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Conserved domains on  [gi|1864381635|ref|YP_009886509|]
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ribonuclease [Acinetobacter phage vB_AbaM_Apostate]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rnh super family cl33687
RnaseH; Provisional
 1-360 3.03e-118

RnaseH; Provisional


The actual alignment was detected with superfamily member PHA02567:

Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 344.35  E-value: 3.03e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   1 MSLDHFYGED--KPGALLIDLSQIALATVAVTYEPGMKFTVPIVRQLVLSTIKHNALKFKSDgYDHVIIAIDNARYGYWR 78
Cdd:PHA02567    1 MDLNSFMDEDddKEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEE-YPEIVLAFDNSKSGYWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  79 RQEEDYYKRNRAIARDAAKeaesFDWDGYFNALGIVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSD 158
Cdd:PHA02567   80 RDIAWYYKKNRKKDREESP----WDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 159 GDFTQLHKLEDVDQYSPIQKKFVKVKTGSPQEDCLTKVLKGDRKDCVASIKVRGDFWLNYEEDERTPSTTAAFVTKLVGK 238
Cdd:PHA02567  156 GDFTQLHKYPGVKQWSPMQKKWVKPKYGSPEKDLMTKIIKGDKKDGVASIKVRSDYILTRVEGERAPSISTKELEAIADA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 239 SDDEVyeALTEEimkkaknkktgvaechkllklqgvqiededgeileqyrtdamamakqiadlQFHRFKRNRILIDFDYI 318
Cdd:PHA02567  236 EDPKV--LLTEE---------------------------------------------------EYERYDENRELIDFDFI 262

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1864381635 319 RDDIRESIINHYKEYKPAPRGKIYPYLVKNQLTKLLKDLNGF 360
Cdd:PHA02567  263 PDDIADKIIEAYNSYKPPPRGKIYSYFVKNGLSKLLQKVNEF 304
 
Name Accession Description Interval E-value
rnh PHA02567
RnaseH; Provisional
 1-360 3.03e-118

RnaseH; Provisional


Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 344.35  E-value: 3.03e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   1 MSLDHFYGED--KPGALLIDLSQIALATVAVTYEPGMKFTVPIVRQLVLSTIKHNALKFKSDgYDHVIIAIDNARYGYWR 78
Cdd:PHA02567    1 MDLNSFMDEDddKEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEE-YPEIVLAFDNSKSGYWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  79 RQEEDYYKRNRAIARDAAKeaesFDWDGYFNALGIVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSD 158
Cdd:PHA02567   80 RDIAWYYKKNRKKDREESP----WDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 159 GDFTQLHKLEDVDQYSPIQKKFVKVKTGSPQEDCLTKVLKGDRKDCVASIKVRGDFWLNYEEDERTPSTTAAFVTKLVGK 238
Cdd:PHA02567  156 GDFTQLHKYPGVKQWSPMQKKWVKPKYGSPEKDLMTKIIKGDKKDGVASIKVRSDYILTRVEGERAPSISTKELEAIADA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 239 SDDEVyeALTEEimkkaknkktgvaechkllklqgvqiededgeileqyrtdamamakqiadlQFHRFKRNRILIDFDYI 318
Cdd:PHA02567  236 EDPKV--LLTEE---------------------------------------------------EYERYDENRELIDFDFI 262

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1864381635 319 RDDIRESIINHYKEYKPAPRGKIYPYLVKNQLTKLLKDLNGF 360
Cdd:PHA02567  263 PDDIADKIIEAYNSYKPPPRGKIYSYFVKNGLSKLLQKVNEF 304
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 15-183 6.26e-35

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: 125.40  E-value: 6.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  15 LLIDLSQIALAT--VAVTYEPGMKFTVpivRQLVLSTIKHNALKFKsdgYDHVIIAIDNAryGYWRRQEEDYYKRNRAia 92
Cdd:cd09860     2 LLIDGNSIGFAAqhSAKLTAGGMEVQA---RFGFLRSIRSYLKRYK---YAKPIVLWDGR--ASWRKDLFPEYKANRK-- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  93 rdaAKEAESFDWDGYFNALGIVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSDGDFTQLHKlEDVDQ 172
Cdd:cd09860    72 ---KTREEKKAWREAFEAQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAFGDKVLLVSGDKDWLQLVY-ENVSW 147

                         170
                  ....*....|.
gi 1864381635 173 YSPIQKKFVKV 183
Cdd:cd09860   148 FSPITDKEVTL 158
RNaseH_C pfam09293
T4 RNase H, C terminal; Members of this family are found in T4 RNaseH ribonuclease, and adopt ...
 186-360 3.72e-32

T4 RNase H, C terminal; Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork.


Pssm-ID: 401290  Cd Length: 124  Bit Score: 117.03  E-value: 3.72e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 186 GSPQEDCLTKVLKGDRKDCVASIKVRGDFWLNYEEDERTPSTTAAFVTKLVGKSDDEVYEALTEEimkkaknkktgvaec 265
Cdd:pfam09293   1 GSAEIDCMTKCIKGDKKDGIAPLKAPSDFWFTHGDGERAPSMKKEELEAIMANDPEEAKKLLTDE--------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 266 hkllklqgvqiededgeileqyrtdamamakqiadlQFHRFKRNRILIDFDYIRDDIRESIINHYKEYKPAPRGKIYPYL 345
Cdd:pfam09293  66 ------------------------------------EYARYEENLKLIDFAFIPDHIADNIIEQFESQKLAPRGKIMMYF 109

                         170
                  ....*....|....*
gi 1864381635 346 VKNQLTKLLKDLNGF 360
Cdd:pfam09293 110 AKAGLDKLIESINEF 124
53EXOc smart00475
5'-3' exonuclease;
57-164 1.92e-08

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 54.52  E-value: 1.92e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   57 FKSDGYDHVIIAIDnARYGYWRRQEEDYYKRNRAIARD-------AAKEAesfdwdgyFNALGIVIQELKDNmpwvvvdv 129
Cdd:smart00475  44 IKEEKPTYVAVVFD-AKGKTFRHELYPEYKANRPKTPDelleqipLIKEL--------LDALGIPVLEVEGY-------- 106

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1864381635  130 rhcEADDCIAVLSSYLSKQGYKVRIISSDGDFTQL 164
Cdd:smart00475 107 ---EADDVIATLAKKAEAEGYEVRIVSGDKDLLQL 138
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
63-164 9.10e-07

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 49.64  E-value: 9.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  63 DHVIIAIDNARYGyWRRQEEDYYKRNRAIARDAAKEAesFDwdgyfnalgiVIQELKDNMPWVVVDVRHCEADDCIAVLS 142
Cdd:COG0258    54 THLAVAFDAKGPT-FRHELYPEYKANRPEMPEELRPQ--IP----------LIKEVLEALGIPVLEVEGYEADDVIGTLA 120

                          90       100
                  ....*....|....*....|..
gi 1864381635 143 SYLSKQGYKVRIISSDGDFTQL 164
Cdd:COG0258   121 KQAEAEGYEVLIVTGDKDLLQL 142
 
Name Accession Description Interval E-value
rnh PHA02567
RnaseH; Provisional
 1-360 3.03e-118

RnaseH; Provisional


Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 344.35  E-value: 3.03e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   1 MSLDHFYGED--KPGALLIDLSQIALATVAVTYEPGMKFTVPIVRQLVLSTIKHNALKFKSDgYDHVIIAIDNARYGYWR 78
Cdd:PHA02567    1 MDLNSFMDEDddKEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEE-YPEIVLAFDNSKSGYWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  79 RQEEDYYKRNRAIARDAAKeaesFDWDGYFNALGIVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSD 158
Cdd:PHA02567   80 RDIAWYYKKNRKKDREESP----WDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 159 GDFTQLHKLEDVDQYSPIQKKFVKVKTGSPQEDCLTKVLKGDRKDCVASIKVRGDFWLNYEEDERTPSTTAAFVTKLVGK 238
Cdd:PHA02567  156 GDFTQLHKYPGVKQWSPMQKKWVKPKYGSPEKDLMTKIIKGDKKDGVASIKVRSDYILTRVEGERAPSISTKELEAIADA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 239 SDDEVyeALTEEimkkaknkktgvaechkllklqgvqiededgeileqyrtdamamakqiadlQFHRFKRNRILIDFDYI 318
Cdd:PHA02567  236 EDPKV--LLTEE---------------------------------------------------EYERYDENRELIDFDFI 262

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1864381635 319 RDDIRESIINHYKEYKPAPRGKIYPYLVKNQLTKLLKDLNGF 360
Cdd:PHA02567  263 PDDIADKIIEAYNSYKPPPRGKIYSYFVKNGLSKLLQKVNEF 304
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 15-183 6.26e-35

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: 125.40  E-value: 6.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  15 LLIDLSQIALAT--VAVTYEPGMKFTVpivRQLVLSTIKHNALKFKsdgYDHVIIAIDNAryGYWRRQEEDYYKRNRAia 92
Cdd:cd09860     2 LLIDGNSIGFAAqhSAKLTAGGMEVQA---RFGFLRSIRSYLKRYK---YAKPIVLWDGR--ASWRKDLFPEYKANRK-- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  93 rdaAKEAESFDWDGYFNALGIVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSDGDFTQLHKlEDVDQ 172
Cdd:cd09860    72 ---KTREEKKAWREAFEAQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAFGDKVLLVSGDKDWLQLVY-ENVSW 147

                         170
                  ....*....|.
gi 1864381635 173 YSPIQKKFVKV 183
Cdd:cd09860   148 FSPITDKEVTL 158
RNaseH_C pfam09293
T4 RNase H, C terminal; Members of this family are found in T4 RNaseH ribonuclease, and adopt ...
 186-360 3.72e-32

T4 RNase H, C terminal; Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork.


Pssm-ID: 401290  Cd Length: 124  Bit Score: 117.03  E-value: 3.72e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 186 GSPQEDCLTKVLKGDRKDCVASIKVRGDFWLNYEEDERTPSTTAAFVTKLVGKSDDEVYEALTEEimkkaknkktgvaec 265
Cdd:pfam09293   1 GSAEIDCMTKCIKGDKKDGIAPLKAPSDFWFTHGDGERAPSMKKEELEAIMANDPEEAKKLLTDE--------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 266 hkllklqgvqiededgeileqyrtdamamakqiadlQFHRFKRNRILIDFDYIRDDIRESIINHYKEYKPAPRGKIYPYL 345
Cdd:pfam09293  66 ------------------------------------EYARYEENLKLIDFAFIPDHIADNIIEQFESQKLAPRGKIMMYF 109

                         170
                  ....*....|....*
gi 1864381635 346 VKNQLTKLLKDLNGF 360
Cdd:pfam09293 110 AKAGLDKLIESINEF 124
PIN_53EXO-like cd00008
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ...
 16-183 6.74e-31

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: 115.05  E-value: 6.74e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  16 LIDLSQIALATVAVTYEPGMKFTVPIVRQLVLSTIKHNAlkfKSDGYDHVIIAIDNARyGYWRRQEEDYYKRNRAIARda 95
Cdd:cd00008     1 LVDGHHLAYRTFHANKGLTTSGEPVQAVYGFAKSILKAL---KEDSGDAVIVVFDAKK-PSFRHEAYGGYKANRAEKY-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  96 akEAESFDWDGYFNALGIVIQELKdNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSDGDFTQLHKlEDVDQYSP 175
Cdd:cd00008    75 --AEEKPTPEDFFEQLALIKELVK-LLGLARLEIPGYEADDVLASLVKKAEKEGYEVRIISADGDLYQLLS-DRVHVLSP 150


                  ....*...
gi 1864381635 176 IQKKFVKV 183
Cdd:cd00008   151 TEGYLITP 158
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
63-164 8.02e-10

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


Pssm-ID: 460672  Cd Length: 163  Bit Score: 57.02  E-value: 8.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  63 DHVIIAIDNAryGYWRRQEEDYYKRNRAIARDAAKEAesFDwdgyfnalgiVIQELKDNMPWVVVDVRHCEADDCIAVLS 142
Cdd:pfam02739  49 THVAVAFDAK--PTFRHELYPEYKANRPPMPEELRPQ--IP----------LIKELLEALGIPVLEVEGYEADDIIGTLA 114

                          90       100
                  ....*....|....*....|..
gi 1864381635 143 SYLSKQGYKVRIISSDGDFTQL 164
Cdd:pfam02739 115 KRAEEEGYEVVIVTGDKDLLQL 136
53EXOc smart00475
5'-3' exonuclease;
57-164 1.92e-08

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 54.52  E-value: 1.92e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   57 FKSDGYDHVIIAIDnARYGYWRRQEEDYYKRNRAIARD-------AAKEAesfdwdgyFNALGIVIQELKDNmpwvvvdv 129
Cdd:smart00475  44 IKEEKPTYVAVVFD-AKGKTFRHELYPEYKANRPKTPDelleqipLIKEL--------LDALGIPVLEVEGY-------- 106

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1864381635  130 rhcEADDCIAVLSSYLSKQGYKVRIISSDGDFTQL 164
Cdd:smart00475 107 ---EADDVIATLAKKAEAEGYEVRIVSGDKDLLQL 138
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 42-167 5.50e-08

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this 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: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 52.10  E-value: 5.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  42 VRQLVLSTIKHNALKFKSDGydHVIIAIDNAR-YGYWRRQEEDYYKRNRAIARDA-----AKEAESFDWDGYFNALGIVI 115
Cdd:cd09853    25 DFQGYFSAVDDLVKKLKPGI--KPILLFDGGKpKAKKGNRDKRRERRAREEDRKKgqlkeHKEFDKRLIELGPEYLIRLF 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1864381635 116 QELKDNMPWVVVDVRHcEADDCIAVLSSYLSKQGYKVRIISSDGDFTQLHKL 167
Cdd:cd09853   103 ELLKHFMGIPVMDAPG-EAEDEIAYLVKKHKHLGTVHLIISTDGDFLLLGTD 153
PRK05755 PRK05755
DNA polymerase I; Provisional
 114-164 5.67e-07

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 51.25  E-value: 5.67e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1864381635 114 VIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGYKVRIISSDGDFTQL 164
Cdd:PRK05755   90 LIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQL 140
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
63-164 9.10e-07

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 49.64  E-value: 9.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  63 DHVIIAIDNARYGyWRRQEEDYYKRNRAIARDAAKEAesFDwdgyfnalgiVIQELKDNMPWVVVDVRHCEADDCIAVLS 142
Cdd:COG0258    54 THLAVAFDAKGPT-FRHELYPEYKANRPEMPEELRPQ--IP----------LIKEVLEALGIPVLEVEGYEADDVIGTLA 120

                          90       100
                  ....*....|....*....|..
gi 1864381635 143 SYLSKQGYKVRIISSDGDFTQL 164
Cdd:COG0258   121 KQAEAEGYEVLIVTGDKDLLQL 142
PRK14976 PRK14976
5'-3' exonuclease; Provisional
 57-164 4.23e-05

5'-3' exonuclease; Provisional


Pssm-ID: 237877 [Multi-domain]  Cd Length: 281  Bit Score: 44.55  E-value: 4.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  57 FKSDGYDHVIIAIDNARYGYwRRQEEDYYKRNRAIARDAAKEAesfdwdgyFNALGIVIQELKDNmpwvVVDVRHCEADD 136
Cdd:PRK14976   50 LKKLNPSYILIAFDAGRKTF-RHQLYDEYKQGRKKTPESLISQ--------IPLLKKILKLAGIK----WEEQPGYEADD 116

                          90       100
                  ....*....|....*....|....*...
gi 1864381635 137 CIAVLSSYLSKQGYKVRIISSDGDFTQL 164
Cdd:PRK14976  117 LIGSLAKKLSKQNITVLIYSSDKDLLQL 144
PHA00439 PHA00439
exonuclease
 8-267 2.84e-04

exonuclease


Pssm-ID: 222794 [Multi-domain]  Cd Length: 286  Bit Score: 42.07  E-value: 2.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635   8 GEDKPGALLIDLSQI---ALATVAVTYEPGMKFTVPI-----VRQLVLSTIKHNALKFKSDGYDHVIIAIDNARYgyWRR 79
Cdd:PHA00439    2 GMSDKGVLVMDGDYLvfqAMAAAEVETDWGEDIWTLEcdhakARQILEDSIKSYKTRKKAWKDAPIVLAFTDSVN--WRK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635  80 QEEDYYKRNRAIARDAAkeaesfdwdGYFNalgiVIQELKDNMPWVVVDVRHCEADDCIAVLSSYLSKQGY-KVRIISSD 158
Cdd:PHA00439   80 EVVPTYKANRKAKRKPV---------GYRK----FLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFkKAVLVSCD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864381635 159 GDFTQlhkLEDVDQYSPIQKKFVKVKTGSPQEDCLTKVLKGDRKDCVASIKVRGDfwlnyeedertpsTTAAFVtklvgk 238
Cdd:PHA00439  147 KDFKT---IPNCDFLWCTTGNILTQTPETADRWHLFQTIKGDSTDGYSGIPGWGD-------------TAEAFL------ 204

                         250       260
                  ....*....|....*....|....*....
gi 1864381635 239 sDDEVYEALTEEIMKKAKNKKTGVAECHK 267
Cdd:PHA00439  205 -ENPYIFEQVEKVLKSGKRKGQTVTKWKK 232
 
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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