|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-604 |
0e+00 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 922.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:PRK08074 75 APEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSD 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLKQLRRLSQHFISDLTHLLDMFIYENRHTEIPGYARFSSFSVREPQSFDEHANEDGNF 160
Cdd:PRK08074 155 AEVTAELFLQLLNKLERLPLVTLQQLRRLSDHLKSDIAELLDENILKKMMHGKPLDEEFDEYRGIALRKREVEKNLEETC 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 161 SFEIENWEAGNEKALSELMPGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTYS 240
Cdd:PRK08074 235 RSDFDAFLEKTEEKLSLAMPKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYT 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 241 TLLQQQILTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPSG 320
Cdd:PRK08074 315 IQLQQQLLEKDIPLLQKIFPFPVEAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSG 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 321 GKLLWDRLAYDDESYKRSRNENVT-GFYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEH 399
Cdd:PRK08074 395 GKLLWNRIASDGESDGGKQSPWFSrCFYQRAKNRAKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEEAASRH 474
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 400 LGKRATYIELHTKLSRIGTLKEQGLLKKMRQLFQRNSL-PVDSFFELEEWIQHIQAESDAFFSSVHSFVKRRKPKEDLNR 478
Cdd:PRK08074 475 LGEQFSYMSFQLLLSRLGTLEEDGLLSKLAKLFKKSDQaSRSSFRDLDESLKELKFEADELFQMLRSFVLKRKKQEQNGR 554
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 479 LVFKVNKES-QDKSWPILTDGAERLCSMLTHLQQLFEAQSALMEKHltsMKSRTVFLADEYqRSMKGLQQYCQTLQKLFF 557
Cdd:PRK08074 555 LIYRYNTESeKGKLWDAITELANRLCYDLRDLLTLLEAQKKELQEK---MESESAFLTGEY-AHLIDLLEKMAQLLQLLF 630
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 124441811 558 ESEDDEAVWIEIDAKGAKNAVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:PRK08074 631 EEDPDYVTWIEIDAKGAINATRLYAQPVEVAERLADEFFAKKKSVIL 677
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
1-604 |
5.22e-114 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 359.89 E-value: 5.22e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:TIGR01407 71 AQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSD 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLKQLRRLSQHFISDLTHLLDMFIYENRHTEIP-GYARFSSFSVREPQSFDEHANedgn 159
Cdd:TIGR01407 151 AQATAELLLLLFEKMEKLPLDTLEQLLELSDQLLYESYDIIQETYRQYKIKPAPkSYEVVEQIAYRKQVASKKPET---- 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 160 fsfEIENWEAGNEKALSELmpGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAkKSKKPVIISTY 239
Cdd:TIGR01407 227 ---NYNTLSSLFSKNIDRL--GLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYA-ITEKPVVISTN 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 240 STLLQQQILTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPS 319
Cdd:TIGR01407 301 TKVLQSQLLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKG 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 320 GGKLLWDRLAYDDESYKRSRNENVTgFYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEH 399
Cdd:TIGR01407 381 GNKMFFAQVRHDGNLSKKDLFYEVD-FYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQ 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 400 LGKRATYIELHTKLSRIGTLKEQGLLKKMRQLFQRNSLPVDSFFELEEWIQHIQAESDAffssvhsfvkrrkpkedlnrl 479
Cdd:TIGR01407 460 LQEELDYADIKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDK--------------------- 518
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 480 vfkvnkesqdkswpiltdgaerlcsmlthLQQLFEAQSALMEKHLTSMksRTVFLADEyqrsmkglqqycqTLQKLFFES 559
Cdd:TIGR01407 519 -----------------------------LNKLLQIFSELSHKTVDQL--RKFDLALK-------------DDFKNIEQS 554
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 124441811 560 EDDEAV-WIEIDAKGAKNAVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:TIGR01407 555 LKEGHTsWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIF 600
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
170-604 |
7.02e-99 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 314.17 E-value: 7.02e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 170 GNEKALSELMPGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTYSTLLQQQILT 249
Cdd:COG1199 1 ADDGLLALAFPGFEPRPGQREMAEAVARALAEGRHLLIEAGTGTGKTLAYLVPALLAARETGKKVVISTATKALQEQLVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 250 KDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPsGGKLLWDRLA 329
Cdd:COG1199 81 KDLPLLRKALGLPLRVALLKGRSNYLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLP-EDDELWRQVT 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 330 YDDESYKRSRNENVTG-FYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEHLGKRATYIE 408
Cdd:COG1199 160 SDADNCLGRRCPYYGVcPYELARRLAREADVVVVNHHLLFADLALGEELLPEDDVLIIDEAHNLPDRARDMFSAELSSRS 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 409 LHTKLSRIGTLKEQGLLKKMRQLFQRnslpvdsffeleewiqhIQAESDAFFSSVHSFVKRRKPkedlnrlvfkvnkesq 488
Cdd:COG1199 240 LLRLLRELRKLGLRPGLKKLLDLLER-----------------LREALDDLFLALEEEEELRLA---------------- 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 489 dksWPILTDGAERLCSMLTHLQQLFEAqsalMEKHLTSMKSRtvflADEYQRSMKGLQQYCQTLQKLFFESEDDEAV-WI 567
Cdd:COG1199 287 ---LGELPDEPEELLEALDALRDALEA----LAEALEEELER----LAELDALLERLEELLFALARFLRIAEDEGYVrWL 355
|
410 420 430
....*....|....*....|....*....|....*..
gi 124441811 568 EIDAKGaknaVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:COG1199 356 EREGGD----VRLHAAPLDPADLLRELLFSRARSVVL 388
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
1-89 |
1.36e-22 |
|
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Pssm-ID: 176648 [Multi-domain] Cd Length: 159 Bit Score: 94.67 E-value: 1.36e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTEL-SEELQLRHDQPHRADS 79
Cdd:cd06127 70 LPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALA 149
|
90
....*....|
gi 124441811 80 DAEVTGLIFL 89
Cdd:cd06127 150 DALATAELLL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
1-96 |
2.14e-18 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 82.73 E-value: 2.14e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHN-IHFDLGFVKYELHKAGFHLP-DCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQ-PHRA 77
Cdd:smart00479 71 LEELLEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKQPpKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRA 150
|
90
....*....|....*....
gi 124441811 78 DSDAEVTGLIFLEILEKLR 96
Cdd:smart00479 151 LDDARATAKLFKKLLERLE 169
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
1-88 |
7.03e-14 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 69.69 E-value: 7.03e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLD-GAYFVAHNIHFDLGFVKYELHKAGF--HLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQ-PHR 76
Cdd:pfam00929 73 LEEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKkpMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGrAHR 152
|
90
....*....|..
gi 124441811 77 ADSDAEVTGLIF 88
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-604 |
0e+00 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 922.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:PRK08074 75 APEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSD 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLKQLRRLSQHFISDLTHLLDMFIYENRHTEIPGYARFSSFSVREPQSFDEHANEDGNF 160
Cdd:PRK08074 155 AEVTAELFLQLLNKLERLPLVTLQQLRRLSDHLKSDIAELLDENILKKMMHGKPLDEEFDEYRGIALRKREVEKNLEETC 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 161 SFEIENWEAGNEKALSELMPGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTYS 240
Cdd:PRK08074 235 RSDFDAFLEKTEEKLSLAMPKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYT 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 241 TLLQQQILTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPSG 320
Cdd:PRK08074 315 IQLQQQLLEKDIPLLQKIFPFPVEAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSG 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 321 GKLLWDRLAYDDESYKRSRNENVT-GFYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEH 399
Cdd:PRK08074 395 GKLLWNRIASDGESDGGKQSPWFSrCFYQRAKNRAKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEEAASRH 474
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 400 LGKRATYIELHTKLSRIGTLKEQGLLKKMRQLFQRNSL-PVDSFFELEEWIQHIQAESDAFFSSVHSFVKRRKPKEDLNR 478
Cdd:PRK08074 475 LGEQFSYMSFQLLLSRLGTLEEDGLLSKLAKLFKKSDQaSRSSFRDLDESLKELKFEADELFQMLRSFVLKRKKQEQNGR 554
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 479 LVFKVNKES-QDKSWPILTDGAERLCSMLTHLQQLFEAQSALMEKHltsMKSRTVFLADEYqRSMKGLQQYCQTLQKLFF 557
Cdd:PRK08074 555 LIYRYNTESeKGKLWDAITELANRLCYDLRDLLTLLEAQKKELQEK---MESESAFLTGEY-AHLIDLLEKMAQLLQLLF 630
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 124441811 558 ESEDDEAVWIEIDAKGAKNAVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:PRK08074 631 EEDPDYVTWIEIDAKGAINATRLYAQPVEVAERLADEFFAKKKSVIL 677
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
1-604 |
5.22e-114 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 359.89 E-value: 5.22e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:TIGR01407 71 AQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSD 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLKQLRRLSQHFISDLTHLLDMFIYENRHTEIP-GYARFSSFSVREPQSFDEHANedgn 159
Cdd:TIGR01407 151 AQATAELLLLLFEKMEKLPLDTLEQLLELSDQLLYESYDIIQETYRQYKIKPAPkSYEVVEQIAYRKQVASKKPET---- 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 160 fsfEIENWEAGNEKALSELmpGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAkKSKKPVIISTY 239
Cdd:TIGR01407 227 ---NYNTLSSLFSKNIDRL--GLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYA-ITEKPVVISTN 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 240 STLLQQQILTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPS 319
Cdd:TIGR01407 301 TKVLQSQLLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKG 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 320 GGKLLWDRLAYDDESYKRSRNENVTgFYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEH 399
Cdd:TIGR01407 381 GNKMFFAQVRHDGNLSKKDLFYEVD-FYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQ 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 400 LGKRATYIELHTKLSRIGTLKEQGLLKKMRQLFQRNSLPVDSFFELEEWIQHIQAESDAffssvhsfvkrrkpkedlnrl 479
Cdd:TIGR01407 460 LQEELDYADIKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDK--------------------- 518
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 480 vfkvnkesqdkswpiltdgaerlcsmlthLQQLFEAQSALMEKHLTSMksRTVFLADEyqrsmkglqqycqTLQKLFFES 559
Cdd:TIGR01407 519 -----------------------------LNKLLQIFSELSHKTVDQL--RKFDLALK-------------DDFKNIEQS 554
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 124441811 560 EDDEAV-WIEIDAKGAKNAVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:TIGR01407 555 LKEGHTsWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIF 600
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
170-604 |
7.02e-99 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 314.17 E-value: 7.02e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 170 GNEKALSELMPGYEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTYSTLLQQQILT 249
Cdd:COG1199 1 ADDGLLALAFPGFEPRPGQREMAEAVARALAEGRHLLIEAGTGTGKTLAYLVPALLAARETGKKVVISTATKALQEQLVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 250 KDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAELNLPsGGKLLWDRLA 329
Cdd:COG1199 81 KDLPLLRKALGLPLRVALLKGRSNYLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLP-EDDELWRQVT 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 330 YDDESYKRSRNENVTG-FYERAKQIAMRSDLVITNHSLLLTDEGSQKKRLPESGTFIIDEAHHFERAASEHLGKRATYIE 408
Cdd:COG1199 160 SDADNCLGRRCPYYGVcPYELARRLAREADVVVVNHHLLFADLALGEELLPEDDVLIIDEAHNLPDRARDMFSAELSSRS 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 409 LHTKLSRIGTLKEQGLLKKMRQLFQRnslpvdsffeleewiqhIQAESDAFFSSVHSFVKRRKPkedlnrlvfkvnkesq 488
Cdd:COG1199 240 LLRLLRELRKLGLRPGLKKLLDLLER-----------------LREALDDLFLALEEEEELRLA---------------- 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 489 dksWPILTDGAERLCSMLTHLQQLFEAqsalMEKHLTSMKSRtvflADEYQRSMKGLQQYCQTLQKLFFESEDDEAV-WI 567
Cdd:COG1199 287 ---LGELPDEPEELLEALDALRDALEA----LAEALEEELER----LAELDALLERLEELLFALARFLRIAEDEGYVrWL 355
|
410 420 430
....*....|....*....|....*....|....*..
gi 124441811 568 EIDAKGaknaVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:COG1199 356 EREGGD----VRLHAAPLDPADLLRELLFSRARSVVL 388
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-455 |
1.26e-50 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 187.59 E-value: 1.26e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVlDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:PRK07246 77 ARHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRV-DTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIAD 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLKQLRRLSQHFISDLTHLLDMFIYENRHTEIPGYARFSSFSVREPQSFDEHANEDGNF 160
Cdd:PRK07246 156 ARATAELFLKLLQKIESLPKECLERLLEYADSLLFESYLVIEEALANAKPYSSPDYIKVQGIVLKKTAASLKPRKLSQDF 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 161 SFEIenweagnekALSELmpgyEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYLIPaaLFAKKSKKPVIISTYS 240
Cdd:PRK07246 236 SINI---------ALLGL----EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLP--LLAQSDQRQIIVSVPT 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 241 TLLQQQILTKDLPIVQDLFPFPVTAaiLKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAEL----- 315
Cdd:PRK07246 301 KILQDQIMAEEVKAIQEVFHIDCHS--LKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIkqkqr 378
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 316 ------NLPSGGKLLWDRLAYDDESYKRSrnenvtgfYERAKQiamrSDLVITNHSLLLT----DEGSQKKRLpesgtFI 385
Cdd:PRK07246 379 yaayfdQLKHDGNLSQSSLFYDYDFWKRS--------YEKAKT----ARLLITNHAYFLTrvqdDKDFARNKV-----LV 441
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124441811 386 IDEAH----HFERAASEHLGKRATYIELHTKLSRIGTLKEQGLLKKMRqlfqrnslpvdsfFELEEWIQHIQAE 455
Cdd:PRK07246 442 FDEAQklmlQLEQLSRHQLNITSFLQTIQKALSGPLPLLQKRLLESIS-------------FELLQLSEQFYQG 502
|
|
| dinG |
PRK11747 |
ATP-dependent DNA helicase DinG; Provisional |
173-604 |
2.30e-35 |
|
ATP-dependent DNA helicase DinG; Provisional
Pssm-ID: 236966 [Multi-domain] Cd Length: 697 Bit Score: 141.50 E-value: 2.30e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 173 KALSELMPGYEKREGQMMMMKEVAEAFA-----NREHALIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTYSTLLQQQI 247
Cdd:PRK11747 15 KALQEQLPGFIPRAGQRQMIAEVAKTLAgeylkDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQL 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 248 LTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEDDDNYDAVLTKAQLLVWLTETDTGDVAEL--NLpSGGK--- 322
Cdd:PRK11747 95 VSKDLPLLLKISGLDFKFTLAKGRGRYVCPRKLAALASDEGTQQDLLLFLDDELTPPDEEEQKLLARLakAL-ATGKwdg 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 323 -----------LLWDRLAYDdesyKRS---RN-ENVTG--FYERAKQIaMRSDLVITNHSLLLTD-EGSQKKRLPE-SGT 383
Cdd:PRK11747 174 drdhwpepiddSLWQRITTD----KHSclgRNcPYFREcpFFKARREI-DEADVVVANHDLVLADlELGGGVVLPDpENL 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 384 F-IIDEAHHFERAASEHLGKRATYielhtkLSRIGTLKEQG-LLKKMRQLFQRNSLPVDSFF-----ELEEWIQHIQAES 456
Cdd:PRK11747 249 LyVLDEGHHLPDVARDHFAASAEL------KGTADWLEKLLkLLTKLVALIMEPPLALPERLnahceELRELLASLNQIL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 457 DAFF-----SSVHSFVKRRKPKEdlnrlvfkvnkesqdkswpiLTDGAERLCSMLTHLQQLFEAQSALMEKHLTSMKSRT 531
Cdd:PRK11747 323 NLFLpaggeEARYRFEMGELPEE--------------------LLELAERLAKLTEKLLGLLEKLLNDLSEAMKTGKIDI 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 532 VfLADEYQRSMKGLQQYCQTLQKLF--FESEDDE-----AVWIEIDAKGAKNAVAIYAQPLEPGELLADQFFARKNSVVL 604
Cdd:PRK11747 383 V-RLERLLLELGRALGRLEALSKLWrlAAKEDQEsgapmARWITREERDGQGDYLFHASPIRVGDQLERLLWSRAPGAVL 461
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
1-104 |
1.58e-32 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 123.33 E-value: 1.58e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLpDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:COG2176 79 LPEFLEFLGDAVLVAHNASFDLGFLNAALKRLGLPF-DNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGD 157
|
90 100
....*....|....*....|....
gi 124441811 81 AEVTGLIFLEILEKLRQLPYPTLK 104
Cdd:COG2176 158 AEATAELFLKLLEKLEEKGITTLR 181
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
1-93 |
2.67e-27 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 107.96 E-value: 2.67e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:COG0847 71 LPELLEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALAD 150
|
90
....*....|...
gi 124441811 81 AEVTGLIFLEILE 93
Cdd:COG0847 151 AEATAELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
1-89 |
1.36e-22 |
|
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Pssm-ID: 176648 [Multi-domain] Cd Length: 159 Bit Score: 94.67 E-value: 1.36e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTEL-SEELQLRHDQPHRADS 79
Cdd:cd06127 70 LPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALA 149
|
90
....*....|
gi 124441811 80 DAEVTGLIFL 89
Cdd:cd06127 150 DALATAELLL 159
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
2-106 |
8.38e-20 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 94.13 E-value: 8.38e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 2 EEVF----HLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRA 77
Cdd:PRK00448 487 EEVLpkfkEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRA 566
|
90 100
....*....|....*....|....*....
gi 124441811 78 DSDAEVTGLIFLEILEKLRQLPYPTLKQL 106
Cdd:PRK00448 567 DYDAEATAYLLIKFLKDLKEKGITNLDEL 595
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
1-96 |
2.14e-18 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 82.73 E-value: 2.14e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHN-IHFDLGFVKYELHKAGFHLP-DCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQ-PHRA 77
Cdd:smart00479 71 LEELLEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKQPpKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRA 150
|
90
....*....|....*....
gi 124441811 78 DSDAEVTGLIFLEILEKLR 96
Cdd:smart00479 151 LDDARATAKLFKKLLERLE 169
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
2-90 |
7.02e-16 |
|
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99834 [Multi-domain] Cd Length: 156 Bit Score: 75.24 E-value: 7.02e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 2 EEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEEL--QLRHdqpHRADS 79
Cdd:cd06130 69 PEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLgiELNH---HDALE 145
|
90
....*....|.
gi 124441811 80 DAEVTGLIFLE 90
Cdd:cd06130 146 DARACAEILLA 156
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
1-88 |
7.03e-14 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 69.69 E-value: 7.03e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLD-GAYFVAHNIHFDLGFVKYELHKAGF--HLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQ-PHR 76
Cdd:pfam00929 73 LEEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKkpMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGrAHR 152
|
90
....*....|..
gi 124441811 77 ADSDAEVTGLIF 88
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
10-110 |
7.27e-13 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 71.10 E-value: 7.27e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 10 GAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFE--GYKLTELSEELQLRHDQPHRADSDAEVTGLI 87
Cdd:PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEapNVRLSTLARLFGATTTPTHRALDDARATVDV 174
|
90 100
....*....|....*....|...
gi 124441811 88 FLEILEKLRQLPYPTLKQLRRLS 110
Cdd:PRK07883 175 LHGLIERLGNLGVHTLEELLTYL 197
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
1-124 |
3.88e-11 |
|
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]
Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 62.85 E-value: 3.88e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDC-EVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHR--- 76
Cdd:TIGR00573 78 AEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTnDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRalh 157
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 124441811 77 -ADSDAEVTGLIFLEILEKlrQLPYPTLKQLRRLSQHFIS---DLTHLLDMF 124
Cdd:TIGR00573 158 gALADAFILAKLYLVMTGK--QTKYGENEGQQSRPYHAIKsivKKDMLLKLI 207
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
1-98 |
4.12e-09 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 58.17 E-value: 4.12e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQPHRADSD 80
Cdd:PRK06063 85 AGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDD 164
|
90
....*....|....*...
gi 124441811 81 AEVTGLIFLEILEKLRQL 98
Cdd:PRK06063 165 ARVLAGILRPSLERARER 182
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-54 |
1.45e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 55.64 E-value: 1.45e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPD----CEVLDTVELSRIVFPG 54
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKtntfCKVTDTLAMARRMFPG 134
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
8-95 |
3.54e-07 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 51.95 E-value: 3.54e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 8 LDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGfEGYKLTELSEELQLRHDQPHRADSDAEVTGLI 87
Cdd:PRK08517 145 LGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEIEVHHRAYADALAAYEI 223
|
....*...
gi 124441811 88 FLEILEKL 95
Cdd:PRK08517 224 FKICLLNL 231
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
1-54 |
1.34e-06 |
|
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99835 [Multi-domain] Cd Length: 167 Bit Score: 48.68 E-value: 1.34e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 124441811 1 AEEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFH---LPDCEVLDTVELSRIVFPG 54
Cdd:cd06131 72 ADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGkkiIDFCRVIDTLALARKKFPG 128
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
14-90 |
1.55e-06 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 50.20 E-value: 1.55e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124441811 14 VAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEELQLRHDQpHRADSDAEVTGLIFLE 90
Cdd:PRK06807 92 VAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAVYQK 167
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
2-96 |
1.62e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 47.08 E-value: 1.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 2 EEVFHLLDGAYFVAHNIHFDLGFVKYELHKAGFHLPDCEVLDTVELSRIVFPGFEGYKLTELSEEL--QLRHdqpHRADS 79
Cdd:PRK06195 72 EKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLgyEFKH---HDALA 148
|
90
....*....|....*..
gi 124441811 80 DAEVTGLIFLEILEKLR 96
Cdd:PRK06195 149 DAMACSNILLNISKELN 165
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
11-95 |
8.07e-04 |
|
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Pssm-ID: 99837 [Multi-domain] Cd Length: 189 Bit Score: 40.74 E-value: 8.07e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 11 AYFVAHNIHFDLGFVKYELHKAG-----FHLPDCevLDTVELSRIVfpgfegYKLTELSEELQ-----LRHDQPHRADSD 80
Cdd:cd06134 103 AILVGHNAHFDLGFLNAAVARCKikrnpFHPFST--FDTATLAGLA------YGQTVLAKACQaagieFDNKEAHSALYD 174
|
90
....*....|....*
gi 124441811 81 AEVTGLIFLEILEKL 95
Cdd:cd06134 175 TQKTAELFCKIVNRW 189
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
203-270 |
9.50e-04 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 40.08 E-value: 9.50e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124441811 203 EHALIEAPPGIGKTIGYLIPAA-LFAKKSKKPVIISTYSTLLQQQiltkdLPIVQDLFPFPVTAAILKG 270
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQT-----AERLRELFGPGIRVAVLVG 65
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
9-109 |
2.67e-03 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 39.81 E-value: 2.67e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 9 DGAYFVAHNIHFDLGFVKYELHKAG--FHLPDCEVLDTVELSRIvFPGFEGYKLTELSEELQLRHDQPHRADSDAEVTGL 86
Cdd:PRK06310 87 EGDYIVGHSVGFDLQVLSQESERIGetFLSKHYYIIDTLRLAKE-YGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINIK 165
|
90 100
....*....|....*....|...
gi 124441811 87 IFLEILEKLRqlpypTLKQLRRL 109
Cdd:PRK06310 166 VFKHLCKRFR-----TLEQLKQI 183
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
162-245 |
2.70e-03 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 39.23 E-value: 2.70e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124441811 162 FEIENWEAGNEKALSELMPGYEKregqmMMMKEVA--EAFAnrehalIEAPPGIGKTIGYLIPAALFAKKSKKPVIISTY 239
Cdd:cd17924 1 KEYEDFEEFFKKKTGFPPWGAQR-----TWAKRLLrgKSFA------IIAPTGVGKTTFGLATSLYLASKGKRSYLIFPT 69
|
....*.
gi 124441811 240 STLLQQ 245
Cdd:cd17924 70 KSLVKQ 75
|
|
| DEXDc2 |
smart00488 |
DEAD-like helicases superfamily; |
182-247 |
3.12e-03 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214693 [Multi-domain] Cd Length: 289 Bit Score: 40.05 E-value: 3.12e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124441811 182 YEKREGQMMMMKEVAEAFANREHALIEAPPGIGKTIGYL--IPAALFAKKSKKPVIISTYSTLLQQQI 247
Cdd:smart00488 7 YEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLclTLTWLRSFPERIQKIKLIYLSRTVSEI 74
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
193-246 |
7.21e-03 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 37.61 E-value: 7.21e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 124441811 193 KEVAEAFANREHALIEAPPGIGKTIGYLIPA-ALFAKKSKKP--VIISTYSTLLQQQ 246
Cdd:pfam00270 5 AEAIPAILEGRDVLVQAPTGSGKTLAFLLPAlEALDKLDNGPqaLVLAPTRELAEQI 61
|
|
| |
