|
Name |
Accession |
Description |
Interval |
E-value |
| PolX |
COG1796 |
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair]; |
3-569 |
0e+00 |
|
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
Pssm-ID: 441401 [Multi-domain] Cd Length: 567 Bit Score: 636.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 3 IHNAECAAVFAEIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMIAKGDdLGKIPSIGADLAAKLREIAATGTCELQ 82
Cdd:COG1796 1 MDNKEIARILEEIADLLELKGENPFKIRAYRRAARAIENLPEDIEELVAEGD-LTEIPGIGKAIAAKIEELLETGRLEEL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 83 QTLRHALPGAIVELLDVPGLGAKRVKALHDALNVDSLEQLRAEAKSGHVRELPGFGAKTEAHLLEAIDdRLQREPQRFLL 162
Cdd:COG1796 80 EELREEVPPGLLELLRIPGLGPKKVKKLYEELGITSLEELEAAAEEGRIRELPGFGEKTEENILKGIE-LLRKRGGRFLL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 163 PDAAHALMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAGAVTAAFVGYDDVARVLAHGKTRSSVMLVNGL 242
Cdd:COG1796 159 GEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVASDDPEAVMDAFVKLPEVKEVLAKGDTKASVRLKSGL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 243 QVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFR-GDERIAGATEASVYAAIGLHEVPPELREGRGE 321
Cdd:COG1796 239 QVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEYGLFDvGGERIAGETEEEVYAALGLPYIPPELREDRGE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 322 IDASRAGTLPALVERKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGFDW--LARQLDDIDR 399
Cdd:COG1796 319 IEAAEEGRLPELVELDDIRGDLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDHSSSLVVA-GGLDEerLLQQEEEIDA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 400 LNATFDDFVLLKGVEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERD 479
Cdd:COG1796 398 LNERLDGIILLLGGEEDILDDGGLDDDDDLLLEDDDVVAAVHHSFLLQDEEMTRRRLAAANEPVVVIIHHPTGRLLLRRR 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 480 ACELDVPRVLAQAAARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLN 559
Cdd:COG1796 478 PYYVDDEAIIAAAAAAGALEEENNAPRRLLLLDDLARAAAEGGVVIIIIDDAHHTDLLLDLMGGGVAARRRWWLEKDVNN 557
|
570
....*....|
gi 1145111223 560 TRTLAQLRPL 569
Cdd:COG1796 558 NTLLLELLLL 567
|
|
| PRK08609 |
PRK08609 |
DNA polymerase/3'-5' exonuclease PolX; |
14-572 |
1.20e-139 |
|
DNA polymerase/3'-5' exonuclease PolX;
Pssm-ID: 236311 [Multi-domain] Cd Length: 570 Bit Score: 417.44 E-value: 1.20e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 14 EIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMiakgDDLGKIPSIGADLAAKLREIAATGTCELQQTLRHALPGAI 93
Cdd:PRK08609 12 TIATYMELKGENPFKISAFRKAAQALELDERSLSEI----DDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 94 VELLDVPGLGAKRVKALHDALNVDSLEQLRAEAKSGHVRELPGFGAKTEAHLLEAIDDRLQRePQRFLLPDAAHALMPLL 173
Cdd:PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKR-PERLPIAQVLPIAQEIE 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 174 ERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAGAVTAAFVGYDDVARVLAHGKTRSSVML--VNGLQVDLRVVDA 251
Cdd:PRK08609 167 EYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEAVREQLLQLPNIVEVIAAGDTKVSVELeyEYTISVDFRLVEP 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 252 DAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFRGD--ERIAGATEASVYAAIGLHEVPPELREGRGEIDASRAgt 329
Cdd:PRK08609 247 EAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQADtgEVKTFESEEAFFAHFGLPFIPPEVREDGSEFERYKD-- 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 330 LPALVERKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGF--DWLARQLDDIDRLNATFDDF 407
Cdd:PRK08609 325 LSNLITLSDIQGDLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDHSQYLKVA-NGLteERLLEQAEEIKALNEKYPEI 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 408 VLLKGVEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERDACELDVPR 487
Cdd:PRK08609 404 DILSGIEMDILPDGSLDYDDEVLAELDYVIAAIHSSFSQSEEEIMKRLENACRNPYVRLIAHPTGRLIGRRDGYDVNIDQ 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 488 VLAQAAARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLNTRTLAQLR 567
Cdd:PRK08609 484 LIELAKETNTALELNANPNRLDLSAEHLKKAQEAGVKLAINTDAHHTEMLDDMKYGVATARKGWIQKDRVINTWSREEFK 563
|
....*
gi 1145111223 568 PLLAR 572
Cdd:PRK08609 564 DFIKR 568
|
|
| NT_POLXc |
cd00141 |
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ... |
6-316 |
4.75e-94 |
|
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 290.64 E-value: 4.75e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 6 AECAAVFAEIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMiakgDDLGKIPSIGADLAAKLREIAATGTCELQQTL 85
Cdd:cd00141 1 QEIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESL----EEAKKLPGIGKKIAEKIEEILETGKLRKLEEL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 86 RHALPGAIVELLDVPGLGAKRVKALHDaLNVDSLEQLRAEAksghvrelpgfGAKTEAHLLEAIDdRLQREPQRFLLPDA 165
Cdd:cd00141 77 REDVPPGLLLLLRVPGVGPKTARKLYE-LGIRTLEDLRKAA-----------GAKLEQNILIGLE-YYEDFQQRIPREEA 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 166 AHALMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAG------AVTAAFVGYDDVARVLAHGKTRSSVML- 238
Cdd:cd00141 144 LAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATsrglleKVVDALVELGFVTEVLSKGDTKASGILk 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 239 ----VNGLQVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFRG--DERIAGATEASVYAAIGLHEVP 312
Cdd:cd00141 224 lpggWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGvdGERLPGETEEEIFEALGLPYIE 303
|
....
gi 1145111223 313 PELR 316
Cdd:cd00141 304 PELR 307
|
|
| POLXc |
smart00483 |
DNA polymerase X family; includes vertebrate polymerase beta and terminal ... |
11-317 |
1.45e-32 |
|
DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Pssm-ID: 214688 Cd Length: 334 Bit Score: 127.87 E-value: 1.45e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 11 VFAEIADMLEIQGANPFRVRAYRNAARTIADYgrdiPTMIAKGDDLGKIPSIGADLAAKLREIAATGTC-ELQQTLRHAL 89
Cdd:smart00483 9 ALEILAENYEVFGENKRKCSYFRKAASVLKSL----PFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSsKVLEILNDEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 90 PGAIVELLDVPGLGAKRVKALHDaLNVDSLEQLRAEA-KSGHVRELPGFgakteaHLLEAIDDRLQREpqrfllpDAAHA 168
Cdd:smart00483 85 YKSLKLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNKeLKLTKQQKAGL------KYYEDILKKVSRA-------EAFAV 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 169 LMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVT-ARDAGAVTAAFVGYDDVAR-------------VLAHGKT-- 232
Cdd:smart00483 151 EYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITsPHPAKEKELEVLDLLLLEStfeelqlpsirvaTLDHGQKkf 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 233 -----------RSSVMLVNG-----LQVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGlKINEYGVFRGD----E 292
Cdd:smart00483 231 milklspsredKEKSGKPDEkgwkaRRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDktkeK 309
|
330 340
....*....|....*....|....*
gi 1145111223 293 RIAGATEASVYAAIGLHEVPPELRE 317
Cdd:smart00483 310 FLKVESEEDIFDHLGLPYIEPEERN 334
|
|
| DNA_pol_B_thumb |
pfam14791 |
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ... |
257-317 |
4.22e-23 |
|
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.
Pssm-ID: 464317 [Multi-domain] Cd Length: 63 Bit Score: 92.43 E-value: 4.22e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1145111223 257 ALVYFTGSKAHNIALRRLAQAGGLKINEYGVFR--GDERIAGATEASVYAAIGLHEVPPELRE 317
Cdd:pfam14791 1 ALLYFTGSKEFNRDLRLLAKKKGLKLNEYGLFDlkDGELLEGETEEDIFEALGLPYIPPELRE 63
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolX |
COG1796 |
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair]; |
3-569 |
0e+00 |
|
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
Pssm-ID: 441401 [Multi-domain] Cd Length: 567 Bit Score: 636.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 3 IHNAECAAVFAEIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMIAKGDdLGKIPSIGADLAAKLREIAATGTCELQ 82
Cdd:COG1796 1 MDNKEIARILEEIADLLELKGENPFKIRAYRRAARAIENLPEDIEELVAEGD-LTEIPGIGKAIAAKIEELLETGRLEEL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 83 QTLRHALPGAIVELLDVPGLGAKRVKALHDALNVDSLEQLRAEAKSGHVRELPGFGAKTEAHLLEAIDdRLQREPQRFLL 162
Cdd:COG1796 80 EELREEVPPGLLELLRIPGLGPKKVKKLYEELGITSLEELEAAAEEGRIRELPGFGEKTEENILKGIE-LLRKRGGRFLL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 163 PDAAHALMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAGAVTAAFVGYDDVARVLAHGKTRSSVMLVNGL 242
Cdd:COG1796 159 GEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVASDDPEAVMDAFVKLPEVKEVLAKGDTKASVRLKSGL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 243 QVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFR-GDERIAGATEASVYAAIGLHEVPPELREGRGE 321
Cdd:COG1796 239 QVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEYGLFDvGGERIAGETEEEVYAALGLPYIPPELREDRGE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 322 IDASRAGTLPALVERKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGFDW--LARQLDDIDR 399
Cdd:COG1796 319 IEAAEEGRLPELVELDDIRGDLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDHSSSLVVA-GGLDEerLLQQEEEIDA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 400 LNATFDDFVLLKGVEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERD 479
Cdd:COG1796 398 LNERLDGIILLLGGEEDILDDGGLDDDDDLLLEDDDVVAAVHHSFLLQDEEMTRRRLAAANEPVVVIIHHPTGRLLLRRR 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 480 ACELDVPRVLAQAAARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLN 559
Cdd:COG1796 478 PYYVDDEAIIAAAAAAGALEEENNAPRRLLLLDDLARAAAEGGVVIIIIDDAHHTDLLLDLMGGGVAARRRWWLEKDVNN 557
|
570
....*....|
gi 1145111223 560 TRTLAQLRPL 569
Cdd:COG1796 558 NTLLLELLLL 567
|
|
| PRK08609 |
PRK08609 |
DNA polymerase/3'-5' exonuclease PolX; |
14-572 |
1.20e-139 |
|
DNA polymerase/3'-5' exonuclease PolX;
Pssm-ID: 236311 [Multi-domain] Cd Length: 570 Bit Score: 417.44 E-value: 1.20e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 14 EIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMiakgDDLGKIPSIGADLAAKLREIAATGTCELQQTLRHALPGAI 93
Cdd:PRK08609 12 TIATYMELKGENPFKISAFRKAAQALELDERSLSEI----DDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 94 VELLDVPGLGAKRVKALHDALNVDSLEQLRAEAKSGHVRELPGFGAKTEAHLLEAIDDRLQRePQRFLLPDAAHALMPLL 173
Cdd:PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKR-PERLPIAQVLPIAQEIE 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 174 ERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAGAVTAAFVGYDDVARVLAHGKTRSSVML--VNGLQVDLRVVDA 251
Cdd:PRK08609 167 EYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEAVREQLLQLPNIVEVIAAGDTKVSVELeyEYTISVDFRLVEP 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 252 DAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFRGD--ERIAGATEASVYAAIGLHEVPPELREGRGEIDASRAgt 329
Cdd:PRK08609 247 EAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQADtgEVKTFESEEAFFAHFGLPFIPPEVREDGSEFERYKD-- 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 330 LPALVERKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGF--DWLARQLDDIDRLNATFDDF 407
Cdd:PRK08609 325 LSNLITLSDIQGDLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDHSQYLKVA-NGLteERLLEQAEEIKALNEKYPEI 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 408 VLLKGVEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERDACELDVPR 487
Cdd:PRK08609 404 DILSGIEMDILPDGSLDYDDEVLAELDYVIAAIHSSFSQSEEEIMKRLENACRNPYVRLIAHPTGRLIGRRDGYDVNIDQ 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 488 VLAQAAARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLNTRTLAQLR 567
Cdd:PRK08609 484 LIELAKETNTALELNANPNRLDLSAEHLKKAQEAGVKLAINTDAHHTEMLDDMKYGVATARKGWIQKDRVINTWSREEFK 563
|
....*
gi 1145111223 568 PLLAR 572
Cdd:PRK08609 564 DFIKR 568
|
|
| NT_POLXc |
cd00141 |
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ... |
6-316 |
4.75e-94 |
|
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 290.64 E-value: 4.75e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 6 AECAAVFAEIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMiakgDDLGKIPSIGADLAAKLREIAATGTCELQQTL 85
Cdd:cd00141 1 QEIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESL----EEAKKLPGIGKKIAEKIEEILETGKLRKLEEL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 86 RHALPGAIVELLDVPGLGAKRVKALHDaLNVDSLEQLRAEAksghvrelpgfGAKTEAHLLEAIDdRLQREPQRFLLPDA 165
Cdd:cd00141 77 REDVPPGLLLLLRVPGVGPKTARKLYE-LGIRTLEDLRKAA-----------GAKLEQNILIGLE-YYEDFQQRIPREEA 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 166 AHALMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVTARDAG------AVTAAFVGYDDVARVLAHGKTRSSVML- 238
Cdd:cd00141 144 LAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATsrglleKVVDALVELGFVTEVLSKGDTKASGILk 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 239 ----VNGLQVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGLKINEYGVFRG--DERIAGATEASVYAAIGLHEVP 312
Cdd:cd00141 224 lpggWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGvdGERLPGETEEEIFEALGLPYIE 303
|
....
gi 1145111223 313 PELR 316
Cdd:cd00141 304 PELR 307
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
335-570 |
9.79e-91 |
|
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213991 [Multi-domain] Cd Length: 237 Bit Score: 279.30 E-value: 9.79e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 335 ERKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGFD--WLARQLDDIDRLNATFDDFVLLKG 412
Cdd:cd07436 1 ELKDIRGDLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDHSKSLRVA-NGLSeeRLREQIEEIDALNEKLPGIRILKG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 413 VEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERDACELDVPRVLAQA 492
Cdd:cd07436 80 IEVDILPDGSLDYPDEVLAELDVVVASVHSGFNQSEEEMTERLLKAIENPHVDILGHPTGRLLGRREGYEVDMERVIEAA 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1145111223 493 AARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLNTRTLAQLRPLL 570
Cdd:cd07436 160 AETGTALEINANPDRLDLDDRHARRAKEAGVKIAINTDAHSTDGLDNMRYGVGTARRGWLEKEDVLNTLPLEELLKFL 237
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
339-569 |
1.72e-72 |
|
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis
Pssm-ID: 440997 [Multi-domain] Cd Length: 232 Bit Score: 231.97 E-value: 1.72e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 339 LHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGARN-GFDWLARQLDDIDRLNATFDDFVLLKGVEAGI 417
Cdd:COG1387 1 MRGDLHTHTTYSDGEGTIEEMVEAAIELGLEYIAITDHSPSLFVANGlSEERLLEYLEEIEELNEKYPDIKILKGIEVDI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 418 REDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSILAHPTGRLLGERDACELDVPRVLAQAAARGC 497
Cdd:COG1387 81 LPDGSLDYPDELLAPLDYVIGSVHSILEEDYEEYTERLLKAIENPLVDILGHPDGRLLGGRPGYEVDIEEVLEAAAENGV 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1145111223 498 FVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVLNTRTLAQLRPL 569
Cdd:COG1387 161 ALEINTRPLRLDPSDELLKLAKELGVKITIGSDAHSPEDLGDLEYGVALARRAGLTKEDVFNTLRKEELLKL 232
|
|
| PRK07945 |
PRK07945 |
PHP domain-containing protein; |
310-567 |
1.65e-40 |
|
PHP domain-containing protein;
Pssm-ID: 236135 [Multi-domain] Cd Length: 335 Bit Score: 150.13 E-value: 1.65e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 310 EVPPELREGRGEIDASRAGTLpalveRKHLHGDLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGArNGF-- 387
Cdd:PRK07945 72 RVPDYLAELRADAEPLGGGAL-----RAALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDHSPRLTVA-NGLsa 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 388 DWLARQLDDIDRLNATFDDFVLLKGVEAGIREDGSLDVPDALLGRLDLVVGAIRDGFDLPRGAQTDRMLRAMDHPHFSIL 467
Cdd:PRK07945 146 ERLRKQLDVVAELNEELAPFRILTGIEVDILDDGSLDQEPELLDRLDVVVASVHSKLRMDAAAMTRRMLAAVANPHTDVL 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 468 AHPTGRLL----GERDACELDVPRVLAQAAARGCFVELDAQPRRFDLPDVWCREAAKAGVPVAIGSDACSADELDNLAFG 543
Cdd:PRK07945 226 GHCTGRLVtgnrGTRPESKFDAEAVFAACREHGTAVEINSRPERRDPPTRLLRLALDAGCLFSIDTDAHAPGQLDWLGYG 305
|
250 260
....*....|....*....|....
gi 1145111223 544 VDQARRGWLTRQDVLNTRTLAQLR 567
Cdd:PRK07945 306 CERAEEAGVPADRIVNTWPADRLL 329
|
|
| POLXc |
smart00483 |
DNA polymerase X family; includes vertebrate polymerase beta and terminal ... |
11-317 |
1.45e-32 |
|
DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Pssm-ID: 214688 Cd Length: 334 Bit Score: 127.87 E-value: 1.45e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 11 VFAEIADMLEIQGANPFRVRAYRNAARTIADYgrdiPTMIAKGDDLGKIPSIGADLAAKLREIAATGTC-ELQQTLRHAL 89
Cdd:smart00483 9 ALEILAENYEVFGENKRKCSYFRKAASVLKSL----PFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSsKVLEILNDEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 90 PGAIVELLDVPGLGAKRVKALHDaLNVDSLEQLRAEA-KSGHVRELPGFgakteaHLLEAIDDRLQREpqrfllpDAAHA 168
Cdd:smart00483 85 YKSLKLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNKeLKLTKQQKAGL------KYYEDILKKVSRA-------EAFAV 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 169 LMPLLERLRAVTGVGQAVPAGSFRRRRETVGDLDILVT-ARDAGAVTAAFVGYDDVAR-------------VLAHGKT-- 232
Cdd:smart00483 151 EYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITsPHPAKEKELEVLDLLLLEStfeelqlpsirvaTLDHGQKkf 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 233 -----------RSSVMLVNG-----LQVDLRVVDADAFGAALVYFTGSKAHNIALRRLAQAGGlKINEYGVFRGD----E 292
Cdd:smart00483 231 milklspsredKEKSGKPDEkgwkaRRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDktkeK 309
|
330 340
....*....|....*....|....*
gi 1145111223 293 RIAGATEASVYAAIGLHEVPPELRE 317
Cdd:smart00483 310 FLKVESEEDIFDHLGLPYIEPEERN 334
|
|
| DNA_pol_B_thumb |
pfam14791 |
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ... |
257-317 |
4.22e-23 |
|
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.
Pssm-ID: 464317 [Multi-domain] Cd Length: 63 Bit Score: 92.43 E-value: 4.22e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1145111223 257 ALVYFTGSKAHNIALRRLAQAGGLKINEYGVFR--GDERIAGATEASVYAAIGLHEVPPELRE 317
Cdd:pfam14791 1 ALLYFTGSKEFNRDLRLLAKKKGLKLNEYGLFDlkDGELLEGETEEDIFEALGLPYIPPELRE 63
|
|
| HHH_8 |
pfam14716 |
Helix-hairpin-helix domain; |
5-75 |
2.25e-20 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434152 [Multi-domain] Cd Length: 67 Bit Score: 84.86 E-value: 2.25e-20
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1145111223 5 NAECAAVFAEIADMLEIQGANPFRVRAYRNAARTIADYGRDIPTMiakgDDLGKIPSIGADLAAKLREIAA 75
Cdd:pfam14716 1 NQEIADALEELADLLELKGEDPFRVRAYRRAARALEALPEEITSL----EELTKLPGIGKKIAAKIEEILE 67
|
|
| PHP_HisPPase_Ycdx_like |
cd07437 |
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
342-531 |
8.60e-14 |
|
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. YcdX may be involved in swarming.
Pssm-ID: 213992 [Multi-domain] Cd Length: 233 Bit Score: 70.93 E-value: 8.60e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 342 DLHAHTDAS------------AGRdglramaaaarARGLAYLAVTDRAP--PDGGA----RNgFDWLARQLDDIDrlnat 403
Cdd:cd07437 4 DLHTHTIASghaystieemarAAA-----------EKGLKLLGITDHGPamPGAPHpwyfGN-LKVIPREIYGVR----- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 404 fddfvLLKGVEAGIR-EDGSLDVPDALLGRLDLVVGAIRDGfDLPRGAQ---TDRMLRAMDHPHFSILAHPtgrllgERD 479
Cdd:cd07437 67 -----ILRGVEANIIdYDGNLDLPERVLKRLDYVIASLHEP-CFAPGTKeenTRAYINAMENPYVDIIGHP------GNP 134
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1145111223 480 ACELDVPRVLAQAAARGCFVELDA---QPRRfdlPDVW--CRE----AAKAGVPVAIGSDA 531
Cdd:cd07437 135 RYPIDYEAVVKAAKEYNVLLEINNsslSPSR---KGSRenCREiaelCKKYGVPVIVGSDA 192
|
|
| PRK09248 |
PRK09248 |
putative hydrolase; Validated |
342-531 |
5.02e-10 |
|
putative hydrolase; Validated
Pssm-ID: 236429 [Multi-domain] Cd Length: 246 Bit Score: 60.24 E-value: 5.02e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 342 DLHAHTDAS----------AgrdglramaAAARARGLAYLAVTDRAP--PDGGARngfdW-------LARQLDDIDrlna 402
Cdd:PRK09248 6 DTHTHTIASghaystlhenA---------AEAKQKGLKLFAITDHGPdmPGAPHY----WhfgnlrvLPRKVDGVG---- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 403 tfddfvLLKGVEAGIR-EDGSLDVPDALLGRLDLVVGAIRD-GFDlPRGAQ--TDRMLRAMDHPHFSILAHPtgrllgER 478
Cdd:PRK09248 69 ------ILRGIEANIKnYDGEIDLPGDMLKKLDIVIAGFHEpVFA-PGDKEtnTQALINAIKNGRVDIIGHP------GN 135
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1145111223 479 DACELDVPRVLAQAAARGCFVELD----------AQPRrfdlpdvwCRE----AAKAGVPVAIGSDA 531
Cdd:PRK09248 136 PKYPIDIEAVVKAAKEHNVALEINnssfghsrkgSEDN--------CRAiaalCKKAGVWVALGSDA 194
|
|
| PRK08392 |
PRK08392 |
hypothetical protein; Provisional |
342-558 |
9.92e-06 |
|
hypothetical protein; Provisional
Pssm-ID: 169423 [Multi-domain] Cd Length: 215 Bit Score: 47.09 E-value: 9.92e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 342 DLHAHTDASAGRDGLRAMAAAARARGLAYLAVTDRAPPDGGARngfdwLARQLDDIDRLNATfDDFVLLKGVEAGIREDG 421
Cdd:PRK08392 2 DLHTHTVYSDGIGSVRDNIAEAERKGLRLVGISDHIHYFTPSK-----FNAYINEIRQWGEE-SEIVVLAGIEANITPNG 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 422 sLDVPDALLGRLDLVVGAIRDGFDLPRGAQ-TDRMLRA-MDH---------PHFSILAHPTgrllgerdacELDVPRVLA 490
Cdd:PRK08392 76 -VDITDDFAKKLDYVIASVHEWFGRPEHHEyIELVKLAlMDEnvdiighfgNSFPYIGYPS----------EEELKEILD 144
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1145111223 491 QAAARGCFVELDAqprRFDLPDV-WCREAAKAGVPVAIGSDACSADELDNLAFGVDQARRGWLTRQDVL 558
Cdd:PRK08392 145 LAEAYGKAFEISS---RYRVPDLeFIRECIKRGIKLTFASDAHRPEDVGNVSWSLKVFKKAGGKKEDLL 210
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
95-151 |
6.30e-05 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 40.93 E-value: 6.30e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1145111223 95 ELLDVPGLGAKRVKALHDALnVDSLEQLrAEAKSGHVRELPGFGAKTEAHLLEAIDD 151
Cdd:pfam14520 3 ELLSISGIGPKTALALLSAG-IGTVEDL-AEADVDELAEIPGIGEKTAQRIILELRD 57
|
|
| PHP_HisPPase_Hisj_like |
cd12110 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; ... |
387-549 |
3.39e-04 |
|
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Bacillus subtilis YtvP HisJ has strong histidinol phosphate phosphatase (HisPPase) activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213994 [Multi-domain] Cd Length: 244 Bit Score: 42.55 E-value: 3.39e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 387 FDWLARQLDDIDRLNATF-DDFVLLKGVEAGIREDGSLDVPDALLG-RLDLVVGAIR----DGFDLPRGAQT-------- 452
Cdd:cd12110 54 EEELEDYVEEIRRLKEKYaDQIEIKLGLEVDYFPGYEEELRELLYGyPLDYVIGSVHflggWGFDFPEDGIAeyfegdid 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1145111223 453 -------DRMLRAMDHPHFSILAHPT-----GRLLGERDACELDVPRVLAQAAARGCFVELDA----QPRRFDLPDVW-C 515
Cdd:cd12110 134 elyeryfDLVEKAIESGLFDIIGHPDlikkfGKNDEPDEDYEELIERILRAIAEAGVALEINTaglrKPVGEPYPSPEfL 213
|
170 180 190
....*....|....*....|....*....|....
gi 1145111223 516 REAAKAGVPVAIGSDACSADELDnlaFGVDQARR 549
Cdd:cd12110 214 ELAKELGIPVTLGSDAHSPEDVG---QGYDEALA 244
|
|
| DNA_pol_B_palm |
pfam14792 |
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ... |
184-210 |
5.05e-03 |
|
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.
Pssm-ID: 464318 Cd Length: 110 Bit Score: 37.16 E-value: 5.05e-03
10 20
....*....|....*....|....*..
gi 1145111223 184 QAVPAGSFRRRRETVGDLDILVTARDA 210
Cdd:pfam14792 26 EVIVCGSYRRGAESSGDVDILITHPDG 52
|
|
| |
