|
Name |
Accession |
Description |
Interval |
E-value |
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
3-1437 |
0e+00 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 2627.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 3 MTEQQKFKVLADQIKISNQLDAEILNSGELTRIDVSNKNRTWEFHITLPQFLAHEDYLLFINAIEQEFKDIAN--VTCRF 80
Cdd:PRK00448 1 NEMQEKFKKLLDQINIPDDLQSEALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFSHIADikVTFSI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 81 TVTNGTNQDEHAIKYFGHCIDQ-TALSPKVKGQLKQKKLIMSGKVLKVMVSNDIERNHFDKACNGSLIKAFRNCGFDIDK 159
Cdd:PRK00448 81 EVENITFTEELLLDYWNEIIEKaKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 160 IIFETNDNDQEqnLASLEAHIQEEDEQSARLATEKLEKMKAEKAKQQDNNESAVDKCQIGKPIQIENIKPIESIIEEEFK 239
Cdd:PRK00448 161 IDFEIDDSKEE--LEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEINEEERR 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 240 VAIEGVIFDINLKELKSGRHIVEIKVTDYTDSLVLKMFTRkNKDDLEHFKALSVGKWVRAQGRIEEDTFIRDLVMMMSDI 319
Cdd:PRK00448 239 VVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSR-DKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQDI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 320 EEIKKATKKDKA-EEKRVEFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME 398
Cdd:PRK00448 318 NEIKHPERKDTAeEEKRVELHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGVE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 399 GMLVDDGVPIAYKPQDVVLKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITD 478
Cdd:PRK00448 398 ANLVDDGVPIVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITD 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 479 DMLVDAPEIEEVLTEFKEWVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYG 558
Cdd:PRK00448 478 DMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFG 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 559 VELTQHHRAIYDTEATAYIFIKMVQQMKELGVLNHNEINKKLSNEDAYKRARPSHVTLIVQNQQGLKNLFKIVSASLVKY 638
Cdd:PRK00448 558 VELEHHHRADYDAEATAYLLIKFLKDLKEKGITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKY 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 639 FYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVEKIAKYYDFIEIQPPALYQDLIDRELIRDTETLHEIYQ 718
Cdd:PRK00448 638 FYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKEIIK 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 719 RLIHAGDTAGIPVIATGNAHYLFEHDGIARKILIASQP-GNPLNRSTLPEAHFRTTDEMLNEFHFLGEEKAHEIVVKNTN 797
Cdd:PRK00448 718 NLIELGKKLNKPVVATGDVHYLDPEDKIYRKILVASQGgGNPLNRHPLPELHFRTTDEMLDEFAFLGEELAKEIVVENTN 797
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 798 ELADRIERVVPIKDELYTPRMEGANEEIRELSYTNARKLYGEDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLD 877
Cdd:PRK00448 798 KIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIYGEPLPEIVEKRIEKELNSIIGNGFAVIYLISQKLVKKSLE 877
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 878 DGYLVGSRGSVGSSFVATMTEITEVNPLPPHYICPNCKTSEFFNDGSVGSGFDLPDKTCETCGAPLIKEGQDIPFETFLG 957
Cdd:PRK00448 878 DGYLVGSRGSVGSSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDGHDIPFETFLG 957
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 958 FKGDKVPDIDLNFSGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAEKTAFGYVKGYLNDQGIHKRGAEIDRLVKGCTGVKR 1037
Cdd:PRK00448 958 FKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTAYGYVKKYEEDTGKFYRNAEIDRLAQGCTGVKR 1037
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1038 TTGQHPGGIIVVPDYMDIYDFTPIQYPADDQNSAWMTTHFDFHSIHDNVLKLDILGHDDPTMIRMLQDLSGIDPKTIPVD 1117
Cdd:PRK00448 1038 TTGQHPGGIIVVPKYMDIYDFTPIQYPADDVNSEWKTTHFDFHSIHDNLLKLDILGHDDPTMIRMLQDLTGIDPKTIPMD 1117
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1118 DKEVMQIFSTPESLGVTEDEILCKTGTFGVPEFGTGFVRQMLEDTKPTTFSELVQISGLSHGTDVWLGNAQELIKTGICD 1197
Cdd:PRK00448 1118 DPKVMKLFSSTEALGVTPEQIGCETGTLGIPEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNAQELIKEGIAT 1197
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1198 LSSVIGCRDDIMVYLMYAGLEPSMAFKIMESVRKGKGLTEEMIETMKENEVPDWYLDSCLKIKYMFPKAHAAAYVLMAVR 1277
Cdd:PRK00448 1198 LSDVIGCRDDIMVYLIHKGLEPKLAFKIMESVRKGKGLTEEEEELMKENNVPDWYIESCKKIKYMFPKAHAAAYVLMAWR 1277
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1278 IAYFKVHHPLYYYASYFTIRASDFDLITMIKDKTSIRNTVKDMYSRYMDLGKKEKDVLTVLEIMNEMAHRGYRMQPISLE 1357
Cdd:PRK00448 1278 IAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEIKSKGNDASNKEKDLLTVLEIALEMLERGFKFQKVDLY 1357
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1358 KSQAFEFIIEGDTLIPPFISVPGLGENVAKRIVEARDDGPFLSKEDLNKKAGLSQKIIEYLDELGSLPNLPDKAQLSIFD 1437
Cdd:PRK00448 1358 KSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIEKLDELGVLDDLPETNQLSLFD 1437
|
|
| polC_Gram_pos |
TIGR01405 |
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain ... |
231-1436 |
0e+00 |
|
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273601 [Multi-domain] Cd Length: 1213 Bit Score: 2168.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 231 ESIIEEEFKVAIEGVIFDINLKELKSGRHIVEIKVTDYTDSLVLKMFTrKNKDDLEHFKALSVGKWVRAQGRIEEDTFIR 310
Cdd:TIGR01405 1 EKINEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFL-KSEEDPEKFDGIKIGKWVRARGKIELDNFSR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 311 DLVMMMSDIEEIKKATKKDKAEEKRVEFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHG 390
Cdd:TIGR01405 80 DLQMIIKDIEEIPYAERKDNAKEKRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 391 IKMIYGMEGMLVDDGVPIAYKPQDVVL-KDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSET 469
Cdd:TIGR01405 160 IKIIYGMEANLVDDRVPIVYNPDDQKLlDDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAF 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 470 IINLTHITDDMLVDAPEIEEVLTEFKEWVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHG 549
Cdd:TIGR01405 240 VTELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 550 LNFLAKKYGVELTQHHRAIYDTEATAYIFIKMVQQMKELGVLNHNEINKKLSNEDAYKRARPSHVTLIVQNQQGLKNLFK 629
Cdd:TIGR01405 320 LGNICKKLGVDLDDHHRADYDAEATAKVFKVMVEQLKEKGITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 630 IVSASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVEKIAKYYDFIEIQPPALYQDLIDRELIRD 709
Cdd:TIGR01405 400 LVSISLTKYFYTRPRILRSLLKKYREGLLIGSACSEGELFDALLSKPDDELEEIAKRYDFIEIQPPGNYAHLIEREQVKD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 710 TETLHEIYQRLIHAGDTAGIPVIATGNAHYLFEHDGIARKILIASQP-GNPLNRSTL----PEAHFRTTDEMLNEFHFLG 784
Cdd:TIGR01405 480 KEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYRKILVASQGlGNPLNRHFNpkevPELHFRTTNEMLDEFSFLG 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 785 EEKAHEIVVKNTNELADRIERVVPIKDELYTPRMEGANEEIRELSYTNARKLYGEDLPQIVIDRLEKELKSIIGNGFAVI 864
Cdd:TIGR01405 560 EEKAYEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIYGDPLPEIVEQRIEKELKSIIGNGFAVI 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 865 YLISQRLVKKSLDDGYLVGSRGSVGSSFVATMTEITEVNPLPPHYICPNCKTSEFFNDGSVGSGFDLPDKTCETCGAPLI 944
Cdd:TIGR01405 640 YLISQLLVQKSLQDGYLVGSRGSVGSSLVATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 945 KEGQDIPFETFLGFKGDKVPDIDLNFSGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAEKTAFGYVKGYLNDQGIHKRGAE 1024
Cdd:TIGR01405 720 KDGQDIPFETFLGFKGDKVPDIDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAYGYVKKYFEDQGKHYRDAE 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1025 IDRLVKGCTGVKRTTGQHPGGIIVVPDYMDIYDFTPIQYPADDQNSAWMTTHFDFHSIHDNVLKLDILGHDDPTMIRMLQ 1104
Cdd:TIGR01405 800 IERLVQGCTGVKRTTGQHPGGIIIVPKYMDVYDFTPVQYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHDDPTMIKMLQ 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1105 DLSGIDPKTIPVDDKEVMQIFSTPESLGVTEDEILCKTGTFGVPEFGTGFVRQMLEDTKPTTFSELVQISGLSHGTDVWL 1184
Cdd:TIGR01405 880 DLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFGTKFVRGMLEETKPKTFADLVRISGLSHGTDVWL 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1185 GNAQELIKTGICDLSSVIGCRDDIMVYLMYAGLEPSMAFKIMESVRKGKGLTEEMIETMKENEVPDWYLDSCLKIKYMFP 1264
Cdd:TIGR01405 960 GNAQDLIKSGIKTLSDVIGCRDDIMVYLIHKGLEPKLAFKIMEKVRKGKGLKAEYIELMKENKVPEWYIESCLKIKYMFP 1039
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1265 KAHAAAYVLMAVRIAYFKVHHPLYYYASYFTIRASDFDLITMIKDKTSIRNTVKDMYSRY--MDLGKKEKDVLTVLEIMN 1342
Cdd:TIGR01405 1040 KAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKAFDLETMIKGKEFIKQKLEEINTRRkiNKASPKEKDLLTVLEIVL 1119
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1343 EMAHRGYRMQPISLEKSQAFEFIIEGDTLIPPFISVPGLGENVAKRIVEARDDGPFLSKEDLNKKAGLSQKIIEYLDELG 1422
Cdd:TIGR01405 1120 EMMARGFKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTKISKTHIEKLDSMG 1199
|
1210
....*....|....
gi 586340297 1423 SLPNLPDKAQLSIF 1436
Cdd:TIGR01405 1200 VLDNLPETNQLSLF 1213
|
|
| PHP_PolIIIA_POLC |
cd07435 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
335-808 |
1.64e-117 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in different location compare to dnaE1, 2, and 3. The PHP domain has four conserved sequence motifs and and contains an invariant histidine that is involved in metal ion coordination.The PHP domain of PolC 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. PHP domains found in dnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. In contrast, PolC PHP lacks detectable nuclease activity.
Pssm-ID: 213990 [Multi-domain] Cd Length: 268 Bit Score: 368.72 E-value: 1.64e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 335 RVEFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIkmiygmegmlvddgvpiaykpqd 414
Cdd:cd07435 1 RVELHAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKNGI----------------------- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 415 vvlkdatyvvfdvettglsnqydKIIelaavkvhngeiidkferfsnpherlsetiinlthitddmlvdapeieevltef 494
Cdd:cd07435 58 -----------------------KVI------------------------------------------------------ 60
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 kewvgdaifvahnasfdmgfidtgyerlgfgpstngvidtlelsrtinteygkhglnflakkYGVEltqhhraiydteat 574
Cdd:cd07435 61 --------------------------------------------------------------YGVE-------------- 64
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 575 AYifikMVQqmkelgvlnhneinkklsnedaykrarPSHVTLIVQNQQGLKNLFKIVSASLVKYFYRTPRIPRSLLDEYR 654
Cdd:cd07435 65 AY----LVD---------------------------PYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKYR 113
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 655 EGLLVGTACDEGELFTAVMQK-DQSQVEKIAKYYDFIEIQPPALYQDLIDRELIRDTETLHEIYQRLIHAGDTAGIPVIA 733
Cdd:cd07435 114 EGLLIGSACENGELFEAALNKkSDEELEEIASFYDYIEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVVA 193
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 734 TGNAHYLFEHDGIARKILIASQPGNPLNRSTLPEAHFRTTDEMLNEFHFLGEEKAHEIVVKNTNELADRIERVVP 808
Cdd:cd07435 194 TGDVHYLDPEDKIYREILLAGQGGGDGRADEQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIEDIKP 268
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
417-593 |
4.99e-81 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 263.93 E-value: 4.99e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKE 496
Cdd:COG2176 5 LEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 497 WVGDAIFVAHNASFDMGFIDTGYERLGFgPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATAY 576
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGL-PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAE 163
|
170
....*....|....*..
gi 586340297 577 IFIKMVQQMKELGVLNH 593
Cdd:COG2176 164 LFLKLLEKLEEKGITTL 180
|
|
| DNA_pol3_alpha |
pfam07733 |
Bacterial DNA polymerase III alpha NTPase domain; |
823-1093 |
1.67e-75 |
|
Bacterial DNA polymerase III alpha NTPase domain;
Pssm-ID: 400196 [Multi-domain] Cd Length: 259 Bit Score: 251.27 E-value: 1.67e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 823 EEIRELSYTNARKLYGEDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVGS-RGSVGSSFVATMTEITE 901
Cdd:pfam07733 1 EYLRKLVEEGLKERYGEGLPEEYQERLEYELNVIIKMGFAGYFLIVWDLVKWAKDNGILVGPgRGSAAGSLVAYLLGITE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 902 VNPLPphyicpncktseffndgsvgsgfdlpdktcetcgaplikegQDIPFETFLGFKGDKVPDIDLNFSGEYQPNAHNY 981
Cdd:pfam07733 81 VDPLK-----------------------------------------HDLLFERFLNPERVSMPDIDIDFEDERREEVIDY 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 982 TKVLFGEDKVFRAGTIGTVAEKTA-------FGYV------------------KGYLNDQ----GIHKRGAEIDRLV--- 1029
Cdd:pfam07733 120 VKEKYGRDRVAQIATFGTYAAKSAirdvgraLGLPydeidrlaklipfelgilEKALEEEpelkELIESDPEVKRLIela 199
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 1030 KGCTGVKRTTGQHPGGIIVVPDymDIYDFTPIQYPADDQNSawmTTHFDFHSIHD-NVLKLDILG 1093
Cdd:pfam07733 200 KKLEGLPRHTGQHAGGVVISPD--PLTDFVPLYKADDDDRP---VTQFDKDDLEDlGLLKMDFLG 259
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
600-1433 |
8.76e-62 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 231.11 E-value: 8.76e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 600 LSNEDAYKRARPSHVTLIVQNQQGLKNLFKIVS-ASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQS 678
Cdd:COG0587 69 LYVAPGSRDDAGYHLVLLAKNREGYRNLCRLLSrAYLEGFYKGKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYD 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 679 QVEKIAKYYdfIEIQPPALYQDLIDRELIRDTETLHeiyqRLIHAGDTAGIPVIATGNAHYLFEHDGIARKILIA----- 753
Cdd:COG0587 149 EAEAALARL--KDIFGDRFYLELQRHGLPEDRRVNA----ALLELARELGLPLVATNDVHYLNPEDAEAHDVLLCirtgk 222
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 754 --SQPGNPLNRStlPEAHFRTTDEMLNEFHFLGEekaheiVVKNTNELADRIE-RVVPIKDEL---YTPRMEGANEEIRE 827
Cdd:COG0587 223 tlDDPGRRRFAN--AERYLKSPEEMAELFADLPE------ALANTLEIAERCNfSLDLGKYQLpkfPVPEGETEEEYLRK 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 828 LSYTNARKLYGEDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVGS-RGSVGSSFVATMTEITEVNPLP 906
Cdd:COG0587 295 LAEEGLERRYPEGIPEEYRERLEYELDVIEKMGFPGYFLIVWDFIRWARSNGIPVGPgRGSAAGSLVAYALGITDVDPIR 374
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 907 phyicpncktseffndgsvgsgFDLpdktcetcgaplikegqdiPFETFLGfkGDKV--PDIDLNFSGEYQPNAHNYTKV 984
Cdd:COG0587 375 ----------------------YDL-------------------LFERFLN--PERVsmPDIDIDFCHERREEVIQYVYE 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 985 LFGEDKVFRAGTIGTVAEKTA-------FGYVKGYL--------NDQGIHKRGA---------------EIDRLVKGCT- 1033
Cdd:COG0587 412 KYGRDRVAQIATFGTMRARAAirdvgrvLGLPYGEVdrlaklipNDPGITLEKAleeepelrelydsdpEVRRLLDLARk 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1034 --GVKRTTGQHPGGIIVVPDymDIYDFTPIQYPADDQNSawmTTHFDFHSIhDNV--LKLDILG-------HDdptMIRM 1102
Cdd:COG0587 492 leGLPRHLSTHAGGVVISDD--PLTDLVPLERAAMGGRP---VTQFDKDDV-EALglLKFDFLGlrtltviRD---ALDL 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1103 LQDLSG--IDPKTIPVDDKEVMQIFSTPESLGVtedeilcktgtfgvpefgtgF------VRQMLEDTKPTTFSELVQIS 1174
Cdd:COG0587 563 IKENRGidIDLADIPLDDPKTYELLQRGDTIGV--------------------FqlesrgMRSLLKRLKPDCFEDLVALV 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1175 GL-----------------SHGtdvwlgnaQELI------------KT-GicdlssvigcrddIMVY---LM-----YAG 1216
Cdd:COG0587 623 ALyrpgpmqggmvppyirrKHG--------REPVeyphpelepilkETyG-------------VIVYqeqVMqiaqvLAG 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1217 LEP--------SMAFKIMESVRKGKgltEEMIETMKENEVPDwylDSCLKI--------KYMFPKAHAAAYVLMAVRIAY 1280
Cdd:COG0587 682 FSLgeadllrrAMGKKKKEEMAKQR---EKFVEGAVANGYDE---EFAEEIfdqiekfaGYGFNKSHAAAYALLAYQTAY 755
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1281 FKVHHPLYYYASYFTIRASDFdlitmikDKTSIrntvkdmysrymdlgkkekdvltvleIMNEMAHRGYRMQPISLEKSQ 1360
Cdd:COG0587 756 LKAHYPAEFMAALLNSQPMGF-------YKPAQ--------------------------YVQEARRHGIEVLPPDVNESD 802
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1361 AfEFIIE-GDTLIPPFISVPGLGENVAKRIVEAR-DDGPFLSKEDLNKKAG---LSQKIIEYL------DELGslpnlPD 1429
Cdd:COG0587 803 W-DFTVEpGGAIRLGLGAIKGVGEAAAEAIVAAReENGPFTSLFDFCRRVDlrkLNKRVLEALikagafDSLG-----PN 876
|
....
gi 586340297 1430 KAQL 1433
Cdd:COG0587 877 RRQL 880
|
|
| polc |
TIGR00594 |
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
599-1433 |
6.55e-59 |
|
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are known are DNA polymerases. 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: 273161 [Multi-domain] Cd Length: 1022 Bit Score: 221.87 E-value: 6.55e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 599 KLSNEDAYKRARPSHVTLIVQNQQGLKNLFKIVSASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQS 678
Cdd:TIGR00594 72 RFDKKRISKGKEAYHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEER 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 679 QVEKIAKYYD-------FIEIQPPALY-QDLIDRELIrdtetlhEIYQRLihagdtaGIPVIATGNAHYLFEHDGIARKI 750
Cdd:TIGR00594 152 LAEEAALKYQeifgddyYLELQDHGIPeQRVVNEALL-------EISEEL-------GIPLVATNDVHYINPEDAHAHEI 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 751 LIASQPGNPL---NRSTLP--EAHFRTTDEMLNEFhflgeeKAHEIVVKNTNELAdriERVVPIKDELYTPRMEGANEE- 824
Cdd:TIGR00594 218 LLCIQTGKTLsdpKRLKFYsdEFYLKSPEEMAELF------ADIPEALANTVEIA---ERCNLVDVKLGPPRLPSYQIPp 288
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 825 --------IRELSYTNARKLYGEDLPQI-----VIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGS 890
Cdd:TIGR00594 289 dftsqedyLRHLADEGLRERLAAGPPGYkrraqYKERLEYELDVINSMGFPGYFLIVWDFIKWAKDHGIPVGpGRGSAAG 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 891 SFVATMTEITEVNPLPPHYIcpncktseffndgsvgsgfdlpdktcetcgaplikegqdipFETFLGFKGDKVPDIDLNF 970
Cdd:TIGR00594 369 SLVAYALKITDIDPIKHGLL-----------------------------------------FERFLNPERISMPDIDIDF 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 971 SGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAEKTAFGYV---------------KGYLNDQGIHKRGA-----------E 1024
Cdd:TIGR00594 408 CDERRDEVIEYVADKYGHDNVAQIITFGTMKAKAALRDVarvldipyaeadriaKLIPPRPGKTLKEAleaspqlrqlyE 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1025 IDRLVK-------GCTGVKRTTGQHPGGIIVVPDYMDiyDFTPIQYPADDQNsawMTTHFDFHSIHD-NVLKLDILGHDD 1096
Cdd:TIGR00594 488 EDPEVKqlidmarKLEGLNRNAGVHAAGVVISSEPLT--DYVPLYKDKEGGA---ISTQYDMDDLEAvGLLKMDFLGLKT 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1097 PTMIRMLQDL------SGIDPKTIPVDDKEVMqifstpeslgvtedEILCKTGTFGVPEFGTGFVRQMLEDTKPTTFSEL 1170
Cdd:TIGR00594 563 LTLIQDATELirkrrgIDLDIASIPLDDKKTF--------------SLLQEGDTTGVFQLESRGMQDLLKRLKPDGFEDI 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1171 VQISGL-------SHGTDVWLG--NAQELIKTGICDLSSVIGCRDDIMVY----LMYAGlepSMA-FKIMES--VRK--G 1232
Cdd:TIGR00594 629 IAVNALyrpgpmeSGMIPDFIDrkHGREPIEYPHPLLEPILKETYGVIVYqeqvMQIAQ---RLAgFSLGEAdlLRRamG 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1233 KGLTEEM-------IETMKENEVPD------WylDSCLKI-KYMFPKAHAAAYVLMAVRIAYFKVHHPLYYYASyftira 1298
Cdd:TIGR00594 706 KKKAEEMakerekfVEGAEKNGYDPeiaenlF--DLIEKFaGYGFNKSHAAAYGMISYQTAYLKANYPAEFMAA------ 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1299 sdfdLITMIKDKtsirntvKDMYSRYMDLGKKekdvltvleimnemahRGYRMQPISLEKSqAFEFIIEGDTLIPPFISV 1378
Cdd:TIGR00594 778 ----LLTSEIND-------IEKVAVYIAEAKK----------------MGIEVLPPDINES-GQDFAVEDKGIRYGLGAI 829
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 586340297 1379 PGLGENVAKRIVEARDD-GPFLSKEDL-----NKKagLSQKIIEYLDELGSLPNL-PDKAQL 1433
Cdd:TIGR00594 830 KGVGESVVKSIIEERNKnGPFKSLFDFinrvdFKK--LNKKVLEALIKAGAFDSLgPNRKTL 889
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
422-583 |
1.97e-58 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 198.48 E-value: 1.97e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGDA 501
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 502 IFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATAYIFIKM 581
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161
|
..
gi 586340297 582 VQ 583
Cdd:COG0847 162 LR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
423-579 |
7.42e-55 |
|
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: 188.28 E-value: 7.42e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKVHNG-EIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGDA 501
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 586340297 502 IFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFL-AKKYGVELTQHHRAIYDTEATAYIFI 579
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAELLL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
421-586 |
1.02e-52 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 182.50 E-value: 1.02e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 421 TYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGD 500
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 501 AIFVAHN-ASFDMGFIDTGYERLG-FGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQ-HHRAIYDTEATAYI 577
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGiKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARATAKL 160
|
....*....
gi 586340297 578 FIKMVQQMK 586
Cdd:smart00479 161 FKKLLERLE 169
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
416-638 |
3.86e-48 |
|
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: 171.09 E-value: 3.86e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 416 VLKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFK 495
Cdd:TIGR00573 3 QLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 496 EWVGDAIFVAHNASFDMGFIDTGYERL-GFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEAT 574
Cdd:TIGR00573 83 DYIRGAELVIHNASFDVGFLNYEFSKLyKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALAD 162
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586340297 575 AYIFIKMVQQMkelgVLNHNEINKKLSNedaykRARPSHVTLIVQNQQGLKNLFKIVSASLVKY 638
Cdd:TIGR00573 163 AFILAKLYLVM----TGKQTKYGENEGQ-----QSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
417-590 |
3.38e-46 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 175.88 E-value: 3.38e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKE 496
Cdd:PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 497 WVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINT--EYGKHGLNFLAKKYGVELTQHHRAIYDTEAT 574
Cdd:PRK07883 92 FARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTPTHRALDDARAT 171
|
170
....*....|....*.
gi 586340297 575 AYIFIKMVQQMKELGV 590
Cdd:PRK07883 172 VDVLHGLIERLGNLGV 187
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
423-578 |
1.11e-44 |
|
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: 159.05 E-value: 1.11e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKVHNGE--IIDKFERFSNPHE--RLSETIINLTHITDDMLVDAPEIEEVLTEFKEWV 498
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 499 G-DAIFVAHNASFDMGFIDTGYERLGFG--PSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQH-HRAIYDTEAT 574
Cdd:pfam00929 81 RkGNLLVAHNASFDVGFLRYDDKRFLKKpmPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160
|
....
gi 586340297 575 AYIF 578
Cdd:pfam00929 161 AKLF 164
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
417-578 |
4.02e-43 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 158.26 E-value: 4.02e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHErLSETIINLTHITDDMLVDAPEIEEVLTEFKE 496
Cdd:PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKE-VPEYITELTGITYEDLENAPSLKEVLEEFRL 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 497 WVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELS-RTINTEygKHGLNFLAKKYGVELTQHHRAIYDTEATA 575
Cdd:PRK08517 144 FLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAkRTIESP--RYGLSFLKELLGIEIEVHHRAYADALAAY 221
|
...
gi 586340297 576 YIF 578
Cdd:PRK08517 222 EIF 224
|
|
| dnaE |
PRK07374 |
DNA polymerase III subunit alpha; Validated |
607-1404 |
3.67e-39 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 159.50 E-value: 3.67e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 607 KRARPSHVTLIVQNQQGLKNLFKIVSASLVK------YFYRtPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQV 680
Cdd:PRK07374 80 KKEKRYHLVVLAKNATGYKNLVKLTTISHLNgmrgrgIFSR-PCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPDVA 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 681 EKIAKYY------DF-IEIQPPALYQD-LIDRELIRdtetlheIYQRLihagdtaGIPVIATGNAHYLFEHDGIARKILI 752
Cdd:PRK07374 159 RDVAAWYkevfgdDFyLEIQDHGSIEDrIVNVELVR-------IAKEL-------GIKLIATNDAHYLSKNDVEAHDALL 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 753 ASQPGNPLN-----RSTLPEaHFRTTDEMLNEF--HfLGEEKAHEiVVKNTNELADRIERVvpikDELYTPRM------E 819
Cdd:PRK07374 225 CVLTGKLISdekrlRYTGTE-YIKSEEEMLRLFrdH-LDPEVIQE-AIANTVEVAEKVEEY----DILGTYRMprfpipE 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 820 G--ANEEIRELSYTNARKLYG----EDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSF 892
Cdd:PRK07374 298 GhtAVSYLTEVTEQGLLKRLKlnslDEIDENYKERLSYELKIIEQMGFPTYFLVVWDYIRFAREQGIPVGpGRGSAAGSL 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 893 VATMTEITEVNPlpphyicpncktseffndgsvgsgfdlpdktcetcgaplIKEGqdIPFETFLGFKGDKVPDIDLNFSG 972
Cdd:PRK07374 378 VAYALGITNIDP---------------------------------------VKNG--LLFERFLNPERKSMPDIDTDFCI 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 973 EYQPNAHNYTKVLFGEDKV-----FRAGTIGTV--------------AEKTA--FGYVKG-------------------- 1011
Cdd:PRK07374 417 ERRGEVIDYVTRRYGEDKVaqiitFNRMTSKAVlkdvarvldipygeADRLAklIPVVRGkpaklkamigkespspefre 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1012 -YLNDQGIhKRGAEIDRLVKgctGVKRTTGQHPGGIIVVPDYMDiyDFTPIQYPADDQnsaWMTTHF--DFHSIhdNVLK 1088
Cdd:PRK07374 497 kYEKDPRV-KKWVDMAMRIE---GTNKTFGVHAAGVVIASDPLD--ELVPLQRNNDGQ---VITQYFmeDIESL--GLLK 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1089 LDILGHDDPTMIRMLQDL----SG--IDPKTIPVDDKEVMQIFSTPESLGVTEDEilcKTGtfgvpefgtgfVRQMLEDT 1162
Cdd:PRK07374 566 MDFLGLKNLTMIEKTLELveqsTGerIDPDNLPLDDEKTFELLARGDLEGIFQLE---SSG-----------MRQVVRDL 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1163 KPTTFSELVQI----------SGL-------SHGTDVwLGNAQELIKTgicDLSSVIGcrddIMVY---LM-----YAG- 1216
Cdd:PRK07374 632 KPSSLEDISSIlalyrpgpldAGLipkfinrKHGREA-IDFAHPLLEP---ILTETYG----IMVYqeqIMkiaqdLAGy 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1217 -------LEPSMAFKIMESVRKGKGLteeMIETMKENEVPDWYLDS-----CLKIKYMFPKAHAAAYVLMAVRIAYFKVH 1284
Cdd:PRK07374 704 slgqadlLRRAMGKKKVSEMQKHRGI---FVEGASKRGVDEKVADElfdqmVLFAEYCFNKSHSTAYGAVTYQTAYLKAH 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1285 HPLYYYASYFTIRASDFDLItmikdktsirntvkdmySRYmdlgkkekdvltvleIMNEMAhRGYRMQPISLEKSqAFEF 1364
Cdd:PRK07374 781 YPVAYMAALLTVNAGSSDKV-----------------QRY---------------ISNCNS-MGIEVMPPDINRS-GIDF 826
|
890 900 910 920
....*....|....*....|....*....|....*....|.
gi 586340297 1365 IIEGDTLIPPFISVPGLGENVAKRIVEARD-DGPFLSKEDL 1404
Cdd:PRK07374 827 TPKGNRILFGLSAVKNLGDGAIRNIIAARDsDGPFKSLADL 867
|
|
| DNA_pol3_finger |
pfam17657 |
Bacterial DNA polymerase III alpha subunit finger domain; |
1096-1246 |
3.71e-39 |
|
Bacterial DNA polymerase III alpha subunit finger domain;
Pssm-ID: 407553 [Multi-domain] Cd Length: 166 Bit Score: 143.44 E-value: 3.71e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1096 DPTMIRMLQDLS------GIDPKTIPVDDKEVMQIFSTPESLGVtedeilcktgtfgvPEFGTGFVRQMLEDTKPTTFSE 1169
Cdd:pfam17657 1 TLTIIRDALDLIkenrgiGIDLATIPLDDPKTYKLLSSGDTLGV--------------FQFESRGMRQMLKRLKPDTFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1170 LVQISGLSHGTDVWLGNAQELI--KTGIC-------DLSSVIGCRDDIMVY--------LMYAGLEPSMAFKIMESVRKG 1232
Cdd:pfam17657 67 LVALSALYRPGPMQGGNVDDYIkrKHGKEkieyphpDLEPILKETYGVIVYqeqvmqiaQILAGFSLGEADLLRRAMGKK 146
|
170
....*....|....*....
gi 586340297 1233 K-----GLTEEMIETMKEN 1246
Cdd:pfam17657 147 KpeemeKLREKFIEGAKEN 165
|
|
| dnaE |
PRK05673 |
DNA polymerase III subunit alpha; Validated |
593-1433 |
1.42e-38 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 157.57 E-value: 1.42e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 593 HNEINKKLSNEDAYkrarpSHVTLIVQNQQGLKNLFKIVS-ASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTA 671
Cdd:PRK05673 69 APEKKDDVSGGGAY-----THLTLLAKNETGYRNLFKLSSrAYLEGQYGYKPRIDREWLAEHSEGLIALSGCPSGEVGTA 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 672 VMQKDQSQVEKIAkyydfieiqppALYQDLI-DR---ELIR---DTETLHEiyQRLIHAGDTAGIPVIATGNAHYLFEHD 744
Cdd:PRK05673 144 LLAGQYDEAEEAA-----------AEYQEIFgDRfylELMRhglPIERRVE--HALLELAKELGLPLVATNDVHYLTPED 210
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 745 GIARKILIASQPGNPLN------RSTlPEAHFRTTDEMLNEFHFLGEekaheiVVKNTNELADRIERVVPIKDELY---- 814
Cdd:PRK05673 211 AEAHEALLCIAEGKTLDdpdrfrFYS-PEQYLKSAEEMRELFADLPE------ALDNTVEIAERCNVEVRLGKPFLprfp 283
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 815 TPRMEGANEEIRELSYT--NAR--KLYGEDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVG 889
Cdd:PRK05673 284 TPDGETEEDYLRKEAKEglEERlaFLFPDEERPEYVERLEYELDVIIQMGFPGYFLIVADFIQWAKDNGIPVGpGRGSGA 363
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 890 SSFVATMTEITEVNPLPphyicpncktseffndgsvgsgFDLpdktcetcgapLikegqdipFETFLgfKGDKV--PDID 967
Cdd:PRK05673 364 GSLVAYALGITDLDPLR----------------------FGL-----------L--------FERFL--NPERVsmPDFD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 968 LNFSGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAEKTAF---GYVKGY-------------------LND--------QG 1017
Cdd:PRK05673 401 IDFCQDRRDEVIRYVAEKYGRDAVAQIITFGTMKAKAVIrdvGRVLGMpygfvdritklippdpgitLAKayeeepelRE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1018 IHKRGAEIDRLV---KGCTGVKRTTGQHPGGIIVVPDymDIYDFTPIQYPADDQNsawMTTHFDFHSIHD-NVLKLDILG 1093
Cdd:PRK05673 481 LYESDPEVKRLIdmaRKLEGLTRNAGVHAAGVVISPT--PLTDFVPLYRDPDSGM---PVTQFDMKDVEAaGLVKFDFLG 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1094 -------HDDPTMIRMlQDLSGIDPKTIPVDDKEVMQIFSTPESLGVtedeilcktgtfgvpeF---GTGFvRQMLEDTK 1163
Cdd:PRK05673 556 lrtltiiDDALKLIKK-RRGIDVDLEAIPLDDPKTYELLQRGETLGV----------------FqleSRGM-RDLLKRLK 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1164 PTTFSELVQISGL-----------------SHGT------DVWLgnaQELIKT--GicdlssvigcrddIMVY---LMya 1215
Cdd:PRK05673 618 PDCFEDIIALVALyrpgpmesgmipnfidrKHGReeieypHPEL---EPILKEtyG-------------IIVYqeqVM-- 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1216 glepSMAFKI--------------MesvrkGKGLTEEM-------IETMKENEVPDwylDSCLKI-----K---YMFPKA 1266
Cdd:PRK05673 680 ----QIAQVLagyslggadllrraM-----GKKKPEEMakqreifVEGAKKNGIDE---EAADAIfdlleKfagYGFNKS 747
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1267 HAAAYVLMAVRIAYFKVHHPLYYYASYFTiraSDFDLitmiKDKTSI-RNTVKDMysrymdlGkkekdvLTVLeimnema 1345
Cdd:PRK05673 748 HAAAYALVSYQTAYLKAHYPAEFMAALLT---SDMDN----TDKVAVyLDECRRM-------G------IKVL------- 800
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1346 hrgyrmqPISLEKSQaFEFIIEGDTLIPPFISVPGLGENVAKRIVEAR-DDGPFLSKEDLNKKAGLSQ---KIIEYL--- 1418
Cdd:PRK05673 801 -------PPDVNESL-YDFTVVDGDIRYGLGAIKGVGEGAVEAIVEAReEGGPFKDLFDFCARVDLKKvnkRVLESLika 872
|
970
....*....|....*...
gi 586340297 1419 ---DELGslpnlPDKAQL 1433
Cdd:PRK05673 873 gafDSLG-----PNRAAL 885
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
422-605 |
1.25e-37 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 144.19 E-value: 1.25e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGDA 501
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 502 IFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQhHRAIYDTEATAYIFIKM 581
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAVYQKC 168
|
170 180
....*....|....*....|....
gi 586340297 582 VQQMKElgvlNHNEINKKLSNEDA 605
Cdd:PRK06807 169 ASIEEE----AKRKSNKEVLDETA 188
|
|
| dnaE |
PRK06826 |
DNA polymerase III DnaE; Reviewed |
610-1418 |
2.82e-37 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 153.51 E-value: 2.82e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 610 RPSHVTLIVQNQQGLKNLFKIVSASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVEKIAKYYD- 688
Cdd:PRK06826 86 ETYHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKd 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 689 -------FIEIQPPAL-YQDLIDRELIRDTETLheiyqrlihagdtaGIPVIATGNAHYLFEHDGIARKILIASQPGNPL 760
Cdd:PRK06826 166 ifgkenfYLELQDHGIpEQRKVNEELIKLSKEL--------------GIPLVATNDVHYIRKEDAKAHDVLLCIQTGKTV 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 761 ---NRSTLPEAHF--RTTDEMLNEFHFLGEekaheiVVKNTNELADRIErvVPIK-DELYTPRM---EG--ANEEIRELS 829
Cdd:PRK06826 232 ddeNRMRFPSDEFylKSPEEMYELFSYVPE------ALENTVKIAERCN--VEFEfGKSKLPKFplpEGydPYEYLRELC 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 830 YTNARKLYgEDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSFVATMTEITEVNPLpph 908
Cdd:PRK06826 304 YEGLKKRY-PNPSEELIERLEYELSVIKQMGYVDYFLIVWDFIRFARENGIMVGpGRGSAAGSLVAYTLGITKIDPI--- 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 909 yicpncKTSeffndgsvgsgfdlpdktcetcgapLIkegqdipFETFLGFKGDKVPDIDLNFSGEYQPNAHNYTKVLFGE 988
Cdd:PRK06826 380 ------KYN-------------------------LL-------FERFLNPERVSMPDIDIDFCYERRQEVIDYVVEKYGK 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 989 DKVFRAGTIGTVAEKTAF---GYVKGYlndqgihkRGAEIDRLVK------GCT-------------------------- 1033
Cdd:PRK06826 422 DRVAQIITFGTMAARAAIrdvGRALNY--------PYAEVDRIAKmiptelGITidkalelnpelkeayendervrelid 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1034 ------GVKRTTGQHPGGIIVVPDymDIYDFTPIQyPADDQnsawMTTHFDFHSIHD-NVLKLDILGHDDPTMIR----M 1102
Cdd:PRK06826 494 taraleGLPRHASTHAAGVVISSE--PLVEYVPLQ-KNDGS----IVTQFTMTTLEElGLLKMDFLGLRTLTVIRdavdL 566
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1103 LQDLSG--IDPKTIPVDDKEVMQIFSTPESLGVTEDEilcktgtfgvpefgTGFVRQMLEDTKPTTFSELvqISGLShgt 1180
Cdd:PRK06826 567 IKKNRGieIDLDKIDYDDKKVYKMIGEGKTVGVFQLE--------------SAGMRSFMKELKPDSLEDI--IAGIS--- 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1181 dvwL---------------GNAQELIKTGICDLSSVI----GCrddiMVY---LM-----YAG--------LEPSMAFK- 1224
Cdd:PRK06826 628 ---LyrpgpmdsipryiknKNNPEKIEYLHPKLEPILkvtyGC----IVYqeqVMqivrdLAGysmgrsdlVRRAMSKKk 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1225 --IMESVRKG--KGLTEEMIETMKENEVPDwylDSCLKI--------KYMFPKAHAAAYVLMAVRIAYFKVHHPLYYYAS 1292
Cdd:PRK06826 701 hdVMEEERKNfiYGIVDEGGPGCIRNGIDE---ETANKIfdsmmdfaSYAFNKSHAAAYAVVAYQTAYLKRYYPVEFMAA 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1293 yftirasdfdLITMIKDKTsirntvkdmysrymdlgkkEKdvltVLEIMNEMAHRGYRMQPISLEKSQAfEFIIEGDTLI 1372
Cdd:PRK06826 778 ----------LLNSVMGNS-------------------DK----VAFYIEECRRLGIEVLPPDINESYS-KFTVEGDKIR 823
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|
gi 586340297 1373 PPFISVPGLGENVAKRIVEARD-DGPFLSKEDLNKKAGLSQ---KIIEYL 1418
Cdd:PRK06826 824 FGLAAVKNVGENAIDSIVEEREkKGKFKSLVDFCERVDTSQinkRAVESL 873
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
421-588 |
1.58e-36 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 150.49 E-value: 1.58e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 421 TYVVFDVETTGLS-NQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVG 499
Cdd:PRK08074 4 RFVVVDLETTGNSpKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 500 DAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATAYIFI 579
Cdd:PRK08074 84 GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAELFL 163
|
....*....
gi 586340297 580 KMVQQMKEL 588
Cdd:PRK08074 164 QLLNKLERL 172
|
|
| dnaE |
PRK06920 |
DNA polymerase III subunit alpha; |
604-1404 |
5.69e-36 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 149.18 E-value: 5.69e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 604 DAYKRARPshVTLIVQNQQGLKNLFKIVSASLVKyfyRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVEKI 683
Cdd:PRK06920 72 EEEEKSYP--LVLLAENEIGYQNLLKISSSIMTK---SKEGIPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQAEEV 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 684 AKYYD--------FIEIQPpalyqdlidrelIRDTETLHEiyqRLIHAGDTAGIPVIATGNAHYLFEHDGIARKILIASQ 755
Cdd:PRK06920 147 ARAYQnmfgnfymSLQHHA------------IQDELLLQE---KLPEFSNRVNIPVVATNDVRYINQSDALVHECLLSVE 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 756 PGNPLN-----RSTLPEAHFRTTDEMLNEFhflgeeKAHEIVVKNTNELADRIERVVPIKD----ELYTPRMEGANEEIR 826
Cdd:PRK06920 212 SGTKMTdpdrpRLKTDQYYLKSSDEMEALF------SHVPEAIYNTVEIAERCRVEIPFHVnqlpKFPVPSNETADMYLR 285
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 827 ELSYTNARKLYGEDlPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSFVATMTEITEVNPL 905
Cdd:PRK06920 286 RVCEEGLQKRYGTP-KEVHINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHILTGpGRGSAAGSLVSYVLEITDIDPI 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 906 PPHYIcpncktseffndgsvgsgfdlpdktcetcgaplikegqdipFETFLGFKGDKVPDIDLNFSGEYQPNAHNYTKVL 985
Cdd:PRK06920 365 EYDLL-----------------------------------------FERFLNPERVTLPDIDIDFPDTRRDEMIRYVKDK 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 986 FGEDKVFRAGTIGTVAEKTAF---GYVKG---------------------------------YLNDQGIHKRGAEIDRLV 1029
Cdd:PRK06920 404 YGQLRVAQIVTFGTLAAKAAIrdiARVMGlpprdidifsklipsklgitlkdayeesqslreFIQGNLLHERVFEIAKRV 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1030 KgctGVKRTTGQHPGGIIVVPDymDIYDFTPIQypaDDQNSAWMTTHFDFHSIHDNVLKLDILGHDDPTMIRMLQDL--- 1106
Cdd:PRK06920 484 E---GLPRHTSIHAAGVIMSQE--PLTGSVAIQ---EGHNDVYVTQYPADALEELGLLKMDFLGLRNLTLLENIIKFieq 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1107 ---SGIDPKTIPVDDKEVMQIFSTPESLGVTEDEilcktgtfgvpefgTGFVRQMLEDTKPTTFSELVQISGL------- 1176
Cdd:PRK06920 556 ktgKEIDIRNLPLQDEKTFQLLGRGDTTGVFQLE--------------SSGMRNVLRGLKPNEFEDIVAVNSLyrpgpme 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1177 --------SHGTdVWLGNAQELIKTGICDLSSVIGCRDDIMVYL-MYAGLEPSMAFKIMESVRKGKgltEEMIETMKENe 1247
Cdd:PRK06920 622 qiptfiesKHGK-RKIEYLHPDLKPILERTYGVIVYQEQIMQIAsKLAGFSLGEADLLRRAVSKKN---RDILDQERKH- 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1248 vpdwYLDSCLK------------------IKYMFPKAHAAAYVLMAVRIAYFKVHHPLYYyasyftirasdfdlitMIKD 1309
Cdd:PRK06920 697 ----FVQGCLQngydetsaekiydlivrfANYGFNRSHAVAYSMIGYQLAYLKANYTLEF----------------MTAL 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1310 KTSIrntvkdmysrymdLGKKEKdvltVLEIMNEMAHRGYRMQPISLEKSqAFEFIIEGDTLIPPFISVPGLGENVAKRI 1389
Cdd:PRK06920 757 LSSA-------------IGNEDK----IVQYIRETKRKGFHVLPPSLQRS-GYNFQIEGNAIRYSLLSIRNIGMATVTAL 818
|
890
....*....|....*
gi 586340297 1390 VEARDDGPFlskEDL 1404
Cdd:PRK06920 819 YEEREKKMF---EDL 830
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
421-588 |
1.40e-34 |
|
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: 143.79 E-value: 1.40e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 421 TYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGD 500
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 501 AIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATAYIFIK 580
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELLLL 160
|
....*...
gi 586340297 581 MVQQMKEL 588
Cdd:TIGR01407 161 LFEKMEKL 168
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
414-601 |
1.40e-33 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 130.17 E-value: 1.40e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 414 DVVLKDATYVVFDVETTGLSNQY-DKIIELAAVKVHNGEII-DKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVL 491
Cdd:PRK07740 53 DIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVL 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 492 TEFKEWVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDT 571
Cdd:PRK07740 133 HRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDA 212
|
170 180 190
....*....|....*....|....*....|
gi 586340297 572 EATAYIFIKMVQQMKELGVLNHNEINKKLS 601
Cdd:PRK07740 213 LMTAKLWAILLVEAQQRGITTLHDLYAALS 242
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
422-581 |
1.83e-31 |
|
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: 121.49 E-value: 1.83e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLS-NQYDKIIELAAVKVHNGEIIDK-FERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVG 499
Cdd:cd06131 1 QIVLDTETTGLDpREGHRIIEIGCVELINRRLTGNtFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 500 DAIFVAHNASFDMGFIDTGYERLGFGPSTN---GVIDTLELSRtinteyGKHG-----LNFLAKKYGVELTQH--HRAIY 569
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLGKKIIdfcRVIDTLALAR------KKFPgkpnsLDALCKRFGIDNSHRtlHGALL 154
|
170
....*....|..
gi 586340297 570 DTEATAYIFIKM 581
Cdd:cd06131 155 DAELLAEVYLEL 166
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
422-579 |
5.50e-31 |
|
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: 119.54 E-value: 5.50e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTglSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGDA 501
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 586340297 502 IFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELtQHHRAIYDTEATAYIFI 579
Cdd:cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILL 155
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
415-593 |
3.21e-29 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 118.01 E-value: 3.21e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 415 VVLKDATYVVFDVETTGLSNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEF 494
Cdd:PRK06310 2 SLLKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 KEWVGDA-IFVAHNASFDMGFIDTGYERLG--FGPSTNGVIDTLELSRtintEYGK---HGLNFLAKKYGVELTQHHRAI 568
Cdd:PRK06310 82 KGFFKEGdYIVGHSVGFDLQVLSQESERIGetFLSKHYYIIDTLRLAK----EYGDspnNSLEALAVHFNVPYDGNHRAM 157
|
170 180
....*....|....*....|....*
gi 586340297 569 YDTEATAYIFIKMVQQMKELGVLNH 593
Cdd:PRK06310 158 KDVEINIKVFKHLCKRFRTLEQLKQ 182
|
|
| PHP_PolIIIA_DnaE3 |
cd12113 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
607-804 |
1.45e-28 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group.
Pssm-ID: 213997 [Multi-domain] Cd Length: 283 Bit Score: 116.77 E-value: 1.45e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 607 KRARPSHVTLIVQNQQGLKNLFKIVSASLVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVEKIAKY 686
Cdd:cd12113 81 GDKRYYHLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALE 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 687 YD--------FIEIQ----PPalyQDLIDRELIrdtetlhEIYQRLihagdtaGIPVIATGNAHYLFEHDGIARKILIAS 754
Cdd:cd12113 161 YRdifgkdnfYLELQdhglPE---QKKVNEGLI-------ELAKEL-------GIPLVATNDVHYLNKEDAEAHDVLLCI 223
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 755 QPGNPLN-----RSTLPEAHFRTTDEMLNEFHFLGEekaheiVVKNTNELADRIE 804
Cdd:cd12113 224 QTGKTLDdpnrmRFDTDEFYLKSPEEMRELFPDVPE------ALENTLEIAERCN 272
|
|
| polC_OBF |
cd04484 |
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
239-322 |
2.48e-28 |
|
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Pssm-ID: 239930 [Multi-domain] Cd Length: 82 Bit Score: 109.23 E-value: 2.48e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 239 KVAIEGVIFDINLKELKSGRHIVEIKVTDYTDSLVLKMFTRKNKDDLEHFKalSVGKWVRAQGRIEEDTFIRDLVMMMSD 318
Cdd:cd04484 1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELK--SKGDWVRVRGKVQYDTFSKELVLMIND 78
|
....
gi 586340297 319 IEEI 322
Cdd:cd04484 79 IEEI 82
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
422-588 |
3.73e-28 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 122.87 E-value: 3.73e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQyDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGDA 501
Cdd:PRK07246 9 YAVVDLEATGAGPN-ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 502 IFVAHNASFDMG------FIDtGYERLgfgpstNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATA 575
Cdd:PRK07246 88 IFVAHNVKFDANllaealFLE-GYELR------TPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATA 160
|
170
....*....|...
gi 586340297 576 YIFIKMVQQMKEL 588
Cdd:PRK07246 161 ELFLKLLQKIESL 173
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
423-619 |
3.72e-25 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 105.71 E-value: 3.72e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSN-QYDKIIELAAVkvhngEIIDK------FERFSNPhERLS-ETIINLTHITDDMLVDAPEIEEVLTEF 494
Cdd:PRK05711 7 IVLDTETTGLNQrEGHRIIEIGAV-----ELINRrltgrnFHVYIKP-DRLVdPEALAVHGITDEFLADKPTFAEVADEF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 KEWVGDAIFVAHNASFDMGFIDTGYERLGFG-PSTN---GVIDTLELSRTINTeyGK-HGLNFLAKKYGVELT--QHHRA 567
Cdd:PRK05711 81 LDFIRGAELIIHNAPFDIGFMDYEFALLGRDiPKTNtfcKVTDTLAMARRMFP--GKrNSLDALCKRYGIDNShrTLHGA 158
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 586340297 568 IYDTEATAYIFIKMVQQMKELGVLNHNEINKKLSNEDAYKRARPSHVTLIVQ 619
Cdd:PRK05711 159 LLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVR 210
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
420-582 |
4.53e-23 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 99.50 E-value: 4.53e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 420 ATYVVFDVETTGLSNQYDKIIELAAvkvHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVG 499
Cdd:PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 500 -DAIFVAHNA-SFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATAYI 577
Cdd:PRK06309 79 tDNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDDVITLHRV 158
|
....*
gi 586340297 578 FIKMV 582
Cdd:PRK06309 159 FSALV 163
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
607-1176 |
9.15e-23 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 105.59 E-value: 9.15e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 607 KRARPSHVTLIVQNQQGLKNLFKIVSASLVKYF-----YRTPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQSQVE 681
Cdd:PRK09532 78 KRRRKYHQVVLAKNTQGYKNLVKLTTISHLQGVqgkgiFARPCINKELLEQYHEGLIVTSACLGGEIPQAILSGRPDAAR 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 682 KIAKYY------DF-IEIQPPALYQD-LIDRELIRdtetlheIYQRLihagdtaGIPVIATGNAHYLFEHDGIARKILIA 753
Cdd:PRK09532 158 KVAKWYkklfgdDFyLEIQDHGSQEDrIVNVEIVK-------IAREL-------GIKIIATNDSHFISCYDVEAHDALLC 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 754 SQPGNPLN-----RSTLPEaHFRTTDEMLNEFHFLGEEKAHEIVVKNTNELADRIERVvPIKDELYTPRM---EGANEEi 825
Cdd:PRK09532 224 IQTGKLITedkrlRYSGTE-YLKSAEEMRLLFRDHLPDDVIAEAIANTLEVADKIEPY-NILGEPRIPNYpvpSGHTPD- 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 826 relSYTNARKLYG----------EDLPQIVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSFVA 894
Cdd:PRK09532 301 ---TYVEEVAWQGllerlncksrSEVEPVYKERLEYELKMLQQMGFSTYFLVVWDYIKYARDNNIPVGpGRGSAAGSLVA 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 895 TMTEITEVNPLppHYicpncktseffndgsvgsgfdlpdktcetcgaplikegqDIPFETFLGFKGDKVPDIDLNFSGEY 974
Cdd:PRK09532 378 YCLKITNIDPV--HH---------------------------------------GLLFERFLNPERKSMPDIDTDFCIER 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 975 QPNAHNYTKVLFGEDKVFRAGTIGTVAEKTAFGYVKGYLN------DQGIH-------------------------KRGA 1023
Cdd:PRK09532 417 RDEMIKYVTEKYGEDRVAQIITFNRMTSKAVLKDVARVLDipygeaDKMAKlipvsrgkptklkvmisdetpepefKEKY 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1024 EIDRLVKG-------CTGVKRTTGQHPGGIIVVPDYMDiyDFTPIQYPADdqnSAWMTTHF--DFHSIhdNVLKLDILGH 1094
Cdd:PRK09532 497 DNDPRVRRwldmairIEGTNKTFGVHAAGVVISSEPLD--EIVPLQKNND---GAVITQYFmeDLESL--GLLKMDFLGL 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1095 DDPTMIRMLQDL------SGIDPKTIPVDDKEVMQIFSTPESLGVTED-----EILCKTGTFGVPEFGTGFVRQMLEDTK 1163
Cdd:PRK09532 570 RNLTTIQKTADLikenrgVEIDLDQLPLDERKALKILAKGEAKKLPKDvqkthKLLERGDLEGIFQLESSGMKQIVRDLK 649
|
650
....*....|...
gi 586340297 1164 PTTFSELVQISGL 1176
Cdd:PRK09532 650 PSNIEDISSILAL 662
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
422-581 |
1.01e-20 |
|
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.
Pssm-ID: 99836 [Multi-domain] Cd Length: 176 Bit Score: 91.13 E-value: 1.01e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQYDK-----IIELAAVKV--HNGEIIDKFERFSNP--HERLSETIINLTHITDDMLVDAPEIEEVLT 492
Cdd:cd06133 1 YLVIDFEATCWEGNSKPdypneIIEIGAVLVdvKTKEIIDTFSSYVKPviNPKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 493 EFKEWVGD---AIFVAhNASFDMGFIDTGYERLGFG---PSTNGVIDtlelsrtINTEYGKH-------GLNFLAKKYGV 559
Cdd:cd06133 81 EFLEWLGKngkYAFVT-WGDWDLKDLLQNQCKYKIInlpPFFRQWID-------LKKEFAKFyglkkrtGLSKALEYLGL 152
|
170 180
....*....|....*....|...
gi 586340297 560 ELT-QHHRAIYDTEATAYIFIKM 581
Cdd:cd06133 153 EFEgRHHRGLDDARNIARILKRL 175
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
337-403 |
1.94e-20 |
|
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Pssm-ID: 197753 [Multi-domain] Cd Length: 67 Bit Score: 86.17 E-value: 1.94e-20
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 586340297 337 EFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGMEGMLVD 403
Cdd:smart00481 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
419-590 |
1.42e-19 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 91.30 E-value: 1.42e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 419 DATYVVFDVETTGLSNQYDKIIELAAVKVH-NGEIIDKFERFSNPherlsETIINLTHI---TDDMLVDAPEIEEVLTEF 494
Cdd:PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLNP-----GVDPGPTHVhglTAEMLEGQPQFADIAGEV 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 KEWVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEAT 574
Cdd:PRK06063 89 AELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVL 168
|
170
....*....|....*.
gi 586340297 575 AYIFIKMVQQMKELGV 590
Cdd:PRK06063 169 AGILRPSLERARERDV 184
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
422-581 |
2.77e-19 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 86.84 E-value: 2.77e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQYDK-----IIELAAVKV-HNGEIIDKFERFSNP--HERLSETIINLTHITDDMLVDAPEIEEVLTE 493
Cdd:COG5018 4 YLVIDLEATCWDGKPPPgfpmeIIEIGAVKVdENGEIIDEFSSFVKPvrRPKLSPFCTELTGITQEDVDSAPSFAEAIED 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 494 FKEWVG--DAIFVAhNASFDMGFIDTGYERLGfgpstngvIDTLELSRTIN--TEYGKH-------GLNFLAKKYGVELT 562
Cdd:COG5018 84 FKKWIGseDYILCS-WGDYDRKQLERNCRFHG--------VPYPFGDRHINlkKLFALYfglkkriGLKKALELLGLEFE 154
|
170 180
....*....|....*....|
gi 586340297 563 -QHHRAIYDTEATAYIFIKM 581
Cdd:COG5018 155 gTHHRALDDARNTAKLFKKI 174
|
|
| DNA_pol3_a_NII |
pfam11490 |
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
94-207 |
1.04e-18 |
|
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam14480.
Pssm-ID: 431908 Cd Length: 117 Bit Score: 83.17 E-value: 1.04e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 94 KYFGHCIDQTA-LSPKVKGQLKQKKLIMSGKVLKVMVSNDIERNHFDKACNGSLIKAFRNCGFDIDKIIFETND-NDQEQ 171
Cdd:pfam11490 1 DYWEEIVEELSkKSPSLKSLLKNQKPEVEGNKLIIKVPNEIEANFLKKKNLDKLLEEYIKFGFGKLSIDVEVDEdESSEE 80
|
90 100 110
....*....|....*....|....*....|....*.
gi 586340297 172 NLASLEAHIQEEDEQSARLATEKLEKMKAEKAKQQD 207
Cdd:pfam11490 81 ELEEFEEQKEEEEQKAIQEAIEALEKKEAEKKSKEK 116
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
424-581 |
7.34e-18 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 84.00 E-value: 7.34e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 424 VFDVETTGLSNqydKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKewvGDAIF 503
Cdd:PRK07983 4 VIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY---GSEWY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 504 VAHNASFDMGFIdtgyerlgfgPSTNGV-IDTLELSRTINTEyGKHGLNFLAKKYGVELT-----QHHRAIYDTEATAYI 577
Cdd:PRK07983 78 VAHNASFDRRVL----------PEMPGEwICTMKLARRLWPG-IKYSNMALYKSRKLNVQtppglHHHRALYDCYITAAL 146
|
....
gi 586340297 578 FIKM 581
Cdd:PRK07983 147 LIDI 150
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
337-398 |
9.78e-18 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 82.21 E-value: 9.78e-18
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 586340297 337 EFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME 398
Cdd:pfam02811 1 HLHVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCE 62
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
603-802 |
3.79e-17 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes.
Pssm-ID: 213988 [Multi-domain] Cd Length: 277 Bit Score: 83.30 E-value: 3.79e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 603 EDAYKRARPSHVTLIVQNQQGLKNLFKIVSASlvkYFYR----TPRIPRSLLDEYREGLLVGTACDEGELFTAVMQKDQS 678
Cdd:cd07433 69 ANPDDADEPFRLTLLAQNEQGYKNLTELISRA---YLEGqrngGPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGNPD 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 679 QVEKIAKYYdfIEIQPPALYQdlidrELIRDTETLHEIY-QRLIHAGDTAGIPVIATGNAHYLFEHDGIARKILIASQPG 757
Cdd:cd07433 146 LAEALLQFL--KKIFPDRFYL-----ELQRHGRPEEEAYeHALIDLAYELGLPLVATNDVRFLKPEDFEAHEARVCIAEG 218
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 586340297 758 NPLN-----RSTLPEAHFRTTDEMLNEFHFLGEekaheiVVKNTNELADR 802
Cdd:cd07433 219 RTLDdprrpRRYSPQQYFKSAEEMAELFADLPE------AIENTVEIAKR 262
|
|
| dnaE |
PRK07279 |
DNA polymerase III DnaE; Reviewed |
554-1301 |
5.20e-16 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 83.93 E-value: 5.20e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 554 AKKYGVeltqHHRAIYDTEA--TAYIFIKMVQQMKELGVLNHnEINKKLSNedaykraRPSHVTLIVQNQQGLKNLFKIV 631
Cdd:PRK07279 27 AKELGY----QTIGIMDKDNlyGAYHFIEGAQKNGLQPILGL-ELNIFVEE-------QEVTLRLIAKNTQGYKNLLKIS 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 632 SASLvkyfyrTPRIPRSLLDEYREGLlvgtacdegelftAVMQKDQSQVEKIAKYYD-FIEIQPpalyqdlidrelirdt 710
Cdd:PRK07279 95 TAKM------SGKKQFSDLSQYLEGI-------------AVIVPYFDWSETLELPFDyYIGVDQ---------------- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 711 ETLHEIYQRlihagdtagiPVIATGNAHYLFEHDGIARKILIASQPGNPLNRSTLPEAH--FRTTDEMLNEFhflgEEKA 788
Cdd:PRK07279 140 ETPGSDFKR----------PILPLRTVRYFESADRETLQMLHAIRDNLSLREVPLVSSDqeLISCQSLETLF----QERF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 789 HEiVVKNTNELADRIErvVPIKDELYTPRME---GANEEIRELSYTN--ARKLYGEDLpqivIDRLEKELKSIIGNGFAV 863
Cdd:PRK07279 206 PQ-ALDNLEKLVSGIS--YDFDTDLKLPRFNrdrPAVEELRELAELGlkEKGLWSSPY----QERLDKELSVIHDMGFDD 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 864 IYLISQRLVKKSLDDGYLVG-SRGSVGSSFVATMTEITEVNPLPphyicpncktseffndgsvgsgfdlpdktcetcgap 942
Cdd:PRK07279 279 YFLIVWDLLRFGRSQGYYMGmGRGSAAGSLVAYALDITGIDPVK------------------------------------ 322
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 943 likegQDIPFETFLGFKGDKVPDIDLNFSGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAEKTA-------FGY------- 1008
Cdd:PRK07279 323 -----HNLLFERFLNKERYSMPDIDIDLPDIYRSEFLRYVRNRYGSDHSAQIVTFSTFGAKQAirdvfkrFGVpeyelsn 397
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1009 ------VKGYLND---------QGIHKRGaEIDR---LVKGCTGVKRTTGQHPGGIIVVPDymDIYDFTPIQYPADdqns 1070
Cdd:PRK07279 398 ltkkisFRDSLASvyeknisfrQIINSKL-EYQKafeIAKRIEGNPRQTSIHAAGVVMSDD--DLTNHIPLKYGDD---- 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1071 aWMTTHFDFHSIHDN-VLKLDILGHDDPTMIRMLQDL------SGIDPKTIPVDDKEVMQIFStpeslgvtedeilcKTG 1143
Cdd:PRK07279 471 -MMITQYDAHAVEANgLLKMDFLGLRNLTFVQKMQEKvakdygIHIDIEAIDLEDKETLALFA--------------AGD 535
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1144 TFGVPEFGTGFVRQMLEDTKPTTFSELVQIS-----GLSHGTD--VWLGNAQE---LIKTGICD-LSSVIGcrddIMVY- 1211
Cdd:PRK07279 536 TKGIFQFEQPGAINLLKRIKPVCFEDIVATTslnrpGASDYTDnfVKRRHGQEkvdLIDPVIAPiLEPTYG----IMLYq 611
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1212 --LM-----YAG--------LEPSMAFKIMESVRKgkgLTEEMIETMKEN----EVPDWYLDSCLKIK-YMFPKAHAAAY 1271
Cdd:PRK07279 612 eqVMqiaqvFAGfslgkadlLRRAMSKKNASEMQK---MEEDFLQGALELghseEKARELFDRMEKFAgYGFNRSHAFAY 688
|
810 820 830
....*....|....*....|....*....|
gi 586340297 1272 VLMAVRIAYFKVHHPLYYYASYFTIRASDF 1301
Cdd:PRK07279 689 SALAFQLAYFKAHYPAVFYDIMLNYSSSDY 718
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
422-607 |
3.05e-15 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 78.28 E-value: 3.05e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTglSNQYDKIIELAAVKVHNGEIIDKFERFSNPHE-RLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVGD 500
Cdd:PRK06195 3 FVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEmRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 501 AIFVAHNASFDMGFIDTGYERLGFGPSTNGVIDTLELSRTINTEYGKHGLNFLAKKYGVELtQHHRAIYDTEATAYIFIK 580
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF-KHHDALADAMACSNILLN 159
|
170 180 190
....*....|....*....|....*....|...
gi 586340297 581 MVqqmKELGVLNHNEINKKLS------NEDAYK 607
Cdd:PRK06195 160 IS---KELNSKDINEISKLLGvtlgyvNENGYK 189
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
423-577 |
7.20e-15 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 76.94 E-value: 7.20e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKV------HNGEIIDKFERFSNPHERLSETIINLTHITDDMlVDAPEIE-EVLTEFk 495
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFeydddgRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEM-VAGQTIDpAAVDAL- 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 496 ewVGDA-IFVAHNASFDMGFIdtgyERlgFGPSTNGVIDTLELSRTINTEYGKHG--LNFLAKKYGVeLTQHHRAIYDTE 572
Cdd:PRK09182 118 --IAPAdLIIAHNAGFDRPFL----ER--FSPVFATKPWACSVSEIDWSARGFEGtkLGYLAGQAGF-FHEGHRAVDDCQ 188
|
....*
gi 586340297 573 ATAYI 577
Cdd:PRK09182 189 ALLEL 193
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
336-408 |
1.03e-13 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such activity has not been found. It has been shown that the PHP domain of PolIIIA has a trinuclear metal complex and is capable of proofreading activity.
Pssm-ID: 213986 [Multi-domain] Cd Length: 179 Bit Score: 70.69 E-value: 1.03e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 336 VEFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGMEGMLVDDGVPI 408
Cdd:cd07431 1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPY 73
|
|
| DNA_pol3_a_NI |
pfam14480 |
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
8-80 |
2.32e-13 |
|
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam11490.
Pssm-ID: 433981 Cd Length: 72 Bit Score: 66.41 E-value: 2.32e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 8 KFKVLADQIKIsNQLDAEILNSGELTRIDVSNKNRTWEFHITLPQFLAHEDYLLFINAIEQEFKDIANVTCRF 80
Cdd:pfam14480 1 RFFELFPQLKL-PDELEELFEDAEIEKVTVHKKSKKWRFYISSPHLLPKEVIYKFEQRLKEQFFHIAKVKVKI 72
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
420-508 |
2.99e-13 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 69.81 E-value: 2.99e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 420 ATYVVFDVETTGLsNQYDKIIELAAVKVHNGEIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVG 499
Cdd:PRK07247 5 ETYIAFDLEFNTV-NGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVG 83
|
....*....
gi 586340297 500 DAIFVAHNA 508
Cdd:PRK07247 84 ELPLIGYNA 92
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
587-693 |
3.62e-13 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 69.11 E-value: 3.62e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 587 ELGVLNHNEINKKLSNEDAYkrarpsHVTLIVQNQQGLKNLFKIVSASLVKYFyrTPRIPRSLLDEYREGLLVGTACDEG 666
Cdd:pfam02811 62 EVYVAPGSREETEKLLAKYF------DLVLLAVHEVGYKNLIKLSSRAYLEGF--KPRIDKELLEEYFEGLIALSGCVLG 133
|
90 100 110
....*....|....*....|....*....|....*.
gi 586340297 667 ELFTAVMQKDQ-SQVEKIAKYYD--------FIEIQ 693
Cdd:pfam02811 134 HLDLILLAPGDyEEAEELAEEYLeifgedgfYLEIN 169
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
718-1424 |
7.02e-13 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 73.74 E-value: 7.02e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 718 QRLIHAGDTAGIPVIATGNAHYlfeHDGIARKI---LIASQPGNPLNRST-----LPEAHFRTTDEMLNEFhflgeeKAH 789
Cdd:PRK05672 182 ARLAALAARAGVPLVATGDVHM---HHRSRRRLqdaMTAIRARRSLAEAGgwlapNGERHLRSGAEMARLF------PDY 252
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 790 EIVVKNTNELADRI----ERVVP-IKDELyTPRMEGANEEIRELSYTNARKLYGEDLPQIVIDRLEKELKSIIGNGFAVI 864
Cdd:PRK05672 253 PEALAETVELAERCafdlDLLAYeYPDEP-VPAGHTPASWLRQLTEAGAARRYGPGIPPKARAQIEHELALIAELGYEGY 331
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 865 YLISQRLVKKSLDDGYLVGSRGSVGSSFVATMTEITEVNPlpphyicpncktseffndgsvgsgfdlpdktcetcgapli 944
Cdd:PRK05672 332 FLTVHDIVRFARSQGILCQGRGSAANSAVCYALGITEVDP---------------------------------------- 371
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 945 kEGQDIPFETFLGFKGDKVPDIDLNFSGEYQPNA--HNYTKvlFGEDK------------------VFRA-----GTIGT 999
Cdd:PRK05672 372 -VQSGLLFERFLSPERDEPPDIDVDFEHDRREEViqYVYRR--YGRDRaaqvanvityrprsavrdVAKAlglspGQVDA 448
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1000 VAeKTAFGYVKGYLNDQGIHKRGAE-----IDR---LVKGCTGVKRTTGQHPGGII--------VVP---DYMDiyDFTP 1060
Cdd:PRK05672 449 WA-KQVSRWSGSADDLQRLRQAGLDpespiPRRvveLAAQLIGFPRHLSQHSGGFVicdrplarLVPvenAAME--GRSV 525
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1061 IQYPADDQNSAWMtthfdfhsihdnvLKLDILG-------HddpTMIRMLQDLSGI--DPKTIPVDDKEVMQIFSTPESL 1131
Cdd:PRK05672 526 IQWDKDDCAAVGL-------------VKVDVLAlgmlsalH---RAFDLIAEHRGRrlTLASIPLDDPAVYDMLCRADSV 589
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1132 GVtedeilcktgtFGVPEfgtgfvR-QM--LEDTKPTTFSELV-QIS---------GLSH-------GTDVWLGNAQELI 1191
Cdd:PRK05672 590 GV-----------FQVES------RaQMamLPRLRPRTFYDLVvEVAivrpgpiqgGMVHpylrrrnGQEPVTYPHPELE 652
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1192 KTgicdLSSVIGC---RDDIMVYLMYAG---------LEPSMA-FKIMESVRKgkgLTEEMIETMKENEVPDWYLDSCL- 1257
Cdd:PRK05672 653 KV----LERTLGVplfQEQVMQIAIDAAgftpgeadqLRRAMAaWRRKGRLER---LRERLYDGMLARGYTGEFADRIFe 725
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1258 KIK----YMFPKAHAAAYVLMAVRIAYFKVHHPLYYYASYftIRA------SDFDLitmikdktsirntVKDmysrymdl 1327
Cdd:PRK05672 726 QIKgfgeYGFPESHAASFAKLVYASSWLKCHHPAAFCAAL--LNSqpmgfySPQQL-------------VQD-------- 782
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1328 gkkekdvltvleimnemAHR-GYRMQPISLEKSQAfEFIIEGDTLIPPFI-----SVPGLGENVAKRIVEARDDGPFLSK 1401
Cdd:PRK05672 783 -----------------ARRhGVEVLPVDVNASGW-DATLEPLPDGGPAVrlglrLVRGLGEEAAERIVAARARGPFTSV 844
|
810 820
....*....|....*....|....*.
gi 586340297 1402 EDLNKKAGLSQKIIEYL---DELGSL 1424
Cdd:PRK05672 845 EDLARRAGLDRRQLEALadaGALRSL 870
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
423-584 |
2.87e-12 |
|
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: 66.93 E-value: 2.87e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKVHNGE--IIDKFERFS---NPHE--RLSETIINLTHIT-DDMLVDAPEIEEVLTEF 494
Cdd:cd06134 8 VVVDVETGGFNPQTDALLEIAAVTLEMDEqgNLYPDETFHfhiLPFEgaNLDPAALEFNGIDpFHPFRFAVDEKEALKEI 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 KEWVGD---------AIFVAHNASFDMGFID-----TGYERLGFGPSTngVIDTLELSRTInteYGKHGLNFLAKKYGVE 560
Cdd:cd06134 88 FKPIRKalkaqgctrAILVGHNAHFDLGFLNaavarCKIKRNPFHPFS--TFDTATLAGLA---YGQTVLAKACQAAGIE 162
|
170 180
....*....|....*....|....*.
gi 586340297 561 L--TQHHRAIYDTEATAYIFIKMVQQ 584
Cdd:cd06134 163 FdnKEAHSALYDTQKTAELFCKIVNR 188
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
336-398 |
4.94e-12 |
|
Polymerase and Histidinol Phosphatase domain; 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. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. 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.
Pssm-ID: 213985 [Multi-domain] Cd Length: 88 Bit Score: 63.21 E-value: 4.94e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 586340297 336 VEFHLHTAMSQMDGIPnIGAYVKQAADWGHPAIAVTDHNVVQAFPDAH--------AAAEKHGIKMIYGME 398
Cdd:cd07309 1 VDLHTHTVFSDGDHAK-LTELVDKAKELGPDALAITDHGNLRGLAEFNtagk*nhiKAAEAAGIKIIIGSE 70
|
|
| HHH_6 |
pfam14579 |
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain. |
1348-1433 |
8.22e-12 |
|
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain.
Pssm-ID: 434050 [Multi-domain] Cd Length: 88 Bit Score: 62.49 E-value: 8.22e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1348 GYRMQPISLEKSQAfEFIIEGDTLIPPFISVPGLGENVAKRIVEARDDGPFLSKEDLNKKAG--LSQKIIEYLDELGSLP 1425
Cdd:pfam14579 1 GIEVLPPDINRSDW-DFTVEGGGIRLGLGAIKGLGEAAAERIVEERENGPFKSLEDFARRVDlkLNKRVLEALIKAGAFD 79
|
....*....
gi 586340297 1426 NL-PDKAQL 1433
Cdd:pfam14579 80 SLgGNRRQL 88
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
772-1418 |
5.19e-11 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 67.41 E-value: 5.19e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 772 TTDEMLNEFHFLGE-EKAHEIVVKNTNELADRIERVVPiKDELYTPRM-----EGANEEIRELSYTNARKLYGEdLP--Q 843
Cdd:PRK07135 173 EENSNFKFFDFEKWfEDIDEKILKRTNYLVENINIEFP-KKEFNLPDFdnnlgLESDLFLKKILKESVINKKAE-LKyyP 250
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 844 IVIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSFVATMTEITEVNPLPphyicpncktseffnd 922
Cdd:PRK07135 251 NVKERINYEYSVIKKLKFSNYFLIIWDFIKWARKNKISIGpGRGSASGSLVSYLLNITSVNPLK---------------- 314
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 923 gsvgsgFDLpdktcetcgaplikegqdiPFETFLGFKGDKVPDIDLNFSGEYQPNAHNYTKVLFGEDKVFRAGTIGTVAE 1002
Cdd:PRK07135 315 ------YDL-------------------LFERFLNPDRITMPDIDIDIQDDRRDEVIDYIFEKYGYEHCATISTFQTLGA 369
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1003 KTAFGYVKGYLN------------------------------------DQGIHKrgaEIDRLVKGCTGVKRTTGQHPGGI 1046
Cdd:PRK07135 370 KSAIRDVGRMLGipesdvnaisklipnnqsleeaydknksffreliskGDPIYK---KLYKIAKKLEGLPRQSGTHAAGI 446
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1047 IVVPDymDIYDFTPIQYPADDQNSAWMTTHF--DFhsihdNVLKLDILGHDDPTMIRMLQDL--------SGIDPKTIPV 1116
Cdd:PRK07135 447 IISNK--PITNYVPTFESKDNYNQVQYSMEFleDF-----GLLKIDLLGLKNLTIIKNIEEKinkellfdHLINFNDLPI 519
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1117 DDKEVMQIFSTpeslGVTEdeilcktGTFGVPEFGtgfVRQMLEDTKPTTFSELVQI-----SGLSHGTDVWLGNAQELI 1191
Cdd:PRK07135 520 IDKKTNNLLSN----GKTE-------GIFQLESPG---MKSTIKKVGIDSFEDIVAIislyrPGPIQYIPIYAKNKKNPK 585
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1192 KTGICD------LSSVIGcrddIMVY---LM-----YAGLEPSMAFKIMESVRKGKgltEEMIETMKE--------NEVP 1249
Cdd:PRK07135 586 NIEKIHpeydeiVAPTYG----IIIYqeqIMqiaqkVAGFSFAQADLLRRAISKKD---ETKLDKIKDkfieggikNGYS 658
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1250 DWYLDSC-LKI----KYMFPKAHAAAYVLMAVRIAYFKVHHPLYYYASyftirasdfdlitMIKDKTSIRNTVKdmysRY 1324
Cdd:PRK07135 659 KKVLEKIySLIekfaDYGFNKSHAVAYATLAYKMAYYKANYPLVFYSA-------------LISNSNGSQENIK----KY 721
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1325 mdlgkkekdvltvleiMNEMAHRGYRMQPISLEKSqAFEFIIEGDTLIPPFISVPGLGENVAKRIVEAR-DDGPFLSKED 1403
Cdd:PRK07135 722 ----------------VKEAKNNGIKVYSPDINFS-TENAVFDNGKIFLPLIMIKGLGSVAIKKIIDERnKNGKYKNFFD 784
|
730
....*....|....*...
gi 586340297 1404 L---NKKAGLSQKIIEYL 1418
Cdd:PRK07135 785 FilrLKFIGISKSIIEKL 802
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
414-578 |
1.59e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 63.02 E-value: 1.59e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 414 DVVLKDATYVVFDVETTGLSNQYDKIIELAAVKVhNGEIIDKFER---FSNPHERLSETIINLTHITDDMLVDAPEIEEV 490
Cdd:PRK09146 41 DTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPF-TLQRIRCRQArhwVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 491 LTEFKEWVGDAIFVAHNASFDMGFIDTGY-ERLGFG---PstngVIDTLELSRTINTEYGKHGLNFLAKK---------- 556
Cdd:PRK09146 120 LDELLEALAGKVVVVHYRRIERDFLDQALrNRIGEGiefP----VIDTMEIEARIQRKQAGGLWNRLKGKkpesirlads 195
|
170 180
....*....|....*....|....*
gi 586340297 557 ---YGVELTQHHRAIYDTEATAYIF 578
Cdd:PRK09146 196 rlrYGLPAYSPHHALTDAIATAELL 220
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
335-398 |
1.52e-09 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 59.15 E-value: 1.52e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586340297 335 RVEFHLHTAMSqmDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME 398
Cdd:COG0613 3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVE 64
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
419-596 |
3.56e-09 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 58.83 E-value: 3.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 419 DATYVVFDVETTGLSNQYDKIIELAAVKVH-NGEIIDKFERFSNPHERLSETIINLTHITDDMLV----DAP----EIEE 489
Cdd:PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDaDGEVVESREWLADPGVEIPEEASAVHGITTEYARahgrPAAevlaEIAD 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 490 VLTEFkeWVGDAIFVAHNASFDMGFIDTGYERLGFGPSTNG-VIDTLELSRTINTeY--GKHGLNFLAKKYGVELTQHHR 566
Cdd:PRK07942 85 ALREA--WARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGpVIDPYVIDKAVDR-YrkGKRTLTALCEHYGVRLDNAHE 161
|
170 180 190
....*....|....*....|....*....|
gi 586340297 567 AIYDTEATAYIFIKMVQQMKELGVLNHNEI 596
Cdd:PRK07942 162 ATADALAAARVAWALARRFPELAALSPAEL 191
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
422-581 |
4.18e-09 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 57.99 E-value: 4.18e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 422 YVVFDVETTGLSNQYDKIIELAAVKVHNGEII--DKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEVLTEFKEWVG 499
Cdd:PRK09145 31 WVALDCETTGLDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIG 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 500 DAIFVAHNASFDMGFIDTGYER-LGFG-PstNGVIDTLEL------SRTINTEYGKHgLNFLAKKYGVELTQHHRAIYDT 571
Cdd:PRK09145 111 NRPLVGYYLEFDVAMLNRYVRPlLGIPlP--NPLIEVSALyydkkeRHLPDAYIDLR-FDAILKHLDLPVLGRHDALNDA 187
|
170
....*....|
gi 586340297 572 EATAYIFIKM 581
Cdd:PRK09145 188 IMAALIFLRL 197
|
|
| HHH_3 |
pfam12836 |
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain. |
1378-1418 |
1.09e-08 |
|
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
Pssm-ID: 463723 [Multi-domain] Cd Length: 62 Bit Score: 52.87 E-value: 1.09e-08
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 586340297 1378 VPGLGENVAKRIVEARDD-GPFLSKEDLNKKAGLSQKIIEYL 1418
Cdd:pfam12836 17 VPGLGPKLAKNIVEYREEnGPFRSREDLLKVKGLGPKTFEQL 58
|
|
| DNA_polA_I_Ecoli_like_exo |
cd06139 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
417-557 |
1.81e-08 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Pssm-ID: 176651 [Multi-domain] Cd Length: 193 Bit Score: 55.99 E-value: 1.81e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDATYVVFDVETTGLSNQYDKIIELAavkvhngeiidkferFS-NPHERLsetIINLTHITDDMLVDapeIEEVLTEFK 495
Cdd:cd06139 2 LEKAKVFAFDTETTSLDPMQAELVGIS---------------FAvEPGEAY---YIPLGHDYGGEQLP---REEVLAALK 60
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 496 EWVGDA--IFVAHNASFDMGFIdtgyERLGFGPstNGVI-DTLELSRTINTEYGKHGLNFLAKKY 557
Cdd:cd06139 61 PLLEDPsiKKVGQNLKFDLHVL----ANHGIEL--RGPAfDTMLASYLLNPGRRRHGLDDLAERY 119
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
423-494 |
2.02e-08 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 58.19 E-value: 2.02e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKV-HNGEIIDKFERFSNPHERLSETiINLTHITDDMLVDAPE-IEEVLTEF 494
Cdd:pfam13361 189 VVFDVETTGLDTTEDEIIQIAAIKLnKKGVVIESFERFLRLKKPVGDS-LQVHGFSDEFLQENGEtPAEALRDF 261
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
336-398 |
5.17e-08 |
|
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. 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. 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: 213987 [Multi-domain] Cd Length: 129 Bit Score: 53.01 E-value: 5.17e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 336 VEFHLHTAMSQmDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME 398
Cdd:cd07432 1 ADLHIHSVFSP-DSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVE 62
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
417-610 |
3.90e-07 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 53.52 E-value: 3.90e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDAT-YVVFDVETTGL---SNQYDKIIELAAVKVHNG--EIIDKFERFSNPHERLSETIINLTHITDDMLVDAPEIEEV 490
Cdd:PRK06722 1 MENAThFIVFDIERNFRpykSEDPSEIVDIGAVKIEAStmKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 491 LTEFKEWVG-DAIFV----------AHNAS--------------FDM-GFIDTGYERL-GFGPSTNGVIDTLelsrtint 543
Cdd:PRK06722 81 IEKFIQFIGeDSIFVtwgkedyrflSHDCTlhsvecpcmekerrIDLqKFVFQAYEELfEHTPSLQSAVEQL-------- 152
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 544 eygkhGLNFLAKKygveltqhHRAIYDTEATAYIFIK------MVQQMKELGVLNHNEiNKKLSnEDAYKRAR 610
Cdd:PRK06722 153 -----GLIWEGKQ--------HRALADAENTANILLKayserdITKRYKRHGELELVK-NGKLT-EKAKKKMR 210
|
|
| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
1377-1416 |
4.71e-07 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 48.32 E-value: 4.71e-07
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 586340297 1377 SVPGLGENVAKRIVEARDD-GPFLSKEDLNKKAGLSQKIIE 1416
Cdd:COG1555 25 TLPGIGPKLAQRIVEYREKnGPFKSVEDLLEVKGIGPKTLE 65
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
336-398 |
5.60e-07 |
|
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). 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 give 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 the 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: 213993 [Multi-domain] Cd Length: 155 Bit Score: 50.85 E-value: 5.60e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 336 VEFHLHTAMSqmDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME 398
Cdd:cd07438 1 IDLHTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVE 61
|
|
| PHP_PolIIIA_DnaE2 |
cd07434 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
356-414 |
9.39e-07 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity.
Pssm-ID: 213989 [Multi-domain] Cd Length: 260 Bit Score: 52.07 E-value: 9.39e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 586340297 356 YVKQAADWGHPAIAVTDHN----VVQAfpdaHAAAEKHGIKMIYGMEGMLVDDGVPIAYkPQD 414
Cdd:cd07434 22 LVARAAELGYRALAITDECslagVVRA----HAAAKELGLKLIVGSELVLADGTRLVLL-ARD 79
|
|
| dnaE |
PRK05898 |
DNA polymerase III subunit alpha; |
818-1137 |
1.13e-06 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 135648 [Multi-domain] Cd Length: 971 Bit Score: 53.31 E-value: 1.13e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 818 MEGANEEIRELSyTNARKLYgedlpqivIDRLEKELKSIIGNGFAVIYLISQRLVKKSLDDGYLVG-SRGSVGSSFVATM 896
Cdd:PRK05898 236 ISGLNKRLNAND-GQVKKIY--------VKRLKYELDIINEKQFDDYFLIVYDFINFAKSNGIIIGpGRGSAAGSLIAYL 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 897 TEITEVNPLPPHYIcpncktseffndgsvgsgfdlpdktcetcgaplikegqdipFETFLGFKGDKVPDIDLNFSGEYQP 976
Cdd:PRK05898 307 LHITDIDPIKYNLI-----------------------------------------FERFLNPTRKSMPDIDTDIMDERRD 345
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 977 NAHNYTKVLFGEDKVFRAGTIGTVAEKTAFGYVKGYLN---------------------DQGIHKRGA---------EID 1026
Cdd:PRK05898 346 EVVEYLFEKYGNDHVAHIITFQRIKAKMAIRDVGRILGidlkvidkicknikpdyeedlDLAIKKNTIlkemyvlhkELF 425
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 1027 RLVKGCTGVKRTTGQHPGGIIVVPDYmdIYDFTPIQYPADDQnsawMTTHFDFHSIHD-NVLKLDILGHDDPT------- 1098
Cdd:PRK05898 426 DLAKKIINAPRQIGTHAAGVVLSNSL--LTNIIPIQLGINDR----PLSQYSMEYLERfGLIKMDLLGLKNLTiidnvlk 499
|
330 340 350
....*....|....*....|....*....|....*....
gi 586340297 1099 MIRMLQDLSgIDPKTIPVDDKEVMQIFSTPESLGVTEDE 1137
Cdd:PRK05898 500 LIKENQNKK-IDLFNINLNDKNVFEDLAKGRTNGIFQLE 537
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
240-322 |
1.18e-05 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 44.53 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 240 VAIEGVIFDINlkelKSGRHIVEIKVTDYTDSLVLKMFtrkNKDDLEHFKALSVGKWVRAQGRIEEDTFiRDLVMMMSDI 319
Cdd:pfam01336 1 VTVAGRVTSIR----RSGGKLLFLTLRDGTGSIQVVVF---KEEAEKLAKKLKEGDVVRVTGKVKKRKG-GELELVVEEI 72
|
...
gi 586340297 320 EEI 322
Cdd:pfam01336 73 ELL 75
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
337-407 |
2.16e-05 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 49.08 E-value: 2.16e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586340297 337 EFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGME---GMLVDDGVP 407
Cdd:PRK05672 7 ELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAElslGPDPDPGGP 80
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
423-574 |
3.64e-05 |
|
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing 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 ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 46.10 E-value: 3.64e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 423 VVFDVETTGLSNQYDKIIELAAVKV-HNGEIIDKFERFS--NPHERLSETIINLTHITDDMLVDAPEIE-EVLTEFKEWV 498
Cdd:cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTdENFNEIEPFNIFCrlPPDVLPSPEALIVTGITPQQLLKEGLSEyEFIAKIHRLF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 499 G--DAIFVAHNA-SFDMGFIDTGYERLGFGPST------NGVIDTLELSR--------TINTEYGKHG-----LNFLAKK 556
Cdd:cd06138 81 NtpGTCIVGYNNiRFDDEFLRFAFYRNLYDPYTwewkngNSRWDLLDVVRayyalrpdGIVWPKNDDGkpsfkLEDLAQA 160
|
170
....*....|....*...
gi 586340297 557 YGVELTQHHRAIYDTEAT 574
Cdd:cd06138 161 NGIEHSNAHDALSDVEAT 178
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
227-337 |
8.30e-05 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 46.97 E-value: 8.30e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 227 IKPIESIIEEEfKVAIEGVIFDINLKELKSGRHIVEIKVTDYTDSLVLKMFtrkNKDDLEhfKALSVGKWVRAQGRIEEd 306
Cdd:COG1200 47 LTPIAELRPGE-TVTVEGTVVSVEVVRRRRRRRILEVTLSDGTGSLTLVFF---NQPYLK--KQLKPGTRVLVSGKVER- 119
|
90 100 110
....*....|....*....|....*....|.
gi 586340297 307 tFIRDLVMMMSDIEeikKATKKDKAEEKRVE 337
Cdd:COG1200 120 -FRGGLQMVHPEYE---LLDEEEAELAGRLT 146
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
336-410 |
5.14e-04 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes.
Pssm-ID: 213988 [Multi-domain] Cd Length: 277 Bit Score: 43.62 E-value: 5.14e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 336 VEFHLHTAMSQMDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAAAEKHGIKMIYGMEGMLVDDGVPIAY 410
Cdd:cd07433 3 VHLRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSNLFGAVKFYKAASKAGIKPIIGADLNVANPDDADEP 77
|
|
| CehA_McbA_metalo |
NF038032 |
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
335-398 |
5.84e-04 |
|
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.
Pssm-ID: 468321 [Multi-domain] Cd Length: 315 Bit Score: 43.85 E-value: 5.84e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586340297 335 RVEFHLHTAMSqmDGIPNIGAYVKQAADWGHPAIAVTDHNVVQAFPDAHAA-AEKHGIKMIYGME 398
Cdd:NF038032 4 SGDLHIHTNHS--DGPTTPEELARAALAEGLDVIALTDHNTISGRAYFAELlASERGLLVIPGME 66
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
417-586 |
1.93e-03 |
|
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
Pssm-ID: 396266 [Multi-domain] Cd Length: 173 Bit Score: 40.75 E-value: 1.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 417 LKDATYVVFDVETTGL-SNQYDKIIELAAVKVHNGE-IIDKFERFSNPHERLSETIINLTHItddmlvdapeieevltef 494
Cdd:pfam01612 17 LLNAPYVAVDTETTSLdTYSYYLRGALIQIGTGEGAyIIDPLALGDDVLSALKRLLEDPNIT------------------ 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 495 keWVGdaifvaHNASFDMGFIDTGyerlgFGPSTNGVIDTlELSRTINTEYGKHGLNFLAKKY-GVELTQHHR------- 566
Cdd:pfam01612 79 --KVG------HNAKFDLEVLARD-----FGIKLRNLFDT-MLAAYLLGYDRSHSLADLAEKYlGVELDKEEQcsdwqar 144
|
170 180
....*....|....*....|....*....
gi 586340297 567 ---------AIYDTEATAYIFIKMVQQMK 586
Cdd:pfam01612 145 plseeqlryAALDADYLLRLYDKLRKELE 173
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
420-578 |
2.06e-03 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 42.35 E-value: 2.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 420 ATYVVFDVETTGLSNQYDKIIELA-AVKvhNGEIIDkferfsnpherlsetiINLTHITDDMLvdapEIEEVLTEFKEWV 498
Cdd:COG0749 1 AGLVAFDTETTSLDPMDAELVGISfAVE--PGEAAY----------------IPLAHGAPEQL----DLDEVLAALKPLL 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 499 GDA--IFVAHNASFDMGFIdtgyERLGFGPstNGVI-DTLELSRTINTEYGKHGLNFLAKKYGVELTQHHRAIYDTEATA 575
Cdd:COG0749 59 EDPaiPKIGQNLKYDLHVL----ARYGIEL--AGVAfDTMLASYLLNPGRRRHGLDDLAERYLGHETISYEELAGKGKKQ 132
|
...
gi 586340297 576 YIF 578
Cdd:COG0749 133 LTF 135
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
610-711 |
4.87e-03 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. 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. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such activity has not been found. It has been shown that the PHP domain of PolIIIA has a trinuclear metal complex and is capable of proofreading activity.
Pssm-ID: 213986 [Multi-domain] Cd Length: 179 Bit Score: 39.49 E-value: 4.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586340297 610 RPSHVTLIVQNQQGLKNLFKIVSAS-LVKYFYRTPRIPRSLLDEYREGLLVGTACDEGELFTavmqkDQSQVEKIA---- 684
Cdd:cd07431 71 EPYPLLLLAKNNEGYQNLLRLSTAAmLGEEKDGVPYLDLEELAEAASGLLVVLLGPLLLLLA-----AEQGLPLVAtndv 145
|
90 100 110
....*....|....*....|....*....|
gi 586340297 685 KY---YDFieiqppALYQDLIDRELIRDTE 711
Cdd:cd07431 146 HYlnpEDA------FAADVLTAFLAVANTV 169
|
|
| |
