~~~l~----~~~~ILDGElVvld~~G~~~F~~Lq~~-------------------~~~-----~~   54 (552)
T TIGR02776         3 NGHDWTKRFPEIVKALALLK----LLPAWIDGEIVVLDERGRADFAALQNA-------------------LSA-----GA   54 (552)
T ss_pred             CcCcchhhhHHHHHHHhhCC----CCCEEEEEEEEEECCCCCCCHHHHHHH-------------------HHh-----cc
Confidence            68999988876654333332    236899999998    44567765331                   010     12


Q ss_pred             ccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-CCCceeeC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423        227 NKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-CGEYSVLS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINC  303 (655)
Q Consensus       227 ~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~-~~~~~~~~-~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (655)
                      ..++.|++|++...++.++ .....+..+.|+++-=+. .....+.. ..++..++++...+      -...|||+|--+
T Consensus        55 ~~pv~~~vFDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~~~~~~~~~~~a~~------~G~EGIV~K~~d  128 (552)
T TIGR02776        55 SRPLTYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHFESDGDALLESACR------LGLEGVVSKRLD  128 (552)
T ss_pred             cCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEeeeecccHHHHHHHHHH------CCCceEEEeCCC
Confidence            3579999999987665443 246777777777652111 11111111 11222355554432      236899999988


Q ss_pred             hhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeE--EEEEEEEECCEE--EEEe-eCCCHHHHHh
Q psy11423        304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV--ALLKPVLIDGIT--ITRA-TLHNESEIYR  376 (655)
Q Consensus       304 ~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPv--A~lePV~l~G~t--Vsra-tLhN~~~i~~  376 (655)
                      ..++  -|   ++..| +-+|. ....+..|.+....-   |++...  +..+    +|.-  |-++ |..+.+..++
T Consensus       129 S~Y~--~G---Rs~~W-lKlK~-~~~~e~vI~Gy~~~~---r~~gslLlg~~d----~g~l~~vgkVgsGfsd~~~~~  192 (552)
T TIGR02776       129 SPYR--SG---RSKDW-LKLKC-RRRQEFVITGYTPPN---RRFGALLVGVYE----GGQLVYAGKVGTGFGADTLKT  192 (552)
T ss_pred             CCCC--CC---CCcch-hcccc-cccceEEEEEEecCC---CceeeEEEEEec----CCeEEEEEEEcCCCCHHHHHH
Confidence            6654  23   55667 44553 344566676655443   222222  1111    5553  3455 6677666653

Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.

>TIGR01083 nth endonuclease III

Probab=83.90  E-value=4.6  Score=40.19  Aligned_cols=41  Identities=20%  Similarity=0.180  Sum_probs=26.3

Q ss_pred             HHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423        470 IEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ  512 (655)
Q Consensus       470 i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~  512 (655)
                      ..+|++. + .++.+|..++.++|..+   -||...+|+.|.+-.+
T Consensus        48 ~~~l~~~-~-pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~   91 (191)
T TIGR01083        48 TKKLFEV-Y-PTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCR   91 (191)
T ss_pred             HHHHHHH-C-CCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence            3445553 2 48899999988887432   2776677777765433

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.

>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=83.68  E-value=3.9  Score=40.55  Aligned_cols=141  Identities=16%  Similarity=0.144  Sum_probs=76.9

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc--cCCccccc--CCCCceEEEEEEEEeehhhHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH--KIPLVLNI--KYPPELLEVRCEVLIYKKDFIKL  194 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~--~iP~~l~~--~~~p~~~evRGEv~~~~~~F~~~  194 (655)
                      .|+|.+|-||+-.-|...++ =+-++.|-         .++..+.  ..|....+  .......-+-||+++....    
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            69999999999998755443 34455653         3344433  24544420  0123468899999987442    


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHh--------C----C-
Q psy11423        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQK--------I----G-  260 (655)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~--------~----G-  260 (655)
                                                  .   .+.+.|.+|++....|... ..+..+.+..|++        .    | 
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   3368999999987655432 1345566666542        1    1 


Q ss_pred             CCC--CCCceeeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423        261 LSI--CGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (655)
Q Consensus       261 F~~--~~~~~~~~~~---~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (655)
                      ...  .+......+.   ..+....  .......+++++||+|+.-.+..+
T Consensus       132 ~~~~~~pf~i~~K~~~~~~~~~~~~--~~~~~~~l~h~~DGLIFtp~~~pY  180 (192)
T PF01331_consen  132 IKKKKEPFSIRIKDFFPIYQIEKLL--FEEFIPKLPHETDGLIFTPVNTPY  180 (192)
T ss_dssp             CTCTTSSSEEEE---EEGGGHHHHC--HHCCCCCTTSTEEEEEEEESSSB-
T ss_pred             ccccccceeeeccccHHHHhhHHHH--HHHhhccCCCCCCEEEEecCCCCc
Confidence            010  1111111211   2222211  334567899999999998877543

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.

>PRK02362 ski2-like helicase; Provisional

Probab=83.61  E-value=3  Score=50.10  Aligned_cols=54  Identities=20%  Similarity=0.345  Sum_probs=47.1

Q ss_pred             HHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       521 r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      ..+.-+.|||+|+++|++|.+. +.|+++|..++.++|.++  +|+++|++|.+-+.
T Consensus       650 ~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~  704 (737)
T PRK02362        650 ELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAG  704 (737)
T ss_pred             HHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence            4444558999999999999874 779999999999999999  99999999988765

>PRK13766 Hef nuclease; Provisional

Probab=83.52  E-value=1.6  Score=52.42  Aligned_cols=50  Identities=12%  Similarity=0.216  Sum_probs=38.4

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .|+|+|++++.+|++.=  .++.+++.++.++|..++|+|++.++.|.+.++
T Consensus       719 ~ipgig~~~a~~Ll~~f--gs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~  768 (773)
T PRK13766        719 SLPDVGPVLARNLLEHF--GSVEAVMTASEEELMEVEGIGEKTAKRIREVVT  768 (773)
T ss_pred             cCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence            67888888888887753  477888888888888888888888887776654

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=83.45  E-value=1.6  Score=45.43  Aligned_cols=51  Identities=22%  Similarity=0.363  Sum_probs=42.8

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      +.|||+|++.+..|++.=  .++.++++++.+.|...+|+|+|.|..|..-+.
T Consensus       185 ~s~pgig~~~a~~ll~~f--gS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~  235 (254)
T COG1948         185 ESIPGIGPKLAERLLKKF--GSVEDVLTASEEELMKVKGIGEKKAREIYRFLR  235 (254)
T ss_pred             HcCCCccHHHHHHHHHHh--cCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence            468899999999998764  488899999989999999999999988776554

>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=82.87  E-value=1.2  Score=32.92  Aligned_cols=28  Identities=21%  Similarity=0.507  Sum_probs=21.8

Q ss_pred             CCCCCCCCcceeec--CceeEEecCCCcCCH
Q psy11423        416 NICPICNSKIIYIE--SNLIARCSGSWIECI  444 (655)
Q Consensus       416 ~~CP~C~~~l~~~~--~~~~~~C~n~~~~C~  444 (655)
                      ..||.||+.|+...  .+..+-|+|.+. |.
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            36999999998553  358899999766 84

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

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=82.42  E-value=2  Score=46.20  Aligned_cols=148  Identities=20%  Similarity=0.338  Sum_probs=73.9

Q ss_pred             CCCCCCCCC-cceeecCceeEEecCCCcCCHHHHHhhccc-------cccccccccCCCCHHHHHHHHHcCCCCChH---
Q psy11423        415 PNICPICNS-KIIYIESNLIARCSGSWIECIAQRKAGLQH-------FSSRKAMNIIGLGKKMIEKLVNANIVVTAV---  483 (655)
Q Consensus       415 P~~CP~C~~-~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~-------F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~---  483 (655)
                      +..||.||+ .++.+.....+.|.+    |-..+-+++..       |..-+..+=.-.|..+-..+.+.|+-+.+.   
T Consensus        11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~----CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~   86 (310)
T PRK00423         11 KLVCPECGSDKLIYDYERGEIVCAD----CGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRN   86 (310)
T ss_pred             CCcCcCCCCCCeeEECCCCeEeecc----cCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCC
Confidence            457999999 455555567899988    87767666653       332222232334443333444444422221   


Q ss_pred             -HHhc--CC---hhhhccccC------CcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC--------
Q psy11423        484 -DLYK--IN---FKNLLRLDR------VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF--------  543 (655)
Q Consensus       484 -DL~~--L~---~~~L~~l~G------fG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f--------  543 (655)
                       |-+.  +.   ...+..|..      ...+...+|..++..     +.++-..|++|..=..+|..|.+.+        
T Consensus        87 ~~~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~-----I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rg  161 (310)
T PRK00423         87 KDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSE-----LDRIASQLGLPRSVREEAAVIYRKAVEKGLIRG  161 (310)
T ss_pred             cccccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHH-----HHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccC
Confidence             0010  10   011111111      112333444444432     4677788899865555665555433        


Q ss_pred             CCHHHHHhc-------------CHHHHhcCCCCCHHHHHHH
Q psy11423        544 KNLECMFKA-------------TEEQLLNIPKIGSTTVKAF  571 (655)
Q Consensus       544 gsl~~l~~a-------------s~eeL~~i~GIG~~~A~~I  571 (655)
                      .+++.+..|             +..|+..+-++..+...+.
T Consensus       162 rs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~  202 (310)
T PRK00423        162 RSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRC  202 (310)
T ss_pred             CCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHH
Confidence            245566554             3456666666665544443

>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]

Probab=82.00  E-value=0.82  Score=44.95  Aligned_cols=52  Identities=17%  Similarity=0.242  Sum_probs=49.0

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      -|++|.+.-+.-++..+|++.....|+.+|+..+.|+|+..|+.+++|++.|
T Consensus       171 ~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~p  222 (224)
T COG5241         171 LIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLP  222 (224)
T ss_pred             EEEeeccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhccc
Confidence            5799999999999999999999999999999999999999999999999865

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=81.93  E-value=1.6  Score=50.68  Aligned_cols=119  Identities=17%  Similarity=0.199  Sum_probs=73.7

Q ss_pred             HHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhc
Q psy11423        372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL  451 (655)
Q Consensus       372 ~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i  451 (655)
                      +.++++||.+- .|-|.|.-+      .++..   +...++.+|..-|.=. -|.+.-|+++-|-... +    +..+.=
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      22221   1223566665433211 1122334555444442 2    233333


Q ss_pred             cccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       452 ~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      .++-| ...+|+|+|+++..+|.+.=  .++.++...+.++|... |++.+.|++|.+.
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            34444 46789999999999999864  48889999999999999 9999999999864

>PRK07758 hypothetical protein; Provisional

Probab=81.90  E-value=3.7  Score=36.38  Aligned_cols=47  Identities=15%  Similarity=0.296  Sum_probs=36.2

Q ss_pred             CCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        529 RHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       529 pgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      |+++....+.|.. .+.++++|...+.+||.++.|+|++..+.|.+-+
T Consensus        40 ~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL   87 (95)
T PRK07758         40 SLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKAL   87 (95)
T ss_pred             ccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHH
Confidence            4444445566654 5789999999999999999999999887776543

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=81.82  E-value=1.2  Score=29.83  Aligned_cols=20  Identities=30%  Similarity=0.602  Sum_probs=16.7

Q ss_pred             HHhcCCCCCHHHHHHHHHHh
Q psy11423        556 QLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       556 eL~~i~GIG~~~A~~I~~~f  575 (655)
                      +|.+++|||+++|+.|.++.
T Consensus         2 ~L~~i~GiG~k~A~~il~~~   21 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHhc
Confidence            57889999999999988754

>TIGR03491 RecB family nuclease, putative, TM0106 family

Probab=81.64  E-value=2.6  Score=47.68  Aligned_cols=64  Identities=19%  Similarity=0.209  Sum_probs=52.0

Q ss_pred             CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      |-+...+. .|     ...++|++.++...|.++| |.|+.||-......|..++|++..++.+|..+.+.
T Consensus       199 C~~~~~~~-~~-----lslv~gi~~~~~~~L~~~G-I~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~a  262 (457)
T TIGR03491       199 CEAVAKEE-GH-----LSLVPGIGPSRYRLLQELG-IHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARA  262 (457)
T ss_pred             HHHHHHhc-CC-----eeecCCCCHHHHHHHHHcC-CCcHHHHhcCCccccccccccCHHHHHHHHHHHHH
Confidence            86665543 33     4579999999999999999 69999999987667888889999999998776654

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.

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=80.86  E-value=1.6  Score=40.55  Aligned_cols=49  Identities=24%  Similarity=0.224  Sum_probs=40.0

Q ss_pred             CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhc
Q psy11423        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL  494 (655)
Q Consensus       443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~  494 (655)
                      |+++.+.++.--+  +.|.|+|+|+..+..|+.+|+ .|+.+|-..+.++|.
T Consensus        41 i~~~~l~~w~~~A--dL~ri~gi~~~~a~LL~~AGv-~Tv~~LA~~~p~~L~   89 (122)
T PF14229_consen   41 ISERNLLKWVNQA--DLMRIPGIGPQYAELLEHAGV-DTVEELAQRNPQNLH   89 (122)
T ss_pred             CCHHHHHHHHhHH--HhhhcCCCCHHHHHHHHHhCc-CcHHHHHhCCHHHHH
Confidence            7788888877766  588999999999999999995 888888776665544

>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=80.81  E-value=1.3  Score=33.32  Aligned_cols=24  Identities=17%  Similarity=0.513  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCcceeecCceeEEecC
Q psy11423        414 IPNICPICNSKIIYIESNLIARCSG  438 (655)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n  438 (655)
                      +-++||.||.||.+..++ ..+|++
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            457999999999984443 578976

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PRK10736 hypothetical protein; Provisional

Probab=80.73  E-value=4.5  Score=44.66  Aligned_cols=67  Identities=6%  Similarity=0.059  Sum_probs=49.7

Q ss_pred             HHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHHcCcc
Q psy11423        522 FIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIY  593 (655)
Q Consensus       522 ~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~  593 (655)
                      ||.-..+||||.++.++|+++|++.+   .++.++|... |++++.+..+.++ ...+..+.++.+...|+.
T Consensus         7 ~l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~   73 (374)
T PRK10736          7 WLRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQL-PRKSLESTLRWLEQPNHH   73 (374)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhcc-CHHHHHHHHHHHHhcCCE
Confidence            44444789999999999999999987   4678888886 9999999888655 333334455666666654

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=80.66  E-value=1.8  Score=50.96  Aligned_cols=49  Identities=24%  Similarity=0.303  Sum_probs=43.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      ..+|+|+|+++...|...-  .|+.+|...+.++|.++  +|+|.|++|.+.+
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  48899999999999988  9999999998764

>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs

Probab=80.17  E-value=1.4  Score=32.05  Aligned_cols=17  Identities=35%  Similarity=0.622  Sum_probs=11.8

Q ss_pred             CCCCccHHHHHHHHHhC
Q psy11423        527 GIRHVGETTAKELANYF  543 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~f  543 (655)
                      ||||||+++|.+|+++|
T Consensus        20 Gv~giG~ktA~~ll~~~   36 (36)
T smart00279       20 GVKGIGPKTALKLLREF   36 (36)
T ss_pred             CCCcccHHHHHHHHHhC
Confidence            67777777777766654

>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins

Probab=80.01  E-value=1.9  Score=30.13  Aligned_cols=26  Identities=27%  Similarity=0.694  Sum_probs=14.2

Q ss_pred             CCCCCCCccee---ec-C-ceeEEecCCCcCCH
Q psy11423        417 ICPICNSKIIY---IE-S-NLIARCSGSWIECI  444 (655)
Q Consensus       417 ~CP~C~~~l~~---~~-~-~~~~~C~n~~~~C~  444 (655)
                      -||.||-.+..   .+ | -..+||.|+ . |.
T Consensus         3 lcpkcgvgvl~pvy~~kgeikvfrcsnp-a-cd   33 (36)
T PF09151_consen    3 LCPKCGVGVLEPVYNQKGEIKVFRCSNP-A-CD   33 (36)
T ss_dssp             B-TTTSSSBEEEEE-TTS-EEEEEES-T-T---
T ss_pred             cCCccCceEEEEeecCCCcEEEEEcCCC-c-cc
Confidence            59999986532   11 2 267899996 6 85

Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	655
2owo_A	671	Last Stop On The Road To Repair: Structure Of E.Col		1e-144
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-104
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
3pn1_A	318	Novel Bacterial Nad+-Dependent Dna Ligase Inhibitor		3e-63
1b04_A	318	Structure Of The Adenylation Domain Of An Nad+ Depe		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		6e-54
1zau_A	328	Adenylation Domain Of Nad+ Dependent Dna Ligase Fro		8e-53
3bac_A	270	Structural Basis For The Inhibition Of Bacterial Na		4e-51
4glw_A	305	Dna Ligase A In Complex With Inhibitor Length = 305		8e-46
1l7b_A	92	Solution Nmr Structure Of Brct Domain Of T. Thermop		6e-04

>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 =  508 bits (1308), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 260/664 (39%), Positives = 392/664 (59%), Gaps = 35/664 (5%)
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----------LNNP-------- 598
           L  +P +G         F  +  +R +IS+L   G++W          +++P        
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVL 605
Query: 599 ----------NTK------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
                     + K      G KV   +SK T+ ++ G+  G KL KA +L I+++DE   
Sbjct: 606 TGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEM 665
Query: 643 VKIV 646
           ++++
Sbjct: 666 LRLL 669

>pdb|4GLX|A Chain A, Dna Ligase A In Complex With Inhibitor Length = 586

Iteration: 1
 Score =  489 bits (1259), 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 =  375 bits (962), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 241/665 (36%), Positives = 373/665 (56%), Gaps = 48/665 (7%)
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 ESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLV--KE 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 KATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW---------------- 594
           +A+ E+L+ + ++G  T +A ++ +  P  R L+ +L++ G+                  
Sbjct: 535 EASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFV 594
Query: 595 ----LNNPNTK--------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
               L+ P  +        G KV + +S+ T+YLV G+ PG KLEKA  L + +L E+ F
Sbjct: 595 LTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEF 654
Query: 643 VKIVK 647
            + +K
Sbjct: 655 WRFLK 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 (955), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 210/591 (35%), Positives = 322/591 (54%), Gaps = 21/591 (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 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN 597
           + +  A+ +QL  +  +G T   A  ++     HR ++ + R  G+  ++ 
Sbjct: 553 DAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDE 603

>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 (614), 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|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 (611), 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|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|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 (544), 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 = 6e-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 (521), Expect = 8e-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 (506), Expect = 4e-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 = 8e-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|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus: Northeast Structural Genomics Consortium Target Wr64tt Length = 92

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
           G KV + +S+ T+YLV G+ PG KLEKA  L +  L E+   ++++ 
Sbjct: 34  GAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEA 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	655
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-145
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	1e-144
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	1e-143
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	1e-141
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
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	3e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	1e-11
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	3e-11
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	1e-07
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	9e-05

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Length = 671

 Score =  826 bits (2137), Expect = 0.0
 Identities = 266/664 (40%), Positives = 397/664 (59%), Gaps = 35/664 (5%)

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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
           L  +P +G         F  +  +R +IS+L   G++W                      
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVL 605

Query: 602 -------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
                              G KV   +SK T+ ++ G+  G KL KA +L I+++DE   
Sbjct: 606 TGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEM 665

Query: 643 VKIV 646
           ++++
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 =  787 bits (2036), Expect = 0.0
 Identities = 241/665 (36%), Positives = 373/665 (56%), Gaps = 46/665 (6%)

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 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK---------- 601
           A+ E+L+ + ++G  T +A ++ +  P  R L+ +L++ G+   +               
Sbjct: 536 ASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFVL 595

Query: 602 ------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFV 643
                             G KV + +S+ T+YLV G+ PG KLEKA  L + +L E+ F 
Sbjct: 596 TGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFW 655

Query: 644 KIVKG 648
           + +K 
Sbjct: 656 RFLKE 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 =  432 bits (1113), 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 (1091), Expect = e-145
 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 (1083), Expect = e-144
 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 =  417 bits (1074), Expect = e-143
 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 (1065), Expect = e-141
 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

>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

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
           G KV + +S+ T+YLV G+ PG KLEKA  L +  L E+   ++++ 
Sbjct: 34  GAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEA 80

>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 = 7e-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 = 61.4 bits (148), Expect = 6e-10
 Identities = 68/438 (15%), Positives = 133/438 (30%), Gaps = 144/438 (32%)

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 IGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNIC--------------PICNS--- 423
                +         K+  ++L LRP         N+                +C S   
Sbjct: 133 RLQPYL---------KLRQALLELRPA-------KNVLIDGVLGSGKTWVALDVCLSYKV 176

Query: 424 ------KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNAN 477
                 KI ++    +  C+ S    +      LQ    +   N            +  +
Sbjct: 177 QCKMDFKIFWLN---LKNCN-SPETVLEM----LQKLLYQIDPNWTSRSDHSSNIKLRIH 228

Query: 478 IVVTAVD--LYKINFKN-LLRLDRVSNKLANNILLA--IQ-KSKLTTFSRFIYALGIRHV 531
            +   +   L    ++N LL L  V N        A  +  K  LTT  RF         
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNA---KAWNAFNLSCKILLTT--RFKQVTDFLSA 283

Query: 532 GETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL----------HR 581
             TT   L ++   L      T +++ ++           +K+++             + 
Sbjct: 284 ATTTHISLDHHSMTL------TPDEVKSL----------LLKYLDCRPQDLPREVLTTNP 327

Query: 582 LLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDE-- 639
             +S +                 + + ++   N+         KL   I+ ++ +L+   
Sbjct: 328 RRLSII--------------AESIRDGLATWDNWK---HVNCDKLTTIIESSLNVLEPAE 370

Query: 640 --KNFVKIVKGFSTETKI 655
             K F ++   F     I
Sbjct: 371 YRKMFDRLSV-FPPSAHI 387

>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 = 61.3 bits (149), Expect = 1e-11
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 647
           GGKV   +SK TNYLV G+  G  K +KA  L  KI+DE   + +++
Sbjct: 50  GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 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 = 59.7 bits (145), Expect = 3e-11
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 647
           GGKV   +SK TNYLV G+  G  K +KA  L  KI+DE   + +++
Sbjct: 60  GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 106

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A Length = 113

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 602 GGKVVNFISKNTNYLVKG---QKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
           GGK+    +K +  +      +K  KK+E+  + NI+++ E     +   
Sbjct: 37  GGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDFLQDVSAS 86

>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 = 9e-05
 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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	655
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
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	99.12
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	99.09
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	99.07
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	98.86
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	98.72
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	98.7
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	98.61
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	98.61
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	98.49
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	98.44
1fvi_A	297	Chlorella virus DNA ligase-adenylate; adenylated D	98.3
1vs0_A	310	Putative DNA ligase-like protein RV0938/MT0965; OB	98.14
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	98.14
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	98.12
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	98.11
3gde_A	558	DNA ligase; DNA-binding domain, adenylation domain	98.08
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	98.04
1a0i_A	348	DNA ligase; DNA replication; HET: DNA ATP; 2.60A {	97.98
2cfm_A	561	Thermostable DNA ligase; protein-nucleotide comple	97.94
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	97.93
3qwu_A	370	DNA ligase; structural genomics, PSI-2, midwest ce	97.92
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	97.83
2hiv_A	621	Thermostable DNA ligase; ATP-dependent, open confo	97.82
1x9n_A	688	DNA ligase I; 5'-adenylated nicked DNA, protein-DN	97.81
3l2p_A	579	DNA ligase 3; DNA ligase, DNA repair, ATP-binding,	97.75
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	97.73
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	97.53
1ckm_A	330	MRNA capping enzyme; nucleotidyltransferase; HET:	97.43
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	97.43
3vnn_A	139	DNA ligase 4; non-homologous END joining, DNA repa	97.31
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	97.21
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	97.12
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	97.12
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	97.08
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	97.08
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	97.08
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	97.06
2duy_A	75	Competence protein comea-related protein; helix-ha	97.05
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	96.96
3b0x_A	575	DNA polymerase beta family (X family); structural	96.9
3b0x_A	575	DNA polymerase beta family (X family); structural	96.9
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	96.87
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	96.85
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	96.84
1u9l_A	70	Transcription elongation protein NUSA; escherichia	96.31
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	96.3
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	96.25
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	96.08
2hvq_A	335	ORF1, hypothetical 37.6 kDa protein in GP24-HOC in	96.04
1p16_A	395	GTP--RNA, mRNA capping enzyme alpha subunit; guany	96.02
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	95.99
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	95.98
1z3e_B	73	DNA-directed RNA polymerase alpha chain; bacterial	95.94
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	95.8
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	95.57
3gfk_B	79	DNA-directed RNA polymerase subunit alpha; protein	95.55
3kyh_C	461	MRNA-capping enzyme subunit alpha; 5' modification	95.5
3k4g_A	86	DNA-directed RNA polymerase subunit alpha; bacteri	95.43
1s68_A	249	RNA ligase 2; ribonucleic acid ligase, RNA repair;	95.39
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	95.37
2duy_A	75	Competence protein comea-related protein; helix-ha	95.27
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	95.21
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	95.15
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	95.06
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	95.02
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	94.9
4id3_A	92	DNA repair protein REV1; BRCT domain, protein bind	94.87
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	94.85
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	94.8
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	94.79
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	94.7
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	94.58
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	94.57
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	94.56
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	94.43
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	94.42
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	94.33
3rtx_A	343	MRNA-capping enzyme; guanylyltransferase, RNA poly	94.31
1coo_A	98	RNA polymerase alpha subunit; transcription regula	94.29
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	94.29
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	94.27
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	94.24
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	94.15
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	93.89
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	93.86
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	93.75
1u9l_A	70	Transcription elongation protein NUSA; escherichia	93.66
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	93.29
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	93.17
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	93.17
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	93.11
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	92.99
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	92.5
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	92.02
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	91.75
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	91.74
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	91.31
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	91.15
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	91.1
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	89.79
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	89.38
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	88.39
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	88.01
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	87.53
1xdn_A	277	RNA editing ligase MP52; HET: MSE ATP; 1.20A {Tryp	87.15
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	87.05
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	86.81
2ziu_A	311	MUS81 protein; helix-hairpin-helix, alternative sp	86.33
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	85.92
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	85.8
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	83.39
2kz3_A	83	Putative uncharacterized protein RAD51L3; RAD51D,	83.33
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	83.21
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	83.06
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	82.83
3bqs_A	93	Uncharacterized protein; 10114F, NYSGXRC, PSI-2, s	82.66
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	81.79
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	81.57
3im1_A	328	Protein SNU246, PRE-mRNA-splicing helicase BRR2; A	80.7
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	80.14

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=100.00  E-value=6.2e-186  Score=1572.56  Aligned_cols=633  Identities=42%  Similarity=0.706  Sum_probs=559.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCC
Q psy11423         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSL   92 (655)
Q Consensus        13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL   92 (655)
                      ++++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.++|||||+||+.+.++|.+|+|++|||||
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             CCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccC
Q psy11423         93 DNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (655)
Q Consensus        93 ~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (655)
                      +|+||.+||.+|++|+.+.++...++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++.
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             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC-CCCCCCHHH
Q psy11423        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG-MNMPSSHSE  251 (655)
Q Consensus       173 ~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~-~~~~~~~~e  251 (655)
                      +.|..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|...++ .. +.+|++
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            2588999999999999999999999999999999999999999999999999999999999999973222 22 489999


Q ss_pred             HHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceee
Q psy11423        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEAL  331 (655)
Q Consensus       252 ~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~  331 (655)
                      .|++|++|||+|+++...|.+++++++|+++|.+.|..+||+|||+||||||+++|+.||+|+|+||||||||||+++++
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             EEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCcc
Q psy11423        332 TKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKI  411 (655)
Q Consensus       332 T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~  411 (655)
                      |+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.++|++.+++
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            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChh
Q psy11423        412 FKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK  491 (655)
Q Consensus       412 ~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~  491 (655)
                      |.+|++||+||++|++.+|++.+||+|.+. ||+|++++|.||+||++|||+|||+|+|.+|+++|+|++++|||.|+.+
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            999999999999999988999999998656 9999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHH
Q psy11423        492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAF  571 (655)
Q Consensus       492 ~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I  571 (655)
                      +|..|+|||+|+++||+++|+.+|+.+|+|||+||||||||+++|+.|+++|+|+++|..|+.++|.+++|||+++|++|
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             HHHhcChhHHHHHHHHHHcCcccc--cC------C--------------------------CCCCCeEecccccCccEEE
Q psy11423        572 IKFINQPLHRLLISQLRDVGIYWL--NN------P--------------------------NTKGGKVVNFISKNTNYLV  617 (655)
Q Consensus       572 ~~~f~~~~n~~li~~L~~~Gi~~~--~~------~--------------------------~~~G~~v~~sVsk~t~ylv  617 (655)
                      ++||++++|+++|++|.+.|+.+.  ..      .                          .++||+|++|||++|||||
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            999999999999999999898543  10      0                          1889999999999999999


Q ss_pred             ecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        618 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       618 ~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      +|+++|||++||++|||+||+|++|++||+
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=1.4e-180  Score=1527.68  Aligned_cols=627  Identities=39%  Similarity=0.662  Sum_probs=551.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCC-Ccceecccccc
Q psy11423         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGEN-SKYVHHTFKMM   90 (655)
Q Consensus        12 ~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~-~~kv~H~~pMl   90 (655)
                      +.+++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.++|||||+||+.+.++ |.+|+|.+|||
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            45678999999999999999999999999999999999999999999999999999999999999888 99999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccc
Q psy11423         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (655)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (655)
                      ||+|+||.+||.+|++|+.+.++  +++.|+|||||||+|| |+|+||+  +|+|||||.+|||||+|+++|++||++|+
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             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccce--EEEEEeccc-ccCCCCCC
Q psy11423        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKIL--HFFAHGVGE-LRGMNMPS  247 (655)
Q Consensus       171 ~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L--~f~~y~~~~-~~~~~~~~  247 (655)
                      +.  |..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|  +||+|+|.. .++.. +.
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 58


Q ss_pred             CHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCc
Q psy11423        248 SHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (655)
Q Consensus       248 ~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (655)
                      +|++.|++|++|||+|+++...|.+++++++|+++|.+.|..+||+|||+||||||+.+|+.||+|+|+||||||||||+
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             ceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCC
Q psy11423        328 KEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPN  407 (655)
Q Consensus       328 ~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~  407 (655)
                      ++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.++|++
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             CCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423        408 DSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (655)
Q Consensus       408 ~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (655)
                      ++++|.+|++||+||+++  .+|++.+||+|. . ||+|++++|.||+||++|||+|||+|+|++|+++|+|++++|||.
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            999999999999999999  567799999996 6 999999999999999999999999999999999999999999999


Q ss_pred             CChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHH
Q psy11423        488 INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT  567 (655)
Q Consensus       488 L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~  567 (655)
                      |+.++|..++|||+|+++||+++|+.+|+.+|+|||+||||||||+++|++|+++|+++++|..|+.++|.+++|||+++
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             HHHHHHHhcChhHHHHHHHHHHcCcccc-c---C-C-----------------------CCCCCeEecccccCccEEEec
Q psy11423        568 VKAFIKFINQPLHRLLISQLRDVGIYWL-N---N-P-----------------------NTKGGKVVNFISKNTNYLVKG  619 (655)
Q Consensus       568 A~~I~~~f~~~~n~~li~~L~~~Gi~~~-~---~-~-----------------------~~~G~~v~~sVsk~t~ylv~g  619 (655)
                      |++|++||++++|++++++|.+.|+.+. .   . .                       .++||+|++|||++|||||+|
T Consensus       552 A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~l~G~~~v~TG~l~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV~G  631 (667)
T 1dgs_A          552 ARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFVLTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVG  631 (667)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHTTCCCBCC--------------------------------------------------
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHcCCccccccccccccCCCEEEEeCCCCCCHHHHHHHHHHcCCEEcCcccCCeeEEEEC
Confidence            9999999999999999999999998653 1   0 0                       188999999999999999999


Q ss_pred             CCCCchHHHHHHcCCeeeCHHHHHHHHhccc
Q psy11423        620 QKPGKKLEKAIKLNIKILDEKNFVKIVKGFS  650 (655)
Q Consensus       620 ~~~g~K~~kA~~lgi~ii~e~~f~~~l~~~~  650 (655)
                      +++|||++||++|||+||+|++|++||+...
T Consensus       632 ~~~gsKl~KA~~lgI~Ii~E~~f~~~l~~~~  662 (667)
T 1dgs_A          632 ENPGSKLEKARALGVAVLTEEEFWRFLKEKG  662 (667)
T ss_dssp             -------------------------------
T ss_pred             CCCChHHHHHHHCCCeEEeHHHHHHHHhcCC
Confidence            9999999999999999999999999997654

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=100.00  E-value=1.1e-175  Score=1471.03  Aligned_cols=585  Identities=43%  Similarity=0.722  Sum_probs=561.5

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11423         11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM   90 (655)
Q Consensus        11 ~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl   90 (655)
                      |+++++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+.++|.||+|++|||
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            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccc
Q psy11423         91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN  170 (655)
Q Consensus        91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~  170 (655)
                      ||+|+||.+||.+|++|+.+.|+...++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|.
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            99999999999999999999886555678999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHH
Q psy11423        171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS  250 (655)
Q Consensus       171 ~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~  250 (655)
                      +.++|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++...++.+++.+|+
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 psy11423        251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEA  330 (655)
Q Consensus       251 e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~  330 (655)
                      +.|++|++|||+|+++...+.+.+++.+|+++|...|.++||+|||||||+|++.+|+.||+|+|+||||||||||++++
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             eEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCc
Q psy11423        331 LTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSK  410 (655)
Q Consensus       331 ~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~  410 (655)
                      +|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|++++|++++.
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             cccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCCh
Q psy11423        411 IFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF  490 (655)
Q Consensus       411 ~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~  490 (655)
                      +|.+|++||+||+++++.++++.+||+|+.. ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|+.
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            9999999999999999999999999999767 999999999999999999999999999999999999999999999999


Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHH
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA  570 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~  570 (655)
                      ++|..|+|||+|||+||+++|++||+.+|+|||+|||||+||+.+|+.|+++|+++++|.+|+.++|.+|+|||+++|++
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 psy11423        571 FIKFINQPLHRLLISQLRDVGIYWLN  596 (655)
Q Consensus       571 I~~~f~~~~n~~li~~L~~~Gi~~~~  596 (655)
                      |++||++++|+++|++|.+.||+|+.
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            99999999999999999999999875

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=100.00  E-value=3.2e-176  Score=1474.60  Aligned_cols=585  Identities=36%  Similarity=0.575  Sum_probs=388.9

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCccc-CCCCcceecc
Q psy11423          8 KINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GENSKYVHHT   86 (655)
Q Consensus         8 ~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~-~~~~~kv~H~   86 (655)
                      ..+..++++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+ ..+|.+|+|.
T Consensus         7 ~~~~~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVGg~~~~~~f~kV~H~   86 (615)
T 3sgi_A            7 DQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHL   86 (615)
T ss_dssp             -CCCSSHHHHHHHHHHHHHHHHHHHHHHSCCCSSCCSSCSSSSHHHHHHTSSGGGCCTTCTTSCCCCCCCSSSCCBCCCS
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhCcCcCCCCCCcccCCCcccccCCCceecC
Confidence            345667788999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC
Q psy11423         87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP  166 (655)
Q Consensus        87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP  166 (655)
                      +|||||+|+||.+||.+|++|+.+.++.  ++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||
T Consensus        87 ~pMlSL~n~f~~eel~~f~~rv~~~l~~--~~~~~~EpKiDGlavsL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP  164 (615)
T 3sgi_A           87 ERMLSLDNAFTADELAAWAGRIHAEVGD--AAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVP  164 (615)
T ss_dssp             SCCCCCEEECSSSCCSTTTTTSTTTTCS--CCCEEEEEEECSEEEEEEEETTEEEEEECCTTSSSCBCCHHHHHSCSSSC
T ss_pred             CccCCccccCCHHHHHHHHHHHHHhcCC--CCeEEEEEEecceEEEEEEECCEEEEEEecCCCcchhhHHHHHHhhcCcc
Confidence            9999999999999999999999888762  46899999999999999999999999999999999999999999999999


Q ss_pred             cccccCC---CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCC
Q psy11423        167 LVLNIKY---PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM  243 (655)
Q Consensus       167 ~~l~~~~---~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~  243 (655)
                      ++|++.+   +|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.
T Consensus       165 ~~L~~~~~~~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqld~~ita~R~L~~f~y~~~~~~~~  244 (615)
T 3sgi_A          165 ERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGF  244 (615)
T ss_dssp             SSCCCCSSCCCCSEEEEEEEEECCHHHHHHHHTTCSSSSSCCCSSHHHHHHHHHTCSSTTHHHHSCCEEEEEEEEEEESC
T ss_pred             hhhcCCcccCCCCeEEEEEEEEEeHHHHHHHHHHHHHcCCCcCCChHHHHHHHHHcCChhhHhhCcceEEEEeccccCCC
Confidence            9998642   5889999999999999999999999999999999999999999999999999999999999999865543


Q ss_pred             CCCCCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEee
Q psy11423        244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAY  323 (655)
Q Consensus       244 ~~~~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~  323 (655)
                      . +.+|++.|++|++|||+|+++...|.+++++.+|+++|.+.|..+||+|||+|||+|++++|+.||+|+|+|||||||
T Consensus       245 ~-~~t~~e~l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~lG~t~k~PRWAiA~  323 (615)
T 3sgi_A          245 R-PATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAY  323 (615)
T ss_dssp             C-CSBTTTHHHHHHHTTCCCCCCCCCBSSHHHHHHHHTTTTTSGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEE
T ss_pred             C-CcCHHHHHHHHHHCCCCCCCCeEeeCCHHHHHHHHHHHHHHhhcCCCCCCeEEEEecCHHHHHHhCCCCCCCCceEEE
Confidence            3 579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeeccccc
Q psy11423        324 KFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILS  403 (655)
Q Consensus       324 Kf~~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~  403 (655)
                      |||+++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.+
T Consensus       324 Kfpaee~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLHN~d~i~~~di~iGD~V~V~rAGdVIP~V~~vv~~  403 (615)
T 3sgi_A          324 KYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVE  403 (615)
T ss_dssp             ECCCSEEEEECCEECCCBCSSSCBCCBEECCCEECSSSEECCCBCCSTTTTTTTCCCBTCEEEEECCSSSSCCCCEECTT
T ss_pred             cCCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEEEEEecCCCHHHHHHcCCCCCCEEEEEEcCCCccceeeeccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCccccCCCCCCCCCCccee-ecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCCh
Q psy11423        404 LRPNDSKIFKIPNICPICNSKIIY-IESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTA  482 (655)
Q Consensus       404 ~r~~~~~~~~~P~~CP~C~~~l~~-~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i  482 (655)
                      .|++++.+|.+|++||+||++|++ .++++.+||+|+.. ||+|++++|.||+||+||||+|||+++|++|+++|+|+++
T Consensus       404 ~R~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~rC~n~~~-CpaQ~~~~l~hf~Sr~amdI~GlG~~~i~~L~~~g~i~~~  482 (615)
T 3sgi_A          404 LRDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARG-CPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADE  482 (615)
T ss_dssp             CCCCCCBCCCCC--------------------------------------------------------------------
T ss_pred             cCCCCCccCCCCCCCCCCCCeeeecCCCCEEEEcCCCCC-CHHHHHHHHHHHhccCccCccccCHHHHHHHHHCCCcCCH
Confidence            999999999999999999999998 67889999999656 9999999999999999999999999999999999999999


Q ss_pred             HHHhcCChhhhccccCC------cHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHH
Q psy11423        483 VDLYKINFKNLLRLDRV------SNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ  556 (655)
Q Consensus       483 ~DL~~L~~~~L~~l~Gf------G~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~ee  556 (655)
                      +|||.|+.++|+.|+||      |+|||+||+++|++||+.+|+|||+||||||||+++|++|+++|+|+++|..|+.++
T Consensus       483 aDly~L~~~~L~~l~~~~~~~g~g~ksa~nLl~aIe~sk~~~l~r~L~aLGIp~VG~~~ak~La~~Fgsle~L~~As~ee  562 (615)
T 3sgi_A          483 GELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQ  562 (615)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHhhCCHHHHhhccccccccCccchHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHH
Confidence            99999999999999977      589999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHHcCccccc
Q psy11423        557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLN  596 (655)
Q Consensus       557 L~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~  596 (655)
                      |.+++|||+++|++|++||++++|+++|++|.+.|+.+..
T Consensus       563 L~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~  602 (615)
T 3sgi_A          563 LAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVD  602 (615)
T ss_dssp             ----------------------------------------
T ss_pred             HhhCCCCCHHHHHHHHHHHcCHHHHHHHHHHHHcCCCccc
Confidence            9999999999999999999999999999999999998754

>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=1.6e-103  Score=825.98  Aligned_cols=320  Identities=43%  Similarity=0.696  Sum_probs=305.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11423         14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD   93 (655)
Q Consensus        14 ~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~   93 (655)
                      +++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+..+|.+|+|++|||||+
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            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHhhcc-CCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccC
Q psy11423         94 NGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (655)
Q Consensus        94 k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (655)
                      |+||.+||.+|++|+.+.++. ..++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|.++
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 1357899999999999999999999999999999999999999999999999999864


Q ss_pred             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHH
Q psy11423        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL  252 (655)
Q Consensus       173 ~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~  252 (655)
                      ++|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++..++.||++.
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            46899999999999999999999999999999999999999999999999999999999999999755443346899999


Q ss_pred             HHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeE
Q psy11423        253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALT  332 (655)
Q Consensus       253 l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T  332 (655)
                      |++|++|||+|+++...|.+++++.+|+++|.+.|..+||+|||||||||++.+|+.||+|+|+||||||||||+++++|
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 psy11423        333 K  333 (655)
Q Consensus       333 ~  333 (655)
                      .
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=5.9e-102  Score=811.88  Aligned_cols=311  Identities=41%  Similarity=0.678  Sum_probs=296.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCC
Q psy11423         13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSL   92 (655)
Q Consensus        13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL   92 (655)
                      ++++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+..+|.+|+|++|||||
T Consensus         3 ~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~p~l~~~dSPTqrVG~~~~~~f~kv~H~~pMlSL   82 (318)
T 3jsl_A            3 DLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSL   82 (318)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCCSCCCCCCEEECSSCCCCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhCcCCCCCCCCccccCccccccCceeecCCcCcCc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccC
Q psy11423         93 DNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK  172 (655)
Q Consensus        93 ~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~  172 (655)
                      +|+||.+||.+|++|+.+.++   ++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++ 
T Consensus        83 ~n~f~~eel~~f~~r~~~~l~---~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~L~~-  158 (318)
T 3jsl_A           83 GNAFNEDDLRKFDQRIREQIG---NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE-  158 (318)
T ss_dssp             EEECSHHHHHHHHHHHHHHTC---SCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSBCSS-
T ss_pred             cccCCHHHHHHHHHHHHhhcC---CceEEEEEeecceEEEEEEECCEEEEEEeCCCCccchhHHHHHHHhcCCccccCC-
Confidence            999999999999999998886   5789999999999999999999999999999999999999999999999999974 


Q ss_pred             CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHH
Q psy11423        173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL  252 (655)
Q Consensus       173 ~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~  252 (655)
                        |..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+|++.
T Consensus       159 --~~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLRqld~~ita~R~L~ff~y~~~~~~~~~-~~t~~e~  235 (318)
T 3jsl_A          159 --PLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFN-ARSQSEA  235 (318)
T ss_dssp             --CCCEEEEEEEECCHHHHHHHHHHHBTTBCCCCSSHHHHHHHHHSCSCHHHHHHSCCEEEEEEESCCTTCC-CSBHHHH
T ss_pred             --CCcEEEEEEEEEcHHHHHHHHHHHHHhCCccccChHHHHHHHHHccChhhhhhCcceEEEEecccccCCC-CCCHHHH
Confidence              5679999999999999999999999999999999999999999999999999999999999998765543 4899999


Q ss_pred             HHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCccee
Q psy11423        253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEA  330 (655)
Q Consensus       253 l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~  330 (655)
                      |++|++|||+|+++..+|.++++|++|+++|.+.|..+||+||||||||||+++|+.||+|+|+||||||||||+++-
T Consensus       236 l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiAyKfp~~~~  313 (318)
T 3jsl_A          236 LDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEH  313 (318)
T ss_dssp             HHHHHHHTCCCCTTCEEESSHHHHHHHHHHHHHHGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBTTEEEEECC----
T ss_pred             HHHHHHCCCCcCCcceEeCCHHHHHHHHHHHHHHHhcCCCCCCcEEEEEeCHHHHHHhCCCCCCCCceEEECCCCccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999864

>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=2.6e-101  Score=812.16  Aligned_cols=322  Identities=39%  Similarity=0.634  Sum_probs=298.2

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecccc
Q psy11423          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFK   88 (655)
Q Consensus         9 ~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~p   88 (655)
                      .+++++++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+.++|.+|+|.+|
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            45667778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcc
Q psy11423         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (655)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (655)
                      ||||+|+||.+||.+|++|+.+.++  .++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++
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             cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCC
Q psy11423        169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS  248 (655)
Q Consensus       169 l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~  248 (655)
                      |.  + |..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+
T Consensus       164 L~--~-p~~leVRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLrqld~~ita~R~L~ff~y~i~~~~~~~-~~t  239 (332)
T 1ta8_A          164 LT--E-PISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK-AKT  239 (332)
T ss_dssp             CS--S-CCCEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHTCSBHHHHHTSCCEEEEEEESCCTTCC-CSB
T ss_pred             cC--C-CCeEEEEEEEEEEHHHHHHHHHHHHhcCCccccChHHHHHHHHHccChhhHhhCCCEEEEEecccccCCC-CCC
Confidence            97  2 7889999999999999999999999999999999999999999999999999999999999997432222 489


Q ss_pred             HHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        249 HSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       249 ~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                      |++.|++|++|||+|+++..+|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||||++
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            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeEEEEE
Q psy11423        329 EALTKIKA  336 (655)
Q Consensus       329 ~~~T~v~~  336 (655)
                      +++|+|+.
T Consensus       320 e~~T~l~~  327 (332)
T 1ta8_A          320 EAETVVZH  327 (332)
T ss_dssp             --------
T ss_pred             eEEEEEec
Confidence            99999974

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2

Probab=100.00  E-value=4.7e-101  Score=806.88  Aligned_cols=315  Identities=42%  Similarity=0.690  Sum_probs=295.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccC
Q psy11423         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMS   91 (655)
Q Consensus        12 ~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlS   91 (655)
                      +.+++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+.+.++|.+|+|.+||||
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             CCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (655)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (655)
                      |+|+||.+||.+|++|+.+.++   .+.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+ 
T Consensus        84 L~n~f~~eel~~f~~rv~~~l~---~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~~L~-  159 (318)
T 1b04_A           84 LANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK-  159 (318)
T ss_dssp             CCEECSTTHHHHHHHHHHHHHS---SCCEEEEEEESSEEEEEEEETTEEEEEEECTTSSCEEBCHHHHHTCTTSCSBCS-
T ss_pred             ccccCCHHHHHHHHHHHHHhcc---CceEEEEEecccEEEEEEEECCEEEEEEccCCCcccHHHHHhHHHhcCCCcccC-
Confidence            9999999999999999988886   378999999999999999999999999999999999999999999999999997 


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (655)
Q Consensus       172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e  251 (655)
                       + |..+||||||||++++|+++|++|.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+|++
T Consensus       160 -~-p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaAAGsLrqld~~ita~R~L~ff~y~~~~~~~~~-~~t~~e  236 (318)
T 1b04_A          160 -E-PVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHSE  236 (318)
T ss_dssp             -S-CCCEEEEEEEECCHHHHHHHHHHHHHC--CCCSCHHHHHHHHHHSSCHHHHHHTCCEEEEEEETTTTTTT-CCBHHH
T ss_pred             -C-CCeEEEEEEEEEEHHHHHHHHHHHHHcCCCccchhhHHHHHHHHccChhhHhhCCCEEEEEecccccCCC-CCCHHH
Confidence             2 7889999999999999999999999999999999999999999999999999999999999997432222 489999


Q ss_pred             HHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceee
Q psy11423        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEAL  331 (655)
Q Consensus       252 ~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~  331 (655)
                      .|++|++|||+|+++..+|.+++++++|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||||+++++
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            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EE
Q psy11423        332 TK  333 (655)
Q Consensus       332 T~  333 (655)
                      |+
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=8.4e-100  Score=800.44  Aligned_cols=317  Identities=37%  Similarity=0.567  Sum_probs=299.8

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcc-cCCCCcceeccc
Q psy11423          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTF   87 (655)
Q Consensus         9 ~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~   87 (655)
                      .++..+++++++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++||||+||+. +.++|.+|+|.+
T Consensus         8 ~~~~~~~~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~lE~~~P~l~~~dSPtqrVG~~~~~~~f~kv~H~~   87 (328)
T 1zau_A            8 QTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLE   87 (328)
T ss_dssp             CCHHHHHTTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHHHHHHTSSTTCCTTCTTTTCSSCCCCCCCCCEECSS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCCccccCCccccccCCccCCCC
Confidence            4566677899999999999999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             cccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCc
Q psy11423         88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPL  167 (655)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~  167 (655)
                      |||||+|+||.+||.+|++|+.+.++  .++.|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||+
T Consensus        88 pMlSL~n~f~~eel~~f~~rv~~~l~--~~~~~~~EpKiDGlaisL~Ye~G~Lv~a~TRGDG~~GEDVT~nvrtI~~IP~  165 (328)
T 1zau_A           88 RMLSLDNAFTADELAAWAGRIHAEVG--DAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPE  165 (328)
T ss_dssp             CCCCCCCBSSHHHHHHHHHGGGTTTC--SCSCEEEEEEECSEEEEEECGGGBCCBCBBCTTSSEECBCHHHHHHSSSCCS
T ss_pred             CCCCccccCCHHHHHHHHHHHHHhcC--CCcceEEeeecceEEEEEEEECCEEEEEEccCCCcccHHHHHHHHHhcCCCh
Confidence            99999999999999999999988775  2478999999999999999999999999999999999999999999999999


Q ss_pred             cc-ccC--CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCC
Q psy11423        168 VL-NIK--YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN  244 (655)
Q Consensus       168 ~l-~~~--~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~  244 (655)
                      +| .+.  +.|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||+++++|+|+||+|+++..++..
T Consensus       166 ~L~~g~~~~~p~~leVRGEv~m~~~~F~~lN~~~~~~g~~~faNPRNaAAGsLrqld~~ita~R~L~f~~y~i~~~~~~~  245 (328)
T 1zau_A          166 RLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR  245 (328)
T ss_dssp             BCCCBTTBCCCSCCEEEEEEBCCHHHHHHHHHSCSSTTSCCCSSHHHHHHHHHTCSSHHHHHHSCCBCCCCBCCCCSSCC
T ss_pred             hhccCCcCCCCCeEEEEEEEEEEHHHHHHHHHHHHHcCCccccChHHHHHHHHHccChhhhhcCcceEEEEeccccCCCC
Confidence            99 542  258889999999999999999999999999999999999999999999999999999999999997432222


Q ss_pred             CCCCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11423        245 MPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK  324 (655)
Q Consensus       245 ~~~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K  324 (655)
                       +.+|++.|++|++|||+|+++...|.+++++.+|+++|.+.|..+||+||||||||||+.+|+.||+|+|+||||||||
T Consensus       246 -~~t~~e~l~~L~~~Gf~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGvViKvn~~~~q~~LG~t~k~PRWAiAyK  324 (328)
T 1zau_A          246 -PATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYK  324 (328)
T ss_dssp             -CSBHHHHHHHHHTTTCCCCCCCCCBCHHHHHHHHHHHTTTTCSSCSSCEEEEEEEECBHHHHTTSCBCSSSBSSCCCEE
T ss_pred             -CCCHHHHHHHHHHcCCCCCCceEEeCCHHHHHHHHHHHHHHHhcCCCCCceEEEEecCHHHHHHhCccCCCCCceeEeC
Confidence             4899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcc
Q psy11423        325 FLSK  328 (655)
Q Consensus       325 f~~~  328 (655)
                      ||++
T Consensus       325 fpae  328 (328)
T 1zau_A          325 YPPE  328 (328)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9985

>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae}

Probab=100.00  E-value=5.2e-98  Score=784.07  Aligned_cols=305  Identities=37%  Similarity=0.600  Sum_probs=265.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11423         14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD   93 (655)
Q Consensus        14 ~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~   93 (655)
                      +++||++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+..+|.+|+|++|||||+
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             CCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCC
Q psy11423         94 NGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKY  173 (655)
Q Consensus        94 k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~  173 (655)
                      |+|+.+||.+|++|+.+.++   ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.  
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            99999999999999988876   4689999999999999999999999999999999999999999999999999974  


Q ss_pred             CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHH
Q psy11423        174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL  253 (655)
Q Consensus       174 ~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l  253 (655)
                       |..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++..+++   +.+|++.|
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             77899999999999999999999999999999999999999999999999999999999999986543   58999999


Q ss_pred             HHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCc
Q psy11423        254 NWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (655)
Q Consensus       254 ~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (655)
                      ++|++|||+++++..+|.+++++++|+++|.+.|.++||+|||||||||++.+|+.||+|+|+|||||||||||
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=4e-38  Score=340.56  Aligned_cols=223  Identities=15%  Similarity=0.141  Sum_probs=190.0

Q ss_pred             CCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHHHHHHHHHHHHhhccCCC
Q psy11423         38 PIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKN  117 (655)
Q Consensus        38 p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~  117 (655)
                      +.-.|++||+|+++|.+||++| ++.        ||+.+..+|+++   .||+||+|+++.     |.+ +         
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            3556999999999999999998 765        899888999988   899999998643     542 1         


Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~  196 (655)
                      ..|+||+|+||+++++.|++|+ ++|.|||+|.  +|||+|  +|++ ||+.|.+.  |..++||||+||+...|+++| 
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 89877532  567999999999998886433 


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCCCCCceeeC--CHH
Q psy11423        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVLS--GVN  274 (655)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~~~~~~~~~--~~~  274 (655)
                               ++||                 .|++.||+|++...++..+ .++.+.+++|+++||++++....+.  +.+
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                 5789999999974332222 6899999999999999998766666  789


Q ss_pred             HHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc---eEeecCCccee
Q psy11423        275 KLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF---ALAYKFLSKEA  330 (655)
Q Consensus       275 ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw---aiA~Kf~~~~~  330 (655)
                      ++.++++.|.      +|++||+|+|+++..  +.+|+|+++|||   |+|||||+++.
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      899999999999987  789999999999   99999999974

>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=99.12  E-value=2.2e-11  Score=105.79  Aligned_cols=51  Identities=37%  Similarity=0.639  Sum_probs=48.5

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHhccc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS  650 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~~~~  650 (655)
                      .+|++|.++||++|||||+|+++|+|++||+++||+||+|++|++||...+
T Consensus        32 ~~Gg~v~~sVskkt~~LV~g~~~gsK~~kA~~lgI~Ii~E~~f~~~l~~~~   82 (92)
T 1l7b_A           32 RLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEART   82 (92)
T ss_dssp             HTTCEEESCCSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHHH
T ss_pred             HcCCEEeCcccCCeeEEEeCCCCChHHHHHHHcCCcEEeHHHHHHHHHhcc
Confidence            789999999999999999999999999999999999999999999997544

>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=99.09  E-value=6.7e-11  Score=105.89  Aligned_cols=49  Identities=43%  Similarity=0.712  Sum_probs=47.3

Q ss_pred             CCCCeEecccccCccEEEecCCCC-chHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG  648 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~  648 (655)
                      .+||+|.+|||++|||||+|+++| +|++||+++||+||+|++|++||+.
T Consensus        58 ~~Gg~v~~sVSkkTd~LV~G~~~g~sK~~kA~~lgI~Ii~E~~f~~ll~~  107 (109)
T 2k6g_A           58 RYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRN  107 (109)
T ss_dssp             HTTCEEESSCCTTCCEEEECBCCCHHHHHHHHHHTCEEECHHHHHHHHHH
T ss_pred             HcCCEeeCcccCCceEEEECCCCChHHHHHHHHcCCeEEeHHHHHHHHHh
Confidence            789999999999999999999999 9999999999999999999999964

>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=99.07  E-value=8.7e-11  Score=105.49  Aligned_cols=50  Identities=42%  Similarity=0.699  Sum_probs=47.9

Q ss_pred             CCCCeEecccccCccEEEecCCCC-chHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF  649 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~~  649 (655)
                      .+|++|.++||++|||||+|+++| +|++||+++||+||+|++|++||+..
T Consensus        48 ~~Ggkv~~sVSkkTd~LV~G~~~g~sKl~KA~~lgI~IisE~~f~~ll~~~   98 (112)
T 2ebu_A           48 RYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRTM   98 (112)
T ss_dssp             HTTCEECSSCCSSCCEEEECSSCCSHHHHHHHHHTCEEEEHHHHHHHHHHS
T ss_pred             HcCCEEeccccCCeeEEEecCCCChHHHHHHHHcCCeEEeHHHHHHHHhhC
Confidence            789999999999999999999999 99999999999999999999999754

>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=98.86  E-value=2e-09  Score=93.05  Aligned_cols=66  Identities=23%  Similarity=0.405  Sum_probs=60.7

Q ss_pred             hcccchhHHHHHh-CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423        514 SKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (655)
Q Consensus       514 sk~~~l~r~L~al-gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~  579 (655)
                      .+..++++++.+| +|||||+++|++|+++|++++++..++.++|.+++|||+++|++|.++|+++.
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            3446678999999 99999999999999999999999999999999999999999999999997654

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=98.72  E-value=2e-08  Score=86.31  Aligned_cols=61  Identities=25%  Similarity=0.440  Sum_probs=56.7

Q ss_pred             chhHHHHHh-CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        518 TFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       518 ~l~r~L~al-gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      .++++..+| +|||||+++|++|+++|++++++..++.++|.+++|||+++|++|..+|+++
T Consensus        13 ~~~~~~~~L~~IpgIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~~   74 (89)
T 1z00_A           13 FVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             HHHHHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            356778888 9999999999999999999999999999999999999999999999999764

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A

Probab=98.70  E-value=4.5e-09  Score=94.53  Aligned_cols=47  Identities=23%  Similarity=0.347  Sum_probs=41.7

Q ss_pred             CCCCeEecccccCccEEEecCC---CCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQK---PGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~---~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||+|.+|||++|||||+|+.   +|+|++||++|||||++|+. +.++.
T Consensus        35 ~~Ggkv~~sVskkT~~lV~g~~~e~~gsKl~kA~~lgI~IvsE~~-l~~~~   84 (113)
T 2cok_A           35 KLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDF-LQDVS   84 (113)
T ss_dssp             HTTCEEESCSTTCSEEECCHHHHHHCCHHHHHHHHTTCCEECTHH-HHHHH
T ss_pred             HCCCEEcCccccCccEEEECCCCCCCChHHHHHHHCCCcEEeHHH-HHHHH
Confidence            7899999999999999999954   88999999999999999995 44443

>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=98.61  E-value=3.5e-08  Score=81.46  Aligned_cols=56  Identities=29%  Similarity=0.478  Sum_probs=52.7

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHH
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHR  581 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~  581 (655)
                      .+|||||+++|++|+++|++++.+..++.++|..++|||+++|.+|..+|+++.+.
T Consensus        17 ~~i~giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~~~~   72 (75)
T 1x2i_A           17 EGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE   72 (75)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC
T ss_pred             cCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCcccc
Confidence            59999999999999999999999999999999999999999999999999876553

>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=98.61  E-value=2.4e-08  Score=80.53  Aligned_cols=50  Identities=20%  Similarity=0.396  Sum_probs=47.9

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHH-HHHHHHHhcCh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT-VKAFIKFINQP  578 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~-A~~I~~~f~~~  578 (655)
                      .|||||+++++.|+++|+|+++|..||.++|.++  +|.+. |+.|++||+.+
T Consensus         8 ~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~v--ig~~~~A~~I~~~l~~~   58 (63)
T 2a1j_A            8 KMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTS   58 (63)
T ss_dssp             TSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHH--HSCHHHHHHHHHHHHCC
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--cCchHHHHHHHHHHhcc
Confidence            8999999999999999999999999999999999  99999 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=98.49  E-value=7.6e-08  Score=80.62  Aligned_cols=50  Identities=20%  Similarity=0.324  Sum_probs=48.8

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +|||||+++|++|+++|++++++..++.++|.+++|||+++|++|.++|+
T Consensus        28 ~I~gIG~~~A~~Ll~~fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~~~   77 (78)
T 1kft_A           28 TIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             GCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999999999999999986

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=98.44  E-value=1.6e-07  Score=79.98  Aligned_cols=52  Identities=19%  Similarity=0.388  Sum_probs=49.1

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHH-HHHHHHHhcChhH
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT-VKAFIKFINQPLH  580 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~-A~~I~~~f~~~~n  580 (655)
                      .|||||++++++|+++|+|+++|..|+.++|.++  ||... |+.|++||+.+..
T Consensus        22 ~IpGIG~kr~~~LL~~FgSl~~i~~AS~eEL~~v--ig~~~~A~~I~~~l~~~~~   74 (84)
T 1z00_B           22 KMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTSFA   74 (84)
T ss_dssp             TCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHH--HSCHHHHHHHHHHHTSBHH
T ss_pred             hCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--hCchHHHHHHHHHHHhhhh
Confidence            8999999999999999999999999999999999  99999 9999999986543

>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=98.30  E-value=5.9e-06  Score=86.29  Aligned_cols=200  Identities=14%  Similarity=0.108  Sum_probs=123.4

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~  197 (655)
                      ..|++|+|+||+-+.+   +|   ++.||    .|+|+|.  ..|.   ..+..  .+ ...+-||+++...+|+.+...
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            4699999999999876   88   78999    6888985  2111   11110  12 356889999988888876443


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhC----C-------CCCCC-
Q psy11423        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI----G-------LSICG-  265 (655)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~----G-------F~~~~-  265 (655)
                                         +++.++.  ...++.|++|++...+ .  .....+..+.|+++    +       +.+++ 
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                               2222222  2357999999998532 2  35677777777665    1       11122 


Q ss_pred             CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCC----CceEeecCCcceeeEEEEEEEEe-
Q psy11423        266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAP----RFALAYKFLSKEALTKIKAINIQ-  340 (655)
Q Consensus       266 ~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~P----rwaiA~Kf~~~~~~T~v~~I~~q-  340 (655)
                      ....+.+.+++.++++...+      -..+|+|+|--+..++-  |   +.+    .| +=+| +.......|.+..+- 
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-LKMK-QFKDAEATIISMTALF  203 (297)
T ss_dssp             CCEEECSHHHHHHHHHHHHH------TTCCSEEEECTTCCCCS--S---BCCTTTTSS-EEEC-CCEEEEEEEEEEEESC
T ss_pred             ceEecCCHHHHHHHHHHHHH------CCCcEEEEECCCCCcCC--C---CCCCCCCCe-EEEC-CCCCEEEEEEEEEeCc
Confidence            02234688999998887643      34699999987655442  3   333    45 3455 345678888888886 


Q ss_pred             --------------------ecC--cceeeeEEEEEEEEECCEEEEEeeCCCHHHHHh
Q psy11423        341 --------------------IGR--TGIITPVALLKPVLIDGITITRATLHNESEIYR  376 (655)
Q Consensus       341 --------------------vGR--TG~itPvA~lePV~l~G~tVsratLhN~~~i~~  376 (655)
                                          -||  +|.+--+..    ...|..+.-.|..+.+..++
T Consensus       204 ~~~~~~~~~~~g~~~r~~~~~G~~~~g~~g~ll~----~~~g~~~~vgtGftd~~~~~  257 (297)
T 1fvi_A          204 KNTNTKTKDNFGYSKRSTHKSGKVEEDVMGSIEV----DYDGVVFSIGTGFDADQRRD  257 (297)
T ss_dssp             C-------------------CCCTTCCCEEEEEE----CSTTCCEEECSSCCHHHHHH
T ss_pred             cccccccccccccccccccCCCcccCCcEEEEEE----ccCCeEEEECCCCCHHHHHH
Confidence                                665  454322211    11265554448888887775

>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=98.14  E-value=3.3e-05  Score=81.05  Aligned_cols=203  Identities=15%  Similarity=0.158  Sum_probs=120.2

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK  193 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~  193 (655)
                      ..|++|+|.||.-+.+...+|. +++.||    .|+|+|+....|..+-..++    +....+-||+++.    ..+|+.
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            3699999999999999888787 689999    68899986654433222221    2478999999994    346665


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhC----CCCCCCCce
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI----GLSICGEYS  268 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~----GF~~~~~~~  268 (655)
                      +...                   +++        ..+.|++|++...++.++ ..+..+..+.|.++    -+.+++.. 
T Consensus        96 l~~r-------------------~~~--------~~~~~~vFDll~~~g~~l~~~pl~eRr~~L~~~~~~~~i~~~~~~-  147 (310)
T 1vs0_A           96 MQNR-------------------GRD--------TRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELL-  147 (310)
T ss_dssp             HHTC-------------------CTT--------SCCEEEEEEEEEETTEECTTSCHHHHHHHHHHHHHHSCCCCCCCC-
T ss_pred             HHhh-------------------ccC--------CcEEEEEEEeEEECCcCcccCCHHHHHHHHHHhccCCcEEECccC-
Confidence            4210                   010        148999999987554332 24677777777654    23333322 


Q ss_pred             eeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-ccee
Q psy11423        269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGII  347 (655)
Q Consensus       269 ~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~i  347 (655)
                       .   .++.++++...+      -..+|+|+|--+..++-  |.  +.+.| +=+| +.......|.+..+.-|| +|.+
T Consensus       148 -~---~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--G~--Rs~~W-lK~K-~~~~~D~vv~G~~~g~G~r~g~~  211 (310)
T 1vs0_A          148 -P---GDGAQAFACSRK------HGWEGVIAKRRDSRYQP--GR--RCASW-VKDK-HWNTQEVVIGGWRAGEGGRSSGV  211 (310)
T ss_dssp             -C---SSHHHHHHHHHH------TTCCEEEEEETTCCCCT--TC--EEEEE-EEEE-SSEEEEEEEEEEEC--------C
T ss_pred             -c---hHHHHHHHHHHH------cCCceEEEeCCCCCcCC--CC--cChHH-hccc-hheEEEEEEEEEEcCCCCccCcc
Confidence             1   135566655432      34799999987755542  21  23333 3455 335667788777766654 3555


Q ss_pred             ee--EEEEEEEEECC-EEEEEe-eCCCHHHHHh
Q psy11423        348 TP--VALLKPVLIDG-ITITRA-TLHNESEIYR  376 (655)
Q Consensus       348 tP--vA~lePV~l~G-~tVsra-tLhN~~~i~~  376 (655)
                      ..  ++..++   +| ..|.++ |..+.+..++
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  233322   23 345566 7788777766

>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=98.14  E-value=2.9e-07  Score=92.15  Aligned_cols=50  Identities=30%  Similarity=0.365  Sum_probs=0.0

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .+|||||++++++|+++|+|+++|..|+.++|.++ |||+++|++|++||+
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            38999999999999999999999999999999999 999999999999986

>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=98.12  E-value=1.1e-06  Score=87.38  Aligned_cols=49  Identities=22%  Similarity=0.388  Sum_probs=46.8

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCH-HHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGS-TTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~-~~A~~I~~~f~  576 (655)
                      .+|||||++++++|+++|+|+++|..|+.++|.++  ||+ ++|++|++||+
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            48999999999999999999999999999999999  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=98.11  E-value=2.5e-06  Score=85.05  Aligned_cols=52  Identities=23%  Similarity=0.451  Sum_probs=50.5

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      +|||||+++|++|+++|++++++..++.++|.+++|||+++|++|++||+++
T Consensus       166 ~i~gVg~~~a~~Ll~~fgs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~~~~  217 (219)
T 2bgw_A          166 SFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP  217 (219)
T ss_dssp             TSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSC
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999999999865

>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=98.08  E-value=4.7e-05  Score=86.03  Aligned_cols=215  Identities=19%  Similarity=0.170  Sum_probs=136.8

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKK----DFIK  193 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~~----~F~~  193 (655)
                      .|++|+|+||.-+.+.+.+|. ++..||+    |+|+|+....|.. +...+     |..+.+-||++.-..    .|+.
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 6999994    9999987654432 12123     334899999999632    6876


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC----
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE----  266 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~----  266 (655)
                      +-...                   +++.+  ......++.|++|++...++ ++ ..+..+..+.|.++--. +..    
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                   11100  00123468999999987655 43 25788888888876322 221    


Q ss_pred             -ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-c
Q psy11423        267 -YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-T  344 (655)
Q Consensus       267 -~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-T  344 (655)
                       ...+.+.+++.++++...+      -..+|+|+|--+..++  .|.  +...| +=+|-........|.+..|--|| +
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             1245788999998887653      2468999997665444  121  23334 34453346788899999998765 5


Q ss_pred             ceeee--EEEEEEEEECCE--EEEEe-eCCCHHHHHhc
Q psy11423        345 GIITP--VALLKPVLIDGI--TITRA-TLHNESEIYRK  377 (655)
Q Consensus       345 G~itP--vA~lePV~l~G~--tVsra-tLhN~~~i~~~  377 (655)
                      |.+..  ++..+|-  +|.  +|-++ |..+-+..+++
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  2333321  243  45565 78888887764

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=98.04  E-value=6.2e-06  Score=87.42  Aligned_cols=100  Identities=15%  Similarity=0.276  Sum_probs=76.7

Q ss_pred             cccC-CCCHHHHHHHHHcCCCCChHHHhc----CChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHH
Q psy11423        460 MNII-GLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGET  534 (655)
Q Consensus       460 l~I~-GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~  534 (655)
                      |-++ |+|..|...|-..-  .++..+-.    ...++|...+|+|+|.+..+..++         .+|  -.|||||+.
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 88888888775432  12222222    456789999999999887776651         111  279999999


Q ss_pred             HHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11423        535 TAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       535 ~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~  573 (655)
                      +|++|+++|||+++++.|+.++|.. +|||++.|..|..
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 9999999998875

>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1

Probab=97.98  E-value=0.00011  Score=78.32  Aligned_cols=230  Identities=16%  Similarity=0.067  Sum_probs=131.7

Q ss_pred             eEEEEEecceeEEEEEEe-CCEEeEEEecCCCCccchhhhhhhhcccCCc---cccc--CCCCceEEEEEEEEeehhhHH
Q psy11423        119 EYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPL---VLNI--KYPPELLEVRCEVLIYKKDFI  192 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~---~l~~--~~~p~~~evRGEv~~~~~~F~  192 (655)
                      .|++|+|+||.-+.+.+. +|. ++..||.    |.|+++-.......|.   .+..  ...|..+.+-||+++....|+
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            699999999999999886 565 6899994    5666653221111111   1110  024668999999999766777


Q ss_pred             HHHHHHHHcC--C----CCCCChhhhHHhHhhhcCcc---cccccceEEEEEeccccc----CCCC----CCCHHHHHHH
Q psy11423        193 KLNKYRYHLG--L----KKFTNPRNAAAGILRQLNPK---INKNKILHFFAHGVGELR----GMNM----PSSHSELLNW  255 (655)
Q Consensus       193 ~~n~~~~~~g--~----~~f~NpRN~aaG~lr~~d~~---~~~~r~L~f~~y~~~~~~----~~~~----~~~~~e~l~~  255 (655)
                      .+........  .    ..+.+-|...     ...+.   .....++.|++|++...+    +.++    .....+..+.
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            6544322100  0    0011111100     00100   123567999999998754    4332    1245566666


Q ss_pred             HHhC--CCC-----CCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        256 YQKI--GLS-----ICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       256 L~~~--GF~-----~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                      |.++  .++     +++ ...+.+.+++.++++...+      -..+|+|+|--+..++.  |..+   .|- =+| +..
T Consensus       177 L~~l~~~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~ds~Y~~--Grr~---~wl-K~K-~~~  242 (348)
T 1a0i_A          177 LPLLQEYFPEIEWQAAE-SYEVYDMVELQQLYEQKRA------EGHEGLIVKDPMCIYKR--GKKS---GWW-KMK-PEN  242 (348)
T ss_dssp             HHHHHHHCTTSEEEECC-EEEESSHHHHHHHHHHHHT------TTCCCEEEECTTCEECS--EEEE---EEE-EES-CCE
T ss_pred             HHHHhhhCCCCeEEEec-cEecCCHHHHHHHHHHHHH------cCCceEEEeCCCCCCCC--CCcc---CcE-EEe-ecc
Confidence            6553  121     222 2345678899998876643      33599999997765552  3221   253 555 445


Q ss_pred             eeeEEEEEEEEeecC---cceeeeEEEEEEEEECCEEEEEeeCCCHHHHHh
Q psy11423        329 EALTKIKAINIQIGR---TGIITPVALLKPVLIDGITITRATLHNESEIYR  376 (655)
Q Consensus       329 ~~~T~v~~I~~qvGR---TG~itPvA~lePV~l~G~tVsratLhN~~~i~~  376 (655)
                      .....|.+..|--||   +|.+....-..   =+|.-+ .+|..+.+..++
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   57665533211   145433 478888776554

>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=97.94  E-value=0.00012  Score=82.76  Aligned_cols=217  Identities=17%  Similarity=0.127  Sum_probs=135.5

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCC-ceEEEEEEEEeeh-----hhH
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPP-ELLEVRCEVLIYK-----KDF  191 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p-~~~evRGEv~~~~-----~~F  191 (655)
                      .|++|+|.||.-+.+.+.+|. ++..||+    |+|+|+....+.. +...+     | ..+.+-||+++-.     ..|
T Consensus       243 ~~~~E~K~DG~R~~i~~~~g~-v~l~SR~----g~~~t~~fPel~~~~~~~l-----~~~~~iLDGElv~~d~~g~~~~F  312 (561)
T 2cfm_A          243 EAEFEIKYDGARVQVHKDGSK-IIVYSRR----LENVTRAIPEIVEALKEAI-----IPEKAIVEGELVAIGENGRPLPF  312 (561)
T ss_dssp             CEEEEEECCSEEEEEEEETTE-EEEECTT----CCBCGGGCHHHHHHHHHHB-----CSSEEEEEEEEEEBCTTSSBCCT
T ss_pred             cEEEEEeEceEEEEEEEECCE-EEEEeCC----CCCchhhhhhHHHHHHHhC-----CCcceEeeeEEEEEcCCCcccCH
Confidence            699999999999999888886 6899995    8999976544321 11122     3 4689999999963     157


Q ss_pred             HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcc--cccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCC---
Q psy11423        192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG---  265 (655)
Q Consensus       192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~--~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~---  265 (655)
                      +.+....                   +++.+.  .....++.|++|++...++.++ ..+..+..+.|.++--+...   
T Consensus       313 ~~L~~r~-------------------~~~~~~~~~~~~~~~~~~vFDlL~l~g~~l~~~pl~eRr~~L~~~~~~~~~i~~  373 (561)
T 2cfm_A          313 QYVLRRF-------------------RRKHNIEEMMEKIPLELNLFDVLYVDGQSLIDTKFIDRRRTLEEIIKQNEKIKV  373 (561)
T ss_dssp             HHHHHHH-------------------HCCSCHHHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCCSSEEE
T ss_pred             HHHHHHh-------------------hcccchhhhcccCceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhCcCCcEEE
Confidence            7654431                   111110  1123479999999987654332 25788888888876322111   


Q ss_pred             -CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-
Q psy11423        266 -EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-  343 (655)
Q Consensus       266 -~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-  343 (655)
                       ....+.+.+++.++++...+      -..+|+|+|--+..++-  |.  +...| +=+|-........|.+..|--|| 
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--GN--RGKKW-LKIKPTMENLDLVIIGAEWGEGRR  442 (561)
T ss_dssp             CCEEEESCHHHHHHHHHHHHH------TTCCEEEEECTTCCCCT--TC--EEEEE-EEECSSCCCEEEEEEEEEECSGGG
T ss_pred             eeeEEcCCHHHHHHHHHHHHH------cCCceeEEeCCCCCCCC--CC--cCCCe-EEEcccCcceeEEEEEEEeCCCCC
Confidence             12246788999998877653      34799999987655542  21  22334 34443334678899898887765 


Q ss_pred             cceeeeE--EEEEEEEECCE--EEEE-eeCCCHHHHHhc
Q psy11423        344 TGIITPV--ALLKPVLIDGI--TITR-ATLHNESEIYRK  377 (655)
Q Consensus       344 TG~itPv--A~lePV~l~G~--tVsr-atLhN~~~i~~~  377 (655)
                      +|.++..  +..+|=  +|.  +|.+ .|..+-+..+++
T Consensus       443 ~g~~g~lllg~~d~~--~~~~~~vgkvgsGftd~~~~~l  479 (561)
T 2cfm_A          443 AHLFGSFILGAYDPE--TGEFLEVGKVGSGFTDDDLVEF  479 (561)
T ss_dssp             TTSEEEEEEEEECTT--TCCEEEEEEECSSCCHHHHHHH
T ss_pred             CCccceEEEEEEeCC--CCeEEEEeEeCCCCCHHHHHHH
Confidence            5655542  233220  132  3444 367777776653

>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=97.93  E-value=1.2e-05  Score=78.69  Aligned_cols=73  Identities=12%  Similarity=0.160  Sum_probs=59.2

Q ss_pred             hhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC---HHHHHhcCHHHHhcCCCCCHHHH
Q psy11423        492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTV  568 (655)
Q Consensus       492 ~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs---l~~l~~as~eeL~~i~GIG~~~A  568 (655)
                      +-..|-||..+....+..            .|  ..|||||+++|.+|+++|++   .+++..++.++|.++||||+++|
T Consensus        55 da~~l~gf~~~~ek~~f~------------~L--~~v~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A  120 (191)
T 1ixr_A           55 EGLSLYGFPDEENLALFE------------LL--LSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLA  120 (191)
T ss_dssp             SCCCEEEESSHHHHHHHH------------HH--HSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHH
T ss_pred             hhHHhhccCCHHHHHHHH------------HH--hcCCCcCHHHHHHHHHhCChHHHHHHHHhCCHHHHHhCCCCCHHHH
Confidence            333477888775543332            22  26999999999999999998   78899999999999999999999


Q ss_pred             HHHHHHhcCh
Q psy11423        569 KAFIKFINQP  578 (655)
Q Consensus       569 ~~I~~~f~~~  578 (655)
                      ++|+..|++.
T Consensus       121 ~rI~~~lk~k  130 (191)
T 1ixr_A          121 ERIALELKGK  130 (191)
T ss_dssp             HHHHHHHTTT
T ss_pred             HHHHHHHHHh
Confidence            9999988653

>3qwu_A DNA ligase; structural genomics, PSI-2, midwest center for structural GE MCSG; HET: DNA ADN; 2.35A {Aquifex aeolicus}

Probab=97.92  E-value=8.6e-05  Score=79.12  Aligned_cols=143  Identities=21%  Similarity=0.205  Sum_probs=98.6

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchh---hhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENI---TTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKL  194 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDv---T~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~  194 (655)
                      -.|++|.|+||-.+.+.|-+|+ +.|.||| |..   +   |..++.+...  .+.. ++| .+.+-||++.+...|.  
T Consensus        73 ~~~~veEKLDG~NVRi~~~dG~-ilA~TRg-G~i---cP~tT~r~~~~~~~--~f~~-~~P-~l~LdGEl~g~~npy~--  141 (370)
T 3qwu_A           73 APFWVEEKVDGYNTRIFKYGDN-YYALSRG-GFI---CPFTTDRLPDLIDL--RILD-ENP-DLVICAEVAGPENPYI--  141 (370)
T ss_dssp             SCEEEEEECSSEEEEEEEETTE-EEEECTT-SCB---CHHHHHHHHHHCCC--HHHH-HCT-TEEEEEEEECTTCSSC--
T ss_pred             CcEEEEEeeCCeEEEEEEECCE-EEEEcCC-Ccc---cCcchhhhhhhcCc--hhhh-cCC-CeEEEEEEEcCCCCcc--
Confidence            3799999999999999889998 5899997 322   2   4444444322  2322 244 6999999998765542  


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCCCCCcee--eC-
Q psy11423        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSV--LS-  271 (655)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~~~~~~~--~~-  271 (655)
                            .+..+|                   ...++.|++|+|.+.+... +-+..+.+++|.++|++.++....  +. 
T Consensus       142 ------~~s~~y-------------------~~~~i~F~VFDV~d~~~~~-~L~~~eR~~ll~~~~lp~V~ii~~~~~~~  195 (370)
T 3qwu_A          142 ------EESPPY-------------------VKEDVQLFVFDFMKKNEQG-FLSQEEKMELIEKYNLPHVEILGRFTASE  195 (370)
T ss_dssp             ------SCCCTT-------------------CCSSCEEEEEEEEETTCCS-CCCHHHHHHHHHHHTCCBCCEEEEECSSH
T ss_pred             ------ccCCcc-------------------cccCceEEEEeCccccCCC-cCCHHHHHHHHHHCCCCCccEEEEeCCCC
Confidence                  011111                   1347999999998753322 358899999999999998875433  34 


Q ss_pred             -CHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423        272 -GVNKLIEFYKKINIKRFNLPYEIDGVVYKINC  303 (655)
Q Consensus       272 -~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~  303 (655)
                       +.+++.++++++.+.      .--|||+|-.+
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             466777777777643      35799999876

>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=97.83  E-value=1.4e-05  Score=79.07  Aligned_cols=72  Identities=17%  Similarity=0.218  Sum_probs=59.5

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC---HHHHHhcCHHHHhcCCCCCHHH
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTT  567 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs---l~~l~~as~eeL~~i~GIG~~~  567 (655)
                      +|-..|-||-.+....+..            .|.  .|+|||+++|.+|+++|++   .+++..++.++|.++||||+++
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------------ELI--KTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT  120 (203)
T ss_dssp             TTEEEEEEESSHHHHHHHH------------HHH--HSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHH
T ss_pred             ehhhhhhccCCHHHHHHHH------------HHh--cCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence            3334488888776655443            222  3999999999999999999   8899999999999999999999


Q ss_pred             HHHHHHHhc
Q psy11423        568 VKAFIKFIN  576 (655)
Q Consensus       568 A~~I~~~f~  576 (655)
                      |++|+..|+
T Consensus       121 A~rI~~elk  129 (203)
T 1cuk_A          121 AERLIVEMK  129 (203)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998875

>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A*

Probab=97.82  E-value=0.00018  Score=82.42  Aligned_cols=217  Identities=14%  Similarity=0.100  Sum_probs=134.7

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCC-ceEEEEEEEEeehh------h
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPP-ELLEVRCEVLIYKK------D  190 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p-~~~evRGEv~~~~~------~  190 (655)
                      .|++|+|+||.-+.+.+.+|. ++..||    .|+|+|+....+.. +...+     | ..+.+-||+++-..      .
T Consensus       274 ~~~~E~K~DG~R~qi~~~g~~-v~l~SR----~g~~~t~~fP~l~~~~~~~l-----~~~~~iLDGElv~~d~~~g~~l~  343 (621)
T 2hiv_A          274 NAIVDYKYDGERAQIHKKEDK-IFIFSR----RLENITSQYPDVVDYVSKYI-----EGKEFIIEGEIVAIDPESGEMRP  343 (621)
T ss_dssp             CEEEEEECSSEEEEEEEETTE-EEEECT----TCCBCGGGCHHHHHHHHHHB-----CCSSEEEEEEEEEBCTTTCCBCC
T ss_pred             cEEEEEEEcceeEEEEEcCCE-EEEEcC----CCcCcHhhhhhHHHHHHHhC-----CCcCeEEeEEEEEeecCCCCcCC
Confidence            699999999999999887776 699999    58999976554321 11122     3 46899999999641      5


Q ss_pred             HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC---
Q psy11423        191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---  266 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~---  266 (655)
                      |+.+...+.+      .+    +.        ......++.|++|++...++.++ ..+..+..+.|.++--+. ..   
T Consensus       344 F~~L~~r~~~------~~----~~--------~~~~~~~v~~~vFDlL~l~G~~l~~~pl~eRr~~L~~~~~~~-~~i~~  404 (621)
T 2hiv_A          344 FQELMHRKRK------SD----IY--------EAIKEYPVNVFLFDLMYYEDVDYTTKPLEARRKLLESIVKPN-DYVKI  404 (621)
T ss_dssp             THHHHHHHHC------SC----HH--------HHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCC-SSEEE
T ss_pred             HHHHhhhccc------cc----hh--------hhcccCceEEEEEeccccCCCccccCCHHHHHHHHHHHhCcC-CcEEE
Confidence            7766433100      00    00        01123479999999987554332 257888888888763221 11   


Q ss_pred             --ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCCc-----ceeeEEEEEE
Q psy11423        267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKAI  337 (655)
Q Consensus       267 --~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~I  337 (655)
                        ...+.+.+++.++++...+      -..+|+|+|--  +..++-  |.  +...| +=+|-..     ......|.+.
T Consensus       405 ~~~~~~~~~~~~~~~~~~~~~------~g~EGlv~K~~~~ds~Y~~--G~--Rs~~W-lK~K~~~~~~~~dt~D~vViG~  473 (621)
T 2hiv_A          405 AHHIQANNVEDLKSFFYRAIS------EGGEGVMVKAIGKDAIYQA--GA--RGWLW-IKLKRDYQSEMADTVDLVVVGG  473 (621)
T ss_dssp             CCEEEESSHHHHHHHHHHHHH------TTCCEEEEECCSTTCCCCT--TC--EEEEE-EEEETTCTTSSCEEEEEEEEEE
T ss_pred             eeeEEeCCHHHHHHHHHHHHh------cCCceEEEEecCCCCCccC--CC--cCCCe-EEEechhccCcCceeEEEEEEE
Confidence              2235688899998887653      34799999986  544431  21  22334 3455433     3678889888


Q ss_pred             EEeecC-cceeeeEE--EEEEEEECCE--EEEE-eeCCCHHHHHhc
Q psy11423        338 NIQIGR-TGIITPVA--LLKPVLIDGI--TITR-ATLHNESEIYRK  377 (655)
Q Consensus       338 ~~qvGR-TG~itPvA--~lePV~l~G~--tVsr-atLhN~~~i~~~  377 (655)
                      .|--|| +|.++..-  ..+|=  +|.  +|.+ .|..+-+..+++
T Consensus       474 ~~g~Gkr~g~~g~lllg~~d~~--~~~l~~vgkvgtGftd~~~~~l  517 (621)
T 2hiv_A          474 FYGKGKRGGKISSLLMAAYNPK--TDSFESVCKVASGFSDEQLDEL  517 (621)
T ss_dssp             EECSGGGTTSEEEEEEEEEETT--TTEEEEEEEECBSCCHHHHHHH
T ss_pred             EcCCCCCCCcccceEEEEEeCC--CCeEEEEeeeCCCCCHHHHHHH
Confidence            887764 56665432  33330  133  3444 467777766643

>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=97.81  E-value=0.00033  Score=81.03  Aligned_cols=220  Identities=15%  Similarity=0.137  Sum_probs=132.6

Q ss_pred             ceEEEEEecceeEEEEEE-eCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCCceEEEEEEEEeeh------h
Q psy11423        118 IEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYK------K  189 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~------~  189 (655)
                      ..|++|+|.||.-+.+.+ .+|. ++..||    .|+|+|+....+.. ++..+..  -...+.+-||+++-.      .
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--SVTSFILDTEAVAWDREKKQIQ  402 (688)
T ss_dssp             SCEEEEEEESSEEEEEEECTTSC-EEEECT----TSCBCTTTCHHHHHTSGGGBCT--TCCCEEEEEEEEEECTTTCSBC
T ss_pred             CeEEEEEccccEeEEEEEcCCCe-EEEEeC----CCCcccccchHHHHHHHHhhcc--CCCCeEEeEEEEEEeCCCCCcC
Confidence            469999999999999988 4665 689999    68899976654432 3322211  023689999999943      2


Q ss_pred             hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc-
Q psy11423        190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY-  267 (655)
Q Consensus       190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~-  267 (655)
                      .|+.+...    .       |..+        +......++.|++|++...++.++ ..+..+..+.|.++--+..... 
T Consensus       403 ~F~~L~~r----~-------r~~~--------~~~~~~~~v~~~vFDlL~l~G~~l~~~Pl~eRr~~L~~~~~~~~~~i~  463 (688)
T 1x9n_A          403 PFQVLTTR----K-------RKEV--------DASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFV  463 (688)
T ss_dssp             CHHHHTTS----C-------SSCC--------CGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBTTTEE
T ss_pred             CHHHHHHH----h-------hccc--------chhhcccceEEEEEechhhcCCccccCCHHHHHHHHHHhhccCCCcEE
Confidence            57654211    0       0000        111124579999999986544332 2578888899988743332222 


Q ss_pred             ----eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCCc-----ceeeEEEEE
Q psy11423        268 ----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKA  336 (655)
Q Consensus       268 ----~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~  336 (655)
                          ..+.+.+++.++++...+      -..+|+|+|--  +..++-  |  .+...| +=+|-..     .+....|.+
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                224678889988876653      34799999996  433331  2  123334 3444331     356677888


Q ss_pred             EEEeecC-cceeeeEE--EEEEEEECCE--EEEEe-eCCCHHHHHh
Q psy11423        337 INIQIGR-TGIITPVA--LLKPVLIDGI--TITRA-TLHNESEIYR  376 (655)
Q Consensus       337 I~~qvGR-TG~itPvA--~lePV~l~G~--tVsra-tLhN~~~i~~  376 (655)
                      ..|--|| +|.++..-  ..+|-  +|.  +|.++ |.++-+..++
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            8877665 56555432  22220  132  44453 5677777665

>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens}

Probab=97.75  E-value=0.00069  Score=76.85  Aligned_cols=215  Identities=15%  Similarity=0.166  Sum_probs=134.9

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhh-hhhcc-cCCcccccCCCCceEEEEEEEEeehh------
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIH-KIPLVLNIKYPPELLEVRCEVLIYKK------  189 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~-~iP~~l~~~~~p~~~evRGEv~~~~~------  189 (655)
                      -.|++|+|+||.-+.+.+.+|. ++..||+    |+|+|.- +..+. .+|..++.   ...+.+-||++.-..      
T Consensus       247 ~~~~~E~K~DG~R~qih~~g~~-v~l~SR~----g~~~~p~~~~~l~~~l~~~~~~---~~~~iLDGElv~~d~~~g~~~  318 (579)
T 3l2p_A          247 NGMFSEIKYDGERVQVHKNGDH-FSYFSRS----LKPVLPHKVAHFKDYIPQAFPG---GHSMILDSEVLLIDNKTGKPL  318 (579)
T ss_dssp             TCEEEEECCCSEEEEEEEETTE-EEEECTT----SCBCCGGGTTTGGGTHHHHSTT---CSEEEEEEEEEEBCTTTCCBC
T ss_pred             CCeEEEEccCcEEEEEEEECCE-EEEECCC----CCccChhHHHHHHHHHHHhcCc---CCceEEEeEEEEEeCCCCccc
Confidence            3689999999999998887775 7999995    7787533 22221 13333321   236899999998542      


Q ss_pred             hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCce
Q psy11423        190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS  268 (655)
Q Consensus       190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~  268 (655)
                      .|+.+..           +.|+.            ....++.|++|++...++.++ ..+..+..+.|.++--+.+....
T Consensus       319 ~F~~L~~-----------~~~~~------------~~~~~v~~~vFDlL~l~G~~L~~~Pl~eRr~~L~~~~~~~~~~i~  375 (579)
T 3l2p_A          319 PFGTLGV-----------HKKAA------------FQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIM  375 (579)
T ss_dssp             CGGGGSH-----------HHHHH------------CSSCCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHCCCBTTTEE
T ss_pred             CHHHHHH-----------Hhhhh------------cccCCeEEEEEEeeccCCCccccCCHHHHHHHHHHHhhcCCCeEE
Confidence            4543311           01110            112479999999987554332 25788999999887544433222


Q ss_pred             -----eeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC-------cceeeEEEEE
Q psy11423        269 -----VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA  336 (655)
Q Consensus       269 -----~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~  336 (655)
                           .+.+.+++.++++...+.      ...|+|+|--+..++-  |.   . .| +=+|-.       .......|.+
T Consensus       376 ~~~~~~~~~~~~~~~~~~~a~~~------g~EGlv~K~~ds~Y~~--Gr---r-~W-lK~K~~y~~~g~~~~t~D~vViG  442 (579)
T 3l2p_A          376 FSEMKRVTKALDLADMITRVIQE------GLEGLVLKDVKGTYEP--GK---R-HW-LKVKKDYLNEGAMADTADLVVLG  442 (579)
T ss_dssp             ECCEEEECSHHHHHHHHHHHHHT------TCCCEEEEESSCCCCT--TC---E-EE-EEECTTTCC---CCEEEEEEEEE
T ss_pred             EeeeEEcCCHHHHHHHHHHHHHh------CCCceEEecCcCCCCC--CC---e-ee-EEEechhhccccccccccEEEEE
Confidence                 356788888888766532      4699999987765542  22   1 23 344432       1466778888


Q ss_pred             EEEeec-CcceeeeE--EEEEEEEECC--EEEEEe-eCCCHHHHHhcC
Q psy11423        337 INIQIG-RTGIITPV--ALLKPVLIDG--ITITRA-TLHNESEIYRKN  378 (655)
Q Consensus       337 I~~qvG-RTG~itPv--A~lePV~l~G--~tVsra-tLhN~~~i~~~~  378 (655)
                      ..|--| |+|.++..  +..+|-  +|  ++|-++ |.++-+.++++.
T Consensus       443 ~~~G~Gkr~g~~g~lllg~~d~~--~~~l~~vgkvgtGftd~~l~~l~  488 (579)
T 3l2p_A          443 AFYGQGSKGGMMSIFLMGCYDPG--SQKWCTVTKCAGGHDDATLARLQ  488 (579)
T ss_dssp             EECCCTTSCSSCCEEEEEEECTT--TSSEEEEEEECTTCCHHHHHHTT
T ss_pred             EEeCCCCCCCceeEEEEEEEeCC--CCeEEEecCccCCCCHHHHHHHH
Confidence            887766 56666643  444431  23  345565 889999888863

>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=97.73  E-value=2e-05  Score=72.21  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=46.0

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++..+|++++++|||++..|+|+++|+++||+|++++.|.+.+.
T Consensus        47 ~~Gg~v~~~~s~~~ThLI~~~~~~~K~~~A~~~gi~IV~~~Wl~d~~~   94 (129)
T 2d8m_A           47 ELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGRIVRKEWVLDCHR   94 (129)
T ss_dssp             HTTEEEESSCCTTCCEEEESSSSCHHHHHHHHHTCEEEETHHHHHHHH
T ss_pred             HcCCEEeCCcCCCCeEEEecCCCChHHHHHHHCCCcEecHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999885

>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=97.53  E-value=7.2e-05  Score=79.84  Aligned_cols=51  Identities=22%  Similarity=0.329  Sum_probs=48.4

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      .||.||++.|++|.++|||++++.+|+.+||.+++|||++.|+.|++-+..
T Consensus       319 ~IPrl~~~iae~Lv~~FGsLq~Il~AS~eEL~~VeGIGe~rAr~IregL~r  369 (377)
T 3c1y_A          319 TVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISS  369 (377)
T ss_dssp             HTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhccCccHHHHHHHHHHHHH
Confidence            699999999999999999999999999999999999999999999987653

>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=97.43  E-value=0.00094  Score=70.64  Aligned_cols=152  Identities=13%  Similarity=0.011  Sum_probs=92.2

Q ss_pred             ceEEEEEecceeEEEEEEe---CCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKL  194 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~  194 (655)
                      ..|++|+|.||+-+.+...   ++.-+...||+    |+++|.-.   +.++..     .+....+-||+++...     
T Consensus        75 ~~y~ve~K~DG~R~ll~~~~~~g~g~v~L~sR~----~~~~t~~f---p~~~~~-----~~~~~vLDGElv~~~~-----  137 (330)
T 1ckm_A           75 NKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRA----MTVYLLPF---KNIPRV-----LFQGSIFDGELCVDIV-----  137 (330)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTEEEEEEECTT----CCEEECCC---SCCCTT-----GGGCEEEEEEEEEETT-----
T ss_pred             CCEEEEECcceEEEEEEEEecCCCCEEEEEeCC----CCEEeccC---hhhhhc-----cCCCeeEEEEEEEEcC-----
Confidence            3699999999999988776   22457899995    78888632   223211     2446899999998431     


Q ss_pred             HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhC--CC---CCCCC-c
Q psy11423        195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI--GL---SICGE-Y  267 (655)
Q Consensus       195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~--GF---~~~~~-~  267 (655)
                                         .|             .+.|++|++...++.++ .....+.++.|+++  +.   ...+. .
T Consensus       138 -------------------~~-------------~~~f~vFDlL~~~G~dl~~~pl~eRr~~L~~~l~~~~~~~~~~~~i  185 (330)
T 1ckm_A          138 -------------------EK-------------KFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAIL  185 (330)
T ss_dssp             -------------------TT-------------EEEEEEEEEEEETTEECTTSCHHHHHHHHHHHHTTCCCCTTSSSEE
T ss_pred             -------------------CC-------------eEEEEEEeeeeeCCcccccCCHHHHHHHHHHHHhhhcccCCCCeEE
Confidence                               01             27899999987655433 24677888888764  21   11111 1


Q ss_pred             eeeC--CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        268 SVLS--GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       268 ~~~~--~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                      ....  .. ++.++++++..... ..|..||+|+|-.+..++-  |   +...| +=||.+
T Consensus       186 ~~~~~~~~-~~~~~~~~~~~~~~-~~yg~EGlI~K~~dspY~~--G---r~~~~-lKwK~~  238 (330)
T 1ckm_A          186 RYKEWIPL-EHPTIIKDHLKKAN-AIYHTDGLIIMSVDEPVIY--G---RNFNL-FKLKPG  238 (330)
T ss_dssp             EECCCEET-TCHHHHHHHHHHHH-HHSCEEEEEEEESSSCCCC--E---EEEEE-EEECST
T ss_pred             EEEEEEeh-hHHHHHHHHHHHHh-ccCCCceEEEeeCCCcccC--C---CccCe-EEEEeC
Confidence            1111  12 34444433222211 1468999999998866552  2   33456 777764

>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens}

Probab=97.31  E-value=0.00055  Score=63.44  Aligned_cols=117  Identities=12%  Similarity=0.134  Sum_probs=70.7

Q ss_pred             EEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-------CCcccccCCCCceEEEEEEEEeehhhHH
Q psy11423        120 YIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-------IPLVLNIKYPPELLEVRCEVLIYKKDFI  192 (655)
Q Consensus       120 ~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-------iP~~l~~~~~p~~~evRGEv~~~~~~F~  192 (655)
                      |++|+|.||.-+.+.+.+|+ ++..||    -|+|+|+....+..       |...+..  ......+-||++.-..+  
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            57899999999999887775 799999    68999997654321       2222221  13579999999995321  


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhC
Q psy11423        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI  259 (655)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~  259 (655)
                                ...|. ++...   ++..........++.|++|++...++.++ ..+..+..+.|.++
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   01111111123478999999987655433 24778888888776

>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=97.21  E-value=0.00048  Score=68.33  Aligned_cols=74  Identities=11%  Similarity=0.152  Sum_probs=54.5

Q ss_pred             hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC---HHHHHhcCHHHHhcCCCCCHH
Q psy11423        490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGST  566 (655)
Q Consensus       490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs---l~~l~~as~eeL~~i~GIG~~  566 (655)
                      .||-..|=||..+....+            -+.|.  .++|||+++|.+|++.|+.   ..++...+.+.|.++||||++
T Consensus        69 RED~~~LyGF~~~~Er~l------------f~~L~--sv~GIGpk~A~~Ils~~~~~~l~~aI~~~d~~~L~~vpGIG~K  134 (212)
T 2ztd_A           69 REDSMTLYGFPDGETRDL------------FLTLL--SVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKR  134 (212)
T ss_dssp             ETTEEEEEEESSHHHHHH------------HHHHH--TSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHH
T ss_pred             ecCCcceEecCcHHHHHH------------HHHhc--CcCCcCHHHHHHHHHhCCHHHHHHHHHhCCHHHHhhCCCCCHH
Confidence            455566666766433222            23333  4999999999999999984   234566789999999999999


Q ss_pred             HHHHHHHHhcC
Q psy11423        567 TVKAFIKFINQ  577 (655)
Q Consensus       567 ~A~~I~~~f~~  577 (655)
                      +|++|+.-+.+
T Consensus       135 tA~rIi~elk~  145 (212)
T 2ztd_A          135 GAERMVLELRD  145 (212)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHHHH
Confidence            99999876654

>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=97.12  E-value=0.00026  Score=58.91  Aligned_cols=53  Identities=19%  Similarity=0.284  Sum_probs=47.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ....|+|+|++++.+|++.  ..++.+|+..+.++|..++|+|++.++.|++.+.
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  2578999999999999999999999999988763

>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=97.12  E-value=5.9e-05  Score=76.30  Aligned_cols=58  Identities=21%  Similarity=0.260  Sum_probs=0.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      ..+.|+|+||+++.+|++.| +.++.+|...+.++|..++|||+|++++|+..++....
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 58999998889999999999999999999998875443

>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=97.08  E-value=8e-05  Score=75.36  Aligned_cols=51  Identities=22%  Similarity=0.300  Sum_probs=0.0

Q ss_pred             hCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +.|||||+++|++|+++ |++++.|..++.++|.+++|||+++|+.|..+++
T Consensus        18 ~~IpGIGpk~a~~Ll~~gf~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~l~   69 (241)
T 1vq8_Y           18 TDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVG   69 (241)
T ss_dssp             ----------------------------------------------------
T ss_pred             hcCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHhccCCCHHHHHHHHHHHH
Confidence            36889999999888887 8889999888889999999999999999888765

>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=97.08  E-value=0.00073  Score=55.32  Aligned_cols=56  Identities=18%  Similarity=0.367  Sum_probs=50.3

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      +.+..+++|+|+.++.+|.++|+ .|+.||-.++..+|..+.|+++..|++|+..-+
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 899999999999999999999999999987654

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=97.08  E-value=0.00073  Score=76.74  Aligned_cols=81  Identities=15%  Similarity=0.284  Sum_probs=63.5

Q ss_pred             hccccCCcHHHHHHHHHHHHHhcccch--------hHHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhc-CHHHHhcCCC
Q psy11423        493 LLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELANY-FKNLECMFKA-TEEQLLNIPK  562 (655)
Q Consensus       493 L~~l~GfG~Ksa~nll~~I~~sk~~~l--------~r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~a-s~eeL~~i~G  562 (655)
                      +..+||+|++.+.++.+.++.-....+        .-|+.-+.|+|||+++|++|.+. |.|++.|..| ....|.+++|
T Consensus        59 ~~~lp~iG~~~~~~i~~~v~~g~~~~~~~~~~~~~~~~~~L~~v~GVGpk~A~~i~~~G~~s~edL~~a~~~~~L~~~~G  138 (578)
T 2w9m_A           59 FTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKG  138 (578)
T ss_dssp             CCSSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTTSTTCCHHHHHHHHHTTCCSHHHHHHHHHHTTTTTSTT
T ss_pred             hhhcCCCChhHHHHHHHHHcCChHHHHHHHhhhhHHHHHHHhCCCCcCHHHHHHHHHcCCCCHHHHHHHHhhCccccCCC
Confidence            999999999999888887754221111        12444469999999999999876 7799999986 4458999999


Q ss_pred             CCHHHHHHHHH
Q psy11423        563 IGSTTVKAFIK  573 (655)
Q Consensus       563 IG~~~A~~I~~  573 (655)
                      ||+|++++|..
T Consensus       139 iG~Ktaq~I~~  149 (578)
T 2w9m_A          139 FGAKSAATILE  149 (578)
T ss_dssp             CCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            99999999954

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=97.06  E-value=0.00031  Score=79.82  Aligned_cols=57  Identities=25%  Similarity=0.167  Sum_probs=50.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSK  515 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk  515 (655)
                      ..+.|+|+|||++.+|++. .+.|++||.. +..+.|..++|||+|++++|+.+|+...
T Consensus        98 ~L~~v~GVGpk~A~~i~~~-G~~s~edL~~a~~~~~L~~~~GiG~Ktaq~I~~~l~~~~  155 (578)
T 2w9m_A           98 DLLGVRGLGPKKIRSLWLA-GIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLF  155 (578)
T ss_dssp             HHTTSTTCCHHHHHHHHHT-TCCSHHHHHHHHHHTTTTTSTTCCHHHHHHHHHHHHHHH
T ss_pred             HHhCCCCcCHHHHHHHHHc-CCCCHHHHHHHHhhCccccCCCCCHHHHHHHHHHHHHHH
Confidence            4688999999999999999 5799999998 4677999999999999999999998543

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=97.05  E-value=0.00026  Score=58.49  Aligned_cols=44  Identities=20%  Similarity=0.333  Sum_probs=33.6

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .|||||+++|++|.+++      ..++.++|.+++|+|+++++.|..|++
T Consensus        31 ~ipGIG~~~A~~Il~~r------~~~s~~eL~~v~Gig~k~~~~i~~~l~   74 (75)
T 2duy_A           31 ALPGIGPVLARRIVEGR------PYARVEDLLKVKGIGPATLERLRPYLR   74 (75)
T ss_dssp             TSTTCCHHHHHHHHHTC------CCSSGGGGGGSTTCCHHHHHHHGGGEE
T ss_pred             hCCCCCHHHHHHHHHHc------ccCCHHHHHhCCCCCHHHHHHHHHhcc
Confidence            46666666666666665      236778899999999999999988864

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=96.96  E-value=0.00094  Score=56.86  Aligned_cols=52  Identities=10%  Similarity=0.092  Sum_probs=47.4

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..|+|+|++++.+|++.-  .++.+++..+.++|..++|+|++.|+.|++.++.
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            489999999999999873  5789999999999999999999999999998864

>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=96.90  E-value=0.00054  Score=77.75  Aligned_cols=58  Identities=21%  Similarity=0.229  Sum_probs=51.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSK  515 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk  515 (655)
                      ..+.|+|+|||++.++++...+.+++||.. +..++|.++||||+|++++|+.+|+...
T Consensus        94 ~l~~v~GvGpk~A~~~~~~lg~~~~~~l~~a~~~~~l~~~~GiG~k~a~~i~~~l~~~~  152 (575)
T 3b0x_A           94 EVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQ  152 (575)
T ss_dssp             HHHTSTTTCHHHHHHHHHTSCCCSHHHHHHHHHHTGGGGSTTCCHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCcCHHHHHHHHHhcCCCCHHHHHHHHHcCCcccCCCCCccHHHHHHHHHHHHH
Confidence            468899999999999999966899999998 6678899999999999999998887543

>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=96.90  E-value=0.0021  Score=72.88  Aligned_cols=95  Identities=19%  Similarity=0.214  Sum_probs=69.2

Q ss_pred             ChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc--------chhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHH
Q psy11423        481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT--------TFSRFIYALGIRHVGETTAKELANY--FKNLECMF  550 (655)
Q Consensus       481 ~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~--------~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~  550 (655)
                      .+.++.....+.+..|||+|++.+.++.+-++.-.-.        ...-|..-+.|+|||+++|.++...  +.+++.|.
T Consensus        43 ~i~~~~~~~~~~~~~lp~iG~~~~~~i~~~v~~g~~~l~~~~~~~~~~~~~~l~~v~GvGpk~A~~~~~~lg~~~~~~l~  122 (575)
T 3b0x_A           43 PIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLK  122 (575)
T ss_dssp             CHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHHTSTTTCHHHHHHHHHTSCCCSHHHHH
T ss_pred             chhhHhhcchhHHHhCCCCCHHHHHHHHHHHHcCcHHHHhhhhhhhHHHHHHHhcCCCcCHHHHHHHHHhcCCCCHHHHH
Confidence            4444443321229999999999999998887652211        1123444469999999999999886  57899998


Q ss_pred             hcC-HHHHhcCCCCCHHHHHHHHHHh
Q psy11423        551 KAT-EEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       551 ~as-~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+- ..+|.++||||+++|++|..-+
T Consensus       123 ~a~~~~~l~~~~GiG~k~a~~i~~~l  148 (575)
T 3b0x_A          123 AALDRGDLTRLKGFGPKRAERIREGL  148 (575)
T ss_dssp             HHHHHTGGGGSTTCCHHHHHHHHHHH
T ss_pred             HHHHcCCcccCCCCCccHHHHHHHHH
Confidence            763 3579999999999999996533

>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=96.87  E-value=0.001  Score=54.27  Aligned_cols=54  Identities=11%  Similarity=0.281  Sum_probs=48.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      ...|+|+|++++.+|++.  ..++.+|+..+.++|..++|+|++.|+.|+..++..
T Consensus        16 L~~i~giG~~~a~~Ll~~--fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~   69 (75)
T 1x2i_A           16 VEGLPHVSATLARRLLKH--FGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAP   69 (75)
T ss_dssp             HTTSTTCCHHHHHHHHHH--HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSC
T ss_pred             HcCCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCc
Confidence            457999999999999985  257899999999999999999999999999988753

>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=96.85  E-value=0.001  Score=56.99  Aligned_cols=52  Identities=10%  Similarity=0.092  Sum_probs=46.8

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..|+|+|++++.+|++.-  .++.+|+..+.++|..++|+|++.|+.|++.+..
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  4789999999999999999999999999998853

>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=96.84  E-value=0.0009  Score=69.76  Aligned_cols=48  Identities=19%  Similarity=0.359  Sum_probs=45.8

Q ss_pred             CCCCeEecccc-cCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFIS-KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVs-k~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++.++++ ++|++||+++..|+|+++|+++||+|++++.|.+.+.
T Consensus       224 ~~GG~~~~~ls~~~~THLI~~~~~g~K~~~A~~~gi~IV~~~Wl~dsi~  272 (298)
T 3olc_X          224 KHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIE  272 (298)
T ss_dssp             HTTCEECSSCCTTTCCEEECSSSCSHHHHHHHHTTCEEECHHHHHHHHH
T ss_pred             HcCCEEeceecCCCceEEEEeCCCchHHHHHHHCCCeEEeHHHHHHHHH
Confidence            78999999999 8999999999999999999999999999999999885

>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=96.31  E-value=0.0049  Score=50.39  Aligned_cols=53  Identities=13%  Similarity=0.241  Sum_probs=48.8

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      |++.|+++..+.+|+++|+ .|+.++-..+.++|..++||.+.++++|.+.-.+
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            6788999999999999997 8999999999999999999999999999887643

>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=96.30  E-value=0.0034  Score=67.44  Aligned_cols=48  Identities=23%  Similarity=0.297  Sum_probs=45.7

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHc-CCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL-NIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~l-gi~ii~e~~f~~~l~  647 (655)
                      .+||+++++++++|++|||+...|+|+.+|+++ ||+|++++.|.+.+.
T Consensus       311 ~lGa~v~~~vs~~vTHLVa~~~~t~K~~~A~~~~~I~IV~~~Wl~~c~~  359 (372)
T 3ef0_A          311 SFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLS  359 (372)
T ss_dssp             HTTCEEESSSSSCCSEEEECSCCCHHHHHHHHSSSCCEEEHHHHHHHHH
T ss_pred             HcCCEEeCcCCCCceEEEEcCCCchHHHHHHhcCCCEEEcHHHHHHHHH
Confidence            889999999999999999999889999999999 899999999999874

>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=96.25  E-value=0.0038  Score=68.29  Aligned_cols=48  Identities=23%  Similarity=0.297  Sum_probs=45.6

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHc-CCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKL-NIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~l-gi~ii~e~~f~~~l~  647 (655)
                      .+||++.++|+++|++|||+...|+|+.+|+++ ||+|++++.|.+.+.
T Consensus       381 ~lGa~~~~~vs~~vTHLVa~~~~t~K~~~A~~~g~IkIVs~~WL~dcl~  429 (442)
T 3ef1_A          381 SFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLS  429 (442)
T ss_dssp             TTTCEECSSSSSCCSEEEECSCCCHHHHHHHHHSSSEEEEHHHHHHHHH
T ss_pred             HcCCEEeCCCCCCceEEEeCCCCCHHHHHHHhcCCCEEEeHHHHHHHHH
Confidence            899999999999999999999889999999999 599999999999875

>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=96.08  E-value=0.0047  Score=55.30  Aligned_cols=50  Identities=24%  Similarity=0.281  Sum_probs=46.8

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      |+|+.++.+|.++|+ .|+.+|...+.++|..++|+++.+|++|+++..+.
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

>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=96.04  E-value=0.026  Score=59.66  Aligned_cols=137  Identities=13%  Similarity=0.059  Sum_probs=82.7

Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccch--------hhhhhh
Q psy11423         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGEN--------ITTNIH  160 (655)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeD--------vT~n~~  160 (655)
                      .-||.|-++    ..|++.+... + .....++++.|+||-++++.+.+|. +.+.|||--. -.+        +++...
T Consensus         6 Y~si~n~~~----~~~i~~~~~~-~-l~~~~vvvtEKlDG~N~~i~~~~~~-i~~~sR~~~l-~~~~~~~~~~~~~~~~~   77 (335)
T 2hvq_A            6 YSSLENHYN----SKFIEKLYSL-G-LTGGEWVAREXIHGTNFSLIIERDK-VTCAKRTGPI-LPAEDFFGYEIILKNYA   77 (335)
T ss_dssp             CCCCEETTC----HHHHHHHHHT-T-CSCSCEEEEECCSSEEEEEEEETTE-EEEEETTEEC-CTTCCCTTTHHHHHHHH
T ss_pred             CCCCcchhh----hhHHHHHHhh-c-cCCCcEEEEEEecCcceEEEEECCE-EEEecCCccc-CCccccchHHHHHHHHH
Confidence            446777775    2345554321 1 1134799999999999999998888 5799998333 222        555542


Q ss_pred             -hcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecc-
Q psy11423        161 -IIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVG-  238 (655)
Q Consensus       161 -~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~-  238 (655)
                       .|..+-..|... .+..+.|-||++=+.                             -|.+-..  . +..|++|+|- 
T Consensus        78 ~~i~~L~~~l~~~-~~~~~~i~GE~~G~~-----------------------------Iq~~i~Y--~-~~~FyvFDI~~  124 (335)
T 2hvq_A           78 DSIKAVQDIMETS-AVVSYQVFGEFAGPG-----------------------------IQKNVDY--G-DKDFYVFDIIV  124 (335)
T ss_dssp             HHHHHHHTTHHHH-TEEEEEEEEEEESBT-----------------------------TBSSCCC--C-SSEEEEEEEEE
T ss_pred             HHHHHHHHHhhcc-CCCcEEEEEEEccCc-----------------------------ccCCccc--C-CCeEEEEEEEE
Confidence             233232233110 135799999998321                             1111111  1 4589999975 


Q ss_pred             cccCC-CCCCCHHHHHHHHHhCCCCCCCC
Q psy11423        239 ELRGM-NMPSSHSELLNWYQKIGLSICGE  266 (655)
Q Consensus       239 ~~~~~-~~~~~~~e~l~~L~~~GF~~~~~  266 (655)
                      +.++. ...-+..+..+++..+||++++.
T Consensus       125 ~~~~~~~~~l~~~~~~~l~~~~gl~~VP~  153 (335)
T 2hvq_A          125 TTESGDVTYVDDYMMESFCNTFKFKMAPL  153 (335)
T ss_dssp             EETTCCEEECCHHHHHHHHHHHTCEESCE
T ss_pred             ecCCCceeeCCHHHHHHHHHHcCCCeece
Confidence            32210 01257788889999999998874

>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=96.02  E-value=0.024  Score=61.29  Aligned_cols=175  Identities=11%  Similarity=-0.003  Sum_probs=97.1

Q ss_pred             ceEEEEEecceeEEEEEEe----CCEEeEEEecCCCCccchhhhhhhhcccCCccccc-CCCCceEEEEEEEEeehhhHH
Q psy11423        118 IEYIAELKFDGIAVNLRYE----YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI-KYPPELLEVRCEVLIYKKDFI  192 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~----~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~-~~~p~~~evRGEv~~~~~~F~  192 (655)
                      ..|++|+|.||+-+.+...    +|.=+...||+    |++++..-...+.+...... ...+....+-||+++....  
T Consensus        60 ~~~~ve~K~DG~R~ll~~~~~~~~g~~v~L~sR~----~~~~~i~~~~FP~~~~~~~~~~~~~~~~vLDGElV~~~~~--  133 (395)
T 1p16_A           60 KDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRE----NDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRN--  133 (395)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTTEEEEEEEETT----CCEEECCSCCCCSCTTCCSSSCCCCSSEEEEEEEEEECCS--
T ss_pred             CCEEEEECccceEEEEEEeecccCCCEEEEEeCC----CceEEeccccCCcccccccchhccCCcceeeeEEEEeccC--
Confidence            3699999999999988663    44557999995    66754211111111111100 0124468999999986421  


Q ss_pred             HHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC--------
Q psy11423        193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI--------  263 (655)
Q Consensus       193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~--------  263 (655)
                                                      ....++.|++|++....+.++ .....+.++.|+++=+..        
T Consensus       134 --------------------------------~~~~~~~f~~FDlL~~~G~dl~~~pl~eR~~~L~~~i~~~~~~~~~~~  181 (395)
T 1p16_A          134 --------------------------------VSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHN  181 (395)
T ss_dssp             --------------------------------SSCCEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHTHHHHHHHHHHC
T ss_pred             --------------------------------CCcceeEEEEEEEEEECCeEcccCCHHHHHHHHHHHhhcccHhhhhcC
Confidence                                            012578999999987665433 246778888887742110        


Q ss_pred             --------CCC-ceee--CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc-eee
Q psy11423        264 --------CGE-YSVL--SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK-EAL  331 (655)
Q Consensus       264 --------~~~-~~~~--~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~-~~~  331 (655)
                              .+. ....  .....+.++++.    -..+.+..||||+|--+..++-  |   +. .--+=||.+.. +..
T Consensus       182 ~~~~~~~~~pf~v~~~~~~~~~~~~~~~~~----~~~~~~g~EGlI~K~~ds~Y~~--G---r~-~~wlKwK~~~~~TvD  251 (395)
T 1p16_A          182 PDIVNSPEFPFKVGFKTMLTSYHADDVLSK----MDKLFHASDGLIYTCAETPYVF--G---TD-QTLLKWKPAEENTVD  251 (395)
T ss_dssp             HHHHSCTTSCCEEEECCCEEGGGTHHHHTT----GGGCSSCEEEEEEEESSSCCCS--E---EE-EEEEEECCGGGCCEE
T ss_pred             ccccccccCceEEEEecchhHHHHHHHHHH----HHhcCCCCCeEEEEeCCCCcCC--C---Cc-cceEEEecCCCeEEE
Confidence                    000 0011  122333444332    1345789999999997765542  3   12 23456666443 333


Q ss_pred             EEEEEEEEe
Q psy11423        332 TKIKAINIQ  340 (655)
Q Consensus       332 T~v~~I~~q  340 (655)
                      ..|.....+
T Consensus       252 fvl~~~~~~  260 (395)
T 1p16_A          252 FQLEFVFNE  260 (395)
T ss_dssp             EEEEEECEE
T ss_pred             EEEEEEecc
Confidence            344433333

>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=95.99  E-value=0.006  Score=48.75  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=45.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHH-HHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKL-ANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ks-a~nll~~I~  512 (655)
                      ..+|||+|+++..+|.+.=  .|+.+|..++.++|.++  +|.+. |++|++.+.
T Consensus         6 L~~IpGIG~kr~~~LL~~F--gs~~~i~~As~eeL~~v--ig~~~~A~~I~~~l~   56 (63)
T 2a1j_A            6 LLKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSI--LGNAANAKQLYDFIH   56 (63)
T ss_dssp             HHTSTTCCHHHHHHHHHHC--SSHHHHHTCCHHHHHHH--HSCHHHHHHHHHHHH
T ss_pred             HHcCCCCCHHHHHHHHHHc--CCHHHHHHCCHHHHHHH--cCchHHHHHHHHHHh
Confidence            3489999999999999864  59999999999999999  88999 999998875

>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=95.98  E-value=0.0062  Score=63.41  Aligned_cols=48  Identities=23%  Similarity=0.227  Sum_probs=45.5

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++.++++++|++||+|+..+.|..+|.++||+|++++.+.+.+.
T Consensus       130 ~~GG~v~~~~t~~tTHLI~~~~~t~Ky~~A~~~gi~IV~~~Wl~~c~~  177 (298)
T 3olc_X          130 MMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWE  177 (298)
T ss_dssp             HTTCEECSSCCTTCCEEEESSSCSHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             HCCCEEecCcCCCeeEEEEeCCCChHHHHHHHCCCeEeeHHHHHHHHH
Confidence            789999999999999999999999999999999999999999998764

>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=95.94  E-value=0.012  Score=48.46  Aligned_cols=51  Identities=12%  Similarity=0.208  Sum_probs=46.2

Q ss_pred             cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      -=+|+.....-|-.+| |.++.||...+.++|.+++|||+|+.+.|.+.++.
T Consensus        13 ~L~LS~Ra~NcLkrag-I~Tv~dL~~~s~~dLlki~n~G~kSl~EI~~~L~~   63 (73)
T 1z3e_B           13 ELDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   63 (73)
T ss_dssp             GSCCBHHHHHHHHHTT-CCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHcC-CCcHHHHHcCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            3378999999998887 79999999999999999999999999999988864

>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=95.80  E-value=0.017  Score=47.14  Aligned_cols=48  Identities=21%  Similarity=0.184  Sum_probs=44.2

Q ss_pred             CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      .+||||+..+.+|.+. |.|++.|..++.++|..|.||++..|+.|+.-
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            6789999999999975 89999999999999999999999999998753

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=95.57  E-value=0.0061  Score=64.97  Aligned_cols=108  Identities=15%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHH--HHHHHh--------------------ccc
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNIL--LAIQKS--------------------KLT  517 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll--~~I~~s--------------------k~~  517 (655)
                      -.|+|+||.+++.|.++=+  |++.+-+.+.++|.. +|+|+|.+..|+  ..+...                    +..
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            4699999999999999743  777888889999977 999999998875  222211                    011


Q ss_pred             chhHHHHHh-----------CCC-----CccHHHHHHHHHhCCCHHHHHhc-CHHHHhcCCCCCHHHHHHHH
Q psy11423        518 TFSRFIYAL-----------GIR-----HVGETTAKELANYFKNLECMFKA-TEEQLLNIPKIGSTTVKAFI  572 (655)
Q Consensus       518 ~l~r~L~al-----------gIp-----gIG~~~Ak~L~~~fgsl~~l~~a-s~eeL~~i~GIG~~~A~~I~  572 (655)
                      |.. -|.-|           |||     +..-.+|..|.+.|++|..+..+ +.++|.. +|+|++.+..|.
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           443     22234567899999999988876 5556555 566666555554

>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=95.55  E-value=0.019  Score=47.92  Aligned_cols=49  Identities=12%  Similarity=0.216  Sum_probs=45.3

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +|+....+-|-.+| |.++.||...+.++|.++.|||+||.+.|.+.++.
T Consensus        22 ~LS~Ra~NcLk~ag-I~Tv~dL~~~se~dLlki~n~G~kSl~EI~~~L~e   70 (79)
T 3gfk_B           22 DLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   70 (79)
T ss_dssp             CCBHHHHHHHHHTT-CCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhC-CCCHHHHHhCCHHHHHHcCCCCHhHHHHHHHHHHH
Confidence            78899999998888 79999999999999999999999999999988764

>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae}

Probab=95.50  E-value=0.087  Score=57.81  Aligned_cols=146  Identities=17%  Similarity=0.113  Sum_probs=86.1

Q ss_pred             ceEEEEEecceeEEEEEEeC----C-EEeEEEecCCCCccchhhhhhhhcccCCcc-----cccCCCCceEEEEEEEEee
Q psy11423        118 IEYIAELKFDGIAVNLRYEY----G-YLKQASTRGDGNIGENITTNIHIIHKIPLV-----LNIKYPPELLEVRCEVLIY  187 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~----G-~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~-----l~~~~~p~~~evRGEv~~~  187 (655)
                      -.|++++|.||+-+.+....    | .=+.++||++-    ++|.+-...+.++..     +.  ..+....+-||+++.
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 34688999644    454221111222221     21  135567899999995


Q ss_pred             hhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCC----
Q psy11423        188 KKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLS----  262 (655)
Q Consensus       188 ~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~----  262 (655)
                      ...+                      +           ....+.|++|++....+.++ .....+.++.|.++=..    
T Consensus       139 ~~~~----------------------~-----------~~~~~~y~~FDlL~~~G~dl~~~pl~eR~~~Le~~I~~P~~~  185 (461)
T 3kyh_C          139 TNPM----------------------T-----------KLQELRYLMFDCLAINGRCLTQSPTSSRLAHLGKEFFKPYFD  185 (461)
T ss_dssp             ECTT----------------------T-----------CCEEEEEEEEEEEEETTEECSSSBHHHHHHHHHHTTHHHHHH
T ss_pred             cCCC----------------------C-----------CccceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhcccchh
Confidence            3210                      0           12479999999987665443 24677888888755110    


Q ss_pred             ----------CCCCceeeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423        263 ----------ICGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (655)
Q Consensus       263 ----------~~~~~~~~~~~---~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (655)
                                ..+......+.   .++.++++    .-..+.+..||+|+|--+..+
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                      01111122222   33444433    124688999999999866544

>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=95.43  E-value=0.021  Score=48.43  Aligned_cols=49  Identities=14%  Similarity=0.056  Sum_probs=45.7

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +|+....+-|-.+| |.++.||...+.++|.+++|||+||.+.|.+.++.
T Consensus        18 ~LSvRa~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   66 (86)
T 3k4g_A           18 ELTVRSANCLXAEA-IHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLAS   66 (86)
T ss_dssp             CCCHHHHHHHHHTT-CCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHcC-CCcHHHHHhCCHHHHhhccccCcccHHHHHHHHHH
Confidence            78999999998888 79999999999999999999999999999988875

>1s68_A RNA ligase 2; ribonucleic acid ligase, RNA repair; HET: AMP; 1.90A {Enterobacteria phage T4} SCOP: d.142.2.4

Probab=95.39  E-value=0.056  Score=54.73  Aligned_cols=148  Identities=15%  Similarity=0.099  Sum_probs=83.1

Q ss_pred             cCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCcc-c------hhhhhh-hh
Q psy11423         90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIG-E------NITTNI-HI  161 (655)
Q Consensus        90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~G-e------DvT~n~-~~  161 (655)
                      -||+|-++    ..|++++... + .....++++.|+||-++++.+.+|. +.+.|||--... +      .+.+.. ..
T Consensus         6 ~~i~n~~~----~~~~~~~~~~-~-~~~~~vvvtEKldG~N~~i~~~~~~-i~~~sR~~~l~~~~~f~~~~~~~~~~~~~   78 (249)
T 1s68_A            6 SSLENHYN----SKFIEKLYSL-G-LTGGEWVAREKIHGTNFSLIIERDK-VTCAKRTGPILPAEDFFGYEIILKNYADS   78 (249)
T ss_dssp             CCCEETTC----HHHHHHHHHH-T-CSCSCEEEEECCCSEEEEEEEESSC-EEEEETTEECCTTCCCTTTHHHHHHTHHH
T ss_pred             Ccccchhh----hHHHHHHHhh-c-cCCCCEEEEEEECCcceEEEEECCE-EEEEeCCcccCCCCccchHHHHHHHHHHH
Confidence            46777665    3445555321 1 1134799999999999999998887 569999833211 1      222211 11


Q ss_pred             cccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecc-cc
Q psy11423        162 IHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVG-EL  240 (655)
Q Consensus       162 i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~-~~  240 (655)
                      +..+-..|... .+..+.|-||++=+.                             -|.+-..  . +..|++|+|- +.
T Consensus        79 ~~~l~~~l~~~-~~~~~~i~GE~~G~~-----------------------------Iq~~v~Y--~-~~~FyvFdI~~~~  125 (249)
T 1s68_A           79 IKAVQDIMETS-AVVSYQVFGEFAGPG-----------------------------IQKNVDY--C-DKDFYVFDIIVTT  125 (249)
T ss_dssp             HHHHHHHHHHH-TEEEEEEEEEEESTT-----------------------------TSSSCCC--C-SCEEEEEEEEEEE
T ss_pred             HHHHHHHhccc-CCCcEEEEEEEcccc-----------------------------ccCCccc--C-CCeEEEEEEEEec
Confidence            11111112100 135799999998321                             1111111  1 4589999985 42


Q ss_pred             cCC-CCCCCHHHHHHHHHhCCCCCCCCceeeCCHHHHHH
Q psy11423        241 RGM-NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIE  278 (655)
Q Consensus       241 ~~~-~~~~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~  278 (655)
                      ++. ...-+..+..+++..+||++++.... .+.+++.+
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 01247778889999999998874322 24444444

>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=95.37  E-value=0.01  Score=51.39  Aligned_cols=22  Identities=23%  Similarity=0.410  Sum_probs=13.4

Q ss_pred             cCHHHHhcCCCCCHHHHHHHHH
Q psy11423        552 ATEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       552 as~eeL~~i~GIG~~~A~~I~~  573 (655)
                      .+.++|.+++|||+++++.|+.
T Consensus        67 ~s~edL~~v~Gig~k~~~~l~~   88 (98)
T 2edu_A           67 SQVEDLERVEGITGKQMESFLK   88 (98)
T ss_dssp             SSGGGGGGSTTCCHHHHHHHHH
T ss_pred             CCHHHHHhCCCCCHHHHHHHHH
Confidence            3445566666666666666654

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=95.27  E-value=0.0056  Score=50.30  Aligned_cols=24  Identities=21%  Similarity=0.326  Sum_probs=10.9

Q ss_pred             hcCChhhhccccCCcHHHHHHHHH
Q psy11423        486 YKINFKNLLRLDRVSNKLANNILL  509 (655)
Q Consensus       486 ~~L~~~~L~~l~GfG~Ksa~nll~  509 (655)
                      -+++.++|..++|+|++.|++|++
T Consensus        22 N~a~~~~L~~ipGIG~~~A~~Il~   45 (75)
T 2duy_A           22 NEASLEELMALPGIGPVLARRIVE   45 (75)
T ss_dssp             TTCCHHHHTTSTTCCHHHHHHHHH
T ss_pred             hhCCHHHHHhCCCCCHHHHHHHHH
Confidence            333444444444444444444444

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A*

Probab=95.21  E-value=0.019  Score=50.66  Aligned_cols=48  Identities=19%  Similarity=0.139  Sum_probs=44.0

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++...+++.++.||+.+..++|+++|++.||+|++.+-+.+-+.
T Consensus        36 ~~GA~v~~~l~~~vTHvV~~~~~~~~~~~A~~~~i~iV~~~Wv~~C~~   83 (107)
T 3pa6_A           36 DMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRT   83 (107)
T ss_dssp             HTTCEECSSCCTTCCEEEEESCCHHHHHHHHHHTCEEECHHHHHHHHH
T ss_pred             HcCCEEecccCCCccEEEEeCCCChHHHHHhcCCCEEECHHHHHHHHH
Confidence            789999999999999999988777999999999999999999888763

>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=95.15  E-value=0.013  Score=57.23  Aligned_cols=54  Identities=22%  Similarity=0.252  Sum_probs=41.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCh-HHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ...|+|+|||++.+|++.-....+ ..+..-+.++|.++||+|+|+|++|+..+.
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 224445778899999999999999988774

>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=95.06  E-value=0.025  Score=59.82  Aligned_cols=62  Identities=16%  Similarity=0.284  Sum_probs=47.6

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcccchh------HHHHHh-CCCCccHHHHHHHHHh-CCCHHHHHhc
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS------RFIYAL-GIRHVGETTAKELANY-FKNLECMFKA  552 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~------r~L~al-gIpgIG~~~Ak~L~~~-fgsl~~l~~a  552 (655)
                      .+|..|||+|++.|++|.+-++.-+-..+.      .++.-+ .|||||+++|+++-+. +.|++.|..+
T Consensus        57 ~~l~~lpGIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k~a~~l~~~Gi~tledL~~a  126 (335)
T 2bcq_A           57 QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQ  126 (335)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHHHH
T ss_pred             HHHhcCCCccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHHHHHHHHHcCCCCHHHHHHH
Confidence            458999999999999999988742211121      356666 9999999999988765 6689998875

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=95.02  E-value=0.017  Score=48.85  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=44.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHH-HHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKL-ANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ks-a~nll~~I~  512 (655)
                      ..+|||+|+++..+|+..-  .++.+|..++.++|..+  +|.+. |++|++.+.
T Consensus        20 L~~IpGIG~kr~~~LL~~F--gSl~~i~~AS~eEL~~v--ig~~~~A~~I~~~l~   70 (84)
T 1z00_B           20 LLKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSI--LGNAANAKQLYDFIH   70 (84)
T ss_dssp             HHTCSSCCHHHHHHHHHHS--SCHHHHHHSCHHHHHHH--HSCHHHHHHHHHHHT
T ss_pred             HHhCCCCCHHHHHHHHHHc--CCHHHHHHCCHHHHHHH--hCchHHHHHHHHHHH
Confidence            3579999999999999864  69999999999999999  89998 999998874

>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=94.90  E-value=0.02  Score=56.64  Aligned_cols=53  Identities=11%  Similarity=0.265  Sum_probs=46.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|+|+|++++..|.+.=  .++.+|+..+.++|..++|+|++.|++|.+.+..
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            3579999999999999973  4789999999999999999999999999988753

>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C}

Probab=94.87  E-value=0.018  Score=48.51  Aligned_cols=47  Identities=30%  Similarity=0.392  Sum_probs=40.9

Q ss_pred             CCCCeEecccc--cCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423        600 TKGGKVVNFIS--KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG  648 (655)
Q Consensus       600 ~~G~~v~~sVs--k~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~~  648 (655)
                      .+||++..+++  +++++|||++..++|+.++  .|++|++++.+.+.+..
T Consensus        32 ~~GG~~~~~~~~~~~~THlI~~~~~~~K~~~~--~~~~iV~~~Wi~dci~~   80 (92)
T 4id3_A           32 LHGGKFLHYLSSKKTVTHIVASNLPLKKRIEF--ANYKVVSPDWIVDSVKE   80 (92)
T ss_dssp             HTTCEEESSCCCTTTCCEEECSCCCHHHHHHT--TTSCEECTHHHHHHHHH
T ss_pred             HCCCEEEEEecCCCceEEEEecCCCHHHHHHc--CCCCEEcccHHHHHHHc
Confidence            78999999999  8999999999888776554  79999999999998853

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=94.85  E-value=0.022  Score=64.40  Aligned_cols=85  Identities=18%  Similarity=0.255  Sum_probs=56.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCC
Q psy11423        457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRH  530 (655)
Q Consensus       457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpg  530 (655)
                      .+.+.++|+|+|.+++|+++     +..=-...-.++   +.++++|++.|..|.+..   +.-.+.+...|   ..|+|
T Consensus       480 ~~L~~l~g~geKsa~nL~~a-----Ie~sk~~~l~r~l~aLGI~~vG~~~a~~La~~f~sl~~l~~a~~e~l---~~i~g  551 (586)
T 4glx_A          480 GKLTGLERMGPKSAQNVVNA-----LEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEEL---QKVPD  551 (586)
T ss_dssp             HHHHTSTTCCHHHHHHHHHH-----HHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHCSHHHHHHCCHHHH---TTSTT
T ss_pred             HHHhcccCccHHHHHHHHHH-----HHHHcCCCHHHHHHHcCCCchhHHHHHHHHHHcCCHHHHHccCHHHH---hcCCC
Confidence            35678999999999999874     111111222222   456889999998887653   33233333322   38999


Q ss_pred             ccHHHHHHHHHhCCCHHHH
Q psy11423        531 VGETTAKELANYFKNLECM  549 (655)
Q Consensus       531 IG~~~Ak~L~~~fgsl~~l  549 (655)
                      ||+.+|+.|.+.|.+-+..
T Consensus       552 iG~~~A~si~~ff~~~~n~  570 (586)
T 4glx_A          552 VGIVVASHVHNFFAEESNR  570 (586)
T ss_dssp             CCHHHHHHHHHHHHSHHHH
T ss_pred             ccHHHHHHHHHHHcCHHHH
Confidence            9999999999999764433

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=94.80  E-value=0.021  Score=65.58  Aligned_cols=81  Identities=19%  Similarity=0.285  Sum_probs=52.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV  531 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI  531 (655)
                      +...++|+|+|++++|+++     +..--.-...++   +.++|+|++.|+.|++.+   +.-++.+...+   ..||||
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            4667889999999998863     221111222332   267889999888888753   33333343322   278999


Q ss_pred             cHHHHHHHHHhCCCH
Q psy11423        532 GETTAKELANYFKNL  546 (655)
Q Consensus       532 G~~~Ak~L~~~fgsl  546 (655)
                      |+++|+.|.+.|..-
T Consensus       553 G~~~A~sI~~ff~~~  567 (671)
T 2owo_A          553 GIVVASHVHNFFAEE  567 (671)
T ss_dssp             CHHHHHHHHHHHTCH
T ss_pred             CHHHHHHHHHHHHhH
Confidence            999999998888753

>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=94.79  E-value=0.026  Score=55.54  Aligned_cols=54  Identities=13%  Similarity=0.258  Sum_probs=42.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCh-HHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ...|+|+|||++.+|++.-....+ ..+..-+.++|.++||+|+|+|++|+..+.
T Consensus        75 L~~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~elk  129 (203)
T 1cuk_A           75 LIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMK  129 (203)
T ss_dssp             HHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HhcCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            457999999999999986532222 234446788999999999999999998885

>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=94.70  E-value=0.019  Score=52.49  Aligned_cols=26  Identities=23%  Similarity=0.370  Sum_probs=20.9

Q ss_pred             HHHhcCChhhhccccCCcHHHHHHHH
Q psy11423        483 VDLYKINFKNLLRLDRVSNKLANNIL  508 (655)
Q Consensus       483 ~DL~~L~~~~L~~l~GfG~Ksa~nll  508 (655)
                      -||-+.+.++|.+|||+|++.|++|+
T Consensus        55 IniNtA~~~eL~~LpGiGp~~A~~II   80 (134)
T 1s5l_U           55 IDLNNTNIAAFIQYRGLYPTLAKLIV   80 (134)
T ss_dssp             EETTTSCGGGGGGSTTCTHHHHHHHH
T ss_pred             eeCcccCHHHHHHCCCCCHHHHHHHH
Confidence            46666778888888888888888887

>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=94.58  E-value=0.1  Score=52.28  Aligned_cols=81  Identities=19%  Similarity=0.181  Sum_probs=51.1

Q ss_pred             HHHHHHHHc-CCC-CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423        468 KMIEKLVNA-NIV-VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (655)
Q Consensus       468 k~i~~L~~~-g~I-~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs  545 (655)
                      +.+.+|++. |.. -++.+|..++.++|..+ ||+..+|..|.+..+..                         .+.+.+
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            455566665 421 38899999998889776 89888888777644322                         222223


Q ss_pred             HHHHHhc----CHHHHhcCCCCCHHHHHHHHHH
Q psy11423        546 LECMFKA----TEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       546 l~~l~~a----s~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      ++.+..+    ..++|.+++|||+++|+.|.-|
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    2356777788888877777765

>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=94.57  E-value=0.049  Score=47.06  Aligned_cols=58  Identities=12%  Similarity=0.027  Sum_probs=40.6

Q ss_pred             hHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc-cchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423        482 AVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL-TTFSRFIYALGIRHVGETTAKELANY  542 (655)
Q Consensus       482 i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~-~~l~r~L~algIpgIG~~~Ak~L~~~  542 (655)
                      +.||.+++.++|..++|+|++.|++|++..+.... .++..+   ..+||||++++++|.+.
T Consensus        31 ~i~iN~a~~~~L~~ipGIG~~~A~~Il~~r~~~g~f~s~edL---~~v~Gig~k~~~~l~~~   89 (98)
T 2edu_A           31 LDLLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVEDL---ERVEGITGKQMESFLKA   89 (98)
T ss_dssp             HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGG---GGSTTCCHHHHHHHHHH
T ss_pred             CeehhhCCHHHHHHCCCCCHHHHHHHHHHHHhcCCcCCHHHH---HhCCCCCHHHHHHHHHC
Confidence            45677777788888888888888888887654222 233343   46788888888877654

>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=94.56  E-value=0.037  Score=63.51  Aligned_cols=80  Identities=21%  Similarity=0.334  Sum_probs=47.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhc---cccCCcHHHHHHHHHH---HHHhcccchhHHHHHhCCCCc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL---RLDRVSNKLANNILLA---IQKSKLTTFSRFIYALGIRHV  531 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~---~l~GfG~Ksa~nll~~---I~~sk~~~l~r~L~algIpgI  531 (655)
                      +.+.++|+|+|+++.|+++-     ..--.-...+++   .++|+|++.|.+|++.   ++.-.+.+...+.   .|+||
T Consensus       476 ~L~~l~g~G~Ksa~nLl~aI-----e~sk~~~l~R~L~alGI~~VG~~~Ak~La~~Fgsl~~l~~As~eeL~---~I~GI  547 (667)
T 1dgs_A          476 DLLGLERMGEKSAQNLLRQI-----EESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELI---EVEEV  547 (667)
T ss_dssp             HHHTTSSCCSTTHHHHHHHH-----HHGGGCCHHHHHHHTTCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHH---TSTTC
T ss_pred             HHhcccccchhhHHHHHHHH-----HHHhcCcHHHhhHhhccCCccHHHHHHHHHHcCCHHHHHhCCHHHHH---hccCc
Confidence            45667788888888777531     111111112221   5677788888777663   3433444433333   67888


Q ss_pred             cHHHHHHHHHhCCC
Q psy11423        532 GETTAKELANYFKN  545 (655)
Q Consensus       532 G~~~Ak~L~~~fgs  545 (655)
                      |+++|+.|.+.|..
T Consensus       548 G~~~A~sI~~ff~~  561 (667)
T 1dgs_A          548 GELTARAILETLKD  561 (667)
T ss_dssp             CHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHhh
Confidence            88888888777764

>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=94.43  E-value=0.16  Score=50.21  Aligned_cols=82  Identities=24%  Similarity=0.316  Sum_probs=51.7

Q ss_pred             HHHHHHHHcCCCCC------hHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHH
Q psy11423        468 KMIEKLVNANIVVT------AVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKE  538 (655)
Q Consensus       468 k~i~~L~~~g~I~~------i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~  538 (655)
                      +.+..|.+.|+ .+      +.+|..++.++|..+   -||...+|.+|.+..+.                         
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            45566777665 35      899999888777322   37887778777654332                         


Q ss_pred             HHHhCCCHHHH-HhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        539 LANYFKNLECM-FKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       539 L~~~fgsl~~l-~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +.+.+++++.+ .....++|.+++|||+++|..|.-|.
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            11222222222 12356788889999999988887753

>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=94.42  E-value=0.063  Score=56.72  Aligned_cols=62  Identities=23%  Similarity=0.287  Sum_probs=47.4

Q ss_pred             hhhccccCCcHHHHHHHHHHHHHhcc--------cc-hhHHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhc
Q psy11423        491 KNLLRLDRVSNKLANNILLAIQKSKL--------TT-FSRFIYALGIRHVGETTAKELANY-FKNLECMFKA  552 (655)
Q Consensus       491 ~~L~~l~GfG~Ksa~nll~~I~~sk~--------~~-l~r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~a  552 (655)
                      .+|..|||+|++.|++|.+-++.-+-        .+ ..-+..-+.|||||+++|+++-+. +.|++.|..+
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            45899999999999999988774221        11 223444459999999999988765 6699999886

>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=94.33  E-value=0.2  Score=50.57  Aligned_cols=118  Identities=20%  Similarity=0.288  Sum_probs=77.1

Q ss_pred             CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhc----CChhhhccccCCcHHHHHHHHHHHHH---hc
Q psy11423        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQK---SK  515 (655)
Q Consensus       443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~GfG~Ksa~nll~~I~~---sk  515 (655)
                      .|.-.-+-|.||-|..  +|-.-.-.-|+.+|++|-++.  +-|.    +....|.+-+|.|.|+|+.|+.++-+   .|
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            6667778889998843  444455677899999997653  3343    22356777799999999999988732   11


Q ss_pred             ----ccch----------hHHHHHh--------CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCH
Q psy11423        516 ----LTTF----------SRFIYAL--------GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGS  565 (655)
Q Consensus       516 ----~~~l----------~r~L~al--------gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~  565 (655)
                          ...+          .|+|.+|        .|.||...+|.+|+++||....+..|..++|.. +|+..
T Consensus       439 qlarefeieklasvegvgervlrslvpgyaslisirgidreraerllkkyggyskvreagveelre-dgltd  509 (519)
T 2csb_A          439 QLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELRE-DGLTD  509 (519)
T ss_dssp             HHHHTTCHHHHHTSTTCSHHHHHHHSTTHHHHHTSTTCCHHHHHHHHHHHTSHHHHHTSCHHHHHH-TTCCH
T ss_pred             HHHHHHhHHHHhhccchHHHHHHHhccchhhheeeccccHHHHHHHHHHhCChhHHHHhhHHHHHH-cCCcH
Confidence                1111          1333332        567777777777777777777777777666654 34444

>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=94.31  E-value=0.079  Score=56.15  Aligned_cols=154  Identities=15%  Similarity=0.123  Sum_probs=82.4

Q ss_pred             eEEEEEecceeEEEEEEe-CCEEeEEEecCCCCccchhhh-hhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITT-NIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~-n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~  196 (655)
                      .|++++|.||.-+.+... +|. +.+.||+    |+++|. +.+. +.+.. +.  ..+....+-||+++...+      
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            699999999999988766 454 6889995    556653 2211 11110 11  023457899999986421      


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhC-----------C----
Q psy11423        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI-----------G----  260 (655)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~-----------G----  260 (655)
                           |                        ...+.|++|++...++.++ ..+..+.++.|.+.           |    
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                        1246999999987666443 24677777777642           2    


Q ss_pred             ----CCCC-CCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        261 ----LSIC-GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       261 ----F~~~-~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                          |.+. .........+++..  .   +....+.+..||+|++-.+ .+.      ++....-+-||.+..
T Consensus       180 ~~~pf~vr~K~~~~~~~~~~ll~--~---~~~~~l~~~~dGlIf~~~~-~Y~------~G~~~~~lKwKp~~~  240 (343)
T 3rtx_A          180 TQEPFSVRPKQFFDINISRKLLE--G---NFAKEVSHEMDGLIFQPIG-KYK------PGRCDDILKWKPPSL  240 (343)
T ss_dssp             TTSSSEEEECCCEEGGGHHHHSC--C-------------CEEEEEESS-CCC------CEEEEEEEEECCSTT
T ss_pred             cCCCcEEEEEEeEehhhHHHHHh--h---hhHhhcCCCCCeEEEEECc-cCc------CCCCcceEEEecCcc
Confidence                1111 00111122233321  0   1234678899999999887 443      222234466776554

>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A

Probab=94.29  E-value=0.039  Score=47.92  Aligned_cols=49  Identities=16%  Similarity=0.086  Sum_probs=44.7

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +|+....+-|-.+| |.++.||...+.++|+++++||+||.+.|.+.++.
T Consensus        30 ~LSvRs~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   78 (98)
T 1coo_A           30 ELTVRSANCLKAEA-IHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   78 (98)
T ss_dssp             TCCTTTHHHHHTTT-CCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcC-CCcHHHHHhCCHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            67888888998777 79999999999999999999999999999998874

>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=94.29  E-value=0.019  Score=56.79  Aligned_cols=54  Identities=15%  Similarity=0.249  Sum_probs=41.6

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChH-HHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAV-DLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~-DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ..|+|+|||++..+++.-....+. .+..=+.+.|.++||+|+|+|++|+..++.
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            349999999999999865333322 133345788999999999999999988854

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=94.27  E-value=0.0079  Score=68.25  Aligned_cols=84  Identities=13%  Similarity=0.116  Sum_probs=0.0

Q ss_pred             cccccCCC------CHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH---HhcccchhHHHHHhCC
Q psy11423        458 KAMNIIGL------GKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ---KSKLTTFSRFIYALGI  528 (655)
Q Consensus       458 ~~l~I~GL------G~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~---~sk~~~l~r~L~algI  528 (655)
                      +.+.++|+      |+|.+++|+++---+.-..|-.+=.  =+.++|+|++.+..|++...   .-++.+...+   ..|
T Consensus       492 ~L~~l~~~~~~~g~g~ksa~nLl~aIe~sk~~~l~r~L~--aLGIp~VG~~~ak~La~~Fgsle~L~~As~eeL---~~I  566 (615)
T 3sgi_A          492 DLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLV--ALSIRHVGPTAARALATEFGSLDAIAAASTDQL---AAV  566 (615)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhhccccccccCccchHHHHHHHHHHHhcCCCHHHHHH--HcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHH---hhC
Confidence            45666644      5788888876532111111111000  14567888888887776542   2222222211   267


Q ss_pred             CCccHHHHHHHHHhCCCH
Q psy11423        529 RHVGETTAKELANYFKNL  546 (655)
Q Consensus       529 pgIG~~~Ak~L~~~fgsl  546 (655)
                      ||||+++|+.|.+.|...
T Consensus       567 ~GIG~~~A~sI~~ff~~~  584 (615)
T 3sgi_A          567 EGVGPTIAAAVTEWFAVD  584 (615)
T ss_dssp             ------------------
T ss_pred             CCCCHHHHHHHHHHHcCH
Confidence            888888888888877643

>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=94.24  E-value=0.042  Score=50.21  Aligned_cols=42  Identities=21%  Similarity=0.302  Sum_probs=35.3

Q ss_pred             CCCCccHHHHHHHHHh--CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~--fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .+||||++.|++|.++  |.        +.|||.+++|||++..+.+.++.+
T Consensus        67 ~LpGiGp~~A~~II~~GpF~--------svedL~~V~GIg~k~~e~l~~~~~  110 (134)
T 1s5l_U           67 QYRGLYPTLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLE  110 (134)
T ss_dssp             GSTTCTHHHHHHHHHTCCCS--------SGGGGGGCTTCCHHHHHHHHHHHT
T ss_pred             HCCCCCHHHHHHHHHcCCCC--------CHHHHHhCCCCCHHHHHHHHHhhc
Confidence            5899999999999976  55        458899999999998888877654

>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=94.15  E-value=0.034  Score=48.25  Aligned_cols=56  Identities=20%  Similarity=0.317  Sum_probs=38.3

Q ss_pred             HHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCC
Q psy11423        483 VDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPK  562 (655)
Q Consensus       483 ~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~G  562 (655)
                      -||-+.+.++|..+||+|++.|++|++      +               |         .|.+        .++|.+++|
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            355666677777777777777777775      0               1         2553        467778888


Q ss_pred             CCHHHHHHHHHHhc
Q psy11423        563 IGSTTVKAFIKFIN  576 (655)
Q Consensus       563 IG~~~A~~I~~~f~  576 (655)
                      ||+++.+++..|+.
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            88888888877654

>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=93.89  E-value=0.094  Score=56.35  Aligned_cols=101  Identities=15%  Similarity=0.115  Sum_probs=63.6

Q ss_pred             CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHh-cCC-hhhhccccCCcHHHHHHHHHHHHHhcccchh
Q psy11423        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY-KIN-FKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (655)
Q Consensus       443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~-~L~-~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~  520 (655)
                      -.+..++.|..     .|.+.| .+-.+...-.+-  ..+..+= .++ ..+|..|||+|++.|++|.+-++.-+-..+.
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            34555565554     456778 776666553321  1111111 121 3459999999999999999887753222222


Q ss_pred             --------H-HHHHhCCCCccHHHHHHHHHh-CCCHHHHHh
Q psy11423        521 --------R-FIYALGIRHVGETTAKELANY-FKNLECMFK  551 (655)
Q Consensus       521 --------r-~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~  551 (655)
                              . +..-+.|||||+++|+++-+. +.|++.|..
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 333459999999999998765 668888883

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=93.86  E-value=0.095  Score=55.92  Aligned_cols=100  Identities=12%  Similarity=0.088  Sum_probs=63.1

Q ss_pred             CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhc-C-ChhhhccccCCcHHHHHHHHHHHHHhcccchh
Q psy11423        443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK-I-NFKNLLRLDRVSNKLANNILLAIQKSKLTTFS  520 (655)
Q Consensus       443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L-~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~  520 (655)
                      -.+..++.|..     .|.+.| .+=.+...-.+-  ..+..+=. + +..+|..|||+|++.|++|.+-++.-+-..+.
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            34555566654     456777 776666553321  11111111 2 23469999999999999999888743222222


Q ss_pred             H---------HHHHhCCCCccHHHHHHHHHh-CCCHHHHH
Q psy11423        521 R---------FIYALGIRHVGETTAKELANY-FKNLECMF  550 (655)
Q Consensus       521 r---------~L~algIpgIG~~~Ak~L~~~-fgsl~~l~  550 (655)
                      .         +..-+.|||||+++|+++-+. +.|++.|.
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            1         233359999999999988765 66888887

>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=93.75  E-value=0.038  Score=47.98  Aligned_cols=48  Identities=8%  Similarity=0.153  Sum_probs=39.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      ...+.++|+|+++++++++.|-.+++        ++|..++|+|++..++|...+.
T Consensus        26 ~eL~~lpGIG~~~A~~IV~~GpF~s~--------edL~~V~Gig~~~~e~l~~~l~   73 (97)
T 3arc_U           26 AAFIQYRGLYPTLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLE   73 (97)
T ss_dssp             GGGGGSTTCTTHHHHHHHHHCCCSSG--------GGGGGCTTCCHHHHHHHHHTGG
T ss_pred             HHHhHCCCCCHHHHHHHHHcCCCCCH--------HHHHhccCCCHHHHHHHHHHhc
Confidence            45668999999999999998877765        5566789999999988877654

>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=93.66  E-value=0.13  Score=41.93  Aligned_cols=52  Identities=27%  Similarity=0.298  Sum_probs=44.0

Q ss_pred             HHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       521 r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      -|...+   ||++..+++|.+. |.|++.+..++.++|..|+||++.+++.|++--
T Consensus         7 ~f~~~l---gI~e~~a~~L~~~Gf~tve~vA~~~~~eL~~I~G~dE~~a~~l~~~A   59 (70)
T 1u9l_A            7 TFTKYL---DIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERA   59 (70)
T ss_dssp             HHHHHH---TCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhC---CCCHHHHHHHHHcCcCcHHHHHcCCHHHHhhccCCCHHHHHHHHHHH
Confidence            345555   5668899888864 999999999999999999999999999998754

>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=93.29  E-value=0.078  Score=56.01  Aligned_cols=74  Identities=16%  Similarity=0.179  Sum_probs=48.7

Q ss_pred             CcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHh-------cCHHHHhcCCCCCHHHHH
Q psy11423        499 VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY--FKNLECMFK-------ATEEQLLNIPKIGSTTVK  569 (655)
Q Consensus       499 fG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~-------as~eeL~~i~GIG~~~A~  569 (655)
                      |.-+...+-...|+.. ..++........|||||+++|++|.+.  -|.+..+..       .+..+|.+|+|||+++|.
T Consensus        34 ~rv~AYr~Aa~~l~~l-~~~i~~~~~l~~LpGIG~~~A~kI~E~l~tG~~~~le~l~~~~~~~~l~~l~~V~GiGpk~a~  112 (335)
T 2fmp_A           34 HKYNAYRKAASVIAKY-PHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAAR  112 (335)
T ss_dssp             HHHHHHHHHHHHHHHC-SSCCCCHHHHHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhC-CccccCHHHHhcCCCCcHHHHHHHHHHHHhCCcHHHHHHHcccchhHHHHHhCCCCCCHHHHH
Confidence            4444444444445432 223444444569999999999988774  345444433       245789999999999999


Q ss_pred             HHHH
Q psy11423        570 AFIK  573 (655)
Q Consensus       570 ~I~~  573 (655)
                      .+++
T Consensus       113 ~l~~  116 (335)
T 2fmp_A          113 KFVD  116 (335)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9876

>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=93.17  E-value=0.35  Score=48.36  Aligned_cols=81  Identities=15%  Similarity=0.163  Sum_probs=54.0

Q ss_pred             HHHHHHHc-CC---CCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCC
Q psy11423        469 MIEKLVNA-NI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK  544 (655)
Q Consensus       469 ~i~~L~~~-g~---I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fg  544 (655)
                      .+.+|.+. |-   --++++|..++.++|..+ ||+..+|..|.+.-+.         +.. |              .+.
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            44555554 41   368999999999999886 9998888877654322         111 0              122


Q ss_pred             CHHHHHhcC----HHHHhcCCCCCHHHHHHHHHH
Q psy11423        545 NLECMFKAT----EEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       545 sl~~l~~as----~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      +++.+...+    .++|.+++|||+++|+.|.-|
T Consensus       136 ~l~~l~~~~~~~~~~~L~~l~GIG~~TA~~ill~  169 (232)
T 4b21_A          136 SKSEIEKMSEEELMESLSKIKGVKRWTIEMYSIF  169 (232)
T ss_dssp             CHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHHH
T ss_pred             CHHHHHcCCHHHHHHHHHhCCCcCHHHHHHHHHH
Confidence            344444443    367899999999999998876

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=93.17  E-value=0.094  Score=55.94  Aligned_cols=74  Identities=9%  Similarity=0.078  Sum_probs=47.3

Q ss_pred             CcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhc-------CHHHHhcCCCCCHHHHH
Q psy11423        499 VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY--FKNLECMFKA-------TEEQLLNIPKIGSTTVK  569 (655)
Q Consensus       499 fG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~a-------s~eeL~~i~GIG~~~A~  569 (655)
                      |.-+...+-...|+.. ..++........|||||+++|++|.+.  -|.+..+...       ...+|.+|+|||+++|+
T Consensus        38 ~r~~AYr~Aa~~l~~l-~~~i~~~~~l~~lpGIG~~~A~kI~E~l~tG~~~~le~L~~d~~~~~l~~l~~I~GvG~kta~  116 (360)
T 2ihm_A           38 GRLLSFSRAASVLKSL-PCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTAN  116 (360)
T ss_dssp             HHHHHHHHHHHHHHHC-SSCCCSGGGGTTCTTCCHHHHHHHHHHHHHSCCHHHHHHHHSHHHHHHHHHHTSTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhC-CcccCCHHHHhcCCCCCHHHHHHHHHHHHcCChHHHHHHhcccchHHHHHHhCCCCCCHHHHH
Confidence            3333333334444432 123333333569999999999988763  4555554432       24689999999999999


Q ss_pred             HHHH
Q psy11423        570 AFIK  573 (655)
Q Consensus       570 ~I~~  573 (655)
                      .+++
T Consensus       117 ~l~~  120 (360)
T 2ihm_A          117 RWYQ  120 (360)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9876

>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=93.11  E-value=0.086  Score=56.68  Aligned_cols=55  Identities=9%  Similarity=0.108  Sum_probs=40.6

Q ss_pred             hhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhc-------CHHHHhcCCCCCHHHHHHHHH
Q psy11423        519 FSRFIYALGIRHVGETTAKELANY--FKNLECMFKA-------TEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       519 l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~a-------s~eeL~~i~GIG~~~A~~I~~  573 (655)
                      +........|||||+++|++|.+.  -|.+..+...       ...+|.+|+|||+++|..+++
T Consensus        76 i~~~~~l~~lpGIG~~ia~kI~E~l~tG~~~~le~l~~d~~~~~l~~l~~I~GvGpk~a~~ly~  139 (381)
T 1jms_A           76 ITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFR  139 (381)
T ss_dssp             CCSGGGGTTCSSCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHHTSTTCCHHHHHHHHH
T ss_pred             ccCHHHHhcCCCCcHHHHHHHHHHHHcCCcHHHHHHhcCcchhHHHHHHccCCCCHHHHHHHHH
Confidence            333334569999999999988773  4555544432       246899999999999999876

>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A

Probab=92.99  E-value=0.25  Score=49.16  Aligned_cols=44  Identities=16%  Similarity=0.080  Sum_probs=30.9

Q ss_pred             HHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        468 KMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      +.+.+|.+.-.--++++|..++.++|..+ ||+..++..|.+.-+
T Consensus        81 ~~~~rL~~~~G~ptp~~la~~~~e~Lr~~-G~~~~KA~~i~~lA~  124 (225)
T 2yg9_A           81 AIYGRLEGLPGGVVPAALLKVSGDDLRGV-GLSWAKVRTVQAAAA  124 (225)
T ss_dssp             HHHHHHHTSTTCSCHHHHTTSCHHHHHHT-TCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcCCHHHHHcCCHHHHHHC-CCcHHHHHHHHHHHH
Confidence            34555655522368899998988888776 888878877766443

>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=92.50  E-value=0.068  Score=47.76  Aligned_cols=46  Identities=20%  Similarity=0.325  Sum_probs=42.6

Q ss_pred             CccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        530 HVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       530 gIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      |||+..+++|.+. |.+++.|..++..+|.+++|||+..|+.|.+..
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            8899999999975 999999999999999999999999999998764

>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=92.02  E-value=0.028  Score=56.09  Aligned_cols=50  Identities=20%  Similarity=0.269  Sum_probs=0.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      ..+|+|+|++++++|.+.=  .|+..|...+.++|.++ |+|++.|++|.+.+
T Consensus       175 L~~IpGIG~k~ak~Ll~~F--GSl~~i~~As~eeL~~V-GIG~~~A~~I~~~f  224 (226)
T 3c65_A          175 LDDIPGVGEKRKKALLNYF--GSVKKMKEATVEELQRA-NIPRAVAEKIYEKL  224 (226)
T ss_dssp             -----------------------------------------------------
T ss_pred             ccccCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence            5579999999999999862  57788888899999999 99999999998765

>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=91.75  E-value=0.18  Score=53.20  Aligned_cols=74  Identities=15%  Similarity=0.121  Sum_probs=48.6

Q ss_pred             CcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhcC-----HHHHhcCCCCCHHHHHHH
Q psy11423        499 VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY--FKNLECMFKAT-----EEQLLNIPKIGSTTVKAF  571 (655)
Q Consensus       499 fG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~as-----~eeL~~i~GIG~~~A~~I  571 (655)
                      |.-..-.+-...|+.. ..++........|||||+++|++|.+.  -|.+..+....     .+.|.+|+|||+++|..+
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            4444445445555432 233444445669999999999988764  45555554432     244569999999999998


Q ss_pred             HH
Q psy11423        572 IK  573 (655)
Q Consensus       572 ~~  573 (655)
                      ++
T Consensus       113 ~~  114 (335)
T 2bcq_A          113 YQ  114 (335)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

>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=91.74  E-value=0.16  Score=54.16  Aligned_cols=52  Identities=15%  Similarity=0.146  Sum_probs=47.8

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      .||+||+++++.|+++=  .++..+++.+.++|...+|+|++.|..|.+++..-
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            49999999999999974  48999999999999999999999999999999764

>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=91.31  E-value=0.51  Score=48.69  Aligned_cols=71  Identities=17%  Similarity=0.174  Sum_probs=45.9

Q ss_pred             CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcC----HH
Q psy11423        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKAT----EE  555 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as----~e  555 (655)
                      -++++|..++.++|..+ |+|-| |..|.+.                         |+.+++...+++.+...+    .+
T Consensus       159 Ptpe~la~~~~e~L~~~-g~g~R-a~~I~~~-------------------------A~~i~~g~~~l~~l~~~~~~~~~~  211 (290)
T 3i0w_A          159 PTVDKLHEFTEKDFEEC-TAGFR-AKYLKDT-------------------------VDRIYNGELNLEYIKSLNDNECHE  211 (290)
T ss_dssp             CCHHHHTTCCHHHHHHT-TCGGG-HHHHHHH-------------------------HHHHHTTSSCHHHHHHSCHHHHHH
T ss_pred             CcHHHHHCCCHHHHHHc-CCchH-HHHHHHH-------------------------HHHHHhCCCCHHHHhcCCHHHHHH
Confidence            58899988888888885 78853 6555543                         222333333444444433    35


Q ss_pred             HHhcCCCCCHHHHHHHHHH-hcC
Q psy11423        556 QLLNIPKIGSTTVKAFIKF-INQ  577 (655)
Q Consensus       556 eL~~i~GIG~~~A~~I~~~-f~~  577 (655)
                      +|.+++|||+++|+.|.-| |..
T Consensus       212 ~L~~lpGIG~~TA~~ill~~lg~  234 (290)
T 3i0w_A          212 ELKKFMGVGPQVADCIMLFSMQK  234 (290)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHHCC
T ss_pred             HHHhCCCcCHHHHHHHHHHhCCC
Confidence            6888888888888888765 443

>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=91.15  E-value=0.061  Score=47.37  Aligned_cols=48  Identities=13%  Similarity=0.167  Sum_probs=43.8

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||+++..++++++.|||.+..+.|+..|.+.||+|++.+-|.+-+.
T Consensus        37 ~~GG~~~~~~~~~~THLV~~~~~~~K~~~a~~~~i~IV~~~Wl~dsi~   84 (109)
T 2cou_A           37 MQGGSYLPVGDERCTHLIVEENTVKDLPFEPSKKLFVVKQEWFWGSIQ   84 (109)
T ss_dssp             HHTCBCCCTTCTTCSEEEECTTTCSSCSSCCCTTSEEECHHHHHHHHH
T ss_pred             HcCCEEecccCCCccEEEEeCCccHHHHHHHHCCCeEecHHHHHHHHH
Confidence            789999999999999999988778899999999999999999988764

>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens}

Probab=91.10  E-value=0.07  Score=47.49  Aligned_cols=48  Identities=17%  Similarity=0.193  Sum_probs=44.4

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||+++..++++++.|||.+..+.|+..|++.||+|++.+-|.+-+.
T Consensus        46 ~~GG~~~~~l~~~cTHLV~~~~~~~K~~~A~~~~i~IVs~eWl~dsi~   93 (112)
T 3l46_A           46 MQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKKLYVVKQEWFWGSIQ   93 (112)
T ss_dssp             HTTCEECCTTCTTCSEEEECTTTBSSCSSCCCSSCEEEEHHHHHHHHH
T ss_pred             HcCCEECcccCCCceEEEecCCchhhHHHHHHCCeeEecHHHHHHHHH
Confidence            889999999999999999998888889889999999999999988774

>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=89.79  E-value=0.43  Score=49.30  Aligned_cols=56  Identities=20%  Similarity=0.360  Sum_probs=50.1

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      +..+++||++..+.+|-++| +.++.|+..+...+|..+.|+.++.+++++.+..+.
T Consensus         4 ~~~~l~gi~~~~~~kL~~~g-i~t~~~~~~~~~~~L~~~~gis~~~a~~~i~~a~~~   59 (322)
T 2i1q_A            4 NLTDLPGVGPSTAEKLVEAG-YIDFMKIATATVGELTDIEGISEKAAAKMIMGARDL   59 (322)
T ss_dssp             -CTTSTTCCHHHHHHHHHHT-CCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             cHhhcCCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHHHhhCcCHHHHHHHHHHHHHh
Confidence            45678999999999999999 589999999999999999999999999999887653

>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=89.38  E-value=0.8  Score=45.25  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=44.1

Q ss_pred             HHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (655)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs  545 (655)
                      ....|++.  ..++.+|..++.++|..+   -||...+|.+|.+..+.....        .+                ++
T Consensus        56 ~~~~l~~~--fptp~~la~a~~e~l~~~i~~~G~~~~KA~~l~~~a~~i~~~--------~~----------------g~  109 (221)
T 1kea_A           56 IYDKFFVK--YKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVIND--------YG----------------GR  109 (221)
T ss_dssp             HHHHHHHH--CCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHH--------HT----------------TS
T ss_pred             HHHHHHHH--CCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH--------hC----------------CC
Confidence            33445544  258899998888777332   277777787776654332110        00                01


Q ss_pred             HHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        546 LECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       546 l~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      ++    .+.++|.+++|||+++|..|..|
T Consensus       110 ~p----~~~~~L~~lpGIG~~TA~~il~~  134 (221)
T 1kea_A          110 VP----RNRKAILDLPGVGKYTCAAVMCL  134 (221)
T ss_dssp             CC----SCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             ch----HHHHHHHhCCCCcHHHHHHHHHH
Confidence            11    23566777777777777777664

>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=88.39  E-value=1  Score=44.77  Aligned_cols=70  Identities=17%  Similarity=0.167  Sum_probs=45.0

Q ss_pred             CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcC----HH
Q psy11423        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKAT----EE  555 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as----~e  555 (655)
                      -++.+|..++.++|..+ ||+..++..|.+.-+...         .-.               +.+++.+...+    .+
T Consensus        85 Ptp~~la~~~~e~Lr~~-G~~~rKa~~i~~~A~~~~---------~g~---------------~p~~~~l~~~~~~e~~~  139 (228)
T 3s6i_A           85 PTPEEIRDMDFEIMRAC-GFSARKIDSLKSIAEATI---------SGL---------------IPTKEEAERLSNEELIE  139 (228)
T ss_dssp             CCHHHHHHSCHHHHHHH-TCCHHHHHHHHHHHHHHH---------HTS---------------SCCHHHHTTSCHHHHHH
T ss_pred             CCHHHHHcCCHHHHHHc-CCCHHHHHHHHHHHHHHH---------cCC---------------CCChHHHhcCCHHHHHH
Confidence            58899999988888776 899888887776433211         111               11233333332    35


Q ss_pred             HHhcCCCCCHHHHHHHHHH
Q psy11423        556 QLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       556 eL~~i~GIG~~~A~~I~~~  574 (655)
                      +|.+++|||+++|+.|.-|
T Consensus       140 ~L~~l~GIG~~TA~~ill~  158 (228)
T 3s6i_A          140 RLTQIKGIGRWTVEMLLIF  158 (228)
T ss_dssp             HHTTSTTCCHHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHHH
Confidence            6777888888888777765

>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=88.01  E-value=1.1  Score=45.13  Aligned_cols=102  Identities=19%  Similarity=0.300  Sum_probs=68.8

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHh-CCCCccHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGET  534 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~al-gIpgIG~~  534 (655)
                      .+|=-||+|..+..|++.-  .+++.+++-+.+.+..+   .++.+..   --.+.+        --|+.| .-.|||.+
T Consensus       356 lidehglspdaadeliehf--esiagilatdleeiermyeegrlseea---yraave--------iqlaeltkkegvgrk  422 (519)
T 2csb_A          356 LIDEHGLSPDAADELIEHF--ESIAGILATDLEEIERMYEEGRLSEEA---YRAAVE--------IQLAELTKKEGVGRK  422 (519)
T ss_dssp             HHHHHCCCHHHHHHHHHHH--SSHHHHHTSCHHHHHHHHHHTSSCHHH---HHHHHH--------HHHHHHHTSTTCCHH
T ss_pred             HHHhcCCCcchHHHHHHHH--HHHHHHHhccHHHHHHHHHcccccHHH---HHHHHH--------HHHHHHhhhcccchh
Confidence            4567799999999998863  57777776444433322   1122211   111111        112222 55799999


Q ss_pred             HHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCHHHHHHHHH
Q psy11423        535 TAKELANYFKNLECMFKA----TEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       535 ~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~~~A~~I~~  573 (655)
                      +|.+|+..||+.+.+++.    ..+.|.++.|+|+.+..+++.
T Consensus       423 taerllrafgnpervkqlarefeieklasvegvgervlrslvp  465 (519)
T 2csb_A          423 TAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVP  465 (519)
T ss_dssp             HHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHHST
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHhHHHHhhccchHHHHHHHhcc
Confidence            999999999999988875    468899999999998888764

>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=87.53  E-value=1.6  Score=43.28  Aligned_cols=70  Identities=17%  Similarity=0.080  Sum_probs=38.8

Q ss_pred             HHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcc---cchhHHHHH-hCCCCccHHHHHHHHH
Q psy11423        470 IEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELAN  541 (655)
Q Consensus       470 i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~---~~l~r~L~a-lgIpgIG~~~Ak~L~~  541 (655)
                      ...|++.-  .++.+|..++.++|..+   -||...+|.+|.+.-+....   ..+...... +.+||||+++|..++.
T Consensus        55 ~~~l~~~f--pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~~TA~~il~  131 (226)
T 1orn_A           55 TKRLFEKY--RTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVS  131 (226)
T ss_dssp             HHHHHHHC--CSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSCCSCHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHC--CCHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHCCCccHHHHHHHHH
Confidence            34455442  58999999988875331   37877788877765543221   111111111 2566666666655543

>1xdn_A RNA editing ligase MP52; HET: MSE ATP; 1.20A {Trypanosoma brucei} SCOP: d.142.2.4

Probab=87.15  E-value=0.84  Score=46.55  Aligned_cols=201  Identities=17%  Similarity=0.112  Sum_probs=105.8

Q ss_pred             cccCCCCCCChHHHHHHHHHHHH-hhccCCCceEEEEEecceeEEEEEE-eCCEE--eEEEecCCCCccch---------
Q psy11423         88 KMMSLDNGFSDEDVIIFNKRITN-ELKLTKNIEYIAELKFDGIAVNLRY-EYGYL--KQASTRGDGNIGEN---------  154 (655)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~-~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l--~~a~TRGdG~~GeD---------  154 (655)
                      ...||+|-|..     |++++.. .+.   ...|+++.||||.-.++++ ++|..  ++.+.| +|..+++         
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            45688887754     4444432 222   3579999999999999998 46777  888898 5666533         


Q ss_pred             ---hhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH---HHcCCCCCCChhhhHHhHhhhcCccccccc
Q psy11423        155 ---ITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR---YHLGLKKFTNPRNAAAGILRQLNPKINKNK  228 (655)
Q Consensus       155 ---vT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~---~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r  228 (655)
                         .+..++.+..+........-+..+.|-||++=..=.+-...+.+   ...|++  ..||-+   +-=|+..=..-..
T Consensus        81 ~~~l~~~~~~l~~~l~~~~~~~~~~~v~VyGELfGg~y~hp~v~~~~~~~~~~~~~--~~p~~~---~~IQ~~i~~~Y~p  155 (277)
T 1xdn_A           81 IDEFTAQIRILNDLLKQKYGLSRVGRLVLNGELFGAKYKHPLVPKSEKWCTLPNGK--KFPIAG---VQIQREPFPQYSP  155 (277)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCSCCSEEEEEEEEEEEECCCTTSCCCCCEEECTTSC--EEEGGG---CCSCCCSSCCCEE
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCccEEEEEEEEecCccCCccccccccccccCccc--cCcccc---cccccccccccCC
Confidence               22233333333221110001568999999993220000000000   000000  012211   1012222001122


Q ss_pred             ceEEEEEecccccC-CC---CCCCHHHHHHHHHhC-CCCCCCCceeeCCHHHHHHHHHH-----HHHh---hc--CCCCc
Q psy11423        229 ILHFFAHGVGELRG-MN---MPSSHSELLNWYQKI-GLSICGEYSVLSGVNKLIEFYKK-----INIK---RF--NLPYE  293 (655)
Q Consensus       229 ~L~f~~y~~~~~~~-~~---~~~~~~e~l~~L~~~-GF~~~~~~~~~~~~~ev~~~~~~-----~~~~---r~--~l~y~  293 (655)
                      .++|++|+|..... .+   .--+..+.++.+.+. ||.+.+. ....+++++++|--+     +.+.   ..  .-+.-
T Consensus       156 ~~~FYaFDI~~~~~~~~~~~~~L~fd~~~~~~~~~~gl~~ap~-L~rGt~~e~~~~~~~~f~s~ip~~~g~~~~~~~~Ni  234 (277)
T 1xdn_A          156 ELHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARA-LVRGTLDECLAFDVENFMTPLPALLGLGNYPLEGNL  234 (277)
T ss_dssp             EEEEEEEEEEEESSCCGGGEEECCHHHHHHHHHTSTTCEECCC-SEEESHHHHHTCCGGGCBCSHHHHTTCTTSCCTTCB
T ss_pred             CceEEEEEEEEecCCCccccccCCHHHHHHHHHHhcCCCeeee-eeecCHHHHhhcccccccccchhhcCCCccCCCCCe
Confidence            69999999964321 11   014667888888885 9998874 345577777774221     1111   10  12223


Q ss_pred             cceEEEEECC
Q psy11423        294 IDGVVYKINC  303 (655)
Q Consensus       294 iDGiVikv~~  303 (655)
                      --|+|||-..
T Consensus       235 aEGvViKp~~  244 (277)
T 1xdn_A          235 AEGVVIRHVR  244 (277)
T ss_dssp             CCEEEEEETT
T ss_pred             eeeEEEeecc
Confidence            5799999875

>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=87.05  E-value=0.65  Score=53.48  Aligned_cols=53  Identities=17%  Similarity=0.277  Sum_probs=45.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      ..+.|||+|..++.+|+++| ++|+.||-.++.++|..++++|++..+.+...+
T Consensus       647 ~L~qlp~v~~~rar~L~~~G-~~s~~dl~~~~~~~l~~~~~~~~~i~~~~~~~~  699 (720)
T 2zj8_A          647 PLMQLPLVGRRRARALYNSG-FRSIEDISQARPEELLKIEGIGVKTVEAIFKFL  699 (720)
T ss_dssp             GGTTSTTCCHHHHHHHHTTT-CCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hhhhCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHhHhHHHHHHHHHHHhc
Confidence            35789999999999999888 599999999999999999999988776665443

>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=86.81  E-value=0.7  Score=48.71  Aligned_cols=54  Identities=24%  Similarity=0.202  Sum_probs=48.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .-.++|+|+.++++|-++|+ .++.++...+..+|..+.|+.+..+++++++..+
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 8999999999999999999999999999988754

>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A

Probab=86.33  E-value=0.54  Score=48.79  Aligned_cols=51  Identities=14%  Similarity=0.279  Sum_probs=42.9

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcC-----HHH----HhcCC-C-----CCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKAT-----EEQ----LLNIP-K-----IGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as-----~ee----L~~i~-G-----IG~~~A~~I~~~f~~  577 (655)
                      .||||+...|..|+++|+|+..|..|.     .++    |..+. |     ||+.+++.|+.+|..
T Consensus       241 ~IpGVs~~~A~~I~~~ypTp~~L~~Ay~~~~~~~e~~~lL~~i~~g~~~r~IG~~lS~kI~~~f~~  306 (311)
T 2ziu_A          241 QISGVSGDKAAAVLEHYSTVSSLLQAYDKCSSETEKEKLLSSVKYGKLKRNLGPALSRTIYQLYCT  306 (311)
T ss_dssp             TBTTCCHHHHHHHHHHCSSHHHHHHHHHHCSSHHHHTTTTTTCEETTTTEECHHHHHHHHHHHHHC
T ss_pred             hccCCCHHHHHHHHHHCCCHHHHHHHHHhcCCHHHHHHHHHhcccCCCCCCcCHHHHHHHHHHhcc
Confidence            899999999999999999999988874     232    56663 3     999999999999864

>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=85.92  E-value=0.7  Score=53.24  Aligned_cols=51  Identities=37%  Similarity=0.578  Sum_probs=47.9

Q ss_pred             hCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +.|||||..+|++|.+. +.|+..|..++.+++..++++|+++++++..++.
T Consensus       649 ~qlp~v~~~rar~L~~~G~~s~~dl~~~~~~~l~~~~~~~~~i~~~~~~~~~  700 (720)
T 2zj8_A          649 MQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLG  700 (720)
T ss_dssp             TTSTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHC
T ss_pred             hhCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHhHhHHHHHHHHHHHhcc
Confidence            48999999999999976 8999999999999999999999999999998886

>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=85.80  E-value=0.35  Score=47.95  Aligned_cols=48  Identities=17%  Similarity=0.297  Sum_probs=41.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcH-HHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLA  510 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~-Ksa~nll~~  510 (655)
                      ..+|+|+|+++.++|.+.=  .++..|...+.++|.++  +|+ +.|++|++.
T Consensus       170 LdgIpGIG~k~ak~Ll~~F--gSl~~i~~As~EeL~~V--IG~~~~A~~I~~~  218 (220)
T 2nrt_A          170 LDNVPGIGPIRKKKLIEHF--GSLENIRSASLEEIARV--IGSTEIARRVLDI  218 (220)
T ss_dssp             HTTSTTCCHHHHHHHHHHH--CSHHHHHTSCHHHHHHH--HTCHHHHHHHHHH
T ss_pred             ccCCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hChHHHHHHHHHH
Confidence            4579999999999999863  48889999999999999  999 999998764

>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family, hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A* 1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A

Probab=83.39  E-value=0.73  Score=43.47  Aligned_cols=72  Identities=11%  Similarity=0.113  Sum_probs=46.7

Q ss_pred             HHHHHHHcCCCCChHHHhcCChhhhccc-c--CCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423        469 MIEKLVNANIVVTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (655)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs  545 (655)
                      ...+|++..  .|+.+|..++.++|.++ .  ||-...|.+|.+.-+                                 
T Consensus        52 ~~~~l~~~~--pt~~~la~a~~~el~~~i~~lG~y~~KAk~i~~~a~---------------------------------   96 (161)
T 4e9f_A           52 VLWKFLEKY--PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSD---------------------------------   96 (161)
T ss_dssp             HHHHHHHHS--CSHHHHTTSCHHHHHHHHGGGSCHHHHHHHHHHHHH---------------------------------
T ss_pred             HHHHHHHHC--CCHHHHhccChHhHHhHhhhcCCHHHHHHHHHHHhC---------------------------------
Confidence            445566654  58888888887766443 2  444566666654211                                 


Q ss_pred             HHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        546 LECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       546 l~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                        .+...+.++|.++||||+.+|.++..|+-+
T Consensus        97 --~~vp~~~~~L~~LpGVG~yTAdav~~F~~~  126 (161)
T 4e9f_A           97 --EYLTKQWKYPIELHGIGKYGNDSYRIFCVN  126 (161)
T ss_dssp             --HHHHSCCSSGGGSTTCCHHHHHHHHHHTSS
T ss_pred             --CcCCCChhhhhcCCCchHHHHHHHHHHHCC
Confidence              111224568889999999999999888654

>2kz3_A Putative uncharacterized protein RAD51L3; RAD51D, homologous recombination, unknown function; NMR {Homo sapiens}

Probab=83.33  E-value=2.3  Score=35.63  Aligned_cols=53  Identities=21%  Similarity=0.260  Sum_probs=47.3

Q ss_pred             ccc-CCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNI-IGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I-~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+. |||.+..++.|-.++ |.|+.|++.++..+|.++=|.+-+.+..|.+.+.+
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 999999999998877 69999999999999999999999999888887754

>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A

Probab=83.21  E-value=3  Score=41.18  Aligned_cols=39  Identities=26%  Similarity=0.216  Sum_probs=24.6

Q ss_pred             HHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423        471 EKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ  512 (655)
Q Consensus       471 ~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~  512 (655)
                      ..|++.-  .++.+|..++.++|..+   =||. .+|.+|.+..+
T Consensus        53 ~~l~~~~--pt~~~la~~~~~~l~~~i~~~G~~-~kA~~l~~~a~   94 (225)
T 1kg2_A           53 ERFMARF--PTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQ   94 (225)
T ss_dssp             HHHHHHC--SSHHHHHHSCHHHHHHHHTTSCCT-HHHHHHHHHHH
T ss_pred             HHHHHHC--CCHHHHHCCCHHHHHHHHHhCChH-HHHHHHHHHHH
Confidence            3454432  58899998888887642   2666 45777665443

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A

Probab=83.06  E-value=0.61  Score=48.21  Aligned_cols=42  Identities=12%  Similarity=0.150  Sum_probs=31.3

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      ||||||+++|.+|++.|||++++...    +.++.  .+++.+++.++
T Consensus       207 GVpGIG~KTA~kLL~~~gsle~i~~~----~~~~~--~~~~~~~L~~~  248 (290)
T 1exn_A          207 GVEGIGAKRGYNIIREFGNVLDIIDQ----LPLPG--KQKYIQNLNAS  248 (290)
T ss_dssp             CCTTCCHHHHHHHHHHHCSHHHHHHH----CSCSC--CCHHHHHHHTC
T ss_pred             CCCcCCHhHHHHHHHHcCCHHHHHHH----HHHhc--cHHHHHHHHHh
Confidence            89999999999999999999988753    22330  33666666654

>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1

Probab=82.83  E-value=1.5  Score=42.89  Aligned_cols=33  Identities=15%  Similarity=0.189  Sum_probs=21.9

Q ss_pred             CChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423        480 VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ  512 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~  512 (655)
                      .++.+|..++.++|..+   -||...+|.+|.+.-+
T Consensus        59 pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~   94 (211)
T 2abk_A           59 NTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCR   94 (211)
T ss_dssp             CSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHH
T ss_pred             CCHHHHHCCCHHHHHHHHHHcCCChHHHHHHHHHHH
Confidence            57888888877776442   2676667777766543

>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens}

Probab=81.79  E-value=3.5  Score=42.44  Aligned_cols=38  Identities=11%  Similarity=-0.003  Sum_probs=23.0

Q ss_pred             HHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHH
Q psy11423        471 EKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAI  511 (655)
Q Consensus       471 ~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I  511 (655)
                      ..|++.-  .++.+|..++.++|..+   =||.. +|.+|.+.-
T Consensus        72 ~rL~~~f--ptpe~La~a~~eel~~~ir~lG~~~-KA~~L~~~A  112 (287)
T 3n5n_X           72 TGWMQKW--PTLQDLASASLEEVNQLWAGLGYYS-RGRRLQEGA  112 (287)
T ss_dssp             HHHHHHC--CSHHHHHTSCHHHHHHHHTTSSCHH-HHHHHHHHH
T ss_pred             HHHHHHC--CCHHHHHcCCHHHHHHHHHHcCCHH-HHHHHHHHH
Confidence            3455442  58888888887776432   26654 576666543

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=81.57  E-value=1.7  Score=46.87  Aligned_cols=54  Identities=20%  Similarity=0.283  Sum_probs=48.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .|.=-||+++++++|-++|+ .++.|+...+..+|..+.|+.+..+++|++++.+
T Consensus        85 ~l~~~gi~~~~~~~L~~ag~-~tv~~~~~~~~~~L~~~~gis~~~~~~i~~~a~~  138 (400)
T 3lda_A           85 KLQVNGITMADVKKLRESGL-HTAEAVAYAPRKDLLEIKGISEAKADKLLNEAAR  138 (400)
T ss_dssp             GGCCTTCCHHHHHHHHHTTC-CBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            34445799999999999996 8999999999999999999999999999988764

>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=80.70  E-value=2.8  Score=43.68  Aligned_cols=64  Identities=14%  Similarity=0.168  Sum_probs=51.5

Q ss_pred             HhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        448 KAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       448 ~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+++-..-+ ..+.+||+|+..+++|.++| ++++.||..++.+++..+-|++++..+.+.+.++.
T Consensus       149 ~q~~w~~~~-pL~Qlp~i~~~~~~~l~~~~-i~s~~~l~~~~~~e~~~ll~~~~~~~~~v~~~~~~  212 (328)
T 3im1_A          149 IQGVWDVDN-PLRQIPHFNNKILEKCKEIN-VETVYDIMALEDEERDEILTLTDSQLAQVAAFVNN  212 (328)
T ss_dssp             HHTSCTTSC-GGGGSTTCCHHHHHHHHHTT-CCSHHHHHHSCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_pred             HhhcCCCCC-ceeCCCCCCHHHHHHHHhCC-CCCHHHHhcCCHHHHHhHhCCCHHHHHHHHHHHHh
Confidence            344444443 57899999999999999877 69999999999988888778888888888777654

>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=80.14  E-value=1.3  Score=37.48  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=38.6

Q ss_pred             CCCCeEecccc-cCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFIS-KNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVs-k~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++....+ .+++++|++...+.|.+.|+  +++|++++-+.+-++
T Consensus        37 ~~GG~~~~~~~~~~~THlI~~~~~~~k~~~~~--~~~iV~p~Wl~dci~   83 (97)
T 2ebw_A           37 LHGGQYHVYYSRSKTTHIIATNLPNAKIKELK--GEKVIRPEWIVESIK   83 (97)
T ss_dssp             HTTCEECSSCCSSSCCEEECSCCCTTHHHHTS--SSCCBCTHHHHHHHH
T ss_pred             HcCCEEeeecCCCCCEEEEecCCChHHHHHhc--CCCEeChHHHHHHHH
Confidence            78898877665 57889999988788888776  999999999988774

---

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	655
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	8e-70
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	9e-68
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	9e-63
d1dgsa1	181	a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, do	7e-24
d1dgsa2	86	b.40.4.6 (A:315-400) NAD+-dependent DNA ligase {Th	1e-22
d2a1jb1	78	a.60.2.5 (B:219-296) DNA excision repair protein E	7e-13
d1l7ba_	92	c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4	4e-10
d1x2ia1	68	a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF201	8e-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	5e-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 = 8e-70
 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 = 9e-68
 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 =  209 bits (531), Expect = 9e-63
 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 = 7e-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 = 89.9 bits (223), 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

>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 = 62.3 bits (151), Expect = 7e-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

>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 = 54.7 bits (132), Expect = 4e-10
 Identities = 19/51 (37%), Positives = 32/51 (62%)

Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFSTE 652
           G KV + +S+ T+YLV G+ PG KLEKA  L +  L E+   ++++  + +
Sbjct: 34  GAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEARTGK 84

>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 = 8e-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 = 5e-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	655
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	100.0
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	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
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	99.29
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	99.2
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	99.16
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	99.13
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	99.05
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	98.89
d1x9na3	220	DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId:	98.8
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	98.64
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	98.62
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	98.57
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	98.54
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	98.52
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	98.43
d1a0ia2	239	ATP-dependent DNA ligase, N-terminal domain {Bacte	97.96
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	97.88
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	97.71
d1fvia2	188	ATP-dependent DNA ligase, N-terminal domain {Chlor	97.66
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	97.56
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	97.52
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	97.48
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	97.45
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	97.41
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	97.4
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	97.21
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	97.11
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	97.04
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	96.77
d1p16a2	245	mRNA capping enzyme alpha subunit {Yeast (Candida	96.47
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	96.19
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	96.18
d1lb2b_	72	C-terminal domain of RNA polymerase alpha subunit	96.17
d1z3eb1	67	C-terminal domain of RNA polymerase alpha subunit	96.14
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	96.11
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.1
d2csba3	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	95.75
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	95.48
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	95.47
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	94.5
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	94.21
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.18
d1xdna_	265	RNA editing ligase MP52 {Trypanosoma brucei [TaxId	94.07
d1ckma2	228	RNA guanylyltransferase (mRNA capping enzyme), N-t	92.84
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	92.53
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	92.19
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	92.13
d1u9la_	68	Transcription elongation protein NusA {Escherichia	92.1
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	92.05
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	91.78
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	91.57
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	91.55
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	91.36
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	90.86
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	90.77
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	90.57
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	90.19
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	89.53
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	88.99
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	88.01
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	87.83
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	87.5
d1u9la_	68	Transcription elongation protein NusA {Escherichia	87.13
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	85.08
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	85.03
d1zeta2	273	DNA polymerase iota {Human (Homo sapiens) [TaxId:	84.62
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	83.07
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	82.85
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	82.4
d1s68a_	233	RNA ligase 2, N-terminal domain {Bacteriophage T4	81.95
d1cmwa1	116	5' to 3' exonuclease domain of DNA polymerase Taq	81.79
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	81.68
d1jx4a2	240	DinB homolog (DBH) {Archaeon Sulfolobus solfataric	81.49
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	81.44
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	80.91
d2q0zx1	176	Protein pro2281 {Human (Homo sapiens) [TaxId: 9606	80.07

>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=1.6e-84  Score=685.65  Aligned_cols=312  Identities=39%  Similarity=0.641  Sum_probs=297.9

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecccc
Q psy11423          9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFK   88 (655)
Q Consensus         9 ~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~p   88 (655)
                      .++..+++|+++|+++|++||++||+.|+|+|||++||+|+++|++||++||++++++|||++||+.+...|.+++|+.|
T Consensus         2 ~~~~~~~~~~~~L~~~i~~~~~~Yy~~~~p~iSD~eYD~L~~~L~~le~~~p~~~~~~s~~~~vg~~~~~~~~~~~h~~p   81 (313)
T d1ta8a_           2 LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIP   81 (313)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCCCBCSSCCEEECSSC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCccccCCCCcccccccccccccccccchhc
Confidence            35677789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcc
Q psy11423         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (655)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (655)
                      |+||+|+++.+++..|..++.+.++.  +..|+||||+||+|++|+|++|+|++|+|||||.+|+|||+|+++|.+||.+
T Consensus        82 m~sl~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~KiDG~si~l~Y~~G~l~~a~TRGdG~~GeDiT~~~~~i~~ip~~  159 (313)
T d1ta8a_          82 MYSLNDGFSKEDIFAFDERVRKAIGK--PVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMR  159 (313)
T ss_dssp             CCCCCEECSHHHHHHHHHHHHHHHSS--CCCEEEEEEECSEEEEEEEETTEEEEEEECTTSSEEEBCHHHHTTCTTSCSB
T ss_pred             ccccccccchhhhhhhhhhhhhhccc--ccceeeeeecccceEEEEecCCcEEEeeecccchHHHHHHHhhhhhcccccc
Confidence            99999999999999999999877753  5689999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCC
Q psy11423        169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS  248 (655)
Q Consensus       169 l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~  248 (655)
                      |+   .|..++||||+||++++|.++|+++.+++++.|+||||+|||+||++++..+..|.|+|++|.+....... ..+
T Consensus       160 l~---~~~~~~iRGEl~~~~~~f~~~n~~~~~~~~~~f~N~RN~vaG~l~~k~~~~~~~~~l~f~~y~v~~~~~~~-~~~  235 (313)
T d1ta8a_         160 LT---EPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK-AKT  235 (313)
T ss_dssp             CS---SCCCEEEEEEEECCHHHHHHHHHHHHHTTCCCCSSHHHHHHHHHTCSBHHHHHTSCCEEEEEEESCCTTCC-CSB
T ss_pred             cc---CCcceeeeeEEEEeccchhhhHHHHHHhcccccccchhhhcccchhcccchhhhccccceeeecceecccc-cch
Confidence            97   47889999999999999999999999999999999999999999999999999999999999998754433 478


Q ss_pred             HHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        249 HSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       249 ~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                      |.+.+.+|+.+||.++++...+.+++++.+|+++|.+.|.+++|+|||||||+||..+|+.||+|+|+||||||||||
T Consensus       236 ~~~~~~~l~~~g~~~~~~~~~~~~~~ei~~~~~~~~~~R~~l~YeIDGIVikvn~~~~q~~lG~ts~~PrwAiA~KfP  313 (313)
T d1ta8a_         236 QFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP  313 (313)
T ss_dssp             HHHHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHTGGGSSSCEEEEEEEESBHHHHHHHCBCSSSBSSEEEEECC
T ss_pred             hHHHhhhhhhcCCcCCCCeEEeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEEeCHHHHHHcCCcCCCCCceEEecCC
Confidence            999999999999999998999999999999999999999999999999999999999999999999999999999998

>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=1.7e-84  Score=685.19  Aligned_cols=310  Identities=42%  Similarity=0.695  Sum_probs=294.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccC
Q psy11423         12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMS   91 (655)
Q Consensus        12 ~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlS   91 (655)
                      .++++||++|+++|++||++||+.|+|+|||++||+|+++|++||++||++..++|||++||+.+...|.+++|+.||+|
T Consensus         3 ~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~l~~~~s~~~~v~~~~~~~~~~~~h~~pmlS   82 (312)
T d1b04a_           3 QQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMS   82 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHHHHHHCGGGCCTTCGGGGTCCCCCSCCCEECCSSCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCCccccccccccccccccccccccc
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423         92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI  171 (655)
Q Consensus        92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~  171 (655)
                      |+|+++.+++..|.+++....+   ...|+|||||||+|++|+|++|+|++|+|||||.+|+|||+|+++|++||+++. 
T Consensus        83 l~~~~~~~~~~~~~~~~~~~~~---~~~~~v~~KlDG~si~l~Y~~G~l~~a~TRGdG~~GeDIT~~~~~i~~iP~~~~-  158 (312)
T d1b04a_          83 LANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK-  158 (312)
T ss_dssp             CCEECSTTHHHHHHHHHHHHHS---SCCEEEEEEESSEEEEEEEETTEEEEEEECTTSSCEEBCHHHHHTCTTSCSBCS-
T ss_pred             cccccchhhccchhhccccccc---ccceeeeeeeecceeeeeecccceEEEeecCCcchhhhHHHHHhhhcCCCCccC-
Confidence            9999999999999999877654   468999999999999999999999999999999999999999999999999996 


Q ss_pred             CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423        172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE  251 (655)
Q Consensus       172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e  251 (655)
                        .|..++||||+||++++|+++|+.+.+.|+++|+||||+|||+||+++|..+..|.|+|++|.++...... +.+|++
T Consensus       159 --~~~~~~irGE~~~~~~~f~~~~~~~~~~~~~~f~NpRN~aAG~l~~k~~~~~~~~~l~~~~y~~~~~~~~~-~~~~~e  235 (312)
T d1b04a_         159 --EPVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHSE  235 (312)
T ss_dssp             --SCCCEEEEEEEECCHHHHHHHHHHHHHC--CCCSCHHHHHHHHHHSSCHHHHHHTCCEEEEEEETTTTTTT-CCBHHH
T ss_pred             --CCcccccccceeeecchhhhhhhhhhhccccccchhhHHhhcccccccchhhhhhhhhheeeecccccccc-chhHHH
Confidence              47899999999999999999999999999999999999999999999999999999999999998755433 589999


Q ss_pred             HHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423        252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK  328 (655)
Q Consensus       252 ~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~  328 (655)
                      .|++|+.+||+++++...+.+++++.+|+++|.+.|..+||+|||||||+||..+|+.||+|+++||||||||||+|
T Consensus       236 ~l~~L~~~gf~~~~~~~~~~~~~~v~~~~~~~~~~R~~l~Y~iDGIVikvn~~~~~~~lG~ts~~PrwAiA~Kfpae  312 (312)
T d1b04a_         236 ALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE  312 (312)
T ss_dssp             HHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHHHSTTCSSCEEEEEEEECBHHHHHHHCCCSSSCTTEEEEECCCC
T ss_pred             HHHHHHhcCcccccceEEECCHHHHHHHHHHHHhhhhcCCCCCCeEEEEEcCHHHHHHcCCcCCCCCceEEeCcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999986

>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=1.7e-84  Score=685.67  Aligned_cols=310  Identities=40%  Similarity=0.595  Sum_probs=290.1

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccC-CCCcceecccc
Q psy11423         10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGG-ENSKYVHHTFK   88 (655)
Q Consensus        10 ~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~-~~~~kv~H~~p   88 (655)
                      +-.+++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||+|..++|||++||+.+. ..|.||+|++|
T Consensus         2 ~~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~le~~~p~l~~~~s~~~~vg~~~~~~~~~kv~h~~p   81 (314)
T d1dgsa3           2 TREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTR   81 (314)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHHHTTSSGGGCCTTSGGGGCSSSCCCCCCCEEECSSC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCccccccccccccccccccccee
Confidence            34567899999999999999999999999999999999999999999999999999999999999875 67999999999


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcc
Q psy11423         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV  168 (655)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~  168 (655)
                      ||||+|+|+.+|+..|.+|+.+.+.  .+..|+|||||||+|+ |+|++|  ++|+|||||.+|+|||+|+++|++||++
T Consensus        82 MlSL~k~~~~~~~~~~~~r~~~~~~--~~~~~~ve~KlDG~Si-L~y~~G--v~~~TRGdG~~GeDiT~~~~~I~~iP~~  156 (314)
T d1dgsa3          82 MYSLDNAFTYEEVLAFEERLEREAE--APSLYTVEHKVDGLSV-LYYEEG--VWSTGSGDGEVGEEVTQNLLTIPTIPRR  156 (314)
T ss_dssp             CCCCCEECSHHHHHHHHHHTTSSSC--SCCEEEEEECCSCEEE-EEEETT--EEEEEECSSSEEEBCTGGGTSSTTSCSB
T ss_pred             eeccccccchhhhhhhhhhhhcccc--ccchhhhhhccCcceE-EEecCC--EeEEeecCCceehhhHhhHhhhcCcchh
Confidence            9999999999999999999876553  2467999999999999 999999  5799999999999999999999999999


Q ss_pred             cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC--CCCC
Q psy11423        169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMP  246 (655)
Q Consensus       169 l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~--~~~~  246 (655)
                      |++  .|..++||||+||++++|+++|+++.+.++++|+||||+|||+||++++.+++.|.|+|++|.++....  ...+
T Consensus       157 l~~--~~~~l~IRGEl~i~~~~F~~~n~~~~~~~~~~f~NpRN~aaG~l~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  234 (314)
T d1dgsa3         157 LKG--VPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGL  234 (314)
T ss_dssp             CSS--CCSEEEEEEEEECCHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHSCSSHHHHHHSCCEEECCCBCTTTTTTSCCC
T ss_pred             ccC--CCccceeeeeEEeecchHHHHHHHHHHhcCCcccccchhhhhhhhcccchhhhhccccceeeeccccccccCCCc
Confidence            974  689999999999999999999999999999999999999999999999999999999999998865322  1235


Q ss_pred             CCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       247 ~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                      .+|.+.+.+|..|||++++....+.+.+++.+++++|.+.|..+||+|||||||+||..+|+.||+|+|+||||||||||
T Consensus       235 ~~~~e~~~~l~~~g~~~~~~~~~~~~~e~l~~~~~~~~~~R~~l~y~iDGiVikvnd~~~q~~LG~ts~~PrwAiA~KfP  314 (314)
T d1dgsa3         235 KSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFP  314 (314)
T ss_dssp             CBHHHHHHHHHHTTCCCCSCEEEEEHHHHHHHHHHHHHHTTTTSSSCCCEEEEEESBTHHHHHSCBCSSCBSSEEEEECC
T ss_pred             ccHHHHHHhhhcccccCCcceEEECCHHHHHHHHHHHHHhhhcCCCCCCceEEEEeCHHHHHHhCcccCCCCceEEecCC
Confidence            89999999999999999998888999999999999999999999999999999999999999999999999999999998

>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=6.4e-49  Score=381.53  Aligned_cols=179  Identities=34%  Similarity=0.675  Sum_probs=173.4

Q ss_pred             CCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh
Q psy11423        414 IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL  493 (655)
Q Consensus       414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L  493 (655)
                      ||++||+||++|+++  +..+||+|+ . ||+|++++|.||+||++|||+|||+++|++|+++|+|++++|||.|+.++|
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 7 999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11423        494 LRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       494 ~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~  573 (655)
                      ..|+|||+|+++||+++|+.||+.+++|||+||||||||+++|+.|+++|+++++|..|+.++|.+|+|||+++|++|++
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 psy11423        574 FINQPLHRLLISQLRDVGIYWLN  596 (655)
Q Consensus       574 ~f~~~~n~~li~~L~~~Gi~~~~  596 (655)
                      ||+++.|++++++|.+.||++..
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=1.1e-31  Score=226.55  Aligned_cols=85  Identities=41%  Similarity=0.696  Sum_probs=81.8

Q ss_pred             cceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCC
Q psy11423        327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP  406 (655)
Q Consensus       327 ~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~  406 (655)
                      +++++|+|++|+|||||||++||||+|+||.|+|++|+||||||+++|+++||++||+|.|.|||||||+|++|+.++|+
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            57899999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             CCCcc
Q psy11423        407 NDSKI  411 (655)
Q Consensus       407 ~~~~~  411 (655)
                      +.++|
T Consensus        81 ~~~~p   85 (86)
T d1dgsa2          81 GKERP   85 (86)
T ss_dssp             SCCCB
T ss_pred             CCCCc
Confidence            77654

>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=99.29  E-value=9.1e-13  Score=109.08  Aligned_cols=71  Identities=23%  Similarity=0.385  Sum_probs=64.6

Q ss_pred             HHH-HhcccchhHHHHHh-CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhH
Q psy11423        510 AIQ-KSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (655)
Q Consensus       510 ~I~-~sk~~~l~r~L~al-gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n  580 (655)
                      +|. ++++.++++++.+| +|||||++.|++|+++|+|+++|..|+.++|.+|+|||+++|++|++||++|..
T Consensus         4 aike~~~~~~~~~~~~~L~~I~gIg~~~a~~L~~~F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~pf~   76 (78)
T d2a1jb1           4 LLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFL   76 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCSC
T ss_pred             HHHHHHcCCcHHHHHHHhcCCCCcCHHHHHHHHHHhCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcCccc
Confidence            443 45566788999999 999999999999999999999999999999999999999999999999998754

>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=99.20  E-value=3.7e-12  Score=98.59  Aligned_cols=51  Identities=20%  Similarity=0.325  Sum_probs=49.9

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      .|||||+++|++|+++|+|+++|.+|+.++|.+|+|||+++|++|++||++
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            799999999999999999999999999999999999999999999999985

>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=99.16  E-value=1.7e-11  Score=98.61  Aligned_cols=55  Identities=29%  Similarity=0.485  Sum_probs=52.4

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhH
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH  580 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n  580 (655)
                      .||||||+++|++|+++|+|++.|.+|+.++|.+|+|||+++|++|++||+.+.+
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            3999999999999999999999999999999999999999999999999987653

>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=99.13  E-value=2.3e-11  Score=98.37  Aligned_cols=53  Identities=23%  Similarity=0.433  Sum_probs=51.3

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP  578 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~  578 (655)
                      .+|||||+++|++|+++|+|++.+.+|+.++|.+|+|||+++|++|++||+.+
T Consensus        16 ~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~~~   68 (70)
T d2bgwa1          16 QSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP   68 (70)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSC
T ss_pred             cCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHhCc
Confidence            39999999999999999999999999999999999999999999999999875

>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=99.05  E-value=3.2e-11  Score=102.67  Aligned_cols=51  Identities=37%  Similarity=0.639  Sum_probs=48.4

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHhccc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGFS  650 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~~~~  650 (655)
                      .+||+++++||++|||||+|+.+|+|+++|+++||+||+|++|++||+..+
T Consensus        32 ~~Gg~v~~sVs~~t~~LV~g~~~g~K~~kA~~~gI~IisE~~f~~~l~~~~   82 (92)
T d1l7ba_          32 RLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEART   82 (92)
T ss_dssp             HTTCEEESCCSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHHH
T ss_pred             HhCCEEcCccccceeEEEECCCCCcHHHHHHHcCCcEecHHHHHHHHHhCC
Confidence            789999999999999999999999999999999999999999999997543

>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=98.89  E-value=4.8e-10  Score=88.27  Aligned_cols=53  Identities=19%  Similarity=0.334  Sum_probs=50.5

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL  579 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~  579 (655)
                      .+|||||++++++|+++|+|+++|.+||.++|.+++| |++.|+.|++||+.+.
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            4899999999999999999999999999999999999 9999999999998753

>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=98.80  E-value=2.2e-08  Score=97.41  Aligned_cols=159  Identities=16%  Similarity=0.175  Sum_probs=104.2

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhccc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK  196 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~  196 (655)
                      ..|++|+|+||+-|.+.+.+|.=+++.||    .|.|+|++...|.. ++. +... .+..+.+-||++.-..+.     
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    58999987765443 332 2211 234688999999754321     


Q ss_pred             HHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc-----eee
Q psy11423        197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY-----SVL  270 (655)
Q Consensus       197 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~-----~~~  270 (655)
                             . --.+.+..++..+...+......++.|++|++...++..+ -.+..+..+.|.++--+.....     ..+
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 1123343444434444444445579999999976544322 2578899999988765544322     235


Q ss_pred             CCHHHHHHHHHHHHHhhcCCCCccceEEEEE
Q psy11423        271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKI  301 (655)
Q Consensus       271 ~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv  301 (655)
                      .+.+++.++++.+.+.      ...|+|+|-
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            7889999988876543      247999995

>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=98.64  E-value=2.1e-08  Score=78.16  Aligned_cols=56  Identities=20%  Similarity=0.324  Sum_probs=51.6

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL  516 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~  516 (655)
                      .+|||+||+++++|+++|+ .|+.+|...+.++|.+++|||++.|++|+++..+..+
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 9999999999999999999999999999998766443

>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=98.62  E-value=2.4e-08  Score=77.83  Aligned_cols=51  Identities=22%  Similarity=0.246  Sum_probs=47.8

Q ss_pred             hCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      ..|||||++++++|.++ |+|++.|..+++++|.+++|||+++|++|++.++
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            37999999999999997 9999999999999999999999999999988754

>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=3.4e-08  Score=77.23  Aligned_cols=57  Identities=25%  Similarity=0.226  Sum_probs=52.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      |...+|||+||+++++|+++|+ .|+.+|...+.++|.+++|+|++.|++|+++..+.
T Consensus         1 ~~L~~i~GIG~~~a~~L~~~g~-~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar~~   57 (61)
T d1pzna1           1 RSIEDLPGVGPATAEKLREAGY-DTLEAIAVASPIELKEVAGISEGTALKIIQAARKA   57 (61)
T ss_dssp             CCSSCCTTCCHHHHHHHHTTTC-CSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CccccCCCCCHHHHHHHHHhcC-CCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence            3467999999999999999986 89999999999999999999999999999987654

>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=98.54  E-value=5.2e-08  Score=76.78  Aligned_cols=56  Identities=20%  Similarity=0.268  Sum_probs=52.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      +.|.++|+|++++++|+++|+ .|+.+|...+.++|..++|||+++|++|+++..+.
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            358899999999999999996 99999999999999999999999999999998764

>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=2.3e-08  Score=80.24  Aligned_cols=57  Identities=21%  Similarity=0.238  Sum_probs=52.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhc
Q psy11423        458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK  515 (655)
Q Consensus       458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk  515 (655)
                      +.|+++|+|++++++|+++|+ .|+.+|..++.++|..++||++++|++|++++++.-
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            357899999999999999996 999999999999999999999999999999987653

>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=98.43  E-value=7.8e-08  Score=75.07  Aligned_cols=50  Identities=24%  Similarity=0.319  Sum_probs=47.1

Q ss_pred             CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      .|||||+++|++|.+. |+|++.|..+++++|.+++|||+++|++|++.++
T Consensus         5 ~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar   55 (61)
T d1pzna1           5 DLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAAR   55 (61)
T ss_dssp             CCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            7999999999999985 8999999999999999999999999999998764

>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=97.96  E-value=3.2e-05  Score=74.86  Aligned_cols=174  Identities=14%  Similarity=0.065  Sum_probs=99.4

Q ss_pred             eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhh------hhhhcccCCccccc--CCCCceEEEEEEEEeehhh
Q psy11423        119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITT------NIHIIHKIPLVLNI--KYPPELLEVRCEVLIYKKD  190 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~------n~~~i~~iP~~l~~--~~~p~~~evRGEv~~~~~~  190 (655)
                      .+++|+|+||+-+.+.+.++.-+...||    .|.++|+      ....   +|..+..  ...|..+.+-||++....+
T Consensus        27 ~~~~E~K~DG~R~~~~~~~~~~~~~~SR----~g~~~~~l~~~~~~~~~---~~~~~~~~~~~~~~~~vLDGEl~~~~~~   99 (239)
T d1a0ia2          27 YLIAEIKYDGVRGNICVDNTANSYWLSR----VSKTIPALEHLNGFDVR---WKRLLNDDRCFYKDGFMLDGELMVKGVD   99 (239)
T ss_dssp             SEEEEECCCSEEEEEEEETTSEEEEECT----TSCBCGGGGGGCEECHH---HHHHHHSTTCCCTTEEEEEEEEEESSSC
T ss_pred             CEEEEEeeceEEEEEEEECCeEEEEEec----CCCcccchhhhhhhhhh---HHHHHHHHhhcCCcceEEeeeEeeccCC
Confidence            5899999999999999987766677788    5556553      2222   2222211  0146679999999999999


Q ss_pred             HHHHHHHHHHcCCCCCC--ChhhhHHhHhhhcCcc--cccccceEEEEEeccccc----CCC--C-CCCHHHHHHHH---
Q psy11423        191 FIKLNKYRYHLGLKKFT--NPRNAAAGILRQLNPK--INKNKILHFFAHGVGELR----GMN--M-PSSHSELLNWY---  256 (655)
Q Consensus       191 F~~~n~~~~~~g~~~f~--NpRN~aaG~lr~~d~~--~~~~r~L~f~~y~~~~~~----~~~--~-~~~~~e~l~~L---  256 (655)
                      |+.++..........-.  .+.+.....+++.+..  ....+++.|++|++...+    +..  . .....+.++.|   
T Consensus       100 f~~~~~~v~~~~~~~~~~~~~f~~l~~r~~~~~~~~~~~~~~~l~~~vfD~l~l~~~~~~~~~~~~~~~~~~r~~~l~~~  179 (239)
T d1a0ia2         100 FNTGSGLLRTKWTDTKNQEFHEELFVEPIRKKDKVPFKLHTGHLHIKLYAILPLHIVESGEDCDVMTLLMQEHVKNMLPL  179 (239)
T ss_dssp             TTTHHHHHHCCSCCSSBSSCC--------CCCSCCCCCBCTTTEEEEEEEEEEHHHHHHCCCEEEEHHHHHHHHHHHHHH
T ss_pred             cccchhhhhhcccccccccCCHHHHHhhhccCccchhhhhcccceEEEEEEeeccccccccchhhccccHHHHHHHHHHH
Confidence            99887765544332222  2334444445554332  334567999999975321    111  0 01223333322   


Q ss_pred             -HhC----CCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423        257 -QKI----GLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (655)
Q Consensus       257 -~~~----GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (655)
                       ...    .+..++ ...+.+.+++.++++...+.    .|  -|+|+|--+..+
T Consensus       180 ~~~~~~~~~~~~~~-~~~~~~~~el~~~~~~~~~~----g~--EGlmiK~~~s~Y  227 (239)
T d1a0ia2         180 LQEYFPEIEWQAAE-SYEVYDMVELQQLYEQKRAE----GH--EGLIVKDPMCIY  227 (239)
T ss_dssp             HHHHCTTSEEEECC-EEEESSHHHHHHHHHHHHTT----TC--CCEEEECTTCEE
T ss_pred             HhhcCCCccEEEee-eEecCCHHHHHHHHHHHHHC----CC--cEEEEeCCCCcc
Confidence             221    112222 34578999999998876432    33  599999766544

>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=97.88  E-value=2.1e-06  Score=65.58  Aligned_cols=52  Identities=19%  Similarity=0.295  Sum_probs=47.7

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .-+|||+||+++++|++. + .++.+|...+.++|.+++|+|++.|++|++.+.
T Consensus         4 L~~I~gVG~~~a~~L~~~-F-~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~l~   55 (56)
T d1kfta_           4 LETIEGVGPKRRQMLLKY-M-GGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   55 (56)
T ss_dssp             GGGCTTCSSSHHHHHHHH-H-SCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             cccCCCccHHHHHHHHHH-h-CCHHHHHHhhHHHHHhcCCCCHHHHHHHHHHHc
Confidence            348999999999999998 3 699999999999999999999999999998764

>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=97.71  E-value=1.7e-05  Score=62.80  Aligned_cols=50  Identities=12%  Similarity=0.321  Sum_probs=47.1

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .|||+|+++...|.+. + .++.+|+..+.++|..++|+|++.|++|.+.+.
T Consensus        14 ~I~gIG~~~a~~L~~~-f-~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~   63 (68)
T d1x2ia1          14 GLPHVSATLARRLLKH-F-GSVERVFTASVAELMKVEGIGEKIAKEIRRVIT   63 (68)
T ss_dssp             TSTTCCHHHHHHHHHH-H-CSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHH-c-CCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHh
Confidence            7999999999999998 4 699999999999999999999999999999875

>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=97.66  E-value=0.00014  Score=67.76  Aligned_cols=141  Identities=12%  Similarity=0.031  Sum_probs=82.7

Q ss_pred             ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423        118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY  197 (655)
Q Consensus       118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~  197 (655)
                      ..+++|||+||+-+..   ++   +..||    .|+++|....... ....     .+  ..+-||++.....|+.+   
T Consensus        19 ~p~~~e~K~DG~R~~~---~~---~l~SR----~g~~~~~~~~~~~-~~~~-----~~--~~lDGEl~~~~~~~~~~---   77 (188)
T d1fvia2          19 FPCLATPKIAGIRSVK---QT---QMLSR----TFKPIRNSVMNRL-LTEL-----LP--EGSDGEISIEGATFQDT---   77 (188)
T ss_dssp             SSEEEEECCCSEEEEE---SS---SEECT----TSCBCSCHHHHHH-HHHH-----SC--TTEEEEEECTTSCHHHH---
T ss_pred             CcEEEEeccccEeEEe---EE---EEEec----CCCccCCcChHHH-HhhC-----cc--ccccceeeccCCchhhh---
Confidence            3578999999988742   44   46899    5888986543211 1110     11  22689999877777543   


Q ss_pred             HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhC-------CCC----C-CC
Q psy11423        198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLS----I-CG  265 (655)
Q Consensus       198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------GF~----~-~~  265 (655)
                                      +|.+++..+.  ....+.|++|++.....   .....+.+..|+++       ...    . ..
T Consensus        78 ----------------~~~~~~~~~~--~~~~~~~~vfD~~~~~~---~~~~~~r~~~l~~~l~~~~~~~~~~~~~~~~~  136 (188)
T d1fvia2          78 ----------------TSAVMTGHKM--YNAKFSYYWFDYVTDDP---LKKYIDRVEDMKNYITVHPHILEHAQVKIIPL  136 (188)
T ss_dssp             ----------------HHHHHSCC------CCEEEEEEEECSSCT---TSCHHHHHHHHHHHHHHCGGGGGCSSEEEEEC
T ss_pred             ----------------HHHHhhcccc--cccccEEEEEEEecCcc---cccHHHHHHHHHHHHHhcccccccCceEEEee
Confidence                            4455544433  23358899999875432   13455555554432       111    0 01


Q ss_pred             CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423        266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST  306 (655)
Q Consensus       266 ~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~  306 (655)
                      ....+.+.+++.++++...+.    .  ..|+|+|--+..+
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~----G--~EGlmiK~~ds~Y  171 (188)
T d1fvia2         137 IPVEINNITELLQYERDVLSK----G--FEGVMIRKPDGKY  171 (188)
T ss_dssp             CCEEECSHHHHHHHHHHHHHT----T--CCSEEEECTTCCC
T ss_pred             eeEecCCHHHHHHHHHHHHHC----C--CcEEEEECCCCcc
Confidence            234577899999988876422    2  3899999755444

>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=97.56  E-value=8.3e-05  Score=59.09  Aligned_cols=53  Identities=17%  Similarity=0.209  Sum_probs=44.4

Q ss_pred             HHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        524 YALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       524 ~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      .-+.++|||+++|-.++..|. ++.|..+    +...|.++||||+++|+.|+--+++
T Consensus        10 ~Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~   66 (71)
T d1bvsa2          10 ALLSVSGVGPRLAMATLAVHD-AAALRQALADSDVASLTRVPGIGRRGAERIVLELAD   66 (71)
T ss_dssp             HHHTSSSCCHHHHHHHHHHSC-HHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHHHSSG
T ss_pred             HHhccCCcCHHHHHHHHHhCC-HHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHHHHHH
Confidence            334899999999999999985 6766654    7889999999999999999876654

>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=97.52  E-value=5.2e-05  Score=59.17  Aligned_cols=51  Identities=18%  Similarity=0.249  Sum_probs=46.9

Q ss_pred             HhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        525 ALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       525 algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .|..+|||+.++++|.+. |.|++.|..++.++|.+++|||++.|++|++-.
T Consensus         5 ~L~~~Gig~~~~~kL~~aG~~Tve~ia~~t~~~L~~i~Gi~e~~a~KIi~~A   56 (64)
T d1szpa1           5 KLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEA   56 (64)
T ss_dssp             GGCCTTCCHHHHHHHHTTSCCSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHhHCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHcCCCCHHHHHHHHHHH
Confidence            467899999999999986 999999999999999999999999999998743

>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=97.48  E-value=0.00012  Score=58.34  Aligned_cols=55  Identities=15%  Similarity=0.166  Sum_probs=44.7

Q ss_pred             HHHHhCCCCccHHHHHHHHHhCCCHHHHH----hcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        522 FIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       522 ~L~algIpgIG~~~Ak~L~~~fgsl~~l~----~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                      |..-.++.|||+++|-.++..|. .+++.    +.+...|.++||||+++|++|+--+++
T Consensus         9 F~~Li~V~GIGpk~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~   67 (73)
T d1ixra1           9 FELLLSVSGVGPKVALALLSALP-PRLLARALLEGDARLLTSASGVGRRLAERIALELKG   67 (73)
T ss_dssp             HHHHHSSSCCCHHHHHHHHHHSC-HHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTT
T ss_pred             HHHHhccCCcCHHHHHHHHHHcc-HHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHHh
Confidence            33344899999999999999886 55554    448899999999999999999876654

>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=97.45  E-value=5.8e-05  Score=59.86  Aligned_cols=51  Identities=12%  Similarity=0.309  Sum_probs=47.1

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .+|||+|++++.+|.++ + .++.+|...+.++|..++|+|++.|+.|.+.++
T Consensus        16 ~~IpgIG~~~a~~L~~~-F-~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~   66 (70)
T d2bgwa1          16 QSFPGIGRRTAERILER-F-GSLERFFTASKAEISKVEGIGEKRAEEIKKILM   66 (70)
T ss_dssp             HTSTTCCHHHHHHHHHH-H-SSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             cCCCCcCHHHHHHHHHH-h-CCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHh
Confidence            38999999999999998 3 689999999999999999999999999998875

>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=97.41  E-value=8e-05  Score=69.92  Aligned_cols=68  Identities=19%  Similarity=0.354  Sum_probs=50.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCC
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGI  528 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algI  528 (655)
                      +|+|+|+|+++++.|.++  ..++++|...+.++|..++|+|++.|+.|.+-+....+..+-.-|...|+
T Consensus       109 aLGI~~vG~~~Ak~La~~--f~sl~~l~~as~eeL~~I~GIG~~~A~si~~ff~~~~n~~~i~~L~~~Gv  176 (181)
T d1dgsa1         109 ALGLPGVGEVLARNLARR--FGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGV  176 (181)
T ss_dssp             HTTCSSCCHHHHHHHHHT--TSBHHHHTTCCHHHHHTSTTCCHHHHHHHHHHHHCHHHHHHHHHHHHTTC
T ss_pred             HHHhhhhhHHHHHHHHHH--hhhhhhhhhhHHHHHhhcCCcCHHHHHHHHHHHCCHHHHHHHHHHHHcCC
Confidence            678888888888888775  36788888888888888888888888888887776555555455555554

>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=97.40  E-value=4.7e-05  Score=61.71  Aligned_cols=51  Identities=10%  Similarity=0.124  Sum_probs=47.4

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .|+|+|++++..|.+. + .|+.+|+..+.++|..++|+|++.|++|.+.+..
T Consensus        23 ~I~gIg~~~a~~L~~~-F-~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~   73 (78)
T d2a1jb1          23 TVKSVNKTDSQTLLTT-F-GSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   73 (78)
T ss_dssp             TSTTCCHHHHHHHHHH-H-SSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS
T ss_pred             CCCCcCHHHHHHHHHH-h-CCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcC
Confidence            7999999999999987 3 6999999999999999999999999999998753

>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=97.21  E-value=0.00019  Score=58.02  Aligned_cols=50  Identities=18%  Similarity=0.281  Sum_probs=42.0

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHHH----hcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l~----~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +.+.|||+++|-.++..|. .+.|.    +-+...|.++||||+++|+.|+--+.
T Consensus        12 i~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk   65 (78)
T d1cuka2          12 IKTNGVGPKLALAILSGMS-AQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMK   65 (78)
T ss_dssp             HHSSSCCHHHHHHHHHHSC-HHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HccCCccHHHHHHHHHhCC-HHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            3799999999999999886 55554    44889999999999999999976554

>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=97.11  E-value=9.3e-05  Score=58.72  Aligned_cols=53  Identities=21%  Similarity=0.286  Sum_probs=47.5

Q ss_pred             HHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        523 IYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       523 L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +.-|.++|||+.++++|.+. |.|++.|..++.++|.+|+||+++.|++|++..
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            44566799999999999975 899999999999999999999999999998754

>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=97.04  E-value=0.00023  Score=54.91  Aligned_cols=52  Identities=15%  Similarity=0.170  Sum_probs=47.1

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS  514 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s  514 (655)
                      ..|||+|++++..|...-  .|+.+|..++.++|.+++| |++.|++|++-+...
T Consensus         6 ~~iPGIg~~~~~~Ll~~f--~Si~~l~~As~~eL~~v~G-~~~~A~~i~~f~~~~   57 (62)
T d2a1ja1           6 LKMPGVNAKNCRSLMHHV--KNIAELAALSQDELTSILG-NAANAKQLYDFIHTS   57 (62)
T ss_dssp             HTSTTCCHHHHHHHHHHC--SSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHCC
T ss_pred             hcCCCCCHHHHHHHHHHh--ccHHHHHhCCHHHHHHCcC-cHHHHHHHHHHHhhh
Confidence            579999999999999754  7999999999999999999 999999999988643

>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=96.77  E-value=0.0011  Score=52.08  Aligned_cols=49  Identities=20%  Similarity=0.399  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +|+..+...|-..| |.++.||..++.++|..++|||+|+.+.|.+.+++
T Consensus        14 ~LS~R~~N~L~~~g-I~tv~dL~~~s~~dLl~i~n~G~ksl~EI~~~L~~   62 (69)
T d1doqa_          14 GLSTRVLHSLKEEG-IESVRALLALNLKDLKNIPGIGERSLEEIKEALEK   62 (69)
T ss_dssp             TCCHHHHHHHHHTT-CCSHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcC-CccHHHHHHCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            78999999998888 69999999999999999999999999999988865

>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=96.47  E-value=0.0091  Score=57.23  Aligned_cols=158  Identities=14%  Similarity=0.036  Sum_probs=82.3

Q ss_pred             eEEEEEecceeEEEEEEe---C-CEEeEEEecCCCCccchhhhhhhhcccCCccc-ccCCCCceEEEEEEEEeehhhHHH
Q psy11423        119 EYIAELKFDGIAVNLRYE---Y-GYLKQASTRGDGNIGENITTNIHIIHKIPLVL-NIKYPPELLEVRCEVLIYKKDFIK  193 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~---~-G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l-~~~~~p~~~evRGEv~~~~~~F~~  193 (655)
                      +|+|++|.||+.+.|.+-   + ..-+..++|.+-..  .++ ++ .+...+... .....-....+.||++..+..+. 
T Consensus        61 ~Y~v~eK~DG~R~lL~i~~~~~~~~~~~li~R~~~~~--~~~-~~-~~~~~~~~~~~~~~~~~~tilDGElv~~~~~~~-  135 (245)
T d1p16a2          61 DYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYY--FIP-NI-HFPLSVNETREKPTYHHGTLLDGELVLENRNVS-  135 (245)
T ss_dssp             CEEEEEEECSEEEEEEEEEETTTEEEEEEEETTCCEE--ECC-SC-CCCSCTTCCSSSCCCCSSEEEEEEEEEECCSSS-
T ss_pred             CEEEEECcCCeEEEEEEEEcCCCceEEEEEeCCCCeE--Ecc-cc-ccccccccccccccccCCeeEEEEEEeecccCC-
Confidence            699999999999988652   1 23356788865422  111 11 111111111 01112234679999998744320 


Q ss_pred             HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCC-----------
Q psy11423        194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL-----------  261 (655)
Q Consensus       194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF-----------  261 (655)
                                                       .....|++|++....+..+ .....+.++.|..+=.           
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                                             1236789999876554332 1355666666644210           


Q ss_pred             -----CCCCCcee---eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423        262 -----SICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL  326 (655)
Q Consensus       262 -----~~~~~~~~---~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~  326 (655)
                           ........   ....+++...+    +....++|.+||+|++-.+..+.  .|      ||.-.||+-
T Consensus       183 ~~~~~~~~~~~~~~k~~~~~~~~~~l~----~~~~~~~~~~DGLIf~p~~~pY~--~G------r~~~~lKWK  243 (245)
T d1p16a2         183 DIVNSPEFPFKVGFKTMLTSYHADDVL----SKMDKLFHASDGLIYTCAETPYV--FG------TDQTLLKWK  243 (245)
T ss_dssp             HHHSCTTSCCEEEECCCEEGGGTHHHH----TTGGGCSSCEEEEEEEESSSCCC--SE------EEEEEEEEC
T ss_pred             ccccchhhhhhhhhhhhhhHHHHHHHH----HHhhhcCCCCCeEEEEcCCCCEe--CC------CCCCeEEeC
Confidence                 00000011   11122333322    34567899999999997665553  12      455556653

>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=96.19  E-value=0.0011  Score=52.73  Aligned_cols=51  Identities=24%  Similarity=0.346  Sum_probs=39.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQ  512 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~  512 (655)
                      .+.|.|+|||++-.+....   ++.+|.. +   +...|..+||+|+|+|++|+-.++
T Consensus        12 Li~V~GIGpk~Al~iLs~~---~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          12 LLSVSGVGPKVALALLSAL---PPRLLARALLEGDARLLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HHSSSCCCHHHHHHHHHHS---CHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HhccCCcCHHHHHHHHHHc---cHHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            6789999999999988643   4566665 2   345688889999999999987663

>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=96.18  E-value=0.0012  Score=52.20  Aligned_cols=50  Identities=18%  Similarity=0.380  Sum_probs=38.8

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      .+.|.|+|||++-.+...-   ++.+|.. +.   ...|..+||+|+|+|++|+-.+
T Consensus        11 Li~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eL   64 (71)
T d1bvsa2          11 LLSVSGVGPRLAMATLAVH---DAAALRQALADSDVASLTRVPGIGRRGAERIVLEL   64 (71)
T ss_dssp             HHTSSSCCHHHHHHHHHHS---CHHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHHHS
T ss_pred             HhccCCcCHHHHHHHHHhC---CHHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHHHH
Confidence            6789999999999888643   6677776 44   3458888999999999988654

>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=96.17  E-value=0.0038  Score=49.33  Aligned_cols=53  Identities=15%  Similarity=0.097  Sum_probs=46.5

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      ++-=+|+..+...|-.+| |.++.||..+++++|..+++||.||.+-|.+.++.
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            344478889999998888 69999999999999999999999999999887765

>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=0.0042  Score=48.44  Aligned_cols=52  Identities=12%  Similarity=0.210  Sum_probs=46.4

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      +-=+|+..+...|-.+| |.++.||..+++++|..+++||+||.+.|.+.++.
T Consensus        10 ~~L~LS~R~~N~Lk~~~-I~tv~dL~~~s~~dLl~~~nfG~kSl~EIk~~L~~   61 (67)
T d1z3eb1          10 EELDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   61 (67)
T ss_dssp             GGSCCBHHHHHHHHHTT-CCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHcC-CcCHHHHHHCCHHHHHhCCCCchhhHHHHHHHHHH
Confidence            44478899999998888 69999999999999999999999999999888764

>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=96.11  E-value=0.0013  Score=52.94  Aligned_cols=52  Identities=15%  Similarity=0.380  Sum_probs=40.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK  513 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~  513 (655)
                      .+.|.|+|||++..+....   ++.+|.. +   +...|..+||+|+|+|++|+-.+..
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   5666665 2   3456888899999999999877753

>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=96.10  E-value=0.00076  Score=63.91  Aligned_cols=60  Identities=18%  Similarity=0.235  Sum_probs=43.7

Q ss_pred             HHhhccccccc---cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccc-cCCcHHHHHHH
Q psy11423        447 RKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL-DRVSNKLANNI  507 (655)
Q Consensus       447 ~~~~i~~F~sk---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~GfG~Ksa~nl  507 (655)
                      +..||.|=+..   ..|.|+|+|++++.+||++| |+|+.||-....+.+..+ +|||+|.+++|
T Consensus       131 L~~Rl~~Gv~~ell~L~~i~gvgr~rAr~L~~~G-i~t~~dl~~a~~~~~~~~~~g~g~ki~~~i  194 (198)
T d2p6ra2         131 LTERIKHGVKEELLELVRIRHIGRVRARKLYNAG-IRNAEDIVRHREKVASLIGRGIAERVVEGI  194 (198)
T ss_dssp             HHHHHHHTCCGGGHHHHTSTTCCHHHHHHHHTTT-CCSHHHHHHTHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHccCCHHHHhHhcCCCCCHHHHHHHHHcC-CCCHHHHHHccHhhHHHHhcchHHHHHHHh
Confidence            55667776654   36789999999999999866 699999998765544443 56666655544

>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=95.75  E-value=0.008  Score=42.39  Aligned_cols=44  Identities=25%  Similarity=0.357  Sum_probs=36.3

Q ss_pred             CCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCHHHHHHH
Q psy11423        528 IRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGSTTVKAF  571 (655)
Q Consensus       528 IpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~~~A~~I  571 (655)
                      -.|+|.++|++|+..||+.+.+.+.    ..+.|.+++|+|+.+..++
T Consensus         7 kegvgrktaerllrafgnpervkqlarefeieklasvegvgervlrsl   54 (55)
T d2csba3           7 KEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSL   54 (55)
T ss_dssp             STTCCHHHHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHH
T ss_pred             hccccHhHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcchHHHHHHhc
Confidence            3688888888888888888887764    4688999999999887765

>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=95.48  E-value=0.0029  Score=49.04  Aligned_cols=57  Identities=23%  Similarity=0.426  Sum_probs=40.6

Q ss_pred             hHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCC
Q psy11423        482 AVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIP  561 (655)
Q Consensus       482 i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~  561 (655)
                      +-||-+++.++|..++|+|++.|++|++.    |                          .|.        +.+||.+++
T Consensus         8 ~idiNtA~~~eL~~lpgig~~~A~~Iv~~----R--------------------------~f~--------s~edL~~v~   49 (65)
T d2duya1           8 PVSLNEASLEELMALPGIGPVLARRIVEG----R--------------------------PYA--------RVEDLLKVK   49 (65)
T ss_dssp             SEETTTCCHHHHTTSTTCCHHHHHHHHHT----C--------------------------CCS--------SGGGGGGST
T ss_pred             CcccccCCHHHHHHCCCCCHHHHHHHHHc----C--------------------------CCC--------CHHHHHhCC
Confidence            34666677778888888888888777742    1                          154        347788888


Q ss_pred             CCCHHHHHHHHHHhc
Q psy11423        562 KIGSTTVKAFIKFIN  576 (655)
Q Consensus       562 GIG~~~A~~I~~~f~  576 (655)
                      |||+.+.+.|..|+.
T Consensus        50 gi~~~~~~~i~~~lr   64 (65)
T d2duya1          50 GIGPATLERLRPYLR   64 (65)
T ss_dssp             TCCHHHHHHHGGGEE
T ss_pred             CCCHHHHHHHHHHcC
Confidence            888888888877763

>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=95.47  E-value=0.0043  Score=51.92  Aligned_cols=24  Identities=21%  Similarity=0.367  Sum_probs=20.3

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        553 TEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       553 s~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      +.++|.+++|||+++.+.|..|+.
T Consensus        51 s~edL~~V~GIg~~~~e~lk~yl~   74 (98)
T d2axtu1          51 SVEDVLNIPGLTERQKQILRENLE   74 (98)
T ss_dssp             SGGGGGGCTTCCTTHHHHHHHHGG
T ss_pred             CHHHHhhCCCCCHHHHHHHHHHHh
Confidence            457888899999999999988875

>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=94.50  E-value=0.0066  Score=50.73  Aligned_cols=53  Identities=19%  Similarity=0.207  Sum_probs=29.7

Q ss_pred             HHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423        484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY  542 (655)
Q Consensus       484 DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~  542 (655)
                      ||-+.+.++|..|||+|++.|++|++      +.|+..+=.-+.++|||+++..+|.+.
T Consensus        20 dlN~As~~eL~~lpGIg~~~A~~Iv~------~gpf~s~edL~~V~GIg~~~~e~lk~y   72 (98)
T d2axtu1          20 DLNNTNIAAFIQYRGLYPTLAKLIVK------NAPYESVEDVLNIPGLTERQKQILREN   72 (98)
T ss_dssp             ESSSSCGGGGTTSTTCTHHHHHHHHH------SCCCSSGGGGGGCTTCCTTHHHHHHHH
T ss_pred             ecccccHHHHHHhhhhcHHHHHHHHH------cCCcCCHHHHhhCCCCCHHHHHHHHHH
Confidence            44455566666666666666666663      234443333446666666665555443

>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=94.21  E-value=0.019  Score=47.18  Aligned_cols=27  Identities=26%  Similarity=0.145  Sum_probs=14.9

Q ss_pred             HHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        484 DLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       484 DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      ||-+.+.++|..+||+|.+.|++|++.
T Consensus        26 ~iNtAs~~eL~~lpgig~~~A~~II~y   52 (91)
T d2edua1          26 LLNEGSARDLRSLQRIGPKKAQLIVGW   52 (91)
T ss_dssp             HHHHSCHHHHHHSTTCCHHHHHHHHHH
T ss_pred             ccccCCHHHHhhCCCCCHHHHHHHHHH
Confidence            344455555555555555555555554

>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=94.18  E-value=0.015  Score=54.59  Aligned_cols=51  Identities=25%  Similarity=0.360  Sum_probs=39.7

Q ss_pred             HHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcC-CCCCHHHHHHHH
Q psy11423        522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNI-PKIGSTTVKAFI  572 (655)
Q Consensus       522 ~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i-~GIG~~~A~~I~  572 (655)
                      +|.-+.|||||.++|++|.+. |.|++.|..++.+.+..+ +|+|++++++|.
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            455569999999999999874 789999999876655554 677777777663

>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=94.07  E-value=0.05  Score=52.61  Aligned_cols=178  Identities=17%  Similarity=0.135  Sum_probs=102.0

Q ss_pred             cccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEe---CCEEeEEEecCCCCccch----------
Q psy11423         88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGEN----------  154 (655)
Q Consensus        88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeD----------  154 (655)
                      +..||+|.+ +.-    ++++.. .+. ..-+|+++.||||.-.++++.   +|..++-+.| +|...++          
T Consensus         6 ~Y~~ien~~-~~~----i~~~k~-~gl-~~~ewVa~EKIHGaNFsii~~~~~dg~~V~~aKR-~~~l~~~e~Ffgy~~i~   77 (265)
T d1xdna_           6 PYIEIDLPS-ESR----IQSLHK-SGL-AAQEWVACEKVHGTNFGIYLINQGDHEVVRFAKR-SGIMDPNENFFGYHILI   77 (265)
T ss_dssp             CCCCCCCCC-HHH----HHHHHH-TTG-GGSCEEEEEECCSEEEEEEEEEETTEEEEEEEET-TEECCTTCCCTTGGGGH
T ss_pred             cchhccCch-HHH----HHHHHh-cCc-ccceEEEEEeecCccEEEEEeecCCCcEEEEeec-ccccCCcccccchhhHH
Confidence            456788865 222    445432 111 134799999999999999873   6788888888 4554333          


Q ss_pred             --hhhhhhhcccCCc---ccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccc
Q psy11423        155 --ITTNIHIIHKIPL---VLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKI  229 (655)
Q Consensus       155 --vT~n~~~i~~iP~---~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~  229 (655)
                        .+..++.+..+=.   .++   -...+.|-||+|=..=.+-..+.... ...-.--+|||. ||.--|++|-+--...
T Consensus        78 ~~l~~~~~~l~~~l~~~~~v~---~~~~~vvyGELfGg~Y~hp~v~~~~~-~~~~~~g~~~~~-~~~~iQk~~~v~Y~p~  152 (265)
T d1xdna_          78 DEFTAQIRILNDLLKQKYGLS---RVGRLVLNGELFGAKYKHPLVPKSEK-WCTLPNGKKFPI-AGVQIQREPFPQYSPE  152 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCS---CCSEEEEEEEEEEEECCCTTSCCCCC-EEECTTSCEEEG-GGCCSCCCSSCCCEEE
T ss_pred             HHHHHHHHHHHHHHHhhhccC---CccEEEEEEEecccccCCCccccccc-ccccccCccccc-cceeeccccccccCCC
Confidence              3444444322111   111   13469999999863222111000000 000112347774 4555577754445557


Q ss_pred             eEEEEEecccccCCC----CCCCHHHHHHHHHh-CCCCCCCCceeeCCHHHHHHH
Q psy11423        230 LHFFAHGVGELRGMN----MPSSHSELLNWYQK-IGLSICGEYSVLSGVNKLIEF  279 (655)
Q Consensus       230 L~f~~y~~~~~~~~~----~~~~~~e~l~~L~~-~GF~~~~~~~~~~~~~ev~~~  279 (655)
                      |+|+||++....+..    ...++-+.++.+.+ .||+..+. ....+++++++|
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            999999996543211    02466777777776 59998874 345678887765

>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=92.84  E-value=0.26  Score=46.27  Aligned_cols=147  Identities=16%  Similarity=0.149  Sum_probs=79.3

Q ss_pred             eEEEEEecceeEEEEEEe--CC-EEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHH
Q psy11423        119 EYIAELKFDGIAVNLRYE--YG-YLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN  195 (655)
Q Consensus       119 ~~~~e~KiDGlsi~l~Y~--~G-~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n  195 (655)
                      +|+|++|.||+-..|...  +| .-+..++|-.-    ..+...   ..+|..+     .....+-||++.....     
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            699999999999877442  33 23556777322    111111   1233333     2236788999864321     


Q ss_pred             HHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhC--CCCCC--------
Q psy11423        196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI--GLSIC--------  264 (655)
Q Consensus       196 ~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~--GF~~~--------  264 (655)
                                                      ....|.+|++....+..+ ...-.+.++.|+++  .+...        
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                                            123577777755443221 24566777776542  11110        


Q ss_pred             -CCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCc
Q psy11423        265 -GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS  327 (655)
Q Consensus       265 -~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~  327 (655)
                       .......+.+.+.+.+.     ...++|.+||+|++=.+..+.      ..  ||.-.||+-|
T Consensus       177 ~k~~~~~~~~~~l~~~~~-----~~~~~y~~DGLIf~p~~~pY~------~G--r~~~~~KWKP  227 (228)
T d1ckma2         177 YKEWIPLEHPTIIKDHLK-----KANAIYHTDGLIIMSVDEPVI------YG--RNFNLFKLKP  227 (228)
T ss_dssp             ECCCEETTCHHHHHHHHH-----HHHHHSCEEEEEEEESSSCCC------CE--EEEEEEEECS
T ss_pred             eeeeeehhhHHHHHHHHh-----hhccCCCCceEEEEeCCCCEe------CC--CCCCeEEeCC
Confidence             01112345555555443     235689999999996554332      22  6776777743

>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=92.53  E-value=0.039  Score=41.31  Aligned_cols=27  Identities=22%  Similarity=0.251  Sum_probs=24.6

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (655)
                      .+|-|+||+++++|++.| ++|++||-.
T Consensus        11 t~I~GvGp~~A~~l~~~G-i~ti~dLr~   37 (57)
T d2bcqa2          11 SNIWGAGTKTAQMWYQQG-FRSLEDIRS   37 (57)
T ss_dssp             HTSTTCCHHHHHHHHHTT-CCSHHHHHH
T ss_pred             hccccccHHHHHHHHHhC-CCCHHHHHh
Confidence            479999999999999997 799999975

>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=92.19  E-value=0.036  Score=46.56  Aligned_cols=25  Identities=20%  Similarity=0.348  Sum_probs=23.5

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFK  551 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~  551 (655)
                      ||||||+++|-+|.++|+|++++..
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            9999999999999999999998875

>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=92.13  E-value=0.038  Score=46.53  Aligned_cols=26  Identities=15%  Similarity=0.341  Sum_probs=23.8

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      |+||||+++|.+|.+.|+|++.+...
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            89999999999999999999988753

>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=92.10  E-value=0.23  Score=38.22  Aligned_cols=53  Identities=28%  Similarity=0.300  Sum_probs=46.0

Q ss_pred             hhHHHHHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        519 FSRFIYALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       519 l~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                      +..|+.+|++.   +..|..|.. -|.|++.|...+.++|..|.|+-+.+|+.+++-
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   678988876 599999999999999999999999999998764

>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=92.05  E-value=0.052  Score=40.59  Aligned_cols=27  Identities=30%  Similarity=0.464  Sum_probs=24.2

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (655)
                      ++|-|+||+++++|++.| ++|++||-.
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 699999964

>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=91.78  E-value=0.15  Score=48.17  Aligned_cols=23  Identities=22%  Similarity=0.488  Sum_probs=19.1

Q ss_pred             CHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        553 TEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       553 s~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      +.++|.++||||+++|..|..|.
T Consensus       111 ~~~~L~~LpGVG~kTA~~il~~~  133 (217)
T d1keaa_         111 NRKAILDLPGVGKYTCAAVMCLA  133 (217)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             hhHHHHHHHhhhhhhhHHHHHHh
Confidence            56788889999999998888864

>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=91.57  E-value=0.042  Score=46.30  Aligned_cols=25  Identities=24%  Similarity=0.258  Sum_probs=23.4

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFK  551 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~  551 (655)
                      ||||||+++|-+|.+.|++++.+..
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            8999999999999999999998875

>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=91.55  E-value=0.14  Score=42.66  Aligned_cols=48  Identities=15%  Similarity=0.038  Sum_probs=41.3

Q ss_pred             CCCCeEecccccCccEEEecCCCC------chHHHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++..+++++++.||+++..+      .|...|...|++|++.+-+.+.+.
T Consensus        23 ~~Gg~~~~~~~~~~THlI~~~~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~   76 (109)
T d1t15a1          23 KHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIK   76 (109)
T ss_dssp             HHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHH
T ss_pred             HcCCEEEeEecCCccEEEEecCcchhhHhhHHHHHHHHCCCccccHHHHHHHHH
Confidence            678999999999999999987654      467779999999999998888763

>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=91.36  E-value=0.28  Score=46.21  Aligned_cols=70  Identities=20%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             ChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHH-hcCHHH
Q psy11423        481 TAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF-KATEEQ  556 (655)
Q Consensus       481 ~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~-~as~ee  556 (655)
                      |+++|..++.++|..+   =||...+|..|.+-                         |+.+.+.|+++..+. ..+.++
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            5777888887776442   26766667666532                         233334455444333 234678


Q ss_pred             HhcCCCCCHHHHHHHHHHh
Q psy11423        557 LLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       557 L~~i~GIG~~~A~~I~~~f  575 (655)
                      |.++||||+++|..|..|.
T Consensus       122 L~~lpGIG~kTA~~vl~~~  140 (217)
T d1pu6a_         122 LLDQKGIGKESADAILCYA  140 (217)
T ss_dssp             HHTSTTCCHHHHHHHHHHT
T ss_pred             HHHHhhhhhHHHHHHHHHH
Confidence            8888888888888887763

>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=90.86  E-value=0.065  Score=43.77  Aligned_cols=28  Identities=25%  Similarity=0.304  Sum_probs=17.1

Q ss_pred             HHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        484 DLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       484 DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      ||-.++.++|..+||+|++.|++|++..
T Consensus        28 diN~As~~~L~~lpGig~~~A~~Iv~~R   55 (90)
T d3bzka1          28 DVNTASAALLARISGLNSTLAQNIVAHR   55 (90)
T ss_dssp             ETTTCCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             ehhhCCHHHHhHCCCCCHHHHHHHHHHH
Confidence            3445556666666666666666666543

>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=90.77  E-value=0.053  Score=40.99  Aligned_cols=27  Identities=22%  Similarity=0.315  Sum_probs=24.7

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423        460 MNIIGLGKKMIEKLVNANIVVTAVDLYK  487 (655)
Q Consensus       460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~  487 (655)
                      ++|-|+||+++++|++.| ++|++||.+
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            579999999999999997 699999984

>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=90.57  E-value=0.075  Score=46.59  Aligned_cols=26  Identities=27%  Similarity=0.438  Sum_probs=24.4

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      ||||||+++|-+|++.|++++.|...
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            99999999999999999999998765

>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=90.19  E-value=0.14  Score=41.18  Aligned_cols=49  Identities=10%  Similarity=0.227  Sum_probs=41.0

Q ss_pred             CCCCeEecccccCccEEEecCCCCchHHHH--HHcCCeeeCHHHHHHHHhc
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKA--IKLNIKILDEKNFVKIVKG  648 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA--~~lgi~ii~e~~f~~~l~~  648 (655)
                      ++||++...++++++++|+....+.+.+.|  +..+++|++++-+.+.+..
T Consensus        31 ~~GG~v~~~~~~~~THvI~~~~~~~~~~~~~~~~~~i~iV~~~Wl~dc~~~   81 (96)
T d1cdza_          31 AFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEK   81 (96)
T ss_dssp             HTTCEECSSCSTTCSEEECSSCCCHHHHHHHTTCTTCEEECTHHHHHHHTT
T ss_pred             HhCCEEeccCCCCceEEEEccCCcceeeehhhhCCCCeEEEEhHHHHHHHc
Confidence            889999999999999999988877665554  4558999999998887743

>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=89.53  E-value=0.09  Score=42.87  Aligned_cols=48  Identities=17%  Similarity=0.236  Sum_probs=36.7

Q ss_pred             hCCCCccHHHHHHHHHhCCCHHHH-HhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423        526 LGIRHVGETTAKELANYFKNLECM-FKATEEQLLNIPKIGSTTVKAFIKFIN  576 (655)
Q Consensus       526 lgIpgIG~~~Ak~L~~~fgsl~~l-~~as~eeL~~i~GIG~~~A~~I~~~f~  576 (655)
                      ..+||+|+..|++|.+.=.   .. .-.+.++|..++|||+++-+++..|+.
T Consensus        38 ~~lpGig~~~A~~Iv~~R~---~~G~f~s~edL~~v~gi~~k~~e~i~~~l~   86 (90)
T d3bzka1          38 ARISGLNSTLAQNIVAHRD---ANGAFRTRDELKKVSRLGEKTFEQAAGFLR   86 (90)
T ss_dssp             TTSTTCCHHHHHHHHHHHH---HHCSCSSSGGGGGSTTCCHHHHHHHHTTEE
T ss_pred             hHCCCCCHHHHHHHHHHHH---HcCCCCCHHHHhhCCCCCHHHHHHhcCCEe
Confidence            3789999999998876311   11 112568899999999999999998875

>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=88.99  E-value=0.44  Score=44.55  Aligned_cols=42  Identities=19%  Similarity=0.139  Sum_probs=23.6

Q ss_pred             HHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHH
Q psy11423        468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAI  511 (655)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I  511 (655)
                      +...+|++..  .++.++..+..+++..+   -||....|.+|++..
T Consensus        50 ~~~~~l~~~~--pt~~~la~~~~~e~~~~i~~~g~y~~ka~~l~~~a   94 (214)
T d1orna_          50 KVTKRLFEKY--RTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLC   94 (214)
T ss_dssp             HHHHHHHHHC--CSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHH
T ss_pred             HHHhhhhccc--CchhhhhhccHHHhhhhhhhhhhhhHHHHHHHHHh
Confidence            4445566554  47788887765443222   355556666665543

>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=88.01  E-value=0.19  Score=40.95  Aligned_cols=64  Identities=16%  Similarity=0.235  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHH-HhcCHHHHhcCCCCCHHHHHHHHH
Q psy11423        501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM-FKATEEQLLNIPKIGSTTVKAFIK  573 (655)
Q Consensus       501 ~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l-~~as~eeL~~i~GIG~~~A~~I~~  573 (655)
                      ++...+++.-|+.+   +...+.   .+||||++.|++|.++   =+.. .-.+.++|..++|||+++.++|..
T Consensus        17 ~~~~~~~l~~iNtA---s~~eL~---~lpgig~~~A~~II~y---R~~~G~f~sledL~~V~Gi~~k~~eki~k   81 (91)
T d2edua1          17 AHGRQKILDLLNEG---SARDLR---SLQRIGPKKAQLIVGW---RELHGPFSQVEDLERVEGITGKQMESFLK   81 (91)
T ss_dssp             HHHHHHHHHHHHHS---CHHHHH---HSTTCCHHHHHHHHHH---HHHHCCCSSGGGGGGSTTCCHHHHHHHHH
T ss_pred             HHhhcccccccccC---CHHHHh---hCCCCCHHHHHHHHHH---HHHcCCCCCHHHHhcCCCCCHHHHHHHHH
Confidence            45556666666543   222222   4678888777777654   2221 112667788888888877777765

>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=87.83  E-value=0.12  Score=39.50  Aligned_cols=28  Identities=21%  Similarity=0.392  Sum_probs=25.3

Q ss_pred             HHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        548 CMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       548 ~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .|..|+.++|..++|||+++|+.|++|-
T Consensus        10 diNtA~~~eL~~lpgig~~~A~~Iv~~R   37 (65)
T d2duya1          10 SLNEASLEELMALPGIGPVLARRIVEGR   37 (65)
T ss_dssp             ETTTCCHHHHTTSTTCCHHHHHHHHHTC
T ss_pred             ccccCCHHHHHHCCCCCHHHHHHHHHcC
Confidence            3678999999999999999999999974

>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=87.50  E-value=0.31  Score=45.58  Aligned_cols=76  Identities=16%  Similarity=0.200  Sum_probs=38.7

Q ss_pred             HHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423        469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN  545 (655)
Q Consensus       469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs  545 (655)
                      ...+|+++.  .++.++..++.++|..+   =||-...|.+|.+..+                         .|.+.|++
T Consensus        50 ~~~~l~~~~--~t~~~la~a~~~~l~~~i~~~G~y~~Ka~~l~~~a~-------------------------~i~~~~~g  102 (211)
T d2abka_          50 ATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCR-------------------------ILLEQHNG  102 (211)
T ss_dssp             HHHHHTTTC--CSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHH-------------------------HHHHHTTT
T ss_pred             HHHHHHHhc--cChHHHHhhhHhHhHHHHHHhhhhhhHHHHHHHHHH-------------------------HHHHHhcC
Confidence            344554443  47777776655544322   2454556655554433                         23333332


Q ss_pred             HHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423        546 LECMFKATEEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       546 l~~l~~as~eeL~~i~GIG~~~A~~I~~~  574 (655)
                         ..-.+.++|.++||||+++|..|..|
T Consensus       103 ---~~p~~~~~L~~LpGVG~~TA~~Il~~  128 (211)
T d2abka_         103 ---EVPEDRAALEALPGVGRKTANVVLNT  128 (211)
T ss_dssp             ---SCCSCHHHHHHSTTCCHHHHHHHHHH
T ss_pred             ---chhHHHHHHHHHHhhchHHHHHHHHH
Confidence               11223456666666666666666664

>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=87.13  E-value=0.68  Score=35.46  Aligned_cols=54  Identities=17%  Similarity=0.311  Sum_probs=44.9

Q ss_pred             ccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        451 LQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       451 i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      +..|+.  .|||   .+..+..|+++|+ +|+.+|-....++|..++||-+..++-|.+.
T Consensus         5 ~~~F~~--~LdV---De~lA~lLv~EGF-~siEeIAyv~~~eL~~IegfDee~a~eL~~R   58 (68)
T d1u9la_           5 IDTFTK--YLDI---DEDFATVLVEEGF-STLEELAYVPMKELLEIEGLDEPTVEALRER   58 (68)
T ss_dssp             HHHHHH--HHTC---CHHHHHHHHHTTC-CCHHHHHHSCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHH--HcCC---cHHHHHHHHHhcc-CcHHHHhcCCHHHHHHhcccCHHHHHHHHHH
Confidence            344553  4655   4789999999998 8999999999999999999999999877654

>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=85.08  E-value=0.39  Score=41.20  Aligned_cols=48  Identities=10%  Similarity=0.145  Sum_probs=40.6

Q ss_pred             CCCCeEecccccCccEEEecCCCCchH--HHHHHcCCeeeCHHHHHHHHh
Q psy11423        600 TKGGKVVNFISKNTNYLVKGQKPGKKL--EKAIKLNIKILDEKNFVKIVK  647 (655)
Q Consensus       600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~--~kA~~lgi~ii~e~~f~~~l~  647 (655)
                      .+||++...+++++++||+++..+.+.  ..|...+++|++++-+.+-+.
T Consensus        65 ~~GG~~~~~~~~~vTHvIv~~~~~~~~~~~~~~~~~i~iV~~~Wl~~c~~  114 (132)
T d1wf6a_          65 SGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWLLECFS  114 (132)
T ss_dssp             HTTCEEESSCCSSCCEEEESSCCSHHHHHHHHSCCCCCEEEHHHHHHHHH
T ss_pred             HcCCEEecccCCCceEEEecCCCccHHHHHHHhcCCCCcCCHHHHHHHHH
Confidence            789999999999999999998877544  446667899999999988764

>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=85.03  E-value=1  Score=40.90  Aligned_cols=69  Identities=13%  Similarity=0.159  Sum_probs=41.7

Q ss_pred             CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCH---HHHHhcC---
Q psy11423        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL---ECMFKAT---  553 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl---~~l~~as---  553 (655)
                      .++.+|..++.+++...-|++.| +.+|.+.                         |+.+.+.+++.   +.+...+   
T Consensus        47 P~~~~la~~~~e~~l~~~~~~~r-a~~i~~~-------------------------a~~i~~~~~~~~~l~~l~~~~~~~  100 (190)
T d2noha1          47 PSLQALAGPEVEAHLRKLGLGYR-ARYVSAS-------------------------ARAILEEQGGLAWLQQLRESSYEE  100 (190)
T ss_dssp             CCHHHHHSTTHHHHHHHTTCTTH-HHHHHHH-------------------------HHHHHHTSCSHHHHHHTTTSCHHH
T ss_pred             CCHHHHHHcchHHHHHhcchHHH-HHHHHHH-------------------------HHHHHHhcccccCHHHhcCCCcHH
Confidence            47777777777777666677654 5555443                         22333333322   2222222   


Q ss_pred             -HHHHhcCCCCCHHHHHHHHHH
Q psy11423        554 -EEQLLNIPKIGSTTVKAFIKF  574 (655)
Q Consensus       554 -~eeL~~i~GIG~~~A~~I~~~  574 (655)
                       .++|.+++|||+.+|+.+.-|
T Consensus       101 ~~~~L~~l~GIG~wTA~~il~~  122 (190)
T d2noha1         101 AHKALCILPGVGTQVADCICLM  122 (190)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCchHHHHHHHHHH
Confidence             357888999999999887765

>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=84.62  E-value=0.33  Score=46.97  Aligned_cols=47  Identities=23%  Similarity=0.203  Sum_probs=40.5

Q ss_pred             ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      +|+|+|+++.++|-+.| |.++.||..+..+.|...  ||.+.++.|++.
T Consensus       212 ~l~GiG~~~~~~L~~~G-I~ti~dl~~~~~~~L~~~--fG~~~g~~l~~~  258 (273)
T d1zeta2         212 EIPGIGYKTAKCLEALG-INSVRDLQTFSPKILEKE--LGISVAQRIQKL  258 (273)
T ss_dssp             GSTTCCHHHHHHHHTTT-CCSHHHHHHSCHHHHHHH--HHHHHHHHHHHH
T ss_pred             HhcCCCHHHHHHHHHhC-CCcHHHHhcCCHHHHHHH--HCHHHHHHHHHH
Confidence            79999999999996655 799999999999999887  998888777654

>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.07  E-value=1.2  Score=38.87  Aligned_cols=72  Identities=10%  Similarity=0.111  Sum_probs=45.0

Q ss_pred             HHHHHHHHcCCCCChHHHhcCChhhh----ccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423        468 KMIEKLVNANIVVTAVDLYKINFKNL----LRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF  543 (655)
Q Consensus       468 k~i~~L~~~g~I~~i~DL~~L~~~~L----~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f  543 (655)
                      +...+|++..  .|+.+|..++.++|    ..+ ||-..+|+.|.+--+.                         +    
T Consensus        40 ~v~~~L~~~~--pt~e~la~a~~~el~~~Ir~~-G~~~~KAk~I~~~a~~-------------------------~----   87 (144)
T d1ngna_          40 PVLWEFLEKY--PSAEVARAADWRDVSELLKPL-GLYDLRAKTIIKFSDE-------------------------Y----   87 (144)
T ss_dssp             HHHHHHHHHS--CSHHHHHHSCHHHHHHHTGGG-SCHHHHHHHHHHHHHH-------------------------H----
T ss_pred             HHHHHHHHhC--CchhhhhccCHHHHHHHHHhh-hhHHHHHHHHHHHHhh-------------------------H----
Confidence            4456666654  48999988887776    344 7777777766542111                         0    


Q ss_pred             CCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423        544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ  577 (655)
Q Consensus       544 gsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~  577 (655)
                            ..-+.++|.++||||+.+|+++.-|..+
T Consensus        88 ------ip~~~~~l~~LpGVG~~tad~~~if~~~  115 (144)
T d1ngna_          88 ------LTKQWRYPIELHGIGKYGNDSYRIFCVN  115 (144)
T ss_dssp             ------HHSCCSSGGGSTTCCHHHHHHHHHHTSS
T ss_pred             ------hhhhhhhHHhcCCccHHHHHHHHHHHcC
Confidence                  0113356777888888888877666544

>d1mpga1 a.96.1.3 (A:100-282) 3-Methyladenine DNA glycosylase II (gene alkA or aidA) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 3-Methyladenine DNA glycosylase II (gene alkA or aidA)
species: Escherichia coli [TaxId: 562]

Probab=82.85  E-value=1.3  Score=40.06  Aligned_cols=95  Identities=13%  Similarity=0.104  Sum_probs=56.6

Q ss_pred             CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc--------cchhHHHHHh-CCCCccHHHHHHHH-HhCCCHHHH
Q psy11423        480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL--------TTFSRFIYAL-GIRHVGETTAKELA-NYFKNLECM  549 (655)
Q Consensus       480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~--------~~l~r~L~al-gIpgIG~~~Ak~L~-~~fgsl~~l  549 (655)
                      .++..|..++.++|..+ |+...++..|....+...+        .+.......| .|||||+.+|.-++ -.++..+.+
T Consensus        57 Ptp~~l~~~~~~~lr~~-Gls~~Ka~~i~~~a~~~~~g~l~~~~~~~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvf  135 (183)
T d1mpga1          57 PTPQRLAAADPQALKAL-GMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVF  135 (183)
T ss_dssp             CCHHHHHTCCHHHHHHT-TSCHHHHHHHHHHHHHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCC
T ss_pred             CcHHHHHcCCHHHHHHc-CCcHHHHHHHHHHHHHHHcCchhhhccccHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCcc
Confidence            57899999999999998 8877777766654443222        2223344444 78888888887654 456655433


Q ss_pred             HhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        550 FKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       550 ~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      -.-+.-=...+.++.++..+.+.+.|
T Consensus       136 P~~D~~lr~~~~~l~~~~~~~~~~~~  161 (183)
T d1mpga1         136 LPDDYLIKQRFPGMTPAQIRRYAERW  161 (183)
T ss_dssp             CTTCHHHHHHSTTCCHHHHHHHHGGG
T ss_pred             ccchHHHHHHhhhCCHHHHHHHHHhc
Confidence            32232222344555555544444444

>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=82.40  E-value=1.3  Score=33.98  Aligned_cols=42  Identities=17%  Similarity=0.324  Sum_probs=33.7

Q ss_pred             HHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        534 TTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       534 ~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+...|.. .+.++..|...+.++|.+++|+|++..+.|.+.+
T Consensus        18 R~~N~L~~~gI~tv~dL~~~s~~dLl~i~n~G~ksl~EI~~~L   60 (69)
T d1doqa_          18 RVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEAL   60 (69)
T ss_dssp             HHHHHHHHTTCCSHHHHHHSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHCCHHHHHhCCCCCHHHHHHHHHHH
Confidence            33344443 4678999999999999999999999999887765

>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=81.95  E-value=1.1  Score=41.76  Aligned_cols=52  Identities=21%  Similarity=0.309  Sum_probs=36.6

Q ss_pred             ccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecC
Q psy11423         89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRG  147 (655)
Q Consensus        89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRG  147 (655)
                      ..|++|.++..    +++++... + .....|++|.|+||-.+++.+.+|++ ++.||+
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            34667766553    34444321 1 12458999999999999999988875 789996

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

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: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=81.79  E-value=0.037  Score=47.06  Aligned_cols=26  Identities=35%  Similarity=0.685  Sum_probs=23.6

Q ss_pred             CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423        527 GIRHVGETTAKELANYFKNLECMFKA  552 (655)
Q Consensus       527 gIpgIG~~~Ak~L~~~fgsl~~l~~a  552 (655)
                      ||||||+++|.+|++.|++++.+...
T Consensus        22 Gv~GiG~KtA~kll~~~gsle~i~~~   47 (116)
T d1cmwa1          22 GVKGIGEKTARKLLEEWGSLEALLKN   47 (116)
T ss_dssp             CCCCSTTCTTTTTGGGGGTTCSSSSS
T ss_pred             cccccCchhHHHHHHhcchHHHHHHH
Confidence            89999999999999999999887753

>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=81.68  E-value=0.61  Score=30.00  Aligned_cols=26  Identities=27%  Similarity=0.687  Sum_probs=17.7

Q ss_pred             CCCCCCCccee---e-cC-ceeEEecCCCcCCH
Q psy11423        417 ICPICNSKIIY---I-ES-NLIARCSGSWIECI  444 (655)
Q Consensus       417 ~CP~C~~~l~~---~-~~-~~~~~C~n~~~~C~  444 (655)
                      -||.||-.+..   . .| -..+||.|+ . |.
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            59999986532   1 12 367899996 6 84

>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=81.49  E-value=0.49  Score=44.85  Aligned_cols=49  Identities=22%  Similarity=0.363  Sum_probs=40.7

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423        459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA  510 (655)
Q Consensus       459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~  510 (655)
                      .=+++|+|+++.++|-..| |.++.||..+..+.|...  ||.+.++.|++.
T Consensus       180 l~~l~GiG~~~~~~L~~~G-i~t~gdl~~~~~~~L~~~--fG~~~g~~l~~~  228 (240)
T d1jx4a2         180 IADVPGIGNITAEKLKKLG-INKLVDTLSIEFDKLKGM--IGEAKAKYLISL  228 (240)
T ss_dssp             GGGSTTCCHHHHHHHHTTT-CCBGGGGGSSCHHHHHHH--HCHHHHHHHHHH
T ss_pred             hhhcCCCCHHHHHHHHHhC-CCcHHHHHcCCHHHHHHH--HCHHHHHHHHHH
Confidence            4479999999999996555 799999999999999876  898777776654

>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=81.44  E-value=0.93  Score=42.46  Aligned_cols=24  Identities=25%  Similarity=0.452  Sum_probs=21.1

Q ss_pred             cCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        552 ATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       552 as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+.++|.++||||+++|..|..|.
T Consensus       106 ~~~~~L~~LpGVG~kTA~~il~~a  129 (224)
T d1kg2a_         106 ETFEEVAALPGVGRSTAGAILSLS  129 (224)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhhhhhhhHHHHHHh
Confidence            367899999999999999998863

>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.91  E-value=1  Score=42.08  Aligned_cols=24  Identities=17%  Similarity=0.342  Sum_probs=21.5

Q ss_pred             cCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423        552 ATEEQLLNIPKIGSTTVKAFIKFI  575 (655)
Q Consensus       552 as~eeL~~i~GIG~~~A~~I~~~f  575 (655)
                      .+.++|.++||||+++|..|..|-
T Consensus       104 ~~~~~Ll~LpGIG~kTA~~il~~a  127 (221)
T d1rrqa1         104 DDPDEFSRLKGVGPYTVGAVLSLA  127 (221)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhhhHHHHHHHHHH
Confidence            467999999999999999999873

>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=80.07  E-value=1.2  Score=39.81  Aligned_cols=55  Identities=7%  Similarity=0.089  Sum_probs=47.1

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423        456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI  511 (655)
Q Consensus       456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I  511 (655)
                      +-..+.+|++|+..+.+|.+.| +.++.||.+++.+++..+-|++++....+++.+
T Consensus       118 ~~~L~Qlp~~~~~~~~kl~~~~-i~sl~~l~~~~~~e~~~ll~~~~~~~~~i~~~~  172 (176)
T d2q0zx1         118 DSYLKQLPHFTSEHIKRCTDKG-VESVFDIMEMEDEERNALLQLTDSQIADVARFC  172 (176)
T ss_dssp             SCGGGGSTTCCHHHHHHHHHTT-CCSHHHHHHSCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             CCCccCCCcCCHHHHHHHHHCC-CCCHHHHHhCCHHHHHHHHcCCHHHHHHHHHHH
Confidence            3357899999999999998877 689999999999999888889998887777654