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Conserved domains on  [gi|444731649|gb|ELW71998|]
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Flap endonuclease GEN like protein 1 [Tupaia chinensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-262 3.51e-122

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member 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: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 366.16  E-value: 3.51e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   2 GVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVKKMIGTVMKPHLRNLFFRISYLTQMDVKLVFVMEGEPPKL 81
Cdd:cd09869    1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQTVLALFETVPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAPEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  82 KADVISKRNQIRYG-PSGKTWSQKRGRSQFKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFL 160
Cdd:cd09869   81 KLQTIKKRNAARFGgAKKKGGSKKRGRSRFSRVLKECEELLELLGVPVVQAPGEAEALCALLNAEGLVDGCITNDGDAFL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 161 YGAQTVYRNFTMNTKDPHVDCYTMScikdklgldrdalvglaillgcdylpkVIEEFLSskdklgkiIRYQRPDLLLFQR 240
Cdd:cd09869  161 YGARTVYRNFSLNTKDGSVECYDMS---------------------------DIEKRLS--------LRWRRPDLDLLQD 205

                        250       260
                 ....*....|....*....|..
gi 444731649 241 FTLEKMEWPNHYACEKLLVLLT 262
Cdd:cd09869  206 FLLKKLDWDEEYAREKLLPLLT 227
Chromo_2 pfam18704
Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, ...
 280-340 1.38e-23

Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired. The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5. Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa).


:

Pssm-ID: 465841  Cd Length: 63  Bit Score: 94.26  E-value: 1.38e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 444731649  280 QPVRIVKTRIRNGVHCFEIEWEKPEHYV-VDDKQCGELGLL-TVEEESLFEAAYPEIVTDYQK 340
Cdd:pfam18704   1 QPIRIVKKRVRKGVPSYEIEWKKPEGYFeEEDDDPGELELLtTIEPQDLVEKAYPELVEAFEK 63
 
Name Accession Description Interval E-value
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-262 3.51e-122

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member 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: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 366.16  E-value: 3.51e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   2 GVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVKKMIGTVMKPHLRNLFFRISYLTQMDVKLVFVMEGEPPKL 81
Cdd:cd09869    1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQTVLALFETVPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAPEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  82 KADVISKRNQIRYG-PSGKTWSQKRGRSQFKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFL 160
Cdd:cd09869   81 KLQTIKKRNAARFGgAKKKGGSKKRGRSRFSRVLKECEELLELLGVPVVQAPGEAEALCALLNAEGLVDGCITNDGDAFL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 161 YGAQTVYRNFTMNTKDPHVDCYTMScikdklgldrdalvglaillgcdylpkVIEEFLSskdklgkiIRYQRPDLLLFQR 240
Cdd:cd09869  161 YGARTVYRNFSLNTKDGSVECYDMS---------------------------DIEKRLS--------LRWRRPDLDLLQD 205

                        250       260
                 ....*....|....*....|..
gi 444731649 241 FTLEKMEWPNHYACEKLLVLLT 262
Cdd:cd09869  206 FLLKKLDWDEEYAREKLLPLLT 227
XPG_I pfam00867
XPG I-region;
125-208 1.76e-34

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 126.09  E-value: 1.76e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  125 GIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMNTKDP---HVDCYTMSCIKDKLGLDRDALVGL 201
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKKKskvPVEEIDLEKILKELGLTREQLIDL 80


                  ....*..
gi 444731649  202 AILLGCD 208
Cdd:pfam00867  81 AILLGCD 87
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 1-213 7.21e-31

flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA


Pssm-ID: 274717 [Multi-domain]  Cd Length: 338  Bit Score: 124.28  E-value: 7.21e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649    1 MGVnDLWQILEpvKQHIDLHNLVGKSIAVDLSLWVCE-AQTVKKMIGTVMK-------PHLRNLFFRISYLTQMDVKLVF 72
Cdd:TIGR03674   1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQfLSSIRQPDGTPLMdsrgritSHLSGLFYRTINLLENGIKPVY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   73 VMEGEPPKLKADVISKRNQIRYGPSGKtWSQ--KRG----------RSQF--KSVLRECLDMLECLGIPWVQAAGEAEAM 138
Cdd:TIGR03674  78 VFDGKPPELKAETLEERREIREEAEEK-WEEalEKGdleearkyaqRSSRltSEIVESSKKLLDLMGIPYVQAPSEGEAQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  139 CAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFT------MNTKDPHVDCY----TMSCIKDKLGLDRDALVGLAILLGCD 208
Cdd:TIGR03674 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTisgkrkLPGKNIYVEVKpeliELEEVLSELGITREQLIDIAILVGTD 236


                  ....*
gi 444731649  209 YLPKV 213
Cdd:TIGR03674 237 YNEGV 241
PRK03980 PRK03980
flap endonuclease-1; Provisional
 52-213 3.14e-29

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 118.38  E-value: 3.14e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  52 HLRNLFFRISYLTQMDVKLVFVMEGEPPKLKADVISKRNQIRYGpSGKTW--SQKRG----------RSQF--KSVLREC 117
Cdd:PRK03980  10 HLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREE-AEEKYeeAKEEGdleearkyaqRSSRltDEIVEDS 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 118 LDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMN--TKDPHVDCY--------TMSCI 187
Cdd:PRK03980  89 KKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISgkRKLPGKNVYvevkpeliELEEV 168

                        170       180
                 ....*....|....*....|....*.
gi 444731649 188 KDKLGLDRDALVGLAILLGCDYLPKV 213
Cdd:PRK03980 169 LKELGITREQLIDIAILVGTDYNPGI 194
Chromo_2 pfam18704
Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, ...
 280-340 1.38e-23

Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired. The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5. Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa).


Pssm-ID: 465841  Cd Length: 63  Bit Score: 94.26  E-value: 1.38e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 444731649  280 QPVRIVKTRIRNGVHCFEIEWEKPEHYV-VDDKQCGELGLL-TVEEESLFEAAYPEIVTDYQK 340
Cdd:pfam18704   1 QPIRIVKKRVRKGVPSYEIEWKKPEGYFeEEDDDPGELELLtTIEPQDLVEKAYPELVEAFEK 63
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-93 7.79e-21

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 87.67  E-value: 7.79e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649     1 MGVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVK-----KMIGTVmkPHLRNLFFRISYLTQMDVKLVFVME 75
Cdd:smart00485   1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACreklgTPLPNS--KHLMGLFYRTCRLLEFGIKPIFVFD 78

                           90
                   ....*....|....*...
gi 444731649    76 GEPPKLKADVISKRNQIR 93
Cdd:smart00485  79 GKPPPLKSETLAKRRERR 96
 
Name Accession Description Interval E-value
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-262 3.51e-122

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member 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: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 366.16  E-value: 3.51e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   2 GVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVKKMIGTVMKPHLRNLFFRISYLTQMDVKLVFVMEGEPPKL 81
Cdd:cd09869    1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQTVLALFETVPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAPEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  82 KADVISKRNQIRYG-PSGKTWSQKRGRSQFKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFL 160
Cdd:cd09869   81 KLQTIKKRNAARFGgAKKKGGSKKRGRSRFSRVLKECEELLELLGVPVVQAPGEAEALCALLNAEGLVDGCITNDGDAFL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 161 YGAQTVYRNFTMNTKDPHVDCYTMScikdklgldrdalvglaillgcdylpkVIEEFLSskdklgkiIRYQRPDLLLFQR 240
Cdd:cd09869  161 YGARTVYRNFSLNTKDGSVECYDMS---------------------------DIEKRLS--------LRWRRPDLDLLQD 205

                        250       260
                 ....*....|....*....|..
gi 444731649 241 FTLEKMEWPNHYACEKLLVLLT 262
Cdd:cd09869  206 FLLKKLDWDEEYAREKLLPLLT 227
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 5-259 9.84e-96

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Nucleases in this subfamily 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: 350206 [Multi-domain]  Cd Length: 235  Bit Score: 297.91  E-value: 9.84e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   5 DLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVKKMIG--TVMKPHLRNLFFRISYLTQMDVKLVFVMEGEPPKLK 82
Cdd:cd09856    1 GFWKIIGPSKRRISLESLRGKRVAIDASIWIYQFLTAVRGQGgnGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  83 ADVISKRNQIRYGPS-------------GKTWSQKRGRSQFKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVD 149
Cdd:cd09856   81 KRTRRKRKERRQGAEesaksavedelfeEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 150 GCLTNDGDAFLYGAQTVYRNFTMNTKDPHVDCYTMSCIKDKLgldrdalvglaillgcdylpkvieeflsskdklgkIIR 229
Cdd:cd09856  161 AVLTEDVDTFLFGSPVVYRNLTSEGKKTHVELYDASSILEGL-----------------------------------FLP 205

                        250       260       270
                 ....*....|....*....|....*....|
gi 444731649 230 YQRPDLLLFQRFTLEKMEWPNHYACEKLLV 259
Cdd:cd09856  206 WSTPDLEGLRKFTREEFDWPFEKLIKVLAP 235
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 6-188 1.84e-60

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1) and exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. 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: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 201.45  E-value: 1.84e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   6 LWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVKKM---IGTVMKPHLRNLFFRISYLTQMDVKLVFVMEGEPPKLK 82
Cdd:cd00128    1 LWQFIGEAKEPISIESLKGKTVAIDASIWVYQFLTAKREqggDIGVTNSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  83 ADVIskrnqirygpsgktwsqkrgrsqFKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYG 162
Cdd:cd00128   81 KETI-----------------------TKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFG 137

                        170       180
                 ....*....|....*....|....*.
gi 444731649 163 AQTVYRNFTMNTkdPHVDCYTMSCIK 188
Cdd:cd00128  138 APRVIRNMTFEG--PHVEEFDASSIL 161
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-257 1.35e-47

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to 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: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 168.60  E-value: 1.35e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   2 GVNDLWQILEPVKQHIDLHNLVGKS-----------IAVDLSLWVCEAQTVKK--MIGTVMKPHLRNLFFRISYLTQMDV 68
Cdd:cd09870    1 GIPGLWDLLEPAAESRSLAELAVVEefnkrggrplrIGIDASIWLFHAQSSFGggHIQAGENPELRTLFYRLARLLSLPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  69 KLVFVmegeppklkADviskrnqiryGPSGKTWsqKRGRSQFKSV---LRECL-DMLECLGIPWVQAAGEAEAMCAYLNA 144
Cdd:cd09870   81 QPVFV---------FD----------GPNRPPF--KRGKKVGKSTphwLTKLFkELLDAFGFPWHEAPGEAEAELARLQR 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 145 CGYVDGCLTNDGDAFLYGAQTVYRNFTMNTKDPHVDCYTMSCIKDKLGLDRDALVGlaillgcdylpkvieeflsskdkl 224
Cdd:cd09870  140 LGVVDAVLTDDSDALVFGATTVLRNFSKKLSDDDVKVYTASAIKDKADLTRTSLRG------------------------ 195

                        250       260       270
                 ....*....|....*....|....*....|...
gi 444731649 225 gkiirYQRPDLLLFQRFTLEKMEWPNHYACEKL 257
Cdd:cd09870  196 -----PREPDLPRLAALCEKYFSWGTKEILKRF 223
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-261 1.07e-43

FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member 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: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 156.91  E-value: 1.07e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   2 GVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVceAQTVKKM----IGTVMKPHLRNLFFRISYLTQMDVKLVFVMEGE 77
Cdd:cd09868    1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWL--HQFVKGMrdneGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  78 PPKLKADVISKRNQIRygpsgktwsqkrgrsqfKSVLRECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGD 157
Cdd:cd09868   79 APALKRRTLARRRSVT-----------------DEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSD 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 158 AFLYGAQTVYRNFTMNTKdpHVDCYTMSCIKDKLgldrdalvglaillgcdylpkvieEFlsskdklgkiiRYQRPDLLL 237
Cdd:cd09868  142 VFLFGAKRVYKNFFNQNK--YVEYYDMEDIEREL------------------------KF-----------SWGKPDLEL 184

                        250       260
                 ....*....|....*....|....
gi 444731649 238 FQRFTLEKMEWPNHYACEKLLVLL 261
Cdd:cd09868  185 LREFCLDKFGWPKEKTDELLLPVL 208
XPG_I pfam00867
XPG I-region;
125-208 1.76e-34

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 126.09  E-value: 1.76e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  125 GIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMNTKDP---HVDCYTMSCIKDKLGLDRDALVGL 201
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKKKskvPVEEIDLEKILKELGLTREQLIDL 80


                  ....*..
gi 444731649  202 AILLGCD 208
Cdd:pfam00867  81 AILLGCD 87
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 1-213 7.21e-31

flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA


Pssm-ID: 274717 [Multi-domain]  Cd Length: 338  Bit Score: 124.28  E-value: 7.21e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649    1 MGVnDLWQILEpvKQHIDLHNLVGKSIAVDLSLWVCE-AQTVKKMIGTVMK-------PHLRNLFFRISYLTQMDVKLVF 72
Cdd:TIGR03674   1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQfLSSIRQPDGTPLMdsrgritSHLSGLFYRTINLLENGIKPVY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   73 VMEGEPPKLKADVISKRNQIRYGPSGKtWSQ--KRG----------RSQF--KSVLRECLDMLECLGIPWVQAAGEAEAM 138
Cdd:TIGR03674  78 VFDGKPPELKAETLEERREIREEAEEK-WEEalEKGdleearkyaqRSSRltSEIVESSKKLLDLMGIPYVQAPSEGEAQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  139 CAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFT------MNTKDPHVDCY----TMSCIKDKLGLDRDALVGLAILLGCD 208
Cdd:TIGR03674 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTisgkrkLPGKNIYVEVKpeliELEEVLSELGITREQLIDIAILVGTD 236


                  ....*
gi 444731649  209 YLPKV 213
Cdd:TIGR03674 237 YNEGV 241
PRK03980 PRK03980
flap endonuclease-1; Provisional
 52-213 3.14e-29

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 118.38  E-value: 3.14e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  52 HLRNLFFRISYLTQMDVKLVFVMEGEPPKLKADVISKRNQIRYGpSGKTW--SQKRG----------RSQF--KSVLREC 117
Cdd:PRK03980  10 HLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREE-AEEKYeeAKEEGdleearkyaqRSSRltDEIVEDS 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 118 LDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMN--TKDPHVDCY--------TMSCI 187
Cdd:PRK03980  89 KKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISgkRKLPGKNVYvevkpeliELEEV 168

                        170       180
                 ....*....|....*....|....*.
gi 444731649 188 KDKLGLDRDALVGLAILLGCDYLPKV 213
Cdd:PRK03980 169 LKELGITREQLIDIAILVGTDYNPGI 194
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 5-171 4.69e-26

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). 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. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 107.87  E-value: 4.69e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   5 DLWQILEpvKQHIDLHNLVGKSIAVDLSLWVceAQ---TVKKMIGTVMK-------PHLRNLFFRISYLTQMDVKLVFVM 74
Cdd:cd09867    2 NLSKLIA--IKEIELKDLSGKKIAIDASNAL--YQflsAIRQPDGTPLTdskgrvtSHLSGLFYRTINLLENGIKPVYVF 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  75 EGEPPKLKADVISKRNQIRYGpSGKTWSQ--KRG-----RSQFKSVLR-------ECLDMLECLGIPWVQAAGEAEAMCA 140
Cdd:cd09867   78 DGKPPELKSGELEKRRERREE-AEEKLEEalEEGdleeaRKYAKRTVRvtkemveEAKKLLDLMGIPYVQAPSEGEAQAA 156

                        170       180       190
                 ....*....|....*....|....*....|.
gi 444731649 141 YLNACGYVDGCLTNDGDAFLYGAQTVYRNFT 171
Cdd:cd09867  157 YLVKKGDVYAVASQDYDSLLFGAPRLVRNLT 187
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 1-240 4.01e-24

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 105.48  E-value: 4.01e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   1 MGVNDLWQILE---P--VKQhIDLHNLVGKSIAVDLSLWVCEAQTVKKMIGTVMK---------PHLRNLFFRISYLTQM 66
Cdd:PTZ00217   1 MGIKGLSKFLAdkaPnaIKE-QELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNltneagevtSHISGLFNRTIRLLEA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  67 DVKLVFVMEGEPPKLKADVISKRNQIRygPSGKTWSQK--------RGRSQFKSVLR-------ECLDMLECLGIPWVQA 131
Cdd:PTZ00217  80 GIKPVYVFDGKPPELKSGELEKRRERR--EEAEEELEKaieegddeEIKKQSKRTVRvtkeqneDAKKLLRLMGIPVIEA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649 132 AGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMN--TKDPHVDcYTMSCIKDKLGLDRDALVGLAILLGCDY 209
Cdd:PTZ00217 158 PCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSeaKKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDY 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 444731649 210 LPKV-----------------IEEFLSSKDKlgkiIRYQRPDLLLFQR 240
Cdd:PTZ00217 237 CDTIkgigpktayklikkyksIEEILEHLDK----TKYPVPENFDYKE 280
Chromo_2 pfam18704
Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, ...
 280-340 1.38e-23

Chromatin organization modifier domain 2; Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired. The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5. Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa).


Pssm-ID: 465841  Cd Length: 63  Bit Score: 94.26  E-value: 1.38e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 444731649  280 QPVRIVKTRIRNGVHCFEIEWEKPEHYV-VDDKQCGELGLL-TVEEESLFEAAYPEIVTDYQK 340
Cdd:pfam18704   1 QPIRIVKKRVRKGVPSYEIEWKKPEGYFeEEDDDPGELELLtTIEPQDLVEKAYPELVEAFEK 63
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-93 7.79e-21

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 87.67  E-value: 7.79e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649     1 MGVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEAQTVK-----KMIGTVmkPHLRNLFFRISYLTQMDVKLVFVME 75
Cdd:smart00485   1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACreklgTPLPNS--KHLMGLFYRTCRLLEFGIKPIFVFD 78

                           90
                   ....*....|....*...
gi 444731649    76 GEPPKLKADVISKRNQIR 93
Cdd:smart00485  79 GKPPPLKSETLAKRRERR 96
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 99-213 1.27e-19

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. 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: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 94.20  E-value: 1.27e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649    99 KTWSQKRGRSQFKSVL-RECLDMLECLGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTmnTKDP 177
Cdd:TIGR00600  758 QKQQQKRIAAEVTGQMiLESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFF--NQNK 835

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 444731649   178 HVDCYTMSCIKDKLGLDRDALVGLAILLGCDY---LPKV 213
Cdd:TIGR00600  836 FVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYtegIPTV 874
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 124-193 1.74e-18

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 80.32  E-value: 1.74e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 444731649   124 LGIPWVQAAGEAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYRNFTMNTKDpHVDCYTM--SCIKDKLGL 193
Cdd:smart00484   3 MGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKK-KLEFRIIdlESVLKELGL 73
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-97 1.68e-14

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. 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: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 77.63  E-value: 1.68e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649     1 MGVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLWVCEA-QTVKKMIGTVMK-PHLRNLFFRISYLTQMDVKLVFVMEGEP 78
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQAlKGVRDREGNAIKnSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90
                   ....*....|....*....
gi 444731649    79 PKLKADVISKRNQIRYGPS 97
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGAS 99
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-189 2.35e-13

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. 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. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 69.36  E-value: 2.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649   1 MGVNDLWQILEPVKQHIDLHNLVGKSIAVDLSLW-----------VCEAQTVKKMIGTVMKphlrnlffRISYLTQMDVK 69
Cdd:cd09857    1 MGIQGLLPFLKPIQRPVHISEYAGKTVAVDAYCWlhrgayscaeeLALGKPTDKYIDYCMK--------RVNMLLHHGIT 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  70 LVFVMEGEPPKLKADVISKRNQIR---------YGPSGKTwsqKRGRSQF-KSV------LRECLDMLECLGIPWVQAAG 133
Cdd:cd09857   73 PILVFDGAPLPSKAGTEEERRERReealekaleLLREGKK---SEARECFqRAVditpemAHELIKALRKENVEYIVAPY 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 444731649 134 EAEAMCAYLNACGYVDGCLTNDGDAFLYGAQTVYrnFTMNtKDPHVDCYTMSCIKD 189
Cdd:cd09857  150 EADAQLAYLAKTGYVDAVITEDSDLLAFGCPKVL--FKLD-KDGNGQEIDRDDLGK 202
XPG_N pfam00752
XPG N-terminal domain;
2-93 8.24e-12

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 61.99  E-value: 8.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649    2 GVNDLWQILEPVK--QHIDLHNLVGKSIAVDLSLWVCEA-QTVKKMIGTVMK--PHLRNLFFRISYLTQMDVKLVFVMEG 76
Cdd:pfam00752   1 GIKGLLPILKPVAliRPVDIEALEGKTLAIDASIWLYQFlKAVRDQLGNALQntSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                          90
                  ....*....|....*..
gi 444731649   77 EPPKLKADVISKRNQIR 93
Cdd:pfam00752  81 GPPPLKAETLQKRSARR 97
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 53-168 5.26e-06

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: 47.48  E-value: 5.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444731649  53 LRNLFF----RISYLTQMDVKLVFVMEGEPPKLKADVISKR--------NQIRYGPSGKTWSQKRGRSQFKSVLRECLDM 120
Cdd:cd09853   25 DFQGYFsavdDLVKKLKPGIKPILLFDGGKPKAKKGNRDKRrerrareeDRKKGQLKEHKEFDKRLIELGPEYLIRLFEL 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 444731649 121 LE-CLGIPWVQAAGEAEAMCAYL----NACGYVDGCLTNDGDAFLYGAQTVYR 168
Cdd:cd09853  105 LKhFMGIPVMDAPGEAEDEIAYLvkkhKHLGTVHLIISTDGDFLLLGTDHPYI 157
 
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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