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Conserved domains on  [gi|18640491|ref|NP_570332|]
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exonuclease [Synechococcus phage P60]

Protein Classification

PHA00439 family protein( domain architecture ID 11475971)

PHA00439 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHA00439 PHA00439
exonuclease
 2-243 5.92e-123

exonuclease


:

Pssm-ID: 222794 [Multi-domain]  Cd Length: 286  Bit Score: 350.62  E-value: 5.92e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    2 KPLTLLIDADYFLYRACNTAEDELEFDFETTLVVGDFRKGQQIFRQSIKDFTTK---FDTDKVLLTFTDSRNFRKDVEPT 78
Cdd:PHA00439   5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRkkaWKDAPIVLAFTDSVNWRKEVVPT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   79 YKGNR-VKRKPCGYKKLKNWAM--KEWPSVMKPGLEADDVMGILATNGSLDNF---VLISPDKDMAQIP-CRIY--DLKH 149
Cdd:PHA00439  85 YKANRkAKRKPVGYRKFLEELMarEEWKSILEPGLEGDDVMGIIGTNPSLFGFkkaVLVSCDKDFKTIPnCDFLwcTTGN 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  150 EYTQTPEKAHELLYLQCLTGDSTDGYSGCPGIGpKRALAILGK----------VKDG-------------------NYWP 200
Cdd:PHA00439 165 ILTQTPETADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENpyifeqvekvLKSGkrkgqtvtkwkkrapepeeTLWD 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 18640491  201 SVVATYEEAGLKEADAVRNLRLANILKAEHWDTKAQQPILITS 243
Cdd:PHA00439 244 CIVTLGAKAGMTEEDAIKQAQMARILRAEDYDFIDKEPILWTP 286
 
Name Accession Description Interval E-value
PHA00439 PHA00439
exonuclease
 2-243 5.92e-123

exonuclease


Pssm-ID: 222794 [Multi-domain]  Cd Length: 286  Bit Score: 350.62  E-value: 5.92e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    2 KPLTLLIDADYFLYRACNTAEDELEFDFETTLVVGDFRKGQQIFRQSIKDFTTK---FDTDKVLLTFTDSRNFRKDVEPT 78
Cdd:PHA00439   5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRkkaWKDAPIVLAFTDSVNWRKEVVPT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   79 YKGNR-VKRKPCGYKKLKNWAM--KEWPSVMKPGLEADDVMGILATNGSLDNF---VLISPDKDMAQIP-CRIY--DLKH 149
Cdd:PHA00439  85 YKANRkAKRKPVGYRKFLEELMarEEWKSILEPGLEGDDVMGIIGTNPSLFGFkkaVLVSCDKDFKTIPnCDFLwcTTGN 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  150 EYTQTPEKAHELLYLQCLTGDSTDGYSGCPGIGpKRALAILGK----------VKDG-------------------NYWP 200
Cdd:PHA00439 165 ILTQTPETADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENpyifeqvekvLKSGkrkgqtvtkwkkrapepeeTLWD 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 18640491  201 SVVATYEEAGLKEADAVRNLRLANILKAEHWDTKAQQPILITS 243
Cdd:PHA00439 244 CIVTLGAKAGMTEEDAIKQAQMARILRAEDYDFIDKEPILWTP 286
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
1-190 4.72e-17

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 78.15  E-value: 4.72e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   1 MKPLtLLIDADYFLYRAcntaedeleF----DFETtlvvgdfRKGQQI-----FRQSIKDFTTKFDTDKVLLTF-TDSRN 70
Cdd:COG0258   4 MKKL-LLIDGSSLLFRA---------FyalpPLTN-------SDGQPTnavygFTNMLLKLLKEEKPTHLAVAFdAKGPT 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  71 FRKDVEPTYKGNRvkrkpcgyKK-----------LKNW--AMKeWPSVMKPGLEADDVMGILATNGSLDNF-VLI-SPDK 135
Cdd:COG0258  67 FRHELYPEYKANR--------PEmpeelrpqiplIKEVleALG-IPVLEVEGYEADDVIGTLAKQAEAEGYeVLIvTGDK 137

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18640491 136 DMAQI---------------PCRIYDLKH---EYTQTPEKAHELLylqCLTGDSTDGYSGCPGIGPKRALAIL 190
Cdd:COG0258 138 DLLQLvddnvtvldpmkgvsELERYDPAEveeKYGVPPEQIIDYL---ALMGDSSDNIPGVPGIGEKTAAKLL 207
53EXOc smart00475
5'-3' exonuclease;
6-225 2.84e-16

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 75.71  E-value: 2.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491      6 LLIDADYFLYRA----CNTAEDELEFdfeTTLVVGdfrkgqqiFRQSIKDFTTKFDTDKVLLTFTDSR-NFRKDVEPTYK 80
Cdd:smart00475   4 LLVDGSSLAFRAyfalPPLKNSKGEP---TNAVYG--------FLRMLLKLIKEEKPTYVAVVFDAKGkTFRHELYPEYK 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491     81 GNRVKRKPCGYKKLKnwAMKEW------PSVMKPGLEADDVMGILATNGSLDNF--VLISPDKDMAQIPC---RIYDL-- 147
Cdd:smart00475  73 ANRPKTPDELLEQIP--LIKELldalgiPVLEVEGYEADDVIATLAKKAEAEGYevRIVSGDKDLLQLVSdkvSVLDPtk 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    148 -------------KHEYTQTPEKAHELLylqCLTGDSTDGYSGCPGIGPKRALAILGKvkdgnyWPSVVATYEEA----- 209
Cdd:smart00475 151 gikefelytpenvIEKYGLTPEQIIDYK---ALMGDSSDNIPGVPGIGEKTAAKLLKE------FGSLENILENLdklkk 221

                          250       260
                   ....*....|....*....|..
gi 18640491    210 GLKE------ADAVRNLRLANI 225
Cdd:smart00475 222 KLREkllahkEDAKLSRKLATI 243
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 5-140 2.49e-11

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


Pssm-ID: 350210  Cd Length: 158  Bit Score: 59.91  E-value: 2.49e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   5 TLLIDADYFLYRACNTAedelefdfeTTLVVGDFRKGQQIFRQSIKDFTTKFDTDKVLLtFTDSRN-FRKDVEPTYKGNR 83
Cdd:cd09860   1 LLLIDGNSIGFAAQHSA---------KLTAGGMEVQARFGFLRSIRSYLKRYKYAKPIV-LWDGRAsWRKDLFPEYKANR 70

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18640491  84 vKRKPC-------GYKKLKNWAMK-----EWPSVMKPGLEADDVMGILA--TNGSLDNFVLISPDKDMAQI 140
Cdd:cd09860  71 -KKTREekkawreAFEAQRPFIEEaleylGVPQIRAPGAEADDLAGVLVkrLAAFGDKVLLVSGDKDWLQL 140
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
6-139 3.33e-11

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 59.72  E-value: 3.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491     6 LLIDADYFLYRA------CNTAEDelefdFETTLVVGdfrkgqqiFRQSIKDFTTKFDTDKVLLTFTDSRNFRKDVEPTY 79
Cdd:pfam02739   3 LLIDGSSLLFRAfyalppLTNSDG-----LPTNAVYG--------FLNMLLKLLKEEKPTHVAVAFDAKPTFRHELYPEY 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18640491    80 KGNRvKRKP----CGYKKLKNW--AMKeWPSVMKPGLEADDVMGILATNGSLDNF-VLI-SPDKDMAQ 139
Cdd:pfam02739  70 KANR-PPMPeelrPQIPLIKELleALG-IPVLEVEGYEADDIIGTLAKRAEEEGYeVVIvTGDKDLLQ 135
 
Name Accession Description Interval E-value
PHA00439 PHA00439
exonuclease
 2-243 5.92e-123

exonuclease


Pssm-ID: 222794 [Multi-domain]  Cd Length: 286  Bit Score: 350.62  E-value: 5.92e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    2 KPLTLLIDADYFLYRACNTAEDELEFDFETTLVVGDFRKGQQIFRQSIKDFTTK---FDTDKVLLTFTDSRNFRKDVEPT 78
Cdd:PHA00439   5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRkkaWKDAPIVLAFTDSVNWRKEVVPT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   79 YKGNR-VKRKPCGYKKLKNWAM--KEWPSVMKPGLEADDVMGILATNGSLDNF---VLISPDKDMAQIP-CRIY--DLKH 149
Cdd:PHA00439  85 YKANRkAKRKPVGYRKFLEELMarEEWKSILEPGLEGDDVMGIIGTNPSLFGFkkaVLVSCDKDFKTIPnCDFLwcTTGN 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  150 EYTQTPEKAHELLYLQCLTGDSTDGYSGCPGIGpKRALAILGK----------VKDG-------------------NYWP 200
Cdd:PHA00439 165 ILTQTPETADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENpyifeqvekvLKSGkrkgqtvtkwkkrapepeeTLWD 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 18640491  201 SVVATYEEAGLKEADAVRNLRLANILKAEHWDTKAQQPILITS 243
Cdd:PHA00439 244 CIVTLGAKAGMTEEDAIKQAQMARILRAEDYDFIDKEPILWTP 286
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
1-190 4.72e-17

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 78.15  E-value: 4.72e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   1 MKPLtLLIDADYFLYRAcntaedeleF----DFETtlvvgdfRKGQQI-----FRQSIKDFTTKFDTDKVLLTF-TDSRN 70
Cdd:COG0258   4 MKKL-LLIDGSSLLFRA---------FyalpPLTN-------SDGQPTnavygFTNMLLKLLKEEKPTHLAVAFdAKGPT 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  71 FRKDVEPTYKGNRvkrkpcgyKK-----------LKNW--AMKeWPSVMKPGLEADDVMGILATNGSLDNF-VLI-SPDK 135
Cdd:COG0258  67 FRHELYPEYKANR--------PEmpeelrpqiplIKEVleALG-IPVLEVEGYEADDVIGTLAKQAEAEGYeVLIvTGDK 137

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18640491 136 DMAQI---------------PCRIYDLKH---EYTQTPEKAHELLylqCLTGDSTDGYSGCPGIGPKRALAIL 190
Cdd:COG0258 138 DLLQLvddnvtvldpmkgvsELERYDPAEveeKYGVPPEQIIDYL---ALMGDSSDNIPGVPGIGEKTAAKLL 207
53EXOc smart00475
5'-3' exonuclease;
6-225 2.84e-16

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 75.71  E-value: 2.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491      6 LLIDADYFLYRA----CNTAEDELEFdfeTTLVVGdfrkgqqiFRQSIKDFTTKFDTDKVLLTFTDSR-NFRKDVEPTYK 80
Cdd:smart00475   4 LLVDGSSLAFRAyfalPPLKNSKGEP---TNAVYG--------FLRMLLKLIKEEKPTYVAVVFDAKGkTFRHELYPEYK 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491     81 GNRVKRKPCGYKKLKnwAMKEW------PSVMKPGLEADDVMGILATNGSLDNF--VLISPDKDMAQIPC---RIYDL-- 147
Cdd:smart00475  73 ANRPKTPDELLEQIP--LIKELldalgiPVLEVEGYEADDVIATLAKKAEAEGYevRIVSGDKDLLQLVSdkvSVLDPtk 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    148 -------------KHEYTQTPEKAHELLylqCLTGDSTDGYSGCPGIGPKRALAILGKvkdgnyWPSVVATYEEA----- 209
Cdd:smart00475 151 gikefelytpenvIEKYGLTPEQIIDYK---ALMGDSSDNIPGVPGIGEKTAAKLLKE------FGSLENILENLdklkk 221

                          250       260
                   ....*....|....*....|..
gi 18640491    210 GLKE------ADAVRNLRLANI 225
Cdd:smart00475 222 KLREkllahkEDAKLSRKLATI 243
PRK05755 PRK05755
DNA polymerase I; Provisional
 1-190 5.75e-16

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 76.67  E-value: 5.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    1 MKPLtLLIDADYFLYRAcntaedeleF-----DFETTlvvgdfrKGQQI-----FRQSIKDFTTKFDTDKVLLTF-TDSR 69
Cdd:PRK05755   1 MKTL-LLIDGSSLLFRA---------FyallpTLRNS-------DGLPTgavygFLNMLLKLLKEEKPTHVAVAFdAKGK 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   70 NFRKDVEPTYKGNRVK-----RKPCGYkkLKNW--AMKeWPSVMKPGLEADDVMGILATNGSLDNF-VLI-SPDKDMAQI 140
Cdd:PRK05755  64 TFRHELYPEYKANRPPmpedlREQIPL--IRELlrALG-IPLLELEGYEADDVIGTLAKQAEAAGYeVLIvTGDKDLLQL 140

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18640491  141 ---------PCRIYDLKH--------EYTQTPEKaheLLYLQCLTGDSTDGYSGCPGIGPKRALAIL 190
Cdd:PRK05755 141 vddnvtlldTMGVSKNEEldpeevveKYGVTPEQ---IIDYLALMGDSSDNIPGVPGIGEKTAAKLL 204
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 5-140 2.49e-11

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


Pssm-ID: 350210  Cd Length: 158  Bit Score: 59.91  E-value: 2.49e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   5 TLLIDADYFLYRACNTAedelefdfeTTLVVGDFRKGQQIFRQSIKDFTTKFDTDKVLLtFTDSRN-FRKDVEPTYKGNR 83
Cdd:cd09860   1 LLLIDGNSIGFAAQHSA---------KLTAGGMEVQARFGFLRSIRSYLKRYKYAKPIV-LWDGRAsWRKDLFPEYKANR 70

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18640491  84 vKRKPC-------GYKKLKNWAMK-----EWPSVMKPGLEADDVMGILA--TNGSLDNFVLISPDKDMAQI 140
Cdd:cd09860  71 -KKTREekkawreAFEAQRPFIEEaleylGVPQIRAPGAEADDLAGVLVkrLAAFGDKVLLVSGDKDWLQL 140
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
6-139 3.33e-11

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 59.72  E-value: 3.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491     6 LLIDADYFLYRA------CNTAEDelefdFETTLVVGdfrkgqqiFRQSIKDFTTKFDTDKVLLTFTDSRNFRKDVEPTY 79
Cdd:pfam02739   3 LLIDGSSLLFRAfyalppLTNSDG-----LPTNAVYG--------FLNMLLKLLKEEKPTHVAVAFDAKPTFRHELYPEY 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18640491    80 KGNRvKRKP----CGYKKLKNW--AMKeWPSVMKPGLEADDVMGILATNGSLDNF-VLI-SPDKDMAQ 139
Cdd:pfam02739  70 KANR-PPMPeelrPQIPLIKELleALG-IPVLEVEGYEADDIIGTLAKRAEEEGYeVVIvTGDKDLLQ 135
PRK14976 PRK14976
5'-3' exonuclease; Provisional
 1-192 4.84e-11

5'-3' exonuclease; Provisional


Pssm-ID: 237877 [Multi-domain]  Cd Length: 281  Bit Score: 61.12  E-value: 4.84e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491    1 MKPLTLLIDADYFLYRAcntaedelefdFETTLVVGDFRKGQQ-IFRQSIKDFTT-------KFDTDKVLLTFTDSR-NF 71
Cdd:PRK14976   1 MMKKALLIDGNSLIFRS-----------YYATLKQGPKLKNNKgLPTNAIHTFLTmifkilkKLNPSYILIAFDAGRkTF 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   72 RKDVEPTYKGNRVKRKPCGYKKLKnwAMKEWPSVMK------PGLEADDVMGILAT-NGSLDNFVLI-SPDKDMAQI--- 140
Cdd:PRK14976  70 RHQLYDEYKQGRKKTPESLISQIP--LLKKILKLAGikweeqPGYEADDLIGSLAKkLSKQNITVLIySSDKDLLQLvne 147

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18640491  141 -----------PCRIYDLKHEYTQTPEKAHELLYLQCLTGDSTDGYSGCPGIGPKRALAILGK 192
Cdd:PRK14976 148 ntdvllkkkgtSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNK 210
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
158-192 9.06e-07

Helix-hairpin-helix class 2 (Pol1 family) motifs;


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 44.36  E-value: 9.06e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 18640491    158 AHELLYLQCLTGDSTDGYSGCPGIGPKRALAILGK 192
Cdd:smart00279   1 PEQFIDYAILVGDYSDNIPGVKGIGPKTALKLLRE 35
PRK09482 PRK09482
flap endonuclease-like protein; Provisional
 56-190 9.49e-07

flap endonuclease-like protein; Provisional


Pssm-ID: 181896 [Multi-domain]  Cd Length: 256  Bit Score: 48.37  E-value: 9.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491   56 FDTDKvlltftDSRNFRKDVEPTYKGNRvkrKPC------GYKKLKN-WAMKEWPSVMKPGLEADDVMGILATNGSLDN- 127
Cdd:PRK09482  54 FDGDA------RSSGWRHQLLPDYKAGR---KPMpealqqGLPAIRAaFEELGIDSWHADGNEADDLIATLAVKVAQAGh 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18640491  128 -FVLISPDKDMAQIP---CRIYD-LKHEYTQTPE-------KAHELLYLQCLTGDSTDGYSGCPGIGPKRALAIL 190
Cdd:PRK09482 125 qATIVSTDKGYCQLLsptIQIRDyFQKRWLDAPFieqefgvEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELL 199
H3TH_53EXO cd09898
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ...
 164-192 3.49e-06

H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188618 [Multi-domain]  Cd Length: 73  Bit Score: 43.54  E-value: 3.49e-06
                        10        20
                ....*....|....*....|....*....
gi 18640491 164 LQCLTGDSTDGYSGCPGIGPKRALAILGK 192
Cdd:cd09898   7 YLALVGDSSDNIPGVPGIGPKTAAKLLQE 35
5_3_exonuc pfam01367
5'-3' exonuclease, C-terminal SAM fold;
167-192 3.00e-05

5'-3' exonuclease, C-terminal SAM fold;


Pssm-ID: 460176 [Multi-domain]  Cd Length: 93  Bit Score: 41.59  E-value: 3.00e-05
                          10        20
                  ....*....|....*....|....*.
gi 18640491   167 LTGDSTDGYSGCPGIGPKRALAILGK 192
Cdd:pfam01367  12 LMGDSSDNIPGVPGIGEKTAAKLLNE 37
PIN_53EXO-like cd00008
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ...
 45-140 4.07e-03

FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs; PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of multi-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350199  Cd Length: 158  Bit Score: 36.85  E-value: 4.07e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18640491  45 FRQSIKDFTTKFDTDKVLLTFTDSRN-FRKDVEPTYKGNRVKRK------PCGYKKLKNWAMKE-----WPSVMKPGLEA 112
Cdd:cd00008  31 FAKSILKALKEDSGDAVIVVFDAKKPsFRHEAYGGYKANRAEKYaeekptPEDFFEQLALIKELvkllgLARLEIPGYEA 110

                        90       100       110
                ....*....|....*....|....*....|
gi 18640491 113 DDVMGILATNGSL--DNFVLISPDKDMAQI 140
Cdd:cd00008 111 DDVLASLVKKAEKegYEVRIISADGDLYQL 140
 
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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