|
Name |
Accession |
Description |
Interval |
E-value |
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
2-1448 |
0e+00 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 2598.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 2 SEKRELFEKLLEQIQLEEaDKQHPLISSGEVERVVVHRKSRLWEFTLHFSQILPIMLYRSLVQHVTLAFHDIA--QVKLN 79
Cdd:PRK00448 1 NEMQEKFKKLLDQINIPD-DLQSEALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFSHIAdiKVTFS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 80 IKAENQQFDEQLLQDYWAQALESQQCDTPLAQQVLKTQVPILKEHKIILPVDSTGALSYLKQQYLPLVESLFVSYGFPKF 159
Cdd:PRK00448 80 IEVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGIL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 160 RIEPEVDEQQAErvLKLFEERKQEQAEAFMKQAAESLIVHEQKKKEKKEQLPALDGPIQLGRNIPTDEPTtPMVNIVEEE 239
Cdd:PRK00448 160 KIDFEIDDSKEE--LEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEIT-PMKEINEEE 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 240 RRVTLEGYVFDKEVRELRSKRKILTLKITDYTSSFIVKKFSNNEKDEQIFEAISTGSWLKVRGSIQEDTFVRDLVMNAQD 319
Cdd:PRK00448 237 RRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQD 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 320 IVEVKHAPRKDYAPEgEKRVELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYG 399
Cdd:PRK00448 317 INEIKHPERKDTAEE-EKRVELHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYG 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 400 VEANVVDDGVPIAYNDVHESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGI 479
Cdd:PRK00448 396 VEANLVDDGVPIVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGI 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 480 TDEMVRGSKSEEEVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKK 559
Cdd:PRK00448 476 TDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 560 FGVSLEQHHRAIYDAEATGHLAWIFIKEAMENhDMFYHDQLNAHIGEGDSYKRARPFHATLLAKNQDGLKDLFKLISMSN 639
Cdd:PRK00448 556 FGVELEHHHRADYDAEATAYLLIKFLKDLKEK-GITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSN 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 640 VEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARNRAKFYDYIEVMPKAVYAPLLEQELVKNERDLEE 719
Cdd:PRK00448 635 TKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKE 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 720 IIQNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKILINSMGGANPLNRHSLPDVHFRTTDEMLTAFNFLGESLAKEIVVE 799
Cdd:PRK00448 715 IIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRKILVASQGGGNPLNRHPLPELHFRTTDEMLDEFAFLGEELAKEIVVE 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 800 NTNKIADSCEEVIPVKDELYTPKIPGSEEEISELSYTKAKQLYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHK 879
Cdd:PRK00448 795 NTNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIYGEPLPEIVEKRIEKELNSIIGNGFAVIYLISQKLVKK 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 880 SNEDGYLVGSRGSVGSSFVATMTGITEVNPLAPHYYCPECQYSEFYEDGTYGSGFDMPEKKCPKCGARLNKDGHDIPFET 959
Cdd:PRK00448 875 SLEDGYLVGSRGSVGSSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDGHDIPFET 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 960 FLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEEYVYRAGTIGTVADKTAYGFVKGYERDHNLQFRSAEVDRLAKGATG 1039
Cdd:PRK00448 955 FLGFKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTAYGYVKKYEEDTGKFYRNAEIDRLAQGCTG 1034
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1040 VKRTTGQHPGGIIVIPDYMDVYDFTPIQFPADDQNSEWKTTHFDFHSIHDNVLKLDILGHDDPTVIRMLQDLSGIDPQTI 1119
Cdd:PRK00448 1035 VKRTTGQHPGGIIVVPKYMDIYDFTPIQYPADDVNSEWKTTHFDFHSIHDNLLKLDILGHDDPTMIRMLQDLTGIDPKTI 1114
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1120 PTDDPEVMRIFAGPEVLNVTQEQINSKTGTLGIPEFGTRFVRGMLEETHPTTFAELLQISGLSHGTDVWLGNAEELIKRG 1199
Cdd:PRK00448 1115 PMDDPKVMKLFSSTEALGVTPEQIGCETGTLGIPEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNAQELIKEG 1194
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1200 DATLAEVIGCRDDIMVYLIHAGLDSGMAFKIMETVRKGLwnkipdELRETYLNAMKENNVPDWYIDSCSKIKYMFPKAHA 1279
Cdd:PRK00448 1195 IATLSDVIGCRDDIMVYLIHKGLEPKLAFKIMESVRKGK------GLTEEEEELMKENNVPDWYIESCKKIKYMFPKAHA 1268
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1280 AAYVLMALRVAYFKVYFPILYYCAYFSVRADDFDLVSMCKGKDAVKQAMKEITDKGMDASVKEKNQLTVLELANEMLERG 1359
Cdd:PRK00448 1269 AAYVLMAWRIAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEIKSKGNDASNKEKDLLTVLEIALEMLERG 1348
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1360 FKFGMIDLYKSDAVNFVIEGDILIAPFRAVPSLGTNVAKQIVEARKDGPFLSKEDLATRGKVSKTLIEYMNDNGVLKDLP 1439
Cdd:PRK00448 1349 FKFQKVDLYKSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIEKLDELGVLDDLP 1428
|
....*....
gi 921163465 1440 DENQLSLFD 1448
Cdd:PRK00448 1429 ETNQLSLFD 1437
|
|
| polC_Gram_pos |
TIGR01405 |
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain ... |
235-1447 |
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: 1941.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 235 IVEEERRVTLEGYVFDKEVRELRSKRKILTLKITDYTSSFIVKKFSNNEKDEQIFEAISTGSWLKVRGSIQEDTFVRDLV 314
Cdd:TIGR01405 3 INEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRDLQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 315 MNAQDIVEVKHAPRKDYAPEgeKRVELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGV 394
Cdd:TIGR01405 83 MIIKDIEEIPYAERKDNAKE--KRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 395 KILYGVEANVVDDGVPIAYNDVHESL-SEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTT 473
Cdd:TIGR01405 161 KIIYGMEANLVDDRVPIVYNPDDQKLlDDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 474 VDLTGITDEMVRGSKSEEEVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGL 553
Cdd:TIGR01405 241 TELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 554 GVLSKKFGVSLEQHHRAIYDAEATGHLAWIFIKEaMENHDMFYHDQLNAHIGEGDSYKRARPFHATLLAKNQDGLKDLFK 633
Cdd:TIGR01405 321 GNICKKLGVDLDDHHRADYDAEATAKVFKVMVEQ-LKEKGITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 634 LISMSNVEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARNRAKFYDYIEVMPKAVYAPLLEQELVKN 713
Cdd:TIGR01405 400 LVSISLTKYFYTRPRILRSLLKKYREGLLIGSACSEGELFDALLSKPDDELEEIAKRYDFIEIQPPGNYAHLIEREQVKD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 714 ERDLEEIIQNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKILINSMGGANPLNRHSL----PDVHFRTTDEMLTAFNFLG 789
Cdd:TIGR01405 480 KEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYRKILVASQGLGNPLNRHFNpkevPELHFRTTNEMLDEFSFLG 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 790 ESLAKEIVVENTNKIADSCEEVIPVKDELYTPKIPGSEEEISELSYTKAKQLYGDPLPEIIQKRLEKELNSINGNGFSVI 869
Cdd:TIGR01405 560 EEKAYEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIYGDPLPEIVEQRIEKELKSIIGNGFAVI 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 870 YLIAQKLVHKSNEDGYLVGSRGSVGSSFVATMTGITEVNPLAPHYYCPECQYSEFYEDGTYGSGFDMPEKKCPKCGARLN 949
Cdd:TIGR01405 640 YLISQLLVQKSLQDGYLVGSRGSVGSSLVATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 950 KDGHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEEYVYRAGTIGTVADKTAYGFVKGYERDHNLQFRSAE 1029
Cdd:TIGR01405 720 KDGQDIPFETFLGFKGDKVPDIDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAYGYVKKYFEDQGKHYRDAE 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1030 VDRLAKGATGVKRTTGQHPGGIIVIPDYMDVYDFTPIQFPADDQNSEWKTTHFDFHSIHDNVLKLDILGHDDPTVIRMLQ 1109
Cdd:TIGR01405 800 IERLVQGCTGVKRTTGQHPGGIIIVPKYMDVYDFTPVQYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHDDPTMIKMLQ 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1110 DLSGIDPQTIPTDDPEVMRIFAGPEVLNVTQEQINSKTGTLGIPEFGTRFVRGMLEETHPTTFAELLQISGLSHGTDVWL 1189
Cdd:TIGR01405 880 DLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFGTKFVRGMLEETKPKTFADLVRISGLSHGTDVWL 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1190 GNAEELIKRGDATLAEVIGCRDDIMVYLIHAGLDSGMAFKIMETVRKGLWnkipdeLRETYLNAMKENNVPDWYIDSCSK 1269
Cdd:TIGR01405 960 GNAQDLIKSGIKTLSDVIGCRDDIMVYLIHKGLEPKLAFKIMEKVRKGKG------LKAEYIELMKENKVPEWYIESCLK 1033
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1270 IKYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAYFSVRADDFDLVSMCKGKDAVKQAMKEITDKG--MDASVKEKNQLT 1347
Cdd:TIGR01405 1034 IKYMFPKAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKAFDLETMIKGKEFIKQKLEEINTRRkiNKASPKEKDLLT 1113
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1348 VLELANEMLERGFKFGMIDLYKSDAVNFVIEGDILIAPFRAVPSLGTNVAKQIVEARKDGPFLSKEDLATRGKVSKTLIE 1427
Cdd:TIGR01405 1114 VLEIVLEMMARGFKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTKISKTHIE 1193
|
1210 1220
....*....|....*....|
gi 921163465 1428 YMNDNGVLKDLPDENQLSLF 1447
Cdd:TIGR01405 1194 KLDSMGVLDNLPETNQLSLF 1213
|
|
| PHP_PolIIIA_POLC |
cd07435 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
338-813 |
4.57e-113 |
|
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: 356.78 E-value: 4.57e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 338 RVELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEahsagkkagvkilygveanvvddgvpiayndvh 417
Cdd:cd07435 1 RVELHAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPE--------------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 418 eslsegtyvvfdvettglsavydtiielaavkmykgnviasfdefidpghplsrttvdltgitdemvrgskseeevlrlf 497
Cdd:cd07435 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 498 lefskdtilvAHNAAfdmgflntsyAKYGIpeapnpvidtlelarylypqfkrfglgvlskkfgvsleqhhRAIYDAEat 577
Cdd:cd07435 48 ----------AYEAA----------KKNGI-----------------------------------------KVIYGVE-- 64
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 578 ghlawifikeamenhdMFYHDqlnahigegdsykrarPFHATLLAKNQDGLKDLFKLISMSNVEYFERVPRIPRSQLNKL 657
Cdd:cd07435 65 ----------------AYLVD----------------PYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKY 112
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 658 RDNLLIGSACDKGEIFEAMMQKG-VEEARNRAKFYDYIEVMPKAVYAPLLEQELVKNERDLEEIIQNLVEIGKSLDKIVV 736
Cdd:cd07435 113 REGLLIGSACENGELFEAALNKKsDEELEEIASFYDYIEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVV 192
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 737 ATGNVHYLNEEDAIYRKILINSMGGANPlNRHSLPDVHFRTTDEMLTAFNFLGESLAKEIVVENTNKIADSCEEVIP 813
Cdd:cd07435 193 ATGDVHYLDPEDKIYREILLAGQGGGDG-RADEQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIEDIKP 268
|
|
| DNA_pol3_alpha |
pfam07733 |
Bacterial DNA polymerase III alpha NTPase domain; |
828-1098 |
3.60e-77 |
|
Bacterial DNA polymerase III alpha NTPase domain;
Pssm-ID: 400196 [Multi-domain] Cd Length: 259 Bit Score: 256.28 E-value: 3.60e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 828 EEISELSYTKAKQLYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVGS-RGSVGSSFVATMTGITE 906
Cdd:pfam07733 1 EYLRKLVEEGLKERYGEGLPEEYQERLEYELNVIIKMGFAGYFLIVWDLVKWAKDNGILVGPgRGSAAGSLVAYLLGITE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 907 VNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNY 986
Cdd:pfam07733 81 VDPLK-----------------------------------------HDLLFERFLNPERVSMPDIDIDFEDERREEVIDY 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 987 TKVLFGEEYVYRAGTIGTVADKTA-------YGFV-------------------KGYERD---HNLQFRSAEVDRL---A 1034
Cdd:pfam07733 120 VKEKYGRDRVAQIATFGTYAAKSAirdvgraLGLPydeidrlaklipfelgileKALEEEpelKELIESDPEVKRLielA 199
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 921163465 1035 KGATGVKRTTGQHPGGIIVIPDymDVYDFTPIQFPADDQNsewKTTHFDFHSIHD-NVLKLDILG 1098
Cdd:pfam07733 200 KKLEGLPRHTGQHAGGVVISPD--PLTDFVPLYKADDDDR---PVTQFDKDDLEDlGLLKMDFLG 259
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
417-590 |
4.41e-77 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 252.76 E-value: 4.41e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 417 HESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRL 496
Cdd:COG2176 2 SLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 497 FLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPeAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEA 576
Cdd:COG2176 82 FLEFLGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEA 160
|
170
....*....|....
gi 921163465 577 TGHLAWIFIKEAME 590
Cdd:COG2176 161 TAELFLKLLEKLEE 174
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
612-1427 |
1.97e-61 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 229.96 E-value: 1.97e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 612 RARPFHATLLAKNQDGLKDLFKLISMSNVE-YFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARNRAKF 690
Cdd:COG0587 77 DDAGYHLVLLAKNREGYRNLCRLLSRAYLEgFYKGKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALAR 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 691 YdyIEVMPKAVYAplleqELVKNERDLEE-IIQNLVEIGKSLDKIVVATGNVHYLNEED--------AIYRKILINSMGG 761
Cdd:COG0587 157 L--KDIFGDRFYL-----ELQRHGLPEDRrVNAALLELARELGLPLVATNDVHYLNPEDaeahdvllCIRTGKTLDDPGR 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 762 ANPLNrhslPDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEVIPVKDELYtPK--IPGSEEEIS---ELSYT 836
Cdd:COG0587 230 RRFAN----AERYLKSPEEMAELFADLPEAL------ANTLEIAERCNFSLDLGKYQL-PKfpVPEGETEEEylrKLAEE 298
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 837 KAKQLYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVH--KSNedGYLVGS-RGSVGSSFVATMTGITEVNPLAph 913
Cdd:COG0587 299 GLERRYPEGIPEEYRERLEYELDVIEKMGFPGYFLIVWDFIRwaRSN--GIPVGPgRGSAAGSLVAYALGITDVDPIR-- 374
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 914 yycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLgfHGDKV--PDIDLNFSGDYQAEAHNYTKVLF 991
Cdd:COG0587 375 ---------------------------------------YDLLFERFL--NPERVsmPDIDIDFCHERREEVIQYVYEKY 413
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 992 GEEYVYRAGTIGTVADKTA-----------YGFV----KGYERDHNLQFRSA---------------EVDRL---AKGAT 1038
Cdd:COG0587 414 GRDRVAQIATFGTMRARAAirdvgrvlglpYGEVdrlaKLIPNDPGITLEKAleeepelrelydsdpEVRRLldlARKLE 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1039 GVKRTTGQHPGGIIVIPDymDVYDFTPIQFPADDQNSewkTTHFDFHSIhDNV--LKLDILGhddpTVIR----MLQDLS 1112
Cdd:COG0587 494 GLPRHLSTHAGGVVISDD--PLTDLVPLERAAMGGRP---VTQFDKDDV-EALglLKFDFLGlrtlTVIRdaldLIKENR 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1113 G--IDPQTIPTDDPEVMRIFagpevlnvtqeqinSKTGTLGIpefgtrF------VRGMLEETHPTTFAEL--------- 1175
Cdd:COG0587 568 GidIDLADIPLDDPKTYELL--------------QRGDTIGV------FqlesrgMRSLLKRLKPDCFEDLvalvalyrp 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1176 --LQiSGL-------SHGtdvwlgnaEELIKRGDATLAEVI----GcrddIMVY------LIH--AGLDSG--------M 1226
Cdd:COG0587 628 gpMQ-GGMvppyirrKHG--------REPVEYPHPELEPILketyG----VIVYqeqvmqIAQvlAGFSLGeadllrraM 694
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1227 AFKIMETVrkglwnkipDELRETYLNAMKENNVPDWYIDSC-SKIK----YMFPKAHAAAYVLMALRVAYFKVYFPILYY 1301
Cdd:COG0587 695 GKKKKEEM---------AKQREKFVEGAVANGYDEEFAEEIfDQIEkfagYGFNKSHAAAYALLAYQTAYLKAHYPAEFM 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1302 CAYFSVRADDFdlvsmckgkDAVKQAMKEITDKGmdasvkeknqLTVLElanemlergfkfgmIDLYKSDAvNFVIE--G 1379
Cdd:COG0587 766 AALLNSQPMGF---------YKPAQYVQEARRHG----------IEVLP--------------PDVNESDW-DFTVEpgG 811
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|..
gi 921163465 1380 DILIApFRAVPSLGTNVAKQIVEARK-DGPFLSKEDLATR---GKVSKTLIE 1427
Cdd:COG0587 812 AIRLG-LGAIKGVGEAAAEAIVAAREeNGPFTSLFDFCRRvdlRKLNKRVLE 862
|
|
| polc |
TIGR00594 |
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
611-1450 |
6.83e-60 |
|
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: 224.95 E-value: 6.83e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 611 KRARPFHATLLAKNQDGLKDLFKLISMSNVEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARNRAKF 690
Cdd:TIGR00594 80 KGKEAYHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALK 159
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 691 YD-------YIEVMPKAvyapLLEQELVkNErdleeiiqNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKILINSMGGAN 763
Cdd:TIGR00594 160 YQeifgddyYLELQDHG----IPEQRVV-NE--------ALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKT 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 764 ----PLNRHSLPDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEvipVKDELYTPKIPG---------SEEEI 830
Cdd:TIGR00594 227 lsdpKRLKFYSDEFYLKSPEEMAELFADIPEAL------ANTVEIAERCNL---VDVKLGPPRLPSyqippdftsQEDYL 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 831 SELSYTKAKQLYGDPLPEI-----IQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATMTGI 904
Cdd:TIGR00594 298 RHLADEGLRERLAAGPPGYkrraqYKERLEYELDVINSMGFPGYFLIVWDFIKWAKDHGIPVGpGRGSAAGSLVAYALKI 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 905 TEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAH 984
Cdd:TIGR00594 378 TDIDPIK-----------------------------------------HGLLFERFLNPERISMPDIDIDFCDERRDEVI 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 985 NYTKVLFGEEYVYRAGTIGTVADKTA-----------YGFV-------------KGYE-RDHNLQFRS--------AEVD 1031
Cdd:TIGR00594 417 EYVADKYGHDNVAQIITFGTMKAKAAlrdvarvldipYAEAdriaklipprpgkTLKEaLEASPQLRQlyeedpevKQLI 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1032 RLAKGATGVKRTTGQHPGGIIVIPDYMDvyDFTPIQFPADDQNSewkTTHFDFHSIHD-NVLKLDILGHDDPTVIRMLQD 1110
Cdd:TIGR00594 497 DMARKLEGLNRNAGVHAAGVVISSEPLT--DYVPLYKDKEGGAI---STQYDMDDLEAvGLLKMDFLGLKTLTLIQDATE 571
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1111 L------SGIDPQTIPTDDPEVMRIFagpevlnvtqeqinSKTGTLGIPEFGTRFVRGMLEETHPTTFAELLQISGL--- 1181
Cdd:TIGR00594 572 LirkrrgIDLDIASIPLDDKKTFSLL--------------QEGDTTGVFQLESRGMQDLLKRLKPDGFEDIIAVNALyrp 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1182 ----SHGTDVWLG--NAEELIKRGDATLAEVIGCRDDIMVY----LIHAGLDSGMAFKIMETVRKGLWNKIPDEL---RE 1248
Cdd:TIGR00594 638 gpmeSGMIPDFIDrkHGREPIEYPHPLLEPILKETYGVIVYqeqvMQIAQRLAGFSLGEADLLRRAMGKKKAEEMakeRE 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1249 TYLNAMKENNVPDwyiDSCSKI--------KYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAYFSVRADDfdlvsmckg 1320
Cdd:TIGR00594 718 KFVEGAEKNGYDP---EIAENLfdliekfaGYGFNKSHAAAYGMISYQTAYLKANYPAEFMAALLTSEIND--------- 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1321 KDAVKQAMKEItdKGMdasvkeknqltvlelanemlerGFKFGMIDLYKSDaVNFVIEGDILIAPFRAVPSLGTNVAKQI 1400
Cdd:TIGR00594 786 IEKVAVYIAEA--KKM----------------------GIEVLPPDINESG-QDFAVEDKGIRYGLGAIKGVGESVVKSI 840
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 921163465 1401 VEARKD-GPFLSKEDLATR---GKVSKTLIEYMNDNGVLkDLPDENQLSLFDML 1450
Cdd:TIGR00594 841 IEERNKnGPFKSLFDFINRvdfKKLNKKVLEALIKAGAF-DSLGPNRKTLLASL 893
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
425-580 |
7.45e-57 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 193.86 E-value: 7.45e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKDT 504
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 921163465 505 ILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEATGHL 580
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAEL 157
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
426-580 |
7.69e-56 |
|
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: 190.97 E-value: 7.69e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAVKMYKG-NVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKDT 504
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 505 ILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVL-SKKFGVSLEQHHRAIYDAEATGHL 580
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAEL 157
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
412-577 |
6.33e-48 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 181.27 E-value: 6.33e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 412 AYNDVHESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEE 491
Cdd:PRK07883 4 SFDDLGTPLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 492 EVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYP--QFKRFGLGVLSKKFGVSLEQHHR 569
Cdd:PRK07883 84 EVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTPTHR 163
|
....*...
gi 921163465 570 AIYDAEAT 577
Cdd:PRK07883 164 ALDDARAT 171
|
|
| dnaE |
PRK06826 |
DNA polymerase III DnaE; Reviewed |
614-1427 |
3.48e-45 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 178.93 E-value: 3.48e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 614 RPFHATLLAKNQDGLKDLFKLISMSNVEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARNRAKFYD- 692
Cdd:PRK06826 86 ETYHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKd 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 693 -------YIEVMpkavYAPLLEQELVKNErdleeiiqnLVEIGKSLDKIVVATGNVHYLNEEDAIYRKIL--INSMGGAN 763
Cdd:PRK06826 166 ifgkenfYLELQ----DHGIPEQRKVNEE---------LIKLSKELGIPLVATNDVHYIRKEDAKAHDVLlcIQTGKTVD 232
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 764 PLNRHSLP--DVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEVIPVkDELYTPKIP-----GSEEEISELSYT 836
Cdd:PRK06826 233 DENRMRFPsdEFYLKSPEEMYELFSYVPEAL------ENTVKIAERCNVEFEF-GKSKLPKFPlpegyDPYEYLRELCYE 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 837 KAKQLYGDPLPEIIQkRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATMTGITEVNPLaphyy 915
Cdd:PRK06826 306 GLKKRYPNPSEELIE-RLEYELSVIKQMGYVDYFLIVWDFIRFARENGIMVGpGRGSAAGSLVAYTLGITKIDPI----- 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 916 cpecQYsefyedgtygsgfdmpekkcpkcgarlnkdghDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEEY 995
Cdd:PRK06826 380 ----KY--------------------------------NLLFERFLNPERVSMPDIDIDFCYERRQEVIDYVVEKYGKDR 423
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 996 VYRAGTIGTVADKTAYgfvkgyeRD--HNLQFRSAEVDRLAK------GAT----------------------------- 1038
Cdd:PRK06826 424 VAQIITFGTMAARAAI-------RDvgRALNYPYAEVDRIAKmiptelGITidkalelnpelkeayendervrelidtar 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1039 ---GVKRTTGQHPGGIIVIPDYMDVYdfTPIQfpaddQNSEWKTTHFDFHSIHD-NVLKLDILGHDDPTVIR----MLQD 1110
Cdd:PRK06826 497 aleGLPRHASTHAAGVVISSEPLVEY--VPLQ-----KNDGSIVTQFTMTTLEElGLLKMDFLGLRTLTVIRdavdLIKK 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1111 LSG--IDPQTIPTDDPEVMRIFagpevlnvtqeqinSKTGTLGIPEFGTRFVRGMLEETHPTTFAELlqISGLSHGTDVW 1188
Cdd:PRK06826 570 NRGieIDLDKIDYDDKKVYKMI--------------GEGKTVGVFQLESAGMRSFMKELKPDSLEDI--IAGISLYRPGP 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1189 LGNAEELIKRG-------------DATLAEVIGCrddiMVY----------LihAGLDSGMAfkimETVRKGLWNKIPD- 1244
Cdd:PRK06826 634 MDSIPRYIKNKnnpekieylhpklEPILKVTYGC----IVYqeqvmqivrdL--AGYSMGRS----DLVRRAMSKKKHDv 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1245 --ELRETYLNAMKENNVPDWY---ID--SCSKI--------KYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAyfsvra 1309
Cdd:PRK06826 704 meEERKNFIYGIVDEGGPGCIrngIDeeTANKIfdsmmdfaSYAFNKSHAAAYAVVAYQTAYLKRYYPVEFMAA------ 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1310 ddfdlvsmckgkdavkqamkeitdkgMDASVKEkNQLTVLELANEMLERGFKFGMIDLYKSDAvNFVIEGDILIAPFRAV 1389
Cdd:PRK06826 778 --------------------------LLNSVMG-NSDKVAFYIEECRRLGIEVLPPDINESYS-KFTVEGDKIRFGLAAV 829
|
890 900 910 920
....*....|....*....|....*....|....*....|..
gi 921163465 1390 PSLGTNVAKQIVEAR-KDGPFLSKEDLATR---GKVSKTLIE 1427
Cdd:PRK06826 830 KNVGENAIDSIVEEReKKGKFKSLVDFCERvdtSQINKRAVE 871
|
|
| DNA_pol3_finger |
pfam17657 |
Bacterial DNA polymerase III alpha subunit finger domain; |
1101-1258 |
2.36e-44 |
|
Bacterial DNA polymerase III alpha subunit finger domain;
Pssm-ID: 407553 [Multi-domain] Cd Length: 166 Bit Score: 158.47 E-value: 2.36e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1101 DPTVIRMLQDLS------GIDPQTIPTDDPEVMRIFAGPEvlnvtqeqinsktgTLGIPEFGTRFVRGMLEETHPTTFAE 1174
Cdd:pfam17657 1 TLTIIRDALDLIkenrgiGIDLATIPLDDPKTYKLLSSGD--------------TLGVFQFESRGMRQMLKRLKPDTFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1175 LLQISGLSHGTDVWLGNAEELIKR---------GDATLAEVIGCRDDIMVY--------LIHAGLDSGMAFKIMETVRKG 1237
Cdd:pfam17657 67 LVALSALYRPGPMQGGNVDDYIKRkhgkekieyPHPDLEPILKETYGVIVYqeqvmqiaQILAGFSLGEADLLRRAMGKK 146
|
170 180
....*....|....*....|.
gi 921163465 1238 lWNKIPDELRETYLNAMKENN 1258
Cdd:pfam17657 147 -KPEEMEKLREKFIEGAKENG 166
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
424-577 |
5.07e-43 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 154.77 E-value: 5.07e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 424 TYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKD 503
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 504 TILVAHN-AAFDMGFLNTSYAKYGIPEAP-NPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQ-HHRAIYDAEAT 577
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGIKQPPkLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARAT 157
|
|
| dnaE |
PRK05673 |
DNA polymerase III subunit alpha; Validated |
605-1427 |
1.14e-41 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 167.59 E-value: 1.14e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 605 GEGDSYKRARPFHATLLAKNQDGLKDLFKLISMSNVE-YFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEE 683
Cdd:PRK05673 72 KKDDVSGGGAYTHLTLLAKNETGYRNLFKLSSRAYLEgQYGYKPRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQYDE 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 684 ARNRAKFY-----D--YIEVMpkavyaplleqelvKNERDLEEII-QNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKIL 755
Cdd:PRK05673 152 AEEAAAEYqeifgDrfYLELM--------------RHGLPIERRVeHALLELAKELGLPLVATNDVHYLTPEDAEAHEAL 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 756 IN-SMGG--ANPlNR--HSLPDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEVIPVKDELYtP--KIPGSEE 828
Cdd:PRK05673 218 LCiAEGKtlDDP-DRfrFYSPEQYLKSAEEMRELFADLPEAL------DNTVEIAERCNVEVRLGKPFL-PrfPTPDGET 289
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 829 EISELSYtKAKQ--------LYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVA 899
Cdd:PRK05673 290 EEDYLRK-EAKEgleerlafLFPDEERPEYVERLEYELDVIIQMGFPGYFLIVADFIQWAKDNGIPVGpGRGSGAGSLVA 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 900 TMTGITEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLgfHGDKV--PDIDLNFSG 977
Cdd:PRK05673 369 YALGITDLDPLR-----------------------------------------FGLLFERFL--NPERVsmPDFDIDFCQ 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 978 DYQAEAHNYTKVLFGEEYVYRAGTIGTVADKTA-----------YGFV----------------KGYERDHNLQFR---S 1027
Cdd:PRK05673 406 DRRDEVIRYVAEKYGRDAVAQIITFGTMKAKAVirdvgrvlgmpYGFVdritklippdpgitlaKAYEEEPELRELyesD 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1028 AEVDRL---AKGATGVKRTTGQHPGGIIVIPDymDVYDFTPIQFPADDQNsewKTTHFDFHSIHD-NVLKLDILGHDDPT 1103
Cdd:PRK05673 486 PEVKRLidmARKLEGLTRNAGVHAAGVVISPT--PLTDFVPLYRDPDSGM---PVTQFDMKDVEAaGLVKFDFLGLRTLT 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1104 VI----RMLQDLSGIDPQ--TIPTDDPEVMRIFAGPEvlnvtqeqinsktgTLGIPEFGTRFVRGMLEETHPTTFAELLQ 1177
Cdd:PRK05673 561 IIddalKLIKKRRGIDVDleAIPLDDPKTYELLQRGE--------------TLGVFQLESRGMRDLLKRLKPDCFEDIIA 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1178 ISGL-----------------SHGtdvwlgnaEELIKRGDATLAEVIGCRDDIMVYL--------IHAGLDSGMAfkimE 1232
Cdd:PRK05673 627 LVALyrpgpmesgmipnfidrKHG--------REEIEYPHPELEPILKETYGIIVYQeqvmqiaqVLAGYSLGGA----D 694
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1233 TVRKGLWNKIPDEL---RETYLNAMKENNVPDwyiDSCSKI-----K---YMFPKAHAAAYVLMALRVAYFKVYFPILYY 1301
Cdd:PRK05673 695 LLRRAMGKKKPEEMakqREIFVEGAKKNGIDE---EAADAIfdlleKfagYGFNKSHAAAYALVSYQTAYLKAHYPAEFM 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1302 CAYFSVRADDfdlvsmckgkdavkqamkeiTDKgmdasvkeknqltVLELANEMLERGFKFGMIDLYKSDAvNF-VIEGD 1380
Cdd:PRK05673 772 AALLTSDMDN--------------------TDK-------------VAVYLDECRRMGIKVLPPDVNESLY-DFtVVDGD 817
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|.
gi 921163465 1381 ILIApFRAVPSLGTNVAKQIVEARKD-GPFLSKEDLATR---GKVSKTLIE 1427
Cdd:PRK05673 818 IRYG-LGAIKGVGEGAVEAIVEAREEgGPFKDLFDFCARvdlKKVNKRVLE 867
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
417-638 |
1.69e-41 |
|
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: 152.22 E-value: 1.69e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 417 HESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRL 496
Cdd:TIGR00573 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 497 FLEFSKDTILVAHNAAFDMGFLNTSYAK-YGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAE 575
Cdd:TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKlYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 921163465 576 ATGH-LAWIFIkeamenhDMFYHdQLNAHIGEGdsyKRARPFHATLLAKNQDGLKDLFKLISMS 638
Cdd:TIGR00573 161 ADAFiLAKLYL-------VMTGK-QTKYGENEG---QQSRPYHAIKSIVKKDMLLKLIKAVSTE 213
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
426-577 |
2.33e-35 |
|
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: 132.48 E-value: 2.33e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAVKM--YKGNVIASFDEFIDPGHP--LSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFS 501
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIdgGENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 502 -KDTILVAHNAAFDMGFLNTSYAKYGIPEAP--NPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQH-HRAIYDAEAT 577
Cdd:pfam00929 81 rKGNLLVAHNASFDVGFLRYDDKRFLKKPMPklNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
424-580 |
6.11e-33 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 138.93 E-value: 6.11e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 424 TYVVFDVETTGLSAVY-DTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSK 502
Cdd:PRK08074 4 RFVVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 921163465 503 DTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEATGHL 580
Cdd:PRK08074 84 GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAEL 161
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
424-590 |
1.41e-32 |
|
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: 137.24 E-value: 1.41e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 424 TYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKD 503
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 504 TILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEATGHLAwI 583
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELL-L 159
|
....*..
gi 921163465 584 FIKEAME 590
Cdd:TIGR01407 160 LLFEKME 166
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
425-573 |
3.72e-32 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 128.39 E-value: 3.72e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKDT 504
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 921163465 505 ILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQhHRAIYD 573
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDD 157
|
|
| dnaE |
PRK07374 |
DNA polymerase III subunit alpha; Validated |
611-1418 |
4.24e-32 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 136.78 E-value: 4.24e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 611 KRARPFHATLLAKNQDGLKDLFKLISMSNVE------YFERvPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEA 684
Cdd:PRK07374 80 KKEKRYHLVVLAKNATGYKNLVKLTTISHLNgmrgrgIFSR-PCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPDVA 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 685 RNRAKFYDyiEVMPKAVYaplLEqelVKNERDLEEIIQN--LVEIGKSLDKIVVATGNVHYLNEEDAIYRKILINSMGGA 762
Cdd:PRK07374 159 RDVAAWYK--EVFGDDFY---LE---IQDHGSIEDRIVNveLVRIAKELGIKLIATNDAHYLSKNDVEAHDALLCVLTGK 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 763 -----NPLnRHSLPDvHFRTTDEMLTAFNflgESLAKEIV---VENTNKIADSCEEVipvkDELYTPKIP--------GS 826
Cdd:PRK07374 231 lisdeKRL-RYTGTE-YIKSEEEMLRLFR---DHLDPEVIqeaIANTVEVAEKVEEY----DILGTYRMPrfpipeghTA 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 827 EEEISELSY----TKAKQLYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATM 901
Cdd:PRK07374 302 VSYLTEVTEqgllKRLKLNSLDEIDENYKERLSYELKIIEQMGFPTYFLVVWDYIRFAREQGIPVGpGRGSAAGSLVAYA 381
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 902 TGITEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQA 981
Cdd:PRK07374 382 LGITNIDPVK-----------------------------------------NGLLFERFLNPERKSMPDIDTDFCIERRG 420
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 982 EAHNYTKVLFGEEYVYRAGT------------IGTV-------ADKTAY-----------------------GFVKGYER 1019
Cdd:PRK07374 421 EVIDYVTRRYGEDKVAQIITfnrmtskavlkdVARVldipygeADRLAKlipvvrgkpaklkamigkespspEFREKYEK 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1020 DHNLQfrsAEVDrLAKGATGVKRTTGQHPGGIIVIPDYMDvyDFTPIQFPADDQNSewkTTHF--DFHSIhdNVLKLDIL 1097
Cdd:PRK07374 501 DPRVK---KWVD-MAMRIEGTNKTFGVHAAGVVIASDPLD--ELVPLQRNNDGQVI---TQYFmeDIESL--GLLKMDFL 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1098 GHDDPTVIRMLQDL----SG--IDPQTIPTDDPEVMRIFAGPEVLNVTQ------------------EQINS-----KTG 1148
Cdd:PRK07374 570 GLKNLTMIEKTLELveqsTGerIDPDNLPLDDEKTFELLARGDLEGIFQlessgmrqvvrdlkpsslEDISSilalyRPG 649
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1149 TLG---IPEFGTRfvrgmleethpttfaellqisglSHGtdvwlgnaEELIKRGDATLAEVIGCRDDIMVYLIH------ 1219
Cdd:PRK07374 650 PLDaglIPKFINR-----------------------KHG--------REAIDFAHPLLEPILTETYGIMVYQEQimkiaq 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1220 --AGLDSGMAfkimETVRKGLWNKIPDEL---RETYLNAMKENNVPdwyidscSKI------------KYMFPKAHAAAY 1282
Cdd:PRK07374 699 dlAGYSLGQA----DLLRRAMGKKKVSEMqkhRGIFVEGASKRGVD-------EKVadelfdqmvlfaEYCFNKSHSTAY 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1283 VLMALRVAYFKVYFPILYYCAYFSVRADDFDLV----SMCKGKdAVKQAMKEITDKGMDASVKEKNQLtvlelanemler 1358
Cdd:PRK07374 768 GAVTYQTAYLKAHYPVAYMAALLTVNAGSSDKVqryiSNCNSM-GIEVMPPDINRSGIDFTPKGNRIL------------ 834
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 921163465 1359 gfkFGMidlyksdavnfviegdiliapfRAVPSLGTNVAKQIVEAR-KDGPFLSKEDLATR 1418
Cdd:PRK07374 835 ---FGL----------------------SAVKNLGDGAIRNIIAARdSDGPFKSLADLCDR 870
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
425-581 |
1.10e-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: 121.85 E-value: 1.10e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTglSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKDT 504
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 505 ILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLeQHHRAIYDAEATGHLA 581
Cdd:cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEIL 154
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
425-575 |
1.60e-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: 1.60e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLS-AVYDTIIELAAVKM----YKGNViasFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLE 499
Cdd:cd06131 1 QIVLDTETTGLDpREGHRIIEIGCVELinrrLTGNT---FHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 500 FSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNP---VIDTLELARYLYPQfKRFGLGVLSKKFGVSLEQH--HRAIYDA 574
Cdd:cd06131 78 FIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARKKFPG-KPNSLDALCKRFGIDNSHRtlHGALLDA 156
|
.
gi 921163465 575 E 575
Cdd:cd06131 157 E 157
|
|
| polC_OBF |
cd04484 |
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
241-323 |
1.55e-30 |
|
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: 115.77 E-value: 1.55e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 241 RVTLEGYVFDKEVRELRSKRKILTLKITDYTSSFIVKKFSnnEKDEQIFEAI-STGSWLKVRGSIQEDTFVRDLVMNAQD 319
Cdd:cd04484 1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFL--RKDEKDKEELkSKGDWVRVRGKVQYDTFSKELVLMIND 78
|
....
gi 921163465 320 IVEV 323
Cdd:cd04484 79 IEEI 82
|
|
| dnaE |
PRK06920 |
DNA polymerase III subunit alpha; |
608-1415 |
3.41e-30 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 130.30 E-value: 3.41e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 608 DSYKRARPFhaTLLAKNQDGLKDLFKLismSNVEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIfEAMMQKGVEEARNR 687
Cdd:PRK06920 72 EEEEKSYPL--VLLAENEIGYQNLLKI---SSSIMTKSKEGIPKKWLAHYAKGLIAISPGKDGEI-EQLLLEDKESQAEE 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 688 A---------KFYDYIEVMPkavyaplleqelVKNERDLEEIIQNLVEigkSLDKIVVATGNVHYLNEEDAIYRKILINS 758
Cdd:PRK06920 146 VarayqnmfgNFYMSLQHHA------------IQDELLLQEKLPEFSN---RVNIPVVATNDVRYINQSDALVHECLLSV 210
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 759 MGGAN----PLNRHSLPDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEVIPV-KDELytPKIPGSEEE---- 829
Cdd:PRK06920 211 ESGTKmtdpDRPRLKTDQYYLKSSDEMEALFSHVPEAI------YNTVEIAERCRVEIPFhVNQL--PKFPVPSNEtadm 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 830 -ISELSYTKAKQLYGDPlPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATMTGITEV 907
Cdd:PRK06920 283 yLRRVCEEGLQKRYGTP-KEVHINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHILTGpGRGSAAGSLVSYVLEITDI 361
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 908 NPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNYT 987
Cdd:PRK06920 362 DPIE-----------------------------------------YDLLFERFLNPERVTLPDIDIDFPDTRRDEMIRYV 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 988 KVLFGEEYVYRAGTIGTVADKTAY---GFVKGYERDHNLQF-----------------RSAEVDR-------------LA 1034
Cdd:PRK06920 401 KDKYGQLRVAQIVTFGTLAAKAAIrdiARVMGLPPRDIDIFsklipsklgitlkdayeESQSLREfiqgnllhervfeIA 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1035 KGATGVKRTTGQHPGGIIVIPDYMDvyDFTPIQfpaDDQNSEWKTTHFDFHSIHDNVLKLDILGHDDPTVIRMLQDL--- 1111
Cdd:PRK06920 481 KRVEGLPRHTSIHAAGVIMSQEPLT--GSVAIQ---EGHNDVYVTQYPADALEELGLLKMDFLGLRNLTLLENIIKFieq 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1112 ---SGIDPQTIPTDDPEVMrifagpevlnvtqeQINSKTGTLGIPEFGTRFVRGMLEETHPTTFAELLQISGL------- 1181
Cdd:PRK06920 556 ktgKEIDIRNLPLQDEKTF--------------QLLGRGDTTGVFQLESSGMRNVLRGLKPNEFEDIVAVNSLyrpgpme 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1182 --------SHGTDVWLGNAEELIKRGDATLAeVIGCRDDIMVYLIH-AGLDSGMAFKIMETVRKGLwNKIPDELRETYLN 1252
Cdd:PRK06920 622 qiptfiesKHGKRKIEYLHPDLKPILERTYG-VIVYQEQIMQIASKlAGFSLGEADLLRRAVSKKN-RDILDQERKHFVQ 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1253 AMKENNVPdwyIDSCSKI--------KYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAYfsvraddfdLVSMCKGKDAV 1324
Cdd:PRK06920 700 GCLQNGYD---ETSAEKIydlivrfaNYGFNRSHAVAYSMIGYQLAYLKANYTLEFMTAL---------LSSAIGNEDKI 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1325 KQAMKEITDKGmdasvkeknqLTVLELAnemlergfkfgmidLYKSdAVNFVIEGDILIAPFRAVPSLGTNVAKQIVEAR 1404
Cdd:PRK06920 768 VQYIRETKRKG----------FHVLPPS--------------LQRS-GYNFQIEGNAIRYSLLSIRNIGMATVTALYEER 822
|
890
....*....|.
gi 921163465 1405 KDGPFlskEDL 1415
Cdd:PRK06920 823 EKKMF---EDL 830
|
|
| PHP_PolIIIA_DnaE3 |
cd12113 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
607-821 |
3.71e-30 |
|
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: 121.78 E-value: 3.71e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 607 GDSYKRARPFHATLLAKNQDGLKDLFKLISMSNVEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEEARN 686
Cdd:cd12113 77 KDKKGDKRYYHLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEARE 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 687 RAKFYD--------YIEVMpkavYAPLLEQelvknerdlEEIIQNLVEIGKSLDKIVVATGNVHYLNEEDAIYRKILI-- 756
Cdd:cd12113 157 AALEYRdifgkdnfYLELQ----DHGLPEQ---------KKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLci 223
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 921163465 757 ---NSMGGANPLnRHSLPDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSCEEVIPvKDELYTP 821
Cdd:cd12113 224 qtgKTLDDPNRM-RFDTDEFYLKSPEEMRELFPDVPEAL------ENTLEIAERCNVELD-FGKLHLP 283
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
417-577 |
4.58e-29 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 117.82 E-value: 4.58e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 417 HESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDpGHPLSRTTVDLTGITDEMVRGSKSEEEVLRL 496
Cdd:PRK08517 62 FTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVK-AKEVPEYITELTGITYEDLENAPSLKEVLEE 140
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 497 FLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQfKRFGLGVLSKKFGVSLEQHHRAIYDAEA 576
Cdd:PRK08517 141 FRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEIEVHHRAYADALA 219
|
.
gi 921163465 577 T 577
Cdd:PRK08517 220 A 220
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
415-590 |
6.15e-29 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 117.08 E-value: 6.15e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 415 DVHESLSEGTYVVFDVETTGLSAVY-DTIIELAAVKMyKGNVIA--SFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEE 491
Cdd:PRK07740 51 VLDIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKT-KGGEVEtdTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLA 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 492 EVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAK-YGIPEApNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRA 570
Cdd:PRK07740 130 EVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRtYRQPFT-HRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHA 208
|
170 180
....*....|....*....|
gi 921163465 571 IYDAEATGHLAWIFIKEAME 590
Cdd:PRK07740 209 LGDALMTAKLWAILLVEAQQ 228
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
426-575 |
3.13e-23 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 100.32 E-value: 3.13e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVY-DTIIELAAVKM----YKGNviaSFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEF 500
Cdd:PRK05711 7 IVLDTETTGLNQREgHRIIEIGAVELinrrLTGR---NFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 501 SKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNP----VIDTLELARYLYPQfKRFGLGVLSKKFGV--SLEQHHRAIYDA 574
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNtfckVTDTLAMARRMFPG-KRNSLDALCKRYGIdnSHRTLHGALLDA 162
|
.
gi 921163465 575 E 575
Cdd:PRK05711 163 E 163
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
425-590 |
4.89e-23 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 106.69 E-value: 4.89e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYdTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKDT 504
Cdd:PRK07246 9 YAVVDLEATGAGPNA-SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 505 ILVAHNAAFDMGFLNTSYAKYGIpEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAEATGHLaWIF 584
Cdd:PRK07246 88 IFVAHNVKFDANLLAEALFLEGY-ELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAEL-FLK 165
|
....*.
gi 921163465 585 IKEAME 590
Cdd:PRK07246 166 LLQKIE 171
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
420-575 |
7.04e-22 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 96.44 E-value: 7.04e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 420 LSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLE 499
Cdd:PRK06310 4 LKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 921163465 500 FSKDT-ILVAHNAAFDMGFLNTSYAKYGIPEAP--NPVIDTLELARyLYPQFKRFGLGVLSKKFGVSLEQHHRAIYDAE 575
Cdd:PRK06310 84 FFKEGdYIVGHSVGFDLQVLSQESERIGETFLSkhYYIIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDVE 161
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
340-406 |
9.45e-22 |
|
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: 90.02 E-value: 9.45e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 340 ELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVD 406
Cdd:smart00481 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
|
|
| DNA_pol3_a_NII |
pfam11490 |
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
94-196 |
3.21e-21 |
|
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: 90.48 E-value: 3.21e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 94 DYWAQALESQQCDTPLAQQVLKTQVPILKEHKIILPVDSTGALSYLKQQYLPLVESLFVSYGFPKFRIEPEVDE-QQAER 172
Cdd:pfam11490 1 DYWEEIVEELSKKSPSLKSLLKNQKPEVEGNKLIIKVPNEIEANFLKKKNLDKLLEEYIKFGFGKLSIDVEVDEdESSEE 80
|
90 100
....*....|....*....|....
gi 921163465 173 VLKLFEERKQEQAEAFMKQAAESL 196
Cdd:pfam11490 81 ELEEFEEQKEEEEQKAIQEAIEAL 104
|
|
| dnaE |
PRK07279 |
DNA polymerase III DnaE; Reviewed |
828-1301 |
3.58e-19 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 94.33 E-value: 3.58e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 828 EEISELSYT--KAKQLYGDPLpeiiQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATMTGI 904
Cdd:PRK07279 240 EELRELAELglKEKGLWSSPY----QERLDKELSVIHDMGFDDYFLIVWDLLRFGRSQGYYMGmGRGSAAGSLVAYALDI 315
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 905 TEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAH 984
Cdd:PRK07279 316 TGIDPVK-----------------------------------------HNLLFERFLNKERYSMPDIDIDLPDIYRSEFL 354
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 985 NYTKVLFGEEYVYRAGTIGTVADKTA-------YGfVKGYE----------RD-------HNLQFRSAEVDRL------- 1033
Cdd:PRK07279 355 RYVRNRYGSDHSAQIVTFSTFGAKQAirdvfkrFG-VPEYElsnltkkisfRDslasvyeKNISFRQIINSKLeyqkafe 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1034 -AKGATGVKRTTGQHPGGIIVIPDymDVYDFTPIQfPADDQnsewKTTHFDFHSIHDN-VLKLDILGHDDPTVIRMLQDL 1111
Cdd:PRK07279 434 iAKRIEGNPRQTSIHAAGVVMSDD--DLTNHIPLK-YGDDM----MITQYDAHAVEANgLLKMDFLGLRNLTFVQKMQEK 506
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1112 ------SGIDPQTIPTDDPEVMRIFAgpevlnvtqeqinsKTGTLGIPEFGTRFVRGMLEETHPTTFAEL-----LQISG 1180
Cdd:PRK07279 507 vakdygIHIDIEAIDLEDKETLALFA--------------AGDTKGIFQFEQPGAINLLKRIKPVCFEDIvattsLNRPG 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1181 LSHGTD--VWLGNAEELIKRGDATLAEVIGCRDDIMVY--------LIHAGLDSGMAfkimETVRKGLWNKIPDE---LR 1247
Cdd:PRK07279 573 ASDYTDnfVKRRHGQEKVDLIDPVIAPILEPTYGIMLYqeqvmqiaQVFAGFSLGKA----DLLRRAMSKKNASEmqkME 648
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 921163465 1248 ETYLNAMKENNvpdwyiDSCSKIK-----------YMFPKAHAAAYVLMALRVAYFKVYFPILYY 1301
Cdd:PRK07279 649 EDFLQGALELG------HSEEKARelfdrmekfagYGFNRSHAFAYSALAFQLAYFKAHYPAVFY 707
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
426-573 |
4.06e-19 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 87.94 E-value: 4.06e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAvkmYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEF-SKDT 504
Cdd:PRK06309 5 IFYDTETTGTQIDKDRIIEIAA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFcGTDN 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 505 ILVAHNA-AFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLEQHHRAIYD 573
Cdd:PRK06309 82 ILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
427-580 |
9.35e-19 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 86.70 E-value: 9.35e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 427 VFDVETTGLSAvydTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEfskDTIL 506
Cdd:PRK07983 4 VIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYG---SEWY 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 921163465 507 VAHNAAFDMGFLntsyakygiPEAPNPVIDTLELARYLYPQFKRFGLGVL-SKKFGVSLEQ---HHRAIYDAEATGHL 580
Cdd:PRK07983 78 VAHNASFDRRVL---------PEMPGEWICTMKLARRLWPGIKYSNMALYkSRKLNVQTPPglhHHRALYDCYITAAL 146
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
340-407 |
3.62e-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: 83.36 E-value: 3.62e-18
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 921163465 340 ELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDD 407
Cdd:pfam02811 1 HLHVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVAPG 68
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
616-1444 |
4.09e-18 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 90.90 E-value: 4.09e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 616 FHATLLAKNQDGLKDLFKLIS--MSNVEyfervprIPRSQLNKlrDNLLIgsacdkgeifeammqkgveearnrakfydy 693
Cdd:PRK07135 72 FRFILLAKNYSGYKLLNELSSkkSKNKE-------IELNDLDS--DNIII------------------------------ 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 694 IEVMPKAVYAPLLEQELVKNERdleeIIQNLVEIGKSldkIVVATGNVhyLNEEDAIYRKILiNSMGGANPLNRhSLPDV 773
Cdd:PRK07135 113 IDHPKNGFYAKNKEQLELKNYY----INSNDPKIENA---VYVQERKL--LFAEDNEYLKIL-NKIGNNKEENS-NFKFF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 774 HFRTTDEMLTafnflgeslakEIVVENTNKIADSCEEVIPvKDELYTPKIPGSEEEISELSY---------TKAKQLYGD 844
Cdd:PRK07135 182 DFEKWFEDID-----------EKILKRTNYLVENINIEFP-KKEFNLPDFDNNLGLESDLFLkkilkesviNKKAELKYY 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 845 PLpeiIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFVATMTGITEVNPLAphyycpecqyse 923
Cdd:PRK07135 250 PN---VKERINYEYSVIKKLKFSNYFLIIWDFIKWARKNKISIGpGRGSASGSLVSYLLNITSVNPLK------------ 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 924 fyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEEYVYRAGTIG 1003
Cdd:PRK07135 315 -----------------------------YDLLFERFLNPDRITMPDIDIDIQDDRRDEVIDYIFEKYGYEHCATISTFQ 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1004 TVADKTAYGFVKGY-----------------------ERDHNLQFRSAEVDR----------LAKGATGVKRTTGQHPGG 1050
Cdd:PRK07135 366 TLGAKSAIRDVGRMlgipesdvnaisklipnnqsleeAYDKNKSFFRELISKgdpiykklykIAKKLEGLPRQSGTHAAG 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1051 IIV--------IPDYMDVYDFTPIQFPAddQNSEwktthfDFhsihdNVLKLDILGHDDPTVIRMLQDL--------SGI 1114
Cdd:PRK07135 446 IIIsnkpitnyVPTFESKDNYNQVQYSM--EFLE------DF-----GLLKIDLLGLKNLTIIKNIEEKinkellfdHLI 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1115 DPQTIPTDDPEvmrifagpevlnvTQEQINSKTgTLGIPEFGTRFVRGMLEETHPTTFAELLQI-----SGLSHGTDVWL 1189
Cdd:PRK07135 513 NFNDLPIIDKK-------------TNNLLSNGK-TEGIFQLESPGMKSTIKKVGIDSFEDIVAIislyrPGPIQYIPIYA 578
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1190 GNAEE--LIKRGDATLAEVIGCRDDIMVY----LIHAGLDSGMAFKIMETVRKGLWNKIPDEL---RETYLNAMKENNVP 1260
Cdd:PRK07135 579 KNKKNpkNIEKIHPEYDEIVAPTYGIIIYqeqiMQIAQKVAGFSFAQADLLRRAISKKDETKLdkiKDKFIEGGIKNGYS 658
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1261 DWYIDSC-SKI----KYMFPKAHAAAYVLMALRVAYFKVYFPILYYCAyfsvraddfdLVSMCKGkdavkqamkeitdkg 1335
Cdd:PRK07135 659 KKVLEKIySLIekfaDYGFNKSHAVAYATLAYKMAYYKANYPLVFYSA----------LISNSNG--------------- 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1336 mdasvkekNQLTVLELANEMLERGFKFGMIDLYKSDAVNFVIEGDILIaPFRAVPSLGTNVAKQIVEARKD-GPFLSKED 1414
Cdd:PRK07135 714 --------SQENIKKYVKEAKNNGIKVYSPDINFSTENAVFDNGKIFL-PLIMIKGLGSVAIKKIIDERNKnGKYKNFFD 784
|
890 900 910
....*....|....*....|....*....|...
gi 921163465 1415 LATRGK---VSKTLIEYMNDNGVLKDLPDENQL 1444
Cdd:PRK07135 785 FILRLKfigISKSIIEKLIKANTLRSFGNQDTL 817
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
426-518 |
1.49e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 85.03 E-value: 1.49e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAVKM-YK-----GNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLE 499
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFeYDddgriGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAAVDALIA 119
|
90
....*....|....*....
gi 921163465 500 fsKDTILVAHNAAFDMGFL 518
Cdd:PRK09182 120 --PADLIIAHNAGFDRPFL 136
|
|
| DNA_pol3_a_NI |
pfam14480 |
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
7-80 |
1.86e-17 |
|
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: 77.97 E-value: 1.86e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 921163465 7 LFEKLLEQIQLEeaDKQHPLISSGEVERVVVHRKSRLWEFTLHFSQILPIMLYRSLVQHVTLAFHDIAQVKLNI 80
Cdd:pfam14480 1 RFFELFPQLKLP--DELEELFEDAEIEKVTVHKKSKKWRFYISSPHLLPKEVIYKFEQRLKEQFFHIAKVKVKI 72
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
425-584 |
3.49e-17 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 84.37 E-value: 3.49e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDTIIELAAVKM-YKGNVIASFDEFIDPGHPLSRTTVDltGITDEMVRGSKSEEEVLRLFLEFSKD 503
Cdd:PRK06063 17 WAVVDVETSGFRPGQARIISLAVLGLdADGNVEQSVVTLLNPGVDPGPTHVH--GLTAEMLEGQPQFADIAGEVAELLRG 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 504 TILVAHNAAFDMGFLNTSYAKYGIpEAP-NPVIDTLELARylypqfkRFGLGV-------LSKKFGVSLEQHHRAIYDAE 575
Cdd:PRK06063 95 RTLVAHNVAFDYSFLAAEAERAGA-ELPvDQVMCTVELAR-------RLGLGLpnlrletLAAHWGVPQQRPHDALDDAR 166
|
....*....
gi 921163465 576 AtghLAWIF 584
Cdd:PRK06063 167 V---LAGIL 172
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
608-808 |
1.12e-16 |
|
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: 82.14 E-value: 1.12e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 608 DSYKRARPFHATLLAKNQDGLKDLFKLISMSnveYFER----VPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQKGVEE 683
Cdd:cd07433 70 NPDDADEPFRLTLLAQNEQGYKNLTELISRA---YLEGqrngGPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGNPDL 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 684 ARNRAKFydYIEVMPKAVYAplleqELVKNERDLEE-IIQNLVEIGKSLDKIVVATGNVHYLNEED--------AIYRKI 754
Cdd:cd07433 147 AEALLQF--LKKIFPDRFYL-----ELQRHGRPEEEaYEHALIDLAYELGLPLVATNDVRFLKPEDfeahearvCIAEGR 219
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 921163465 755 LINSMgganplNRHSL--PDVHFRTTDEMLTAFNFLGESLakeivvENTNKIADSC 808
Cdd:cd07433 220 TLDDP------RRPRRysPQQYFKSAEEMAELFADLPEAI------ENTVEIAKRC 263
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
605-1131 |
1.39e-16 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 85.56 E-value: 1.39e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 605 GEGDSYKRARPFHATLLAKNQDGLKDLFKLISMSNVE------YFERvPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQ 678
Cdd:PRK09532 72 GDIEKQKRRRKYHQVVLAKNTQGYKNLVKLTTISHLQgvqgkgIFAR-PCINKELLEQYHEGLIVTSACLGGEIPQAILS 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 679 KGVEEARNRAKFYDyiEVMPKAVYaplLEqelVKNERDLEEIIQN--LVEIGKSLDKIVVATGNVHYLNEEDAIYRKILI 756
Cdd:PRK09532 151 GRPDAARKVAKWYK--KLFGDDFY---LE---IQDHGSQEDRIVNveIVKIARELGIKIIATNDSHFISCYDVEAHDALL 222
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 757 NSMGGA----NPLNRHSLPDvHFRTTDEMLTAF-NFLGESLAKEiVVENTNKIADSCEEVipvkDELYTPKIPGSEEEIS 831
Cdd:PRK09532 223 CIQTGKliteDKRLRYSGTE-YLKSAEEMRLLFrDHLPDDVIAE-AIANTLEVADKIEPY----NILGEPRIPNYPVPSG 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 832 ELSYTKAKQLYGDPL------------PEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKSNEDGYLVG-SRGSVGSSFV 898
Cdd:PRK09532 297 HTPDTYVEEVAWQGLlerlncksrsevEPVYKERLEYELKMLQQMGFSTYFLVVWDYIKYARDNNIPVGpGRGSAAGSLV 376
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 899 ATMTGITEVNPLapHyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFETFLGFHGDKVPDIDLNFSGD 978
Cdd:PRK09532 377 AYCLKITNIDPV--H---------------------------------------HGLLFERFLNPERKSMPDIDTDFCIE 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 979 YQAEAHNYTKVLFGEEyvyRAGTIGTVADKTAYGFVKGYERDHNLQFrsAEVDRLAK----------------------- 1035
Cdd:PRK09532 416 RRDEMIKYVTEKYGED---RVAQIITFNRMTSKAVLKDVARVLDIPY--GEADKMAKlipvsrgkptklkvmisdetpep 490
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1036 --------------------GATGVKRTTGQHPGGIIVIPDYMDvyDFTPIQfpaddQNSEWK--TTHF--DFHSIhdNV 1091
Cdd:PRK09532 491 efkekydndprvrrwldmaiRIEGTNKTFGVHAAGVVISSEPLD--EIVPLQ-----KNNDGAviTQYFmeDLESL--GL 561
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 921163465 1092 LKLDILGHDDPTVIRMLQDL------SGIDPQTIPTDDPEVMRIFA 1131
Cdd:PRK09532 562 LKMDFLGLRNLTTIQKTADLikenrgVEIDLDQLPLDERKALKILA 607
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
339-418 |
1.67e-16 |
|
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: 75.93 E-value: 1.67e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 339 VELHVHSKMSTMDATNnISDIVAQAGKWGHRAIAITDHGGAQAFPEAH--------SAGKKAGVKILYGVEANVVDDGVP 410
Cdd:cd07309 1 VDLHTHTVFSDGDHAK-LTELVDKAKELGPDALAITDHGNLRGLAEFNtagk*nhiKAAEAAGIKIIIGSEVNLTVLAHP 79
|
....*....
gi 921163465 411 IAYN-DVHE 418
Cdd:cd07309 80 VVATsDSHY 88
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
426-580 |
7.39e-15 |
|
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: 74.64 E-value: 7.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAV--KMYKGNVIA---SFDEFIDP--GHPLSRTTVDLTGIT-DEMVRGSKSEEEVL-RL 496
Cdd:cd06134 8 VVVDVETGGFNPQTDALLEIAAVtlEMDEQGNLYpdeTFHFHILPfeGANLDPAALEFNGIDpFHPFRFAVDEKEALkEI 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 497 FLEFSKD--------TILVAHNAAFDMGFLNTSYAKYGI---PEAPNPVIDTLELARYLYPQfkrfglGVLSK-----KF 560
Cdd:cd06134 88 FKPIRKAlkaqgctrAILVGHNAHFDLGFLNAAVARCKIkrnPFHPFSTFDTATLAGLAYGQ------TVLAKacqaaGI 161
|
170 180
....*....|....*....|
gi 921163465 561 GVSLEQHHRAIYDAEATGHL 580
Cdd:cd06134 162 EFDNKEAHSALYDTQKTAEL 181
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
412-586 |
2.01e-14 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 73.40 E-value: 2.01e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 412 AYNDVHESLSEGTYVVFDVETTGLSAVYDTIIELAAVKMyKGNVI---ASFDEFIDPGHPLSRTTVDLTGITDEMVRGSK 488
Cdd:PRK09145 18 RYAFLFEPPPPDEWVALDCETTGLDPRRAEIVSIAAVKI-RGNRIltsERLELLVRPPQSLSAESIKIHRLRHQDLEDGL 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 489 SEEEVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKY-GIPeAPNPVIDTLEL-ARYLYPQFK------RFglGVLSKKF 560
Cdd:PRK09145 97 SEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLlGIP-LPNPLIEVSALyYDKKERHLPdayidlRF--DAILKHL 173
|
170 180
....*....|....*....|....*.
gi 921163465 561 GVSLEQHHRAIYDAEATghlAWIFIK 586
Cdd:PRK09145 174 DLPVLGRHDALNDAIMA---ALIFLR 196
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
419-582 |
4.34e-14 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 73.47 E-value: 4.34e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 419 SLSEGTYVVFDVETTGLSAVYDTIIELAAVKM-YKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVR--GSKSEE---E 492
Cdd:PRK07942 2 SWHPGPLAAFDLETTGVDPETARIVTAALVVVdADGEVVESREWLADPGVEIPEEASAVHGITTEYARahGRPAAEvlaE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 493 VLRLFLE-FSKDTILVAHNAAFDMGFLNTSYAKYGIPE-APNPVIDTLELARYL--YPQFKRfGLGVLSKKFGVSLEQHH 568
Cdd:PRK07942 82 IADALREaWARGVPVVVFNAPYDLTVLDRELRRHGLPSlVPGPVIDPYVIDKAVdrYRKGKR-TLTALCEHYGVRLDNAH 160
|
170
....*....|....
gi 921163465 569 RAIYDAEATGHLAW 582
Cdd:PRK07942 161 EATADALAAARVAW 174
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
425-582 |
5.04e-14 |
|
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: 71.48 E-value: 5.04e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDT-----IIELAAVKM--YKGNVIASFDEFIDP--GHPLSRTTVDLTGITDEMVRGSKSEEEVLR 495
Cdd:cd06133 1 YLVIDFEATCWEGNSKPdypneIIEIGAVLVdvKTKEIIDTFSSYVKPviNPKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 496 LFLEFSKDTIlvahNAAF------DMGFLNTSYAKYGI---PEAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLE- 565
Cdd:cd06133 81 EFLEWLGKNG----KYAFvtwgdwDLKDLLQNQCKYKIinlPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEg 156
|
170
....*....|....*..
gi 921163465 566 QHHRAIYDAEATGHLAW 582
Cdd:cd06133 157 RHHRGLDDARNIARILK 173
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
425-580 |
2.71e-13 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 69.50 E-value: 2.71e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDT-----IIELAAVKM-YKGNVIASFDEFIDP-GHP-LSRTTVDLTGITDEMVRGSKSEEEVLRL 496
Cdd:COG5018 4 YLVIDLEATCWDGKPPPgfpmeIIEIGAVKVdENGEIIDEFSSFVKPvRRPkLSPFCTELTGITQEDVDSAPSFAEAIED 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 497 FLEF--SKDTILVAhNAAFDMGFLNTSYAKYGIP-EAPNPVIDTLELARYLYPQFKRFGLGVLSKKFGVSLE-QHHRAIY 572
Cdd:COG5018 84 FKKWigSEDYILCS-WGDYDRKQLERNCRFHGVPyPFGDRHINLKKLFALYFGLKKRIGLKKALELLGLEFEgTHHRALD 162
|
....*...
gi 921163465 573 DAEATGHL 580
Cdd:COG5018 163 DARNTAKL 170
|
|
| dnaE |
PRK05898 |
DNA polymerase III subunit alpha; |
732-1450 |
3.78e-13 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 135648 [Multi-domain] Cd Length: 971 Bit Score: 74.49 E-value: 3.78e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 732 DKIVVATGNVHYLNEEDaiyrKILINSMGGANplNRHSLPDVHfrtTDEMLTAFNFLGESLAK----EIVVENTNKIADS 807
Cdd:PRK05898 134 APNAIAFNSVFYANKND----KIVFNAMLAIK--NDLKIDELK---NCQDFDNNHFLNDNEAQslfsPIQLDNLNKVLNE 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 808 CE---EVIPVKDELY-TPKIPGSEEEISELSYTKAKQLYGD---PLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVHKS 880
Cdd:PRK05898 205 LKveiHDLPINIIKYdKQNSIISSEILKQLCISGLNKRLNAndgQVKKIYVKRLKYELDIINEKQFDDYFLIVYDFINFA 284
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 881 NEDGYLVG-SRGSVGSSFVATMTGITEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFET 959
Cdd:PRK05898 285 KSNGIIIGpGRGSAAGSLIAYLLHITDIDPIK-----------------------------------------YNLIFER 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 960 FLGFHGDKVPDIDLNFSGDYQAEAHNYTKVLFGEEYVYRAGT------------IG-------TVADKTAYGFVKGYERD 1020
Cdd:PRK05898 324 FLNPTRKSMPDIDTDIMDERRDEVVEYLFEKYGNDHVAHIITfqrikakmairdVGrilgidlKVIDKICKNIKPDYEED 403
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1021 HNLQFR-----------SAEVDRLAKGATGVKRTTGQHPGGIIVIPDYMDvyDFTPIQFPADDQnsewKTTHFDFHSIHD 1089
Cdd:PRK05898 404 LDLAIKkntilkemyvlHKELFDLAKKIINAPRQIGTHAAGVVLSNSLLT--NIIPIQLGINDR----PLSQYSMEYLER 477
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1090 -NVLKLDILGHDDPTVI-------RMLQDLSgIDPQTIPTDDPEVMRIFAgpevlnvtqeqinsKTGTLGIPEFGTRFVR 1161
Cdd:PRK05898 478 fGLIKMDLLGLKNLTIIdnvlkliKENQNKK-IDLFNINLNDKNVFEDLA--------------KGRTNGIFQLESPGMK 542
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1162 GMLEETHPTTFAELLQISGLSHGTDvwLGNAEELIKRG---------DATLAEVIGCRDDIMVY--------LIHAGLDS 1224
Cdd:PRK05898 543 KVLKKVKPQNIEDISIVSALFRPGP--QQNIKTFVERRfkreefsywNEATKKILEPTHGIIVYqeqvinlvKTIANFDI 620
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1225 GMA--FKIMETVRKGlwnKIPDELRETYLNAMKENNVPD-------WYIDSCSkiKYMFPKAHAAAYVLMALRVAYFKVY 1295
Cdd:PRK05898 621 ATAdnFRRAISKKDE---KILIQLKKDFIEGALKNNYKQplvnqifEYIFSFA--DYGFNHSHSLAYSYISYWMAYLKHY 695
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1296 FPILYYCAYFSVRADDfdlvsmckgkdavkqamkeitdkgmdasvKEKnqltVLELANEMLERGFKFGMIDLYKSDAvNF 1375
Cdd:PRK05898 696 YPLEFLSILLSHTSAS-----------------------------KDK----LLSYLNEAKEFNISIKKPDINYSSN-SF 741
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1376 VIEGD--ILIAPFRAVPSLGTNVAKQIVEARKDGP---FLSKEDLATRGKVSKTLIEYMNDNGVLkdlpDENQLSLFDML 1450
Cdd:PRK05898 742 VLDTQkqIIRFGFNTIKGFGDELLKKIKSALQNKTfsdFISYIDALKKNNVSLSNIEILINVGTF----DSFKLSRLFLL 817
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
339-415 |
5.60e-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: 68.77 E-value: 5.60e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 339 VELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDDGVP-----IAY 413
Cdd:cd07431 1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPyplllLAK 80
|
..
gi 921163465 414 ND 415
Cdd:cd07431 81 NN 82
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
735-1438 |
3.13e-12 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 71.81 E-value: 3.13e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 735 VVATGNVHYLNEED--------AIYRKILINSMGGANPLNrhslPDVHFRTTDEMLTAFNFLGESLAkeivveNTNKIAD 806
Cdd:PRK05672 195 LVATGDVHMHHRSRrrlqdamtAIRARRSLAEAGGWLAPN----GERHLRSGAEMARLFPDYPEALA------ETVELAE 264
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 807 SC----EEVIP-VKDELytpkIPGSEEEIS---ELSYTKAKQLYGDPLPEIIQKRLEKELNSINGNGFSVIYLIAQKLVH 878
Cdd:PRK05672 265 RCafdlDLLAYeYPDEP----VPAGHTPASwlrQLTEAGAARRYGPGIPPKARAQIEHELALIAELGYEGYFLTVHDIVR 340
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 879 KSNEDGYLVGSRGSVGSSFVATMTGITEVNPLAphyycpecqysefyedgtygsgfdmpekkcpkcgarlnkdgHDIPFE 958
Cdd:PRK05672 341 FARSQGILCQGRGSAANSAVCYALGITEVDPVQ-----------------------------------------SGLLFE 379
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 959 TFLGFHGDKVPDIDLNFSGDYQAEA--HNYTKvlFGEEYV--------YR-AGTIGTVAdkTAYGF--------VKGYER 1019
Cdd:PRK05672 380 RFLSPERDEPPDIDVDFEHDRREEViqYVYRR--YGRDRAaqvanvitYRpRSAVRDVA--KALGLspgqvdawAKQVSR 455
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1020 -----DHNLQFRSAEVDR----------LAKGATGVKRTTGQHPGGiIVIPDYmDVYDFTPIQFPADDQNS--EW-KTth 1081
Cdd:PRK05672 456 wsgsaDDLQRLRQAGLDPespiprrvveLAAQLIGFPRHLSQHSGG-FVICDR-PLARLVPVENAAMEGRSviQWdKD-- 531
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1082 fDFHSIhdNVLKLDILGHDDPTVIR----MLQDLSGI--DPQTIPTDDPEVMrifagpevlnvtqEQInSKTGTLGIPEF 1155
Cdd:PRK05672 532 -DCAAV--GLVKVDVLALGMLSALHrafdLIAEHRGRrlTLASIPLDDPAVY-------------DML-CRADSVGVFQV 594
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1156 GTRFVRGMLEETHPTTFAEL-LQIS---------GLSH-------GTDVWLGNAEELIKrgdaTLAEVIGC---RDDIM- 1214
Cdd:PRK05672 595 ESRAQMAMLPRLRPRTFYDLvVEVAivrpgpiqgGMVHpylrrrnGQEPVTYPHPELEK----VLERTLGVplfQEQVMq 670
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1215 VYLIHAGLDSG--------MA-FKIMETVRKglwnkipdeLRETYLNAMKENNVPDWYIDSC-SKIK----YMFPKAHAA 1280
Cdd:PRK05672 671 IAIDAAGFTPGeadqlrraMAaWRRKGRLER---------LRERLYDGMLARGYTGEFADRIfEQIKgfgeYGFPESHAA 741
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1281 AYVLMALRVAYFKVYFPILYYCAYfsVRAddfdlvsmckgkdavkQAMkeitdkGM--------DASvkeKNQLTVLEla 1352
Cdd:PRK05672 742 SFAKLVYASSWLKCHHPAAFCAAL--LNS----------------QPM------GFyspqqlvqDAR---RHGVEVLP-- 792
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 1353 nemlergfkfgmIDLYKSDAVNfVIEGDILIAP-----FRAVPSLGTNVAKQIVEARKDGPFLSKEDLATRGKVSKTLIE 1427
Cdd:PRK05672 793 ------------VDVNASGWDA-TLEPLPDGGPavrlgLRLVRGLGEEAAERIVAARARGPFTSVEDLARRAGLDRRQLE 859
|
810
....*....|.
gi 921163465 1428 YMNDNGVLKDL 1438
Cdd:PRK05672 860 ALADAGALRSL 870
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
600-697 |
1.38e-11 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 64.49 E-value: 1.38e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 600 LNAHIGEGDSYKRARPFHATLLAKNQDGLKDLFKLISMSNVEYFErvPRIPRSQLNKLRDNLLIGSACDKGEIFEAMMQK 679
Cdd:pfam02811 65 VAPGSREETEKLLAKYFDLVLLAVHEVGYKNLIKLSSRAYLEGFK--PRIDKELLEEYFEGLIALSGCVLGHLDLILLAP 142
|
90 100
....*....|....*....|....*..
gi 921163465 680 G-VEEARNRAKFYD--------YIEVM 697
Cdd:pfam02811 143 GdYEEAEELAEEYLeifgedgfYLEIN 169
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
478-576 |
1.74e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 64.03 E-value: 1.74e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 478 GITDEMVRGSKSEEEVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKYGIPEAPNPVIDTLELARYLYPQFKRFGLGVLS 557
Cdd:PRK06195 55 GIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVN 134
|
90
....*....|....*....
gi 921163465 558 KKFGVSLeQHHRAIYDAEA 576
Cdd:PRK06195 135 NFLGYEF-KHHDALADAMA 152
|
|
| HHH_6 |
pfam14579 |
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain. |
1366-1429 |
2.37e-10 |
|
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain.
Pssm-ID: 434050 [Multi-domain] Cd Length: 88 Bit Score: 58.25 E-value: 2.37e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 921163465 1366 DLYKSDAvNFVIEGDILIAPFRAVPSLGTNVAKQIVEARKDGPFLSKEDLATR--GKVSKTLIEYM 1429
Cdd:pfam14579 8 DINRSDW-DFTVEGGGIRLGLGAIKGLGEAAAERIVEERENGPFKSLEDFARRvdLKLNKRVLEAL 72
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
338-411 |
4.15e-10 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 60.69 E-value: 4.15e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 921163465 338 RVELHVHSKMStmDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDDGVPI 411
Cdd:COG0613 3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTRWEGREV 74
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
339-405 |
9.42e-10 |
|
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: 58.02 E-value: 9.42e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 921163465 339 VELHVHSKMSTmDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVV 405
Cdd:cd07432 1 ADLHIHSVFSP-DSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEVTLV 66
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
425-580 |
2.29e-09 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 60.07 E-value: 2.29e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGL---SAVYDTIIELAAVKMYKGN--VIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLE 499
Cdd:PRK06722 7 FIVFDIERNFRpykSEDPSEIVDIGAVKIEASTmkVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQ 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 500 F-SKDTILVAHNAAfDMGFLNTSYAKYGIpEAPNPVIDT-LELARYLYPQFKRF-----GLGVLSKKFGVSLE-QHHRAI 571
Cdd:PRK06722 87 FiGEDSIFVTWGKE-DYRFLSHDCTLHSV-ECPCMEKERrIDLQKFVFQAYEELfehtpSLQSAVEQLGLIWEgKQHRAL 164
|
....*....
gi 921163465 572 YDAEATGHL 580
Cdd:PRK06722 165 ADAENTANI 173
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
339-411 |
3.99e-09 |
|
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: 57.02 E-value: 3.99e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 921163465 339 VELHVHSKMStmDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDDGVPI 411
Cdd:cd07438 1 IDLHTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVEISTEYEGREV 71
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
424-512 |
5.66e-09 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 57.48 E-value: 5.66e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 424 TYVVFDVETTGLSAVyDTIIELAAVKMYKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLFLEFSKD 503
Cdd:PRK07247 6 TYIAFDLEFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVGE 84
|
....*....
gi 921163465 504 TILVAHNAA 512
Cdd:PRK07247 85 LPLIGYNAQ 93
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
418-499 |
1.44e-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: 58.57 E-value: 1.44e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 418 ESLSEGTYVVFDVETTGLSAVYDTIIELAAVKM-YKGNVIASFDEFIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRL 496
Cdd:pfam13361 181 IALEQDNIVVFDVETTGLDTTEDEIIQIAAIKLnKKGVVIESFERFLRLKKPVGDSLQVHGFSDEFLQENGETPAEALRD 260
|
...
gi 921163465 497 FLE 499
Cdd:pfam13361 261 FLE 263
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
242-323 |
2.88e-08 |
|
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: 51.85 E-value: 2.88e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 242 VTLEGYVFDKEvrelRSKRKILTLKITDYTSSFIVKKFsnNEKDEQIFEAISTGSWLKVRGSIQEDTFvRDLVMNAQDIV 321
Cdd:pfam01336 1 VTVAGRVTSIR----RSGGKLLFLTLRDGTGSIQVVVF--KEEAEKLAKKLKEGDVVRVTGKVKKRKG-GELELVVEEIE 73
|
..
gi 921163465 322 EV 323
Cdd:pfam01336 74 LL 75
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
338-408 |
3.69e-08 |
|
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis
Pssm-ID: 440997 [Multi-domain] Cd Length: 232 Bit Score: 55.93 E-value: 3.69e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 338 RVELHVHSKMStmDATNNISDIVAQAGKWGHRAIAITDHggAQAFPEAHS----------------AGKKAGVKILYGVE 401
Cdd:COG1387 2 RGDLHTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDH--SPSLFVANGlseerlleyleeieelNEKYPDIKILKGIE 77
|
....*..
gi 921163465 402 ANVVDDG 408
Cdd:COG1387 78 VDILPDG 84
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
330-410 |
6.72e-07 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 54.09 E-value: 6.72e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 330 DYApegekrvELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVE---ANVVD 406
Cdd:PRK05672 4 PYA-------ELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAElslGPDPD 76
|
....
gi 921163465 407 DGVP 410
Cdd:PRK05672 77 PGGP 80
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
428-562 |
5.94e-06 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 47.98 E-value: 5.94e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 428 FDVETTGLSAVYDTIIeLAAVKMYKGNVIASFDEFIDPGHPLsrttvdltgitdemvrgsksEEEVLRLFLEFSKDTILV 507
Cdd:pfam13482 3 FDIETTGLSPGKNTIY-LIGVYDVDGDKVRTFVQYLAEGPTE--------------------EAAILQLFELLADYPLLV 61
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 921163465 508 AHN-AAFDMGFLNTSYAKYGIPEaPNPVIDtleLARYLYPQFKRFGLGVLSKKFGV 562
Cdd:pfam13482 62 TFNgKSFDVPFIKRRFKRYDLDE-LFRHID---LLHPLRKLGLESGLKSVERELGI 113
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
451-577 |
6.71e-06 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins 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. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.
Pssm-ID: 99847 Cd Length: 152 Bit Score: 47.51 E-value: 6.71e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 451 YKGNVIasFDEFIDPGHPLS--RTTVdlTGITDEMVRGSKSEEEVLRLFLEFSKDTILVAHNAAFDMGFLNTSYAKYGIP 528
Cdd:cd06144 27 EDGNVV--YDTYVKPQEPVTdyRTAV--SGIRPEHLKDAPDFEEVQKKVAELLKGRILVGHALKNDLKVLKLDHPKKLIR 102
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 921163465 529 eapnpviDTlelARYLY----PQFKRFGLGVLSKKF-GVSLEQ-HHRAIYDAEAT 577
Cdd:cd06144 103 -------DT---SKYKPlrktAKGKSPSLKKLAKQLlGLDIQEgEHSSVEDARAA 147
|
|
| PRK09248 |
PRK09248 |
putative hydrolase; Validated |
339-406 |
1.16e-05 |
|
putative hydrolase; Validated
Pssm-ID: 236429 [Multi-domain] Cd Length: 246 Bit Score: 48.30 E-value: 1.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 339 VELHVHSKMSTmDATNNISDIVAQAGKWGHRAIAITDHG----GA---------QAFPEahsagKKAGVKILYGVEANVV 405
Cdd:PRK09248 5 VDTHTHTIASG-HAYSTLHENAAEAKQKGLKLFAITDHGpdmpGAphywhfgnlRVLPR-----KVDGVGILRGIEANIK 78
|
.
gi 921163465 406 D 406
Cdd:PRK09248 79 N 79
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
420-580 |
1.45e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 48.00 E-value: 1.45e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 420 LSEGTYVVFDVETTGLSAVYDTIIELAAVKMYKGNVIASFDE--FIDPGHPLSRTTVDLTGITDEMVRGSKSEEEVLRLF 497
Cdd:PRK09146 44 LSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARhwVVKPRRPLEEESVVIHGITHSELQDAPDLERILDEL 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 498 LEFSKDTILVAHNAAFDMGFLNT---SYAKYGIpeaPNPVIDTLELARYLYPQ-----FKRFG--------LGVLSKKFG 561
Cdd:PRK09146 124 LEALAGKVVVVHYRRIERDFLDQalrNRIGEGI---EFPVIDTMEIEARIQRKqagglWNRLKgkkpesirLADSRLRYG 200
|
170
....*....|....*....
gi 921163465 562 VSLEQHHRAIYDAEATGHL 580
Cdd:PRK09146 201 LPAYSPHHALTDAIATAEL 219
|
|
| PHP_HisPPase_Ycdx_like |
cd07437 |
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
339-407 |
1.46e-05 |
|
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. YcdX may be involved in swarming.
Pssm-ID: 213992 [Multi-domain] Cd Length: 233 Bit Score: 47.82 E-value: 1.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 339 VELHVHSKMSTmDATNNISDIVAQAGKWGHRAIAITDHG----GA---------QAFPEAHSagkkaGVKILYGVEANVV 405
Cdd:cd07437 3 ADLHTHTIASG-HAYSTIEEMARAAAEKGLKLLGITDHGpampGAphpwyfgnlKVIPREIY-----GVRILRGVEANII 76
|
..
gi 921163465 406 DD 407
Cdd:cd07437 77 DY 78
|
|
| DNA_polA_I_Ecoli_like_exo |
cd06139 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
420-560 |
1.48e-05 |
|
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: 47.51 E-value: 1.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 420 LSEGTYVVFDVETTGLSAVYDTIIelaavkmykGNVIAsFDE----FIDPGHPLSRTTVDLTGItdemvrgskseEEVLR 495
Cdd:cd06139 2 LEKAKVFAFDTETTSLDPMQAELV---------GISFA-VEPgeayYIPLGHDYGGEQLPREEV-----------LAALK 60
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 921163465 496 LFLEFSKDTIlVAHNAAFDMGFLntsyAKYGIpEAPNPVIDTLELARYLYPQFKRFGLGVLSKKF 560
Cdd:cd06139 61 PLLEDPSIKK-VGQNLKFDLHVL----ANHGI-ELRGPAFDTMLASYLLNPGRRRHGLDDLAERY 119
|
|
| REX1_like |
cd06145 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ... |
444-581 |
5.00e-05 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Pssm-ID: 99848 Cd Length: 150 Bit Score: 44.78 E-value: 5.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 444 ELAAVKM--YKGNVIasFDEFIDPGHPLsrttVDL----TGITDEMVRG-SKSEEEVLRLFLEF-SKDTILVAHNAAFDM 515
Cdd:cd06145 15 ELTRVTVvdENGKVV--LDELVKPDGEI----VDYntrfSGITEEMLENvTTTLEDVQKKLLSLiSPDTILVGHSLENDL 88
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 921163465 516 GFLNTSYAKygipeapnpVIDTlelaRYLYPQF----KRFGLGVLSKKF----GVSLEQHHRAIYDAEATGHLA 581
Cdd:cd06145 89 KALKLIHPR---------VIDT----AILFPHPrgppYKPSLKNLAKKYlgrdIQQGEGGHDSVEDARAALELV 149
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
341-408 |
5.80e-05 |
|
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213991 [Multi-domain] Cd Length: 237 Bit Score: 46.26 E-value: 5.80e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 341 LHVHSKMStmDATNNISDIVAQAGKWGHRAIAITDH----GGAQAFPEA-----HSA-----GKKAGVKILYGVEANVVD 406
Cdd:cd07436 9 LHVHTTWS--DGRNSIEEMAEAARALGYEYIAITDHskslRVANGLSEErlreqIEEidalnEKLPGIRILKGIEVDILP 86
|
..
gi 921163465 407 DG 408
Cdd:cd07436 87 DG 88
|
|
| DnaQ_like_exo |
cd06125 |
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ... |
426-543 |
1.29e-04 |
|
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which 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 conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.
Pssm-ID: 176647 [Multi-domain] Cd Length: 96 Bit Score: 42.43 E-value: 1.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAVKMYKGnVIASFDefidpghplsrttvdltgitdemvrgskseeevLRLFLEFSKDTI 505
Cdd:cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPE-DTAVID---------------------------------LKDILRDKPLAI 46
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 921163465 506 LVAHNAAFDMGFLNTSYAKYGI--PEAPNPVIDTLELARY 543
Cdd:cd06125 47 LVGHNGSFDLPFLNNRCAELGLkyPLLAGSWIDTIKLAAD 86
|
|
| RPA2_OBF_family |
cd03524 |
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ... |
243-316 |
6.55e-04 |
|
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).
Pssm-ID: 239601 [Multi-domain] Cd Length: 75 Bit Score: 39.65 E-value: 6.55e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 921163465 243 TLEGYVfdKEVRELRSKRKILTLKITDYTSSFIVKKFSNNEKDEQIFEaISTGSWLKVRGSIQEDTFVRDLVMN 316
Cdd:cd03524 1 TIVGIV--VAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENL-LKEGQVVYIKGKVKKFRGRLQLIVE 71
|
|
| PHP_PolIIIA_DnaE2 |
cd07434 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
360-411 |
2.22e-03 |
|
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: 41.67 E-value: 2.22e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 921163465 360 VAQAGKWGHRAIAITDH---GGAqafPEAHSAGKKAGVKILYGVEAnVVDDGVPI 411
Cdd:cd07434 23 VARAAELGYRALAITDEcslAGV---VRAHAAAKELGLKLIVGSEL-VLADGTRL 73
|
|
| PRK08392 |
PRK08392 |
hypothetical protein; Provisional |
340-411 |
2.70e-03 |
|
hypothetical protein; Provisional
Pssm-ID: 169423 [Multi-domain] Cd Length: 215 Bit Score: 40.92 E-value: 2.70e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 921163465 340 ELHVHSKMStmDATNNISDIVAQAGKWGHRAIAITDH------GGAQAF-PEAHSAGKKAGVKILYGVEANVVDDGVPI 411
Cdd:PRK08392 2 DLHTHTVYS--DGIGSVRDNIAEAERKGLRLVGISDHihyftpSKFNAYiNEIRQWGEESEIVVLAGIEANITPNGVDI 78
|
|
| DEDDh_RNase |
cd06137 |
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ... |
426-581 |
2.83e-03 |
|
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.
Pssm-ID: 99840 Cd Length: 161 Bit Score: 39.96 E-value: 2.83e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 426 VVFDVETTGLSAVYDTIIELAAVKMYKGNVIasFDEFIDPGHPLSRTTVDLTGIT----DEMVRGSKS---EEEVLRLFL 498
Cdd:cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL--IDSLVRPSVRVTDWRTRFSGVTpadlEEAAKAGKTifgWEAARAALW 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 499 EFS-KDTILVAHNAAFDMGFLNTSYAKygipeapnpVIDTLELARylYPQFKRF-----GLGVLSKKF-GVSLEQH---H 568
Cdd:cd06137 79 KFIdPDTILVGHSLQNDLDALRMIHTR---------VVDTAILTR--EAVKGPLakrqwSLRTLCRDFlGLKIQGGgegH 147
|
170
....*....|...
gi 921163465 569 RAIYDAEATGHLA 581
Cdd:cd06137 148 DSLEDALAAREVV 160
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
425-578 |
3.41e-03 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 41.96 E-value: 3.41e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 425 YVVFDVETTGLSAVYDTIIELA-AVKmyKGNVIasfdeFIDPGHP----LSRTTVdltgitdemvrgskseEEVLRLFLE 499
Cdd:COG0749 3 LVAFDTETTSLDPMDAELVGISfAVE--PGEAA-----YIPLAHGapeqLDLDEV----------------LAALKPLLE 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 500 fSKDTILVAHNAAFDMGFLntsyAKYGIPEAPnPVIDTLeLARY-LYPQFKRFGLGVLSKKFGvsleqHHRAIYDAEATG 578
Cdd:COG0749 60 -DPAIPKIGQNLKYDLHVL----ARYGIELAG-VAFDTM-LASYlLNPGRRRHGLDDLAERYL-----GHETISYEELAG 127
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
614-732 |
8.35e-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: 39.11 E-value: 8.35e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 921163465 614 RPFHATLLAKNQDGLKDLFKLISMSN-VEYFERVPRIPRSQLNKLRDNLLIGSACDKGEIFEAmmQKGVEE-ARNRAKF- 690
Cdd:cd07431 71 EPYPLLLLAKNNEGYQNLLRLSTAAMlGEEKDGVPYLDLEELAEAASGLLVVLLGPLLLLLAA--EQGLPLvATNDVHYl 148
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 921163465 691 ----YDYIEVMPKAvyaplleqelvknerdleEIIQNLVEIGKSLD 732
Cdd:cd07431 149 npedAFAADVLTAF------------------LAVANTVRIAKECA 176
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
339-413 |
9.01e-03 |
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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: 39.77 E-value: 9.01e-03
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gi 921163465 339 VELHVHSKMSTMDATNNISDIVAQAGKWGHRAIAITDHGGAQAFPEAHSAGKKAGVKILYGVEANVVDDGVPIAY 413
Cdd:cd07433 3 VHLRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSNLFGAVKFYKAASKAGIKPIIGADLNVANPDDADEP 77
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