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Conserved domains on  [gi|1491344480|gb|RLJ03624|]
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MAG: hypothetical protein DRP11_00065 [Candidatus Aenigmatarchaeota archaeon]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CDC9 super family cl43518
ATP-dependent DNA ligase [Replication, recombination and repair];
679-907 1.06e-24

ATP-dependent DNA ligase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1793:

Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 108.85  E-value: 1.06e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  679 KGEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMV-WFKDGK-------ARE 749
Cdd:COG1793    127 DGGDWAYEPKWDGYRVQAHRDGGEVRLYS--RNgEDITDRFPELVEALRALPADDAVLDGEIVaLDEDGRppfqalqQRL 204

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  750 REEAmgiiAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLvsDYDNFVKAFKKFSE 829
Cdd:COG1793    205 GRKR----DVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVI--DWGEGEALFAAARE 278

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIKKSYDIEVQVA-------KRVPKISSatgkpipgqylYEIQTKDDKGRIVPM 902
Cdd:COG1793    279 -AGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGgatpgkgRRAGGFGS-----------LLLGVYDPGGELVYV 346


                   ....*
gi 1491344480  903 GRTFS 907
Cdd:COG1793    347 GKVGT 351
COG3392 super family cl42426
Adenine-specific DNA methylase [Replication, recombination and repair];
9-290 4.73e-20

Adenine-specific DNA methylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3392:

Pssm-ID: 442619  Cd Length: 338  Bit Score: 93.02  E-value: 4.73e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480    9 FNYLGSKKRQVD---SIMSEIPKTAKTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAILG---QTKFSK---- 78
Cdd:COG3392      5 IRYIGSKRKLLPfieEVISEVVIEGESFLDLFAGTGVVSRAFKKHGKRVIANDLEYYSYVLNKAYIEnnsEPLFEKlgpy 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   79 EDAEKLLSA-RPVKGYLYH----AKTIAGRPKSR-------ILRQVIDGIctYAHQLPPGKKEFALGAM---ADCLSSLF 143
Cdd:COG3392     85 EELLAYLNRlPPEDGFISEnycpAGSGERLYFSDenakkidAIREEIEEL--KLDGINENEYAILLASLiyaADKVANTA 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  144 GSFGFFRKapeeqglytvsKFKKKLLRSIISLNSKVIPQGSA-AVTRKDAFTIPIP-KVDIIYFDPPYdisgtSEVPYAK 221
Cdd:COG3392    163 GVYGAYLK-----------DWLKRAEKPLELEPPEFIDNGKEnEVFNGDANELIKKiEADLVYLDPPY-----NSRQYGS 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  222 HYALLNSI-------------LMQREVNLPPF-PRERIP----ELIKRFanKCKILLVSSSSQPNLKY---RQILKEHfG 280
Cdd:COG3392    227 NYHLLETIarydkpeikgktgLRDWREYRSPFcSKRGALdafeDLISNA--KAKYILLSYNSEGLISLeeiIEILSKY-G 303

                          330
                   ....*....|
gi 1491344480  281 NTRLKRITFK 290
Cdd:COG3392    304 KVEVFEIDYK 313
LigD_N super family cl11819
DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.
 1065-1118 1.05e-03

DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.


The actual alignment was detected with superfamily member pfam13298:

Pssm-ID: 448346 [Multi-domain]  Cd Length: 103  Bit Score: 39.77  E-value: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480 1065 WLTLEGIVPPGKPGAtknypGVFIIRDKGTFE------EGTRKPYLyEYFLHGKHLKGRY 1118
Cdd:pfam13298   49 YADFEGTIPEGEYGA-----GTVIIWDRGTYEplgdlrEALQKGKL-KFRLHGEKLKGGY 102
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
679-907 1.06e-24

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 108.85  E-value: 1.06e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  679 KGEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMV-WFKDGK-------ARE 749
Cdd:COG1793    127 DGGDWAYEPKWDGYRVQAHRDGGEVRLYS--RNgEDITDRFPELVEALRALPADDAVLDGEIVaLDEDGRppfqalqQRL 204

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  750 REEAmgiiAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLvsDYDNFVKAFKKFSE 829
Cdd:COG1793    205 GRKR----DVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVI--DWGEGEALFAAARE 278

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIKKSYDIEVQVA-------KRVPKISSatgkpipgqylYEIQTKDDKGRIVPM 902
Cdd:COG1793    279 -AGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGgatpgkgRRAGGFGS-----------LLLGVYDPGGELVYV 346


                   ....*
gi 1491344480  903 GRTFS 907
Cdd:COG1793    347 GKVGT 351
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 680-858 1.05e-21

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 94.27  E-value: 1.05e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  680 GEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALP---VKQCVFFGEMV-WFKD-GKAREREEA 753
Cdd:pfam01068   18 GGAFIAEYKYDGERAQIHKDGDEVKLFS--RNlENITRHYPEIVEALKEAFkpdEKSFILDGEIVaVDPEtGEILPFQVL 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  754 MGIIAGKEPLADEDIR----FFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLVSDYDNFVKAFKKFSE 829
Cdd:pfam01068   96 ADRKKKKVDVEELAEKvpvcLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVTKDVEEAQEFLEEAIS 175

                          170       180
                   ....*....|....*....|....*....
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIK 858
Cdd:pfam01068  176 -EGLEGLVVKDPDSTYEPGKRGKNWLKIK 203
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 686-858 2.13e-21

Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; 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 common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.


Pssm-ID: 185715 [Multi-domain]  Cd Length: 190  Bit Score: 92.99  E-value: 2.13e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKDGK--------AREReeamgi 756
Cdd:cd07906     21 EIKWDGYRALARVDGGRVRLYS--RNgLDWTARFPELAEALAALPVRDAVLDGEIVVLDEGGrpdfqalqNRLR------ 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  757 iAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHImKTPRVLVSDYDNFVKAFKKFseieGSEGV 836
Cdd:cd07906     93 -LRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRL-RVSEHFEGGGAALFAAACEL----GLEGI 166

                          170       180
                   ....*....|....*....|..
gi 1491344480  837 MVKKQDFIYEKDGRTSNMAKIK 858
Cdd:cd07906    167 VAKRADSPYRSGRRSRDWLKIK 188
COG3392 COG3392
Adenine-specific DNA methylase [Replication, recombination and repair];
9-290 4.73e-20

Adenine-specific DNA methylase [Replication, recombination and repair];


Pssm-ID: 442619  Cd Length: 338  Bit Score: 93.02  E-value: 4.73e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480    9 FNYLGSKKRQVD---SIMSEIPKTAKTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAILG---QTKFSK---- 78
Cdd:COG3392      5 IRYIGSKRKLLPfieEVISEVVIEGESFLDLFAGTGVVSRAFKKHGKRVIANDLEYYSYVLNKAYIEnnsEPLFEKlgpy 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   79 EDAEKLLSA-RPVKGYLYH----AKTIAGRPKSR-------ILRQVIDGIctYAHQLPPGKKEFALGAM---ADCLSSLF 143
Cdd:COG3392     85 EELLAYLNRlPPEDGFISEnycpAGSGERLYFSDenakkidAIREEIEEL--KLDGINENEYAILLASLiyaADKVANTA 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  144 GSFGFFRKapeeqglytvsKFKKKLLRSIISLNSKVIPQGSA-AVTRKDAFTIPIP-KVDIIYFDPPYdisgtSEVPYAK 221
Cdd:COG3392    163 GVYGAYLK-----------DWLKRAEKPLELEPPEFIDNGKEnEVFNGDANELIKKiEADLVYLDPPY-----NSRQYGS 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  222 HYALLNSI-------------LMQREVNLPPF-PRERIP----ELIKRFanKCKILLVSSSSQPNLKY---RQILKEHfG 280
Cdd:COG3392    227 NYHLLETIarydkpeikgktgLRDWREYRSPFcSKRGALdafeDLISNA--KAKYILLSYNSEGLISLeeiIEILSKY-G 303

                          330
                   ....*....|
gi 1491344480  281 NTRLKRITFK 290
Cdd:COG3392    304 KVEVFEIDYK 313
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 686-865 1.56e-17

DNA ligase D, ligase domain; 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.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 84.66  E-value: 1.56e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKD-GKAR----EREEAMGiiag 759
Cdd:TIGR02779   17 EVKYDGYRCLARIEGGKVRLIS--RNgHDWTEKFPILAAALAALPILPAVLDGEIVVLDEsGRSDfsalQNRLRAG---- 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  760 keplADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRAdTRHIMKTPRVLVSDYDNFVKAFKKFSEIeGSEGVMVK 839
Cdd:TIGR02779   91 ----RDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKA-IKGPLAPDRYSVHFEGDGQALLEAACRL-GLEGVVAK 164

                          170       180
                   ....*....|....*....|....*.
gi 1491344480  840 KQDFIYEKdGRTSNMAKIKKSYDIEV 865
Cdd:TIGR02779  165 RRDSPYRS-GRSADWLKLKCRRRQEF 189
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 675-858 2.40e-15

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 80.39  E-value: 2.40e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  675 LKRAKGEkVYVEPKWDGFTFGVKKDGKEVQLITedrR--RDRSSILPQIVEDVRALPVKQCVFFGEMVWFK-DGKARERE 751
Cdd:PRK03180   199 LARLGGP-AAVEAKLDGARVQVHRDGDDVRVYT---RtlDDITARLPEVVEAVRALPVRSLVLDGEAIALRpDGRPRPFQ 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  752 EAM---GIIAGKEPLADED-IRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRhimkTPRVLVSDYDNfVKAFKKF 827
Cdd:PRK03180   275 VTAsrfGRRVDVAAARATQpLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHR----VPRLVTADPAA-AAAFLAA 349

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1491344480  828 SEIEGSEGVMVKKQDFIYEKDGRTSNMAKIK 858
Cdd:PRK03180   350 ALAAGHEGVMVKSLDAPYAAGRRGAGWLKVK 380
MethyltransfD12 pfam02086
D12 class N6 adenine-specific DNA methyltransferase;
11-210 5.62e-08

D12 class N6 adenine-specific DNA methyltransferase;


Pssm-ID: 396593  Cd Length: 254  Bit Score: 55.45  E-value: 5.62e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   11 YLGSKKRQVDSIMSEIPKT-AKTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAILG-QTKFSKEDAEKLL--S 86
Cdd:pfam02086    1 YIGGKRKLLPEIKEHIPKGgDRRFVEPFAGGGAVFFEAKKQGKKVLINDINYDLINLYKALIKnNPDDLIKDLEALLelE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   87 ARPVKGYLYHAKTIAGRpkSRILRQVIDGI-CTYAHqlppgkkefALGAMADCLSSLFGSFGFfrkapeEQGLYTvsKFK 165
Cdd:pfam02086   81 ELNSREYFYELREEFNA--IDAIREVIRAIdFLYLN---------RLLFSGLYRVNKKGNFNV------PYGAYK--KPW 141

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1491344480  166 KKLLRSIISLNSKVIPQGSAAVTRKDAFT-IPIPKVDIIYFDPPYD 210
Cdd:pfam02086  142 KFALKELKLRALKLQNNATIECGDFDAVLlAANISDDFVYLDPPYN 187
LigD_N pfam13298
DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.
 1065-1118 1.05e-03

DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.


Pssm-ID: 433097 [Multi-domain]  Cd Length: 103  Bit Score: 39.77  E-value: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480 1065 WLTLEGIVPPGKPGAtknypGVFIIRDKGTFE------EGTRKPYLyEYFLHGKHLKGRY 1118
Cdd:pfam13298   49 YADFEGTIPEGEYGA-----GTVIIWDRGTYEplgdlrEALQKGKL-KFRLHGEKLKGGY 102
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
679-907 1.06e-24

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 108.85  E-value: 1.06e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  679 KGEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMV-WFKDGK-------ARE 749
Cdd:COG1793    127 DGGDWAYEPKWDGYRVQAHRDGGEVRLYS--RNgEDITDRFPELVEALRALPADDAVLDGEIVaLDEDGRppfqalqQRL 204

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  750 REEAmgiiAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLvsDYDNFVKAFKKFSE 829
Cdd:COG1793    205 GRKR----DVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVI--DWGEGEALFAAARE 278

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIKKSYDIEVQVA-------KRVPKISSatgkpipgqylYEIQTKDDKGRIVPM 902
Cdd:COG1793    279 -AGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGgatpgkgRRAGGFGS-----------LLLGVYDPGGELVYV 346


                   ....*
gi 1491344480  903 GRTFS 907
Cdd:COG1793    347 GKVGT 351
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 680-858 1.05e-21

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 94.27  E-value: 1.05e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  680 GEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALP---VKQCVFFGEMV-WFKD-GKAREREEA 753
Cdd:pfam01068   18 GGAFIAEYKYDGERAQIHKDGDEVKLFS--RNlENITRHYPEIVEALKEAFkpdEKSFILDGEIVaVDPEtGEILPFQVL 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  754 MGIIAGKEPLADEDIR----FFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLVSDYDNFVKAFKKFSE 829
Cdd:pfam01068   96 ADRKKKKVDVEELAEKvpvcLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVTKDVEEAQEFLEEAIS 175

                          170       180
                   ....*....|....*....|....*....
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIK 858
Cdd:pfam01068  176 -EGLEGLVVKDPDSTYEPGKRGKNWLKIK 203
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 686-858 2.13e-21

Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; 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 common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.


Pssm-ID: 185715 [Multi-domain]  Cd Length: 190  Bit Score: 92.99  E-value: 2.13e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKDGK--------AREReeamgi 756
Cdd:cd07906     21 EIKWDGYRALARVDGGRVRLYS--RNgLDWTARFPELAEALAALPVRDAVLDGEIVVLDEGGrpdfqalqNRLR------ 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  757 iAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHImKTPRVLVSDYDNFVKAFKKFseieGSEGV 836
Cdd:cd07906     93 -LRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRL-RVSEHFEGGGAALFAAACEL----GLEGI 166

                          170       180
                   ....*....|....*....|..
gi 1491344480  837 MVKKQDFIYEKDGRTSNMAKIK 858
Cdd:cd07906    167 VAKRADSPYRSGRRSRDWLKIK 188
COG3392 COG3392
Adenine-specific DNA methylase [Replication, recombination and repair];
9-290 4.73e-20

Adenine-specific DNA methylase [Replication, recombination and repair];


Pssm-ID: 442619  Cd Length: 338  Bit Score: 93.02  E-value: 4.73e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480    9 FNYLGSKKRQVD---SIMSEIPKTAKTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAILG---QTKFSK---- 78
Cdd:COG3392      5 IRYIGSKRKLLPfieEVISEVVIEGESFLDLFAGTGVVSRAFKKHGKRVIANDLEYYSYVLNKAYIEnnsEPLFEKlgpy 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   79 EDAEKLLSA-RPVKGYLYH----AKTIAGRPKSR-------ILRQVIDGIctYAHQLPPGKKEFALGAM---ADCLSSLF 143
Cdd:COG3392     85 EELLAYLNRlPPEDGFISEnycpAGSGERLYFSDenakkidAIREEIEEL--KLDGINENEYAILLASLiyaADKVANTA 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  144 GSFGFFRKapeeqglytvsKFKKKLLRSIISLNSKVIPQGSA-AVTRKDAFTIPIP-KVDIIYFDPPYdisgtSEVPYAK 221
Cdd:COG3392    163 GVYGAYLK-----------DWLKRAEKPLELEPPEFIDNGKEnEVFNGDANELIKKiEADLVYLDPPY-----NSRQYGS 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  222 HYALLNSI-------------LMQREVNLPPF-PRERIP----ELIKRFanKCKILLVSSSSQPNLKY---RQILKEHfG 280
Cdd:COG3392    227 NYHLLETIarydkpeikgktgLRDWREYRSPFcSKRGALdafeDLISNA--KAKYILLSYNSEGLISLeeiIEILSKY-G 303

                          330
                   ....*....|
gi 1491344480  281 NTRLKRITFK 290
Cdd:COG3392    304 KVEVFEIDYK 313
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 677-860 1.67e-18

Adenylation domain of archaeal and bacterial LigB-like 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. 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 adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185711 [Multi-domain]  Cd Length: 207  Bit Score: 85.28  E-value: 1.67e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  677 RAKGEKVYVEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPV-KQCVFFGEMVWF-KDGKAREREEA 753
Cdd:cd07901     21 IKEGGEAAVEYKYDGIRVQIHKDGDEVRIFS--RRlEDITNALPEVVEAVRELVKaEDAILDGEAVAYdPDGRPLPFQET 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  754 MGIIAGKEPLAD--EDIRF--FAFDITNFDGKDISNLPYYERVKYLDRLLRaDTRHIMKTPRVLVSDYDNFVKAFKKFSE 829
Cdd:cd07901     99 LRRFRRKYDVEEaaEEIPLtlFLFDILYLDGEDLLDLPLSERRKILEEIVP-ETEAILLAPRIVTDDPEEAEEFFEEALE 177

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1491344480  830 iEGSEGVMVKKQDFIYEKDGRTSNMAKIKKS 860
Cdd:cd07901    178 -AGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 671-861 1.69e-18

Adenylation domain of DNA Ligase IV; 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 discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185713 [Multi-domain]  Cd Length: 225  Bit Score: 85.71  E-value: 1.69e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  671 KNWYLKRAKGEKVYVEPKWDGFTFGVKKDGKEVQLITedRRR-----------DRSSILPQIVeDVRALPVKQCVFFGEM 739
Cdd:cd07903     23 GYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFS--RNGndytylygaslTPGSLTPYIH-LAFNPKVKSCILDGEM 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  740 V-------------WFKDGKAREREEamgiIAGKEPLadedirFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHI 806
Cdd:cd07903    100 VvwdketkrflpfgTLKDVAKLREVE----DSDLQPC------FVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPGRL 169

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1491344480  807 MKTPRVLVSDYDNFVKAFKKFSEiEGSEGVMVKKQDFIYEKDGRTSNMAKIKKSY 861
Cdd:cd07903    170 EVVKRTEASTKEEIEEALNEAID-NREEGIVVKDLDSKYKPGKRGGGWIKIKPEY 223
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 686-865 1.56e-17

DNA ligase D, ligase domain; 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.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 84.66  E-value: 1.56e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKD-GKAR----EREEAMGiiag 759
Cdd:TIGR02779   17 EVKYDGYRCLARIEGGKVRLIS--RNgHDWTEKFPILAAALAALPILPAVLDGEIVVLDEsGRSDfsalQNRLRAG---- 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  760 keplADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRAdTRHIMKTPRVLVSDYDNFVKAFKKFSEIeGSEGVMVK 839
Cdd:TIGR02779   91 ----RDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKA-IKGPLAPDRYSVHFEGDGQALLEAACRL-GLEGVVAK 164

                          170       180
                   ....*....|....*....|....*.
gi 1491344480  840 KQDFIYEKdGRTSNMAKIKKSYDIEV 865
Cdd:TIGR02779  165 RRDSPYRS-GRSADWLKLKCRRRQEF 189
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 675-858 2.40e-15

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 80.39  E-value: 2.40e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  675 LKRAKGEkVYVEPKWDGFTFGVKKDGKEVQLITedrR--RDRSSILPQIVEDVRALPVKQCVFFGEMVWFK-DGKARERE 751
Cdd:PRK03180   199 LARLGGP-AAVEAKLDGARVQVHRDGDDVRVYT---RtlDDITARLPEVVEAVRALPVRSLVLDGEAIALRpDGRPRPFQ 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  752 EAM---GIIAGKEPLADED-IRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRhimkTPRVLVSDYDNfVKAFKKF 827
Cdd:PRK03180   275 VTAsrfGRRVDVAAARATQpLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHR----VPRLVTADPAA-AAAFLAA 349

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1491344480  828 SEIEGSEGVMVKKQDFIYEKDGRTSNMAKIK 858
Cdd:PRK03180   350 ALAAGHEGVMVKSLDAPYAAGRRGAGWLKVK 380
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 674-859 3.23e-15

Adenylation domain of 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. 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-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185709 [Multi-domain]  Cd Length: 201  Bit Score: 75.45  E-value: 3.23e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  674 YLKRAKGEKVYVEPKWDGFTFGVKKDGKEVQLITEDRRRDRSSIlPQIVEDVRALPVkQCVFFGEMVWFKDGKAREREEA 753
Cdd:cd07898     14 AAKAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQF-PELAAAAKALPH-EFILDGEILAWDDNRGLPFSEL 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  754 MGIIAGK--EPLADEDIR--FFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLVSDYDNFVKAFKKfSE 829
Cdd:cd07898     92 FKRLGRKfrDKFLDEDVPvvLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPALPVESAEELEAAFAR-AR 170

                          170       180       190
                   ....*....|....*....|....*....|
gi 1491344480  830 IEGSEGVMVKKQDFIYEKDGRTSNMAKIKK 859
Cdd:cd07898    171 ARGNEGLMLKDPDSPYEPGRRGLAWLKLKK 200
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 679-861 1.08e-12

DNA ligase I, ATP-dependent (dnl1); 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). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 71.96  E-value: 1.08e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  679 KGEKVYVEPKWDGFTFGVKKDGKEVQLITedrrRDRSSILPQIVEDV-----RALP-VKQCVFFGEMVW----------F 742
Cdd:TIGR00574  185 KGNGFYVEYKYDGERVQVHKDGDKFKIFS----RRLENYTYQYPEIFtefikEAFPgIKSCILDGEMVAidpetgkplpF 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  743 KDGKAREREEAMGIIAGKEPLadediRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRHIMKTPRVLVSDYDNFVK 822
Cdd:TIGR00574  261 GTLLRRKRKYDIKAMDQKVPV-----CLFVFDILYLNGKSLIDEPLIERREILESILKPIPNRIEIAEMKIVSNVEELEK 335

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1491344480  823 AFKKFSEiEGSEGVMVKKQDFIYEKDGRTSNMAKIKKSY 861
Cdd:TIGR00574  336 FLNEAIS-EGCEGLMLKDLKSIYEPGKRGWLWLKIKPEY 373
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 686-858 1.60e-12

Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; 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 common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185714 [Multi-domain]  Cd Length: 194  Bit Score: 67.66  E-value: 1.60e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKDGKA-----REREEAMGiiAG 759
Cdd:cd07905     21 EPKWDGFRCLAFRDGDEVRLQS--RSgKPLTRYFPELVAAARALLPPGCVLDGELVVWRGGRLdfdalQQRIHPAA--SR 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  760 KEPLADEDI-RFFAFDITNFDGKDISNLPYYERVKyldRLLRADTRHimkTPRVLVS----DYDNFVKAFKKFSEIeGSE 834
Cdd:cd07905     97 VRRLAEETPaSFVAFDLLALGGRDLRGRPLRERRA---ALEALLAGW---GPPLHLSpattDRAEAREWLEEFEGA-GLE 169

                          170       180
                   ....*....|....*....|....
gi 1491344480  835 GVMVKKQDFIYEKDGRTsnMAKIK 858
Cdd:cd07905    170 GVVAKRLDGPYRPGERA--MLKVK 191
ligD PRK09633
DNA ligase D;
686-858 6.40e-11

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 66.60  E-value: 6.40e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITEDRRRdRSSILPQIVEDVR--------ALPVkqcVFFGEMVWFKDGKARE-------- 749
Cdd:PRK09633    21 EVKYDGFRCLLIIDETGITLISRNGRE-LTNTFPEIIEFCEsnfehlkeELPL---TLDGELVCLVNPYRSDfehvqqrg 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  750 ---REEAMGIIAGKEPLadediRFFAFDITNFDGKDISNLPYYERVKYLDRLLRA----DTRHIMKTPRV-LVSDYDNFV 821
Cdd:PRK09633    97 rlkNTEVIAKSANARPC-----QLLAFDLLELKGESLTSLPYLERKKQLDKLMKAaklpASPDPYAKARIqYIPSTTDFD 171

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1491344480  822 KAFKKFSEIEGsEGVMVKKQDFIYEKDGRTSNMAKIK 858
Cdd:PRK09633   172 ALWEAVKRYDG-EGIVAKKKTSKWLENKRSKDWLKIK 207
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 712-858 7.76e-11

DNA ligase D; 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; it only represents 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. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274293 [Multi-domain]  Cd Length: 552  Bit Score: 66.19  E-value: 7.76e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  712 RDRSSILPQIVEDVRALPVKQCVFFGEMVWFkDGKAREREEAMGIIAGKEplADEDIRFFAFDITNFDGKDISNLPYYER 791
Cdd:TIGR02776    5 HDWTKRFPEIVKALALLKLLPAWIDGEIVVL-DERGRADFAALQNALSAG--ASRPLTYYAFDLLFLSGEDLRDLPLEER 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491344480  792 VKYLDRLLRA-DTRHIMKTPRVLvSDYDNFVKAFKKFseieGSEGVMVKKQDFIYEKdGRTSNMAKIK 858
Cdd:TIGR02776   82 KKRLKQLLKAqDEPAIRYSDHFE-SDGDALLESACRL----GLEGVVSKRLDSPYRS-GRSKDWLKLK 143
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 685-867 1.17e-09

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 62.71  E-value: 1.17e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  685 VEPKWDGFTFGVKKDGKEVQLITedRR-RDRSSILPQIVEDVRALPVKQCVFFGEMVWFKD------GKAREREEamgii 757
Cdd:PRK09632   481 FEGKWDGYRLLAEADHGALRLRS--RSgRDVTAEYPELAALAEDLADHHVVLDGEIVALDDsgvpsfGLLQNRGR----- 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  758 agkeplaDEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRhiMKTPRVLVSDYDNFVKAfkkfSEIEGSEGVM 837
Cdd:PRK09632   554 -------DTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGGS--LTVPPLLPGDGAEALAY----SRELGWEGVV 620

                          170       180       190
                   ....*....|....*....|....*....|
gi 1491344480  838 VKKQDFIYEKDGRTSNMAKIKKSYDIEVQV 867
Cdd:PRK09632   621 AKRRDSTYQPGRRSSSWIKDKHWRTQEVVI 650
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 686-912 1.05e-08

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 58.75  E-value: 1.05e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLitedrrRDRSS-----ILPQIVEDVRALPVKQCVFFGEMVWFKDGK------------AR 748
Cdd:PRK08224    29 EPKWDGFRCLVFRDGDEVEL------GSRNGkpltrYFPELVAALRAELPERCVLDGEIVVARDGGldfealqqrihpAA 102

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  749 EREEAmgiiagkepLADED-IRFFAFDITNFDGKDISNLPYYERVKYLDRLLrADTRHIMKTPRVLvsDYDNFVKAFKKF 827
Cdd:PRK08224   103 SRVRK---------LAEETpASFVAFDLLALGDRDLTGRPFAERRAALEAAA-AGSGPVHLTPATT--DPATARRWFEEF 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  828 sEIEGSEGVMVKKQDFIYEKDGRTsnMAKIKKSYDIEVQVAK-RVPKISSATGKPIPGqyLYeiqtkDDKGRIVPMGrtF 906
Cdd:PRK08224   171 -EGAGLDGVIAKPLDGPYQPGKRA--MFKVKHERTADCVVAGyRYHKSGPVVGSLLLG--LY-----DDDGQLHHVG--V 238


                   ....*.
gi 1491344480  907 STSIKA 912
Cdd:PRK08224   239 TSAFPM 244
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 680-864 3.45e-08

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 57.67  E-value: 3.45e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  680 GEKVYVEPKWDGFTFGVKKDGKEVqLITEDRRRDRSSILPQIVEDVR-ALPVKQCVFFGEMVW----------FKDGKAR 748
Cdd:PRK01109   247 GGEALVEYKYDGERAQIHKKGDKV-KIFSRRLENITHQYPDVVEYAKeAIKAEEAIVEGEIVAvdpetgemrpFQELMHR 325

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  749 ER----EEAMGIIAgkepladedIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRaDTRHIMKTPRVLVSDYDNFVKAF 824
Cdd:PRK01109   326 KRkydiEEAIKEYP---------VNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVK-ENDKVKLAERIITDDVEELEKFF 395

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1491344480  825 KKFSEiEGSEGVMVK--KQDFIYEKDGRTSNMAKIKKSYDIE 864
Cdd:PRK01109   396 HRAIE-EGCEGLMAKslGKDSIYQAGARGWLWIKYKRDYQSE 436
MethyltransfD12 pfam02086
D12 class N6 adenine-specific DNA methyltransferase;
11-210 5.62e-08

D12 class N6 adenine-specific DNA methyltransferase;


Pssm-ID: 396593  Cd Length: 254  Bit Score: 55.45  E-value: 5.62e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   11 YLGSKKRQVDSIMSEIPKT-AKTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAILG-QTKFSKEDAEKLL--S 86
Cdd:pfam02086    1 YIGGKRKLLPEIKEHIPKGgDRRFVEPFAGGGAVFFEAKKQGKKVLINDINYDLINLYKALIKnNPDDLIKDLEALLelE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480   87 ARPVKGYLYHAKTIAGRpkSRILRQVIDGI-CTYAHqlppgkkefALGAMADCLSSLFGSFGFfrkapeEQGLYTvsKFK 165
Cdd:pfam02086   81 ELNSREYFYELREEFNA--IDAIREVIRAIdFLYLN---------RLLFSGLYRVNKKGNFNV------PYGAYK--KPW 141

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1491344480  166 KKLLRSIISLNSKVIPQGSAAVTRKDAFT-IPIPKVDIIYFDPPYD 210
Cdd:pfam02086  142 KFALKELKLRALKLQNNATIECGDFDAVLlAANISDDFVYLDPPYN 187
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 679-859 7.21e-08

Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; 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 sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity.


Pssm-ID: 185704 [Multi-domain]  Cd Length: 182  Bit Score: 53.58  E-value: 7.21e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  679 KGEKVYVEPKWDGFTFGVKKDGKEVQLITedrrRDRSSI-LPQIVEDVRALP--VKQCVFFGEMVwfkdgkarereeamg 755
Cdd:cd06846     17 EQDEYYVQEKYDGKRALIVALNGGVFAIS----RTGLEVpLPSILIPGRELLtlKPGFILDGELV--------------- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  756 iiAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADT-------RHIMKTPRVLVSDYDNFVKAFKKfs 828
Cdd:cd06846     78 --VENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEgldpvklVPLENAPSYDETLDDLLEKLKKK-- 153

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1491344480  829 eieGSEGVMVKKQDFIY-EKDGRTSNMAKIKK 859
Cdd:cd06846    154 ---GKEGLVFKHPDAPYkGRPGSSGNQLKLKP 182
PRK09125 PRK09125
DNA ligase; Provisional
 751-928 2.35e-07

DNA ligase; Provisional


Pssm-ID: 181662 [Multi-domain]  Cd Length: 282  Bit Score: 53.72  E-value: 2.35e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  751 EEAMGIIAGKEPLADE--DIRFFAFDITNFDGkdisnlPYYERVKYLDRLL-RADTRHIMKTPRVLVSDYDNFvkaFKKF 827
Cdd:PRK09125    98 EAISSIVRDKTPDDAAwrKVRFMVFDLPDAPG------DFEERLAVLKKLLaKLPSPYIKIIEQIRVRSEAAL---QQFL 168

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  828 SEIE--GSEGVMVKKQDFIYEKdGRTSNMAKIKKSYDIEVQVAKRVPkissatGKpipGQYL-----YEIQTKDdkGRIV 900
Cdd:PRK09125   169 DQIVaaGGEGLMLHRPDAPYEA-GRSDDLLKLKPYYDAEATVIGHLP------GK---GKFAgmlgaLLVETPD--GREF 236

                          170       180
                   ....*....|....*....|....*...
gi 1491344480  901 PMGRTFSTSIKASPGDILTVRTARIRGF 928
Cdd:PRK09125   237 KIGSGFSDAERENPPKIGSIITYKYRGL 264
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 686-858 2.34e-06

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 52.22  E-value: 2.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedrRR--DRSSILPQIVEDVRALPVKQCVFFGEMV---------------WFKDGKar 748
Cdd:PRK05972   254 EIKFDGYRILARIEGGEVRLFT---RNglDWTAKLPALAKAAAALGLPDAWLDGEIVvldedgvpdfqalqnAFDEGR-- 328

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  749 ereeamgiiagkeplaDEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRADTRhimktPRVlvsdydNFVKAFkkfs 828
Cdd:PRK05972   329 ----------------TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARS-----DRI------RFSEHF---- 377

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1491344480  829 EIEGS-----------EGVMVKKQDFIYeKDGRTSNMAKIK 858
Cdd:PRK05972   378 DAGGDavlasacrlglEGVIGKRADSPY-VSGRSEDWIKLK 417
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 685-845 5.11e-06

Adenylation domain of putative bacterial ATP-dependent DNA ligases; 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.


Pssm-ID: 185708 [Multi-domain]  Cd Length: 207  Bit Score: 48.70  E-value: 5.11e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  685 VEPKWDGFtfgvkkdgkEVQLITEDRRR--------DRSSILPQIVEDVRALPvKQCVFFGEMVWFKDGKA--------- 747
Cdd:cd07897     28 AEWKWDGI---------RGQLIRRGGEVflwsrgeeLITGSFPELLAAAEALP-DGTVLDGELLVWRDGRPlpfndlqqr 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  748 --REReeamgiiAGKEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLradTRHimKTPRVLVSDydnfVKAFK 825
Cdd:cd07897     98 lgRKT-------VGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALL---ARL--PPPRLDLSP----LIAFA 161

                          170       180
                   ....*....|....*....|....*....
gi 1491344480  826 KFSEIE---------GSEGVMVKKQDFIY 845
Cdd:cd07897    162 DWEELAalraqsrerGAEGLMLKRRDSPY 190
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 751-859 6.11e-06

Adenylation domain of kDNA ligases and similar proteins; 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 members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues.


Pssm-ID: 185707 [Multi-domain]  Cd Length: 174  Bit Score: 47.95  E-value: 6.11e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  751 EEAMGIIAGKEPLADE--DIRFFAFDITNFDGkdisnlPYYERVKYLDRLLR-ADTRHIMKTPRVLVSDYDNFVKAFKKF 827
Cdd:cd07896     71 EQTSSIVRSKKPDDEDwrKVKFMVFDLPSAKG------PFEERLERLKNLLEkIPNPHIKIVPQIPVKSNEALDQYLDEV 144

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1491344480  828 SEIEGsEGVMVKKQDFIYEkDGRTSNMAKIKK 859
Cdd:cd07896    145 VAAGG-EGLMLRRPDAPYE-TGRSDNLLKLKP 174
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 685-851 6.76e-06

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 50.22  E-value: 6.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  685 VEPKWDGFtfgvkkdgkEVQLItedRRRDRSSI-----------LPQIVEDVRALPvKQCVFFGEM-VW-FKDGKAR--- 748
Cdd:PRK09247   229 AEWKWDGI---------RVQLV---RRGGEVRLwsrgeeliterFPELAEAAEALP-DGTVLDGELlVWrPEDGRPQpfa 295

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  749 ---EReeamgiIAGKEP----LADEDIRFFAFDITNFDGKDISNLPYYERVKYLDRLL-RADTRHIMKTPRVLVSDYDNF 820
Cdd:PRK09247   296 dlqQR------IGRKTVgkklLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIaRLPDPRLDLSPLVPFSDWDEL 369

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1491344480  821 vKAFKKFSEIEGSEGVMVKKQDFIYEKdGRT 851
Cdd:PRK09247   370 -AALRAAARERGVEGLMLKRRDSPYLV-GRK 398
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 686-857 3.53e-05

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 47.06  E-value: 3.53e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  686 EPKWDGFTFGVKKDGKEVQLITedrrRDRSSILPQIVEDVRALPVKQCVFFGEMVWFKDGKAREREEAMGIIAGKEPLAD 765
Cdd:PRK07636    23 EPKFDGIRLIASKNNGLIRLYT----RHNNEVTAKFPELLNLDIPDGTVLDGELIVLGSTGAPDFEAVMERFQSKKSTKI 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  766 EDIRFFAFDITNFDGKDISNLPYYERVKYLDRLLRaDTRHIMKTPRVlvsdyDNFVKAFKKFSEIEGSEGVMVKKQDFIY 845
Cdd:PRK07636    99 HPVVFCVFDVLYINGVSLTALPLSERKEILASLLL-PHPNVKIIEGI-----EGHGTAYFELVEERELEGIVIKKANSPY 172

                          170
                   ....*....|..
gi 1491344480  846 EKDGRTSNMAKI 857
Cdd:PRK07636   173 EINKRSDNWLKV 184
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 31-84 4.36e-05

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 45.32  E-value: 4.36e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1491344480   31 KTIFDPMCGSSAVLYECKKRGMHIIANDISPMAYYYSKAIL---GQTKFS--KEDAEKL 84
Cdd:COG1041     28 DTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLehyGYEDADviRGDARDL 86
30 PHA02587
DNA ligase; Provisional
 743-867 4.94e-05

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 47.39  E-value: 4.94e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  743 KDGKAREREEAMGI----IAGKEPLAD-EDIRFFAFDITNFD---GKDISNLPYYERVKYLDRLL-RADTRHIMKTPRVL 813
Cdd:PHA02587   239 FVGVVADRATGNGIvnksLKGTISKEEaQEIVFQVWDIVPLEvyyGKEKSDMPYDDRFSKLAQMFeDCGYDRVELIENQV 318

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1491344480  814 VSDYDNFVKAFKKFSEiEGSEGVMVKKQDFIYEkDGRTSNMAKIKKSYDIEVQV 867
Cdd:PHA02587   319 VNNLEEAKEIYKRYVD-QGLEGIILKNTDGLWE-DGRSKDQIKFKEVIDIDLEI 370
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 760-861 3.02e-04

Adenylation domain of DNA Ligase III; 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 nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. 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. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185712 [Multi-domain]  Cd Length: 213  Bit Score: 43.48  E-value: 3.02e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  760 KEPLADEDIRFFAFDITNFDGKDISNLPYYERVKYLdrllradTRHIMKTP-RVLVSDYdNFVKAFKKFSEI------EG 832
Cdd:cd07902    115 KSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKIL-------EDNMVEIPnRIMLSEM-KFVKKADDLSAMiarvikEG 186

                           90       100
                   ....*....|....*....|....*....
gi 1491344480  833 SEGVMVKKQDFIYEKDGRtsNMAKIKKSY 861
Cdd:cd07902    187 LEGLVLKDLKSVYEPGKR--HWLKVKKDY 213
LigD_N pfam13298
DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.
 1065-1118 1.05e-03

DNA polymerase Ligase (LigD); This is the N terminal region of ATP dependant DNA ligase.


Pssm-ID: 433097 [Multi-domain]  Cd Length: 103  Bit Score: 39.77  E-value: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480 1065 WLTLEGIVPPGKPGAtknypGVFIIRDKGTFE------EGTRKPYLyEYFLHGKHLKGRY 1118
Cdd:pfam13298   49 YADFEGTIPEGEYGA-----GTVIIWDRGTYEplgdlrEALQKGKL-KFRLHGEKLKGGY 102
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 771-861 7.96e-03

Adenylation domain of eukaryotic DNA Ligase I; 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/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 39.08  E-value: 7.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491344480  771 FAFDITNFDGKDISNLPYYERvkylDRLLRAdtrHIMKTPRVLV----SDYDNfVKAFKKFSE--IEGS-EGVMVK--KQ 841
Cdd:cd07900    128 FAFDLLYLNGESLLKKPLRER----RELLHS---LFKEVPGRFQfatsKDSED-TEEIQEFLEeaVKNNcEGLMVKtlDS 199

                           90       100
                   ....*....|....*....|
gi 1491344480  842 DFIYEKDGRTSNMAKIKKSY 861
Cdd:cd07900    200 DATYEPSKRSHNWLKLKKDY 219
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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