|
Name |
Accession |
Description |
Interval |
E-value |
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
1-1460 |
0e+00 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 2562.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1 MSDKFQLLLQQIGMPLDARQSgAFSTATIEKVVLHKVSKLWEFTFRFETPLPLMDYQLFKARLATEFEKV-GNKIQFSIV 79
Cdd:PRK00448 3 MQEKFKKLLDQINIPDDLQSE-ALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFSHIaDIKVTFSIE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 80 SDAEAFEAGLVEAYYPEAFTEDLCQSAGFKALFQPLEVAYRDGVLWIKGPETIDTDHFRKNHLPNLVEQYKRFGFGNLAV 159
Cdd:PRK00448 82 VENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILKI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 160 DIQVCQEMtqQQAEIFHAQNAEIYQQANEENLAALEQLAQMAPPPEAAQPFvpeYKKNRPAKVNIEKAEITPMIEVDSEE 239
Cdd:PRK00448 162 DFEIDDSK--EELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDP---KEGPVQIGKKIDKEEITPMKEINEEE 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 240 NRIVFEGLVFEVEQKTTKTGRVIINFKMTDYTSSFTLQKWAKNEEEAQKFDMVKKGNWLRVRGNVETNNFTRDLTMNVQE 319
Cdd:PRK00448 237 RRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQD 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 320 VQEVKKEIRKDLMPEgEKRVEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFG 399
Cdd:PRK00448 317 INEIKHPERKDTAEE-EKRVELHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYG 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 400 MEANIVEDSVPIAYNEADVVLSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGI 479
Cdd:PRK00448 396 VEANLVDDGVPIVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGI 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 480 TDEHVRGSKPLEQVLREFQDFCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKR 559
Cdd:PRK00448 476 TDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 560 FGVALEHHHMANYDAEATGRLLFIFLKDALEKhNLTNLNQLNTELIAEDSYKKARVKHATLYVINQVGLKNMFKLVSLSN 639
Cdd:PRK00448 556 FGVELEHHHRADYDAEATAYLLIKFLKDLKEK-GITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSN 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 640 TKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYDFIEVMPPALYAPMIAKEQFKDMAEIEE 719
Cdd:PRK00448 635 TKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKE 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 720 TIKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVRALGQGAPINWTigngenaqpaPLPKAHFRTTSEMLDEFAFLG 799
Cdd:PRK00448 715 IIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRKILVASQGGGNPLNRH----------PLPELHFRTTDEMLDEFAFLG 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 800 ESLAREIVITNPNAMLDRFEDVQVVKTDLYTPYIEKAEETVAELTYQKAFEIYGNPLPDIIDLRIEKELTSILGNGFAVI 879
Cdd:PRK00448 785 EELAKEIVVENTNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIYGEPLPEIVEKRIEKELNSIIGNGFAVI 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 880 YLASQMLVHRSNERGYLVGSRGSVGSSFVATMIGITEVNPMPPHYVCPNCQHSEFITDGSYGSGFDLPDKDCEKCGTKYK 959
Cdd:PRK00448 865 YLISQKLVKKSLEDGYLVGSRGSVGSSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLK 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 960 KDGQDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTAYGFVRGYERDYGKFYRDVE 1039
Cdd:PRK00448 945 KDGHDIPFETFLGFKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTAYGYVKKYEEDTGKFYRNAE 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1040 VERLAAGAAGVKRTTGQHPGGIIVFPDYMDVYDFTPVQYPADDVTASWQTTHFNFHDIDENVLKLDILGHDDPTMVRKLQ 1119
Cdd:PRK00448 1025 IDRLAQGCTGVKRTTGQHPGGIIVVPKYMDIYDFTPIQYPADDVNSEWKTTHFDFHSIHDNLLKLDILGHDDPTMIRMLQ 1104
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1120 DLSGIDPQTIPADDKGVMALFSGTEILGVTPEQIGTPTGMLGIPEFGTNFVRGMVEETKPTTFSELLQLSGLSHGTDVWL 1199
Cdd:PRK00448 1105 DLTGIDPKTIPMDDPKVMKLFSSTEALGVTPEQIGCETGTLGIPEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWL 1184
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1200 GNAQDLIKAGIANLSTVIGCRDDIMVYLMHAGLPPKMAFNIMERVRKGlwLKISEEerngYIQAMKDNKVPDWYIESCGK 1279
Cdd:PRK00448 1185 GNAQELIKEGIATLSDVIGCRDDIMVYLIHKGLEPKLAFKIMESVRKG--KGLTEE----EEELMKENNVPDWYIESCKK 1258
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1280 IKYMFPKAHAAAYVMMALRVAYFKVHHPLYYYCAYFSIRAKAFDLATMSGGLERVKAKMEEIalKKKNNEASNVEQDLYT 1359
Cdd:PRK00448 1259 IKYMFPKAHAAAYVLMAWRIAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEI--KSKGNDASNKEKDLLT 1336
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1360 TLELVNEMLERGFKFGKLDLYKSHATDFLIEEDTLIPPFVAMDGLGENVAKQVVAARAEGEFLSKTELRKRGGLSGTLVE 1439
Cdd:PRK00448 1337 VLEIALEMLERGFKFQKVDLYKSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIE 1416
|
1450 1460
....*....|....*....|.
gi 500942978 1440 KMDEMGILGKMPEDNQLSLFD 1460
Cdd:PRK00448 1417 KLDELGVLDDLPETNQLSLFD 1437
|
|
| polC_Gram_pos |
TIGR01405 |
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain ... |
233-1459 |
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: 2010.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 233 IEVDSEENRIVFEGLVFEVEQKTTKTGRVIINFKMTDYTSSFTLQKWAKNEEEAQKFDMVKKGNWLRVRGNVETNNFTRD 312
Cdd:TIGR01405 1 EKINEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 313 LTMNVQEVQEVKKEIRKDLMPEgeKRVEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKA 392
Cdd:TIGR01405 81 LQMIIKDIEEIPYAERKDNAKE--KRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKD 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 393 GIKPLFGMEANIVEDSVPIAYNEADVVL-SDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQ 471
Cdd:TIGR01405 159 GIKIIYGMEANLVDDRVPIVYNPDDQKLlDDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSA 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 472 FTTDLTGITDEHVRGSKPLEQVLREFQDFCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRH 551
Cdd:TIGR01405 239 FVTELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSH 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 552 GLGPLTKRFGVALEHHHMANYDAEATGRLLFIFLKDALEKhNLTNLNQLNTELIAEDSYKKARVKHATLYVINQVGLKNM 631
Cdd:TIGR01405 319 RLGNICKKLGVDLDDHHRADYDAEATAKVFKVMVEQLKEK-GITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNL 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 632 FKLVSLSNTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYDFIEVMPPALYAPMIAKEQF 711
Cdd:TIGR01405 398 YKLVSISLTKYFYTRPRILRSLLKKYREGLLIGSACSEGELFDALLSKPDDELEEIAKRYDFIEIQPPGNYAHLIEREQV 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 712 KDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVRALGQGAPINWTIGNGEnaqpapLPKAHFRTTSEM 791
Cdd:TIGR01405 478 KDKEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYRKILVASQGLGNPLNRHFNPKE------VPELHFRTTNEM 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 792 LDEFAFLGESLAREIVITNPNAMLDRFEDVQVVKTDLYTPYIEKAEETVAELTYQKAFEIYGNPLPDIIDLRIEKELTSI 871
Cdd:TIGR01405 552 LDEFSFLGEEKAYEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIYGDPLPEIVEQRIEKELKSI 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 872 LGNGFAVIYLASQMLVHRSNERGYLVGSRGSVGSSFVATMIGITEVNPMPPHYVCPNCQHSEFITDGSYGSGFDLPDKDC 951
Cdd:TIGR01405 632 IGNGFAVIYLISQLLVQKSLQDGYLVGSRGSVGSSLVATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDC 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 952 EKCGTKYKKDGQDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTAYGFVRGYERDY 1031
Cdd:TIGR01405 712 PKCGAPLKKDGQDIPFETFLGFKGDKVPDIDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAYGYVKKYFEDQ 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1032 GKFYRDVEVERLAAGAAGVKRTTGQHPGGIIVFPDYMDVYDFTPVQYPADDVTASWQTTHFNFHDIDENVLKLDILGHDD 1111
Cdd:TIGR01405 792 GKHYRDAEIERLVQGCTGVKRTTGQHPGGIIIVPKYMDVYDFTPVQYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHDD 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1112 PTMVRKLQDLSGIDPQTIPADDKGVMALFSGTEILGVTPEQIGTPTGMLGIPEFGTNFVRGMVEETKPTTFSELLQLSGL 1191
Cdd:TIGR01405 872 PTMIKMLQDLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFGTKFVRGMLEETKPKTFADLVRISGL 951
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1192 SHGTDVWLGNAQDLIKAGIANLSTVIGCRDDIMVYLMHAGLPPKMAFNIMERVRKGLWLKiseeerNGYIQAMKDNKVPD 1271
Cdd:TIGR01405 952 SHGTDVWLGNAQDLIKSGIKTLSDVIGCRDDIMVYLIHKGLEPKLAFKIMEKVRKGKGLK------AEYIELMKENKVPE 1025
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1272 WYIESCGKIKYMFPKAHAAAYVMMALRVAYFKVHHPLYYYCAYFSIRAKAFDLATMSGGLERVKAKMEEIALKKKNNEAS 1351
Cdd:TIGR01405 1026 WYIESCLKIKYMFPKAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKAFDLETMIKGKEFIKQKLEEINTRRKINKAS 1105
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1352 NVEQDLYTTLELVNEMLERGFKFGKLDLYKSHATDFLIEEDTLIPPFVAMDGLGENVAKQVVAARAEGEFLSKTELRKRG 1431
Cdd:TIGR01405 1106 PKEKDLLTVLEIVLEMMARGFKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRT 1185
|
1210 1220
....*....|....*....|....*...
gi 500942978 1432 GLSGTLVEKMDEMGILGKMPEDNQLSLF 1459
Cdd:TIGR01405 1186 KISKTHIEKLDSMGVLDNLPETNQLSLF 1213
|
|
| PHP_PolIIIA_POLC |
cd07435 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
616-822 |
1.14e-87 |
|
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: 286.29 E-value: 1.14e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 616 KHATLYVINQVGLKNMFKLVSLSNTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVK-TAAYYDFI 694
Cdd:cd07435 71 YHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNKKSDEELEeIASFYDYI 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 695 EVMPPALYAPMIAKEQFKDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVRALGqgapinwtiGNGEN 774
Cdd:cd07435 151 EIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVVATGDVHYLDPEDKIYREILLAGQG---------GGDGR 221
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 500942978 775 AQpaPLPKAHFRTTSEMLDEFAFLGESLAREIVITNPNAMLDRFEDVQ 822
Cdd:cd07435 222 AD--EQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIEDIK 267
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
420-597 |
3.52e-73 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 241.59 E-value: 3.52e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 420 LSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQD 499
Cdd:COG2176 5 LEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 500 FCQDSVMVAHNATFDVGFMNVNYERAGLPiISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEATGR 579
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAE 163
|
170
....*....|....*...
gi 500942978 580 LLFIFLKDaLEKHNLTNL 597
Cdd:COG2176 164 LFLKLLEK-LEEKGITTL 180
|
|
| DNA_pol3_alpha |
pfam07733 |
Bacterial DNA polymerase III alpha NTPase domain; |
842-1108 |
4.42e-68 |
|
Bacterial DNA polymerase III alpha NTPase domain;
Pssm-ID: 400196 [Multi-domain] Cd Length: 259 Bit Score: 230.08 E-value: 4.42e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 842 ELTYQKAFEIYGNPLPDIIDLRIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVGS-RGSVGSSFVATMIGITEVNPM 920
Cdd:pfam07733 5 KLVEEGLKERYGEGLPEEYQERLEYELNVIIKMGFAGYFLIVWDLVKWAKDNGILVGPgRGSAAGSLVAYLLGITEVDPL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 921 pphyvcpncqhsefitdgsygsgfdlpdkdcekcgtKYkkdgqDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDI 1000
Cdd:pfam07733 85 ------------------------------------KH-----DLLFERFLNPERVSMPDIDIDFEDERREEVIDYVKEK 123
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1001 FGEENAFRAGTVGTVAAKTA-------YGFVRGY---------------------ERDYGKFY-RDVEVERL---AAGAA 1048
Cdd:pfam07733 124 YGRDRVAQIATFGTYAAKSAirdvgraLGLPYDEidrlaklipfelgilekaleeEPELKELIeSDPEVKRLielAKKLE 203
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500942978 1049 GVKRTTGQHPGGIIVFPDymDVYDFTPVQYPADDVTaswQTTHFNFHDIDE-NVLKLDILG 1108
Cdd:pfam07733 204 GLPRHTGQHAGGVVISPD--PLTDFVPLYKADDDDR---PVTQFDKDDLEDlGLLKMDFLG 259
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
425-581 |
3.98e-55 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 189.23 E-value: 3.98e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDS 504
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500942978 505 VMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEATGRLL 581
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELF 158
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
426-582 |
1.96e-51 |
|
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: 178.26 E-value: 1.96e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 426 VVFDVETTGLSAVNNALIQIAASKMHKGNIIAE-FDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDS 504
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVErFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500942978 505 VMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLT-KRFGVALEHHHMANYDAEATGRLLF 582
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLaERYGIPLEGAHRALADALATAELLL 159
|
|
| polc |
TIGR00594 |
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
617-1429 |
5.94e-46 |
|
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: 181.04 E-value: 5.94e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 617 HATLYVINQVGLKNMFKLVSLSNTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYD---- 692
Cdd:TIGR00594 86 HLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALKYQeifg 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 693 ---FIEVMPPAlyapmIAKEQFKDmaeieetiKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVrALGQGAPInwti 769
Cdd:TIGR00594 166 ddyYLELQDHG-----IPEQRVVN--------EALLEISEELGIPLVATNDVHYINPEDAHAHEILL-CIQTGKTL---- 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 770 gNGENAQPAPLPKAHFRTTSEMLDEFAFLGESLAREIVITnpnamldrfEDVQVVKTDLYTPYI---------EKAEETV 840
Cdd:TIGR00594 228 -SDPKRLKFYSDEFYLKSPEEMAELFADIPEALANTVEIA---------ERCNLVDVKLGPPRLpsyqippdfTSQEDYL 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 841 AELTYQKAFEIYGNPLPDIIDL-----RIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG-SRGSVGSSFVATMIGI 914
Cdd:TIGR00594 298 RHLADEGLRERLAAGPPGYKRRaqykeRLEYELDVINSMGFPGYFLIVWDFIKWAKDHGIPVGpGRGSAAGSLVAYALKI 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 915 TEVNPMPphyvcpncqhsefitdgsygsgFDLpdkdcekcgtkykkdgqdiPFETFLGFDGDKVPDIDLNFSGDDQPSAH 994
Cdd:TIGR00594 378 TDIDPIK----------------------HGL-------------------LFERFLNPERISMPDIDIDFCDERRDEVI 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 995 LDVRDIFGEENAFRAGTVGTVAAKTAygfVRGYERDYGKFYRDV------------------------------------ 1038
Cdd:TIGR00594 417 EYVADKYGHDNVAQIITFGTMKAKAA---LRDVARVLDIPYAEAdriaklipprpgktlkealeaspqlrqlyeedpevk 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1039 EVERLAAGAAGVKRTTGQHPGGIIVFPDYMDvyDFTPVQYPADDVTASwqtTHFNFHDIDE-NVLKLDILG-------HD 1110
Cdd:TIGR00594 494 QLIDMARKLEGLNRNAGVHAAGVVISSEPLT--DYVPLYKDKEGGAIS---TQYDMDDLEAvGLLKMDFLGlktltliQD 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1111 DPTMVRKLQDLSgIDPQTIPADDKGVMALFSGTEILGVTpeQIGTpTGMlgipefgtnfvRGMVEETKPTTFSELLQLSG 1190
Cdd:TIGR00594 569 ATELIRKRRGID-LDIASIPLDDKKTFSLLQEGDTTGVF--QLES-RGM-----------QDLLKRLKPDGFEDIIAVNA 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1191 LSHGTDVWLGNAQDLI--KAGIANLSTVIGCRDDI-------MVY---LMH-----AGLPPKMAfNIMERVRKGLWLKIS 1253
Cdd:TIGR00594 634 LYRPGPMESGMIPDFIdrKHGREPIEYPHPLLEPIlketygvIVYqeqVMQiaqrlAGFSLGEA-DLLRRAMGKKKAEEM 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1254 EEERNGYIQAMKDNKVPDWYIESCGKI-----KYMFPKAHAAAYVMMALRVAYFKVHHPLYYycayfsirakafdlatMS 1328
Cdd:TIGR00594 713 AKEREKFVEGAEKNGYDPEIAENLFDLiekfaGYGFNKSHAAAYGMISYQTAYLKANYPAEF----------------MA 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1329 GGLERVKAKMEEIALkkknneasnveqdlyttleLVNEMLERGFKFGKLDLYKShATDFLIEEDTLIPPFVAMDGLGENV 1408
Cdd:TIGR00594 777 ALLTSEINDIEKVAV-------------------YIAEAKKMGIEVLPPDINES-GQDFAVEDKGIRYGLGAIKGVGESV 836
|
890 900
....*....|....*....|....*...
gi 500942978 1409 AKQVVAARAEG-------EFLSKTELRK 1429
Cdd:TIGR00594 837 VKSIIEERNKNgpfkslfDFINRVDFKK 864
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
617-1430 |
1.10e-45 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 180.27 E-value: 1.10e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 617 HATLYVINQVGLKNMFKLVSLSNTK-YFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYD--- 692
Cdd:COG0587 82 HLVLLAKNREGYRNLCRLLSRAYLEgFYKGKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALARLKdif 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 693 ----FIEVMPPalyapmiakeqfkDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEE-EIYReiIVRALGQGAPIN- 766
Cdd:COG0587 162 gdrfYLELQRH-------------GLPEDRRVNAALLELARELGLPLVATNDVHYLNPEDaEAHD--VLLCIRTGKTLDd 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 767 ---WTIGNGEnaqpaplpkAHFRTTSEMLDEFAFLGESLAREIVItnpnamLDRFEdvqvVKTDLYTPYI--------EK 835
Cdd:COG0587 227 pgrRRFANAE---------RYLKSPEEMAELFADLPEALANTLEI------AERCN----FSLDLGKYQLpkfpvpegET 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 836 AEETVAELTYQKAFEIYGNPLPDIIDLRIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVGS-RGSVGSSFVATMIGI 914
Cdd:COG0587 288 EEEYLRKLAEEGLERRYPEGIPEEYRERLEYELDVIEKMGFPGYFLIVWDFIRWARSNGIPVGPgRGSAAGSLVAYALGI 367
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 915 TEVNPMPphyvcpncqhsefitdgsygsgFDLpdkdcekcgtkykkdgqdiPFETFLGFDGDKVPDIDLNFSGDDQpsah 994
Cdd:COG0587 368 TDVDPIR----------------------YDL-------------------LFERFLNPERVSMPDIDIDFCHERR---- 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 995 lD-----VRDIFGEENAFRAGTVGTVAAKTA-----------YGFV----RGYERDYG--------------KFYR-DVE 1039
Cdd:COG0587 403 -EeviqyVYEKYGRDRVAQIATFGTMRARAAirdvgrvlglpYGEVdrlaKLIPNDPGitlekaleeepelrELYDsDPE 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1040 VERL---AAGAAGVKRTTGQHPGGIIVFPDymDVYDFTPVQYPADDvtaSWQTTHFNFHDIDE-NVLKLDILG------- 1108
Cdd:COG0587 482 VRRLldlARKLEGLPRHLSTHAGGVVISDD--PLTDLVPLERAAMG---GRPVTQFDKDDVEAlGLLKFDFLGlrtltvi 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1109 HDDPTMVRKLQDLSgIDPQTIPADDKGVMALFSGTEILGVTpeQIGTPtGMlgipefgtnfvRGMVEETKPTTFSellql 1188
Cdd:COG0587 557 RDALDLIKENRGID-IDLADIPLDDPKTYELLQRGDTIGVF--QLESR-GM-----------RSLLKRLKPDCFE----- 616
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1189 sglshgtdvwlgnaqDLIkAGIA--------------------NLSTVI--------------GcrddIMVY---LMH-- 1229
Cdd:COG0587 617 ---------------DLV-ALVAlyrpgpmqggmvppyirrkhGREPVEyphpelepilketyG----VIVYqeqVMQia 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1230 ---AGLPPKMAfnimERVRKGLWLKISEE---ERNGYIQAMKDNKVPDWYIESC-GKIK----YMFPKAHAAAYVMMALR 1298
Cdd:COG0587 677 qvlAGFSLGEA----DLLRRAMGKKKKEEmakQREKFVEGAVANGYDEEFAEEIfDQIEkfagYGFNKSHAAAYALLAYQ 752
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1299 VAYFKVHHPLYYYCayfsirakafdlATMsgglervkakmeeialkkknneaSNVEQDLYTTLELVNEMLERGFKFGKLD 1378
Cdd:COG0587 753 TAYLKAHYPAEFMA------------ALL-----------------------NSQPMGFYKPAQYVQEARRHGIEVLPPD 797
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 500942978 1379 LYKSHAtDFLIEEDTLIP-PFVAMDGLGENVAKQVVAARAE-GEFLSKTELRKR 1430
Cdd:COG0587 798 VNESDW-DFTVEPGGAIRlGLGAIKGVGEAAAEAIVAAREEnGPFTSLFDFCRR 850
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
412-577 |
6.32e-43 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 166.25 E-value: 6.32e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 412 AYNEADVVLSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLE 491
Cdd:PRK07883 4 SFDDLGTPLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 492 QVLREFQDFCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYP--DFKRHGLGPLTKRFGVALEHHHM 569
Cdd:PRK07883 84 EVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTPTHR 163
|
....*...
gi 500942978 570 ANYDAEAT 577
Cdd:PRK07883 164 ALDDARAT 171
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
424-587 |
1.99e-40 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 147.45 E-value: 1.99e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 424 TYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQD 503
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 504 SVMVAHN-ATFDVGFMNVNYERAGLPIISQ-PVIDTLEFARNLYPDFKRHGLGPLTKRFGVALE-HHHMANYDAEATGRL 580
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGIKQPPKlPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARATAKL 160
|
....*..
gi 500942978 581 LFIFLKD 587
Cdd:smart00479 161 FKKLLER 167
|
|
| DNA_pol3_finger |
pfam17657 |
Bacterial DNA polymerase III alpha subunit finger domain; |
1111-1267 |
3.33e-38 |
|
Bacterial DNA polymerase III alpha subunit finger domain;
Pssm-ID: 407553 [Multi-domain] Cd Length: 166 Bit Score: 140.75 E-value: 3.33e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1111 DPTMVRKLQDLS------GIDPQTIPADDKGVMALFSGTEILGVtpeqigtptgmlgiPEFGTNFVRGMVEETKPTTFSE 1184
Cdd:pfam17657 1 TLTIIRDALDLIkenrgiGIDLATIPLDDPKTYKLLSSGDTLGV--------------FQFESRGMRQMLKRLKPDTFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1185 LLQLSGLSHGTDVWLGNAQDLI--KAGIAN-------LSTVIGCRDDIMVY--------LMHAGLPPKMAFNIMERVRKG 1247
Cdd:pfam17657 67 LVALSALYRPGPMQGGNVDDYIkrKHGKEKieyphpdLEPILKETYGVIVYqeqvmqiaQILAGFSLGEADLLRRAMGKK 146
|
170 180
....*....|....*....|
gi 500942978 1248 lWLKISEEERNGYIQAMKDN 1267
Cdd:pfam17657 147 -KPEEMEKLREKFIEGAKEN 165
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
424-600 |
3.24e-36 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 149.33 E-value: 3.24e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 424 TYVVFDVETTGLSAVNNA-LIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQ 502
Cdd:PRK08074 4 RFVVVDLETTGNSPKKGDkIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 503 DSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGvaLEHH--HMANYDAEATGrL 580
Cdd:PRK08074 84 GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELG--LEHDqpHRADSDAEVTA-E 160
|
170 180
....*....|....*....|
gi 500942978 581 LFIFLKDALEKHNLTNLNQL 600
Cdd:PRK08074 161 LFLQLLNKLERLPLVTLQQL 180
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
424-618 |
9.29e-34 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 141.09 E-value: 9.29e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 424 TYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQD 503
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 504 SVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEATGRLLfI 583
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELL-L 159
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 500942978 584 FLKDALEKHNLTNLNQL---------NTELIAEDSYKKARVKHA 618
Cdd:TIGR01407 160 LLFEKMEKLPLDTLEQLlelsdqllyESYDIIQETYRQYKIKPA 203
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
424-638 |
2.13e-32 |
|
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: 126.03 E-value: 2.13e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 424 TYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQD 503
Cdd:TIGR00573 8 TETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 504 SVMVAHNATFDVGFMNVNYERAGLPI-ISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEATGRLLF 582
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKLYKVEpKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILA 167
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 500942978 583 IFLKDALEKHnltnlnqlntELIAEDSYKKARVKHATLYVINQVGLKNMFKLVSLS 638
Cdd:TIGR00573 168 KLYLVMTGKQ----------TKYGENEGQQSRPYHAIKSIVKKDMLLKLIKAVSTE 213
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
425-581 |
1.44e-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: 121.46 E-value: 1.44e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTglSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDS 504
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500942978 505 VMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHmANYDAEATGRLL 581
Cdd:cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHD-ALEDARACAEIL 154
|
|
| dnaE |
PRK06826 |
DNA polymerase III DnaE; Reviewed |
617-1462 |
2.46e-31 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 134.25 E-value: 2.46e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 617 HATLYVINQVGLKNMFKLVSLSNTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYD---- 692
Cdd:PRK06826 89 HLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKdifg 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 693 ----FIEVmppalyapmiakeQFKDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVrALGQGAPInwt 768
Cdd:PRK06826 169 kenfYLEL-------------QDHGIPEQRKVNEELIKLSKELGIPLVATNDVHYIRKEDAKAHDVLL-CIQTGKTV--- 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 769 igNGENAQPAPLPKAHFRTTSEMLDEFAFLGESLAREIVITNP-NAMLDrFEDVQVVKTDL---YTPYiekaeETVAELT 844
Cdd:PRK06826 232 --DDENRMRFPSDEFYLKSPEEMYELFSYVPEALENTVKIAERcNVEFE-FGKSKLPKFPLpegYDPY-----EYLRELC 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 845 YQKAFEIYGNPLPDIIDlRIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG-SRGSVGSSFVATMIGITEVNPMpph 923
Cdd:PRK06826 304 YEGLKKRYPNPSEELIE-RLEYELSVIKQMGYVDYFLIVWDFIRFARENGIMVGpGRGSAAGSLVAYTLGITKIDPI--- 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 924 yvcpncqhsefitdgsygsgfdlpdkdcekcgtKYkkdgqDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGE 1003
Cdd:PRK06826 380 ---------------------------------KY-----NLLFERFLNPERVSMPDIDIDFCYERRQEVIDYVVEKYGK 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1004 ENAFRAGTVGTVAAKTA-----------YGFV--------------------------RGYERDYgkfyrdvEVERL--- 1043
Cdd:PRK06826 422 DRVAQIITFGTMAARAAirdvgralnypYAEVdriakmiptelgitidkalelnpelkEAYENDE-------RVRELidt 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1044 AAGAAGVKRTTGQHPGGIIVFPDYMDVYdfTPVQYPADDVtaswqTTHFNFHDIDE-NVLKLDILG-------HDDPTMV 1115
Cdd:PRK06826 495 ARALEGLPRHASTHAAGVVISSEPLVEY--VPLQKNDGSI-----VTQFTMTTLEElGLLKMDFLGlrtltviRDAVDLI 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1116 RKLQDLSgIDPQTIPADDKGVMALFSGTEILGVTpeQIGTPtGMlgipefgTNFVRgmveETKPTTFsellqlsglshgt 1195
Cdd:PRK06826 568 KKNRGIE-IDLDKIDYDDKKVYKMIGEGKTVGVF--QLESA-GM-------RSFMK----ELKPDSL------------- 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1196 dvwlgnaQDLIkAGIAnLstvigCR----DDIMVYL-----------MHAGLPP--KMAFN-------IMERVRK--GLW 1249
Cdd:PRK06826 620 -------EDII-AGIS-L-----YRpgpmDSIPRYIknknnpekieyLHPKLEPilKVTYGcivyqeqVMQIVRDlaGYS 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1250 L---------------KISEEERNGYIQAMKDNKVPDWY-----IESCGKI--------KYMFPKAHAAAYVMMALRVAY 1301
Cdd:PRK06826 686 MgrsdlvrramskkkhDVMEEERKNFIYGIVDEGGPGCIrngidEETANKIfdsmmdfaSYAFNKSHAAAYAVVAYQTAY 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1302 FKVHHPLYYYCAYfsirakafdlatmsggLERVKAKMEEIAlkkknneasnveqdlyttlELVNEMLERGFKFGKLDLYK 1381
Cdd:PRK06826 766 LKRYYPVEFMAAL----------------LNSVMGNSDKVA-------------------FYIEECRRLGIEVLPPDINE 810
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1382 SHAtDFLIEEDTLIPPFVAMDGLGENVAKQVVAARAEG-------EFLSKTELR---------------------KRGGL 1433
Cdd:PRK06826 811 SYS-KFTVEGDKIRFGLAAVKNVGENAIDSIVEEREKKgkfkslvDFCERVDTSqinkraveslikagafdslgvYRSQL 889
|
970 980
....*....|....*....|....*....
gi 500942978 1434 SGTLVEKMDEMGILGKMPEDNQLSLFDDL 1462
Cdd:PRK06826 890 LAVYEKILDSISKQRKKNIEGQISLFDLI 918
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
425-567 |
3.76e-29 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 119.53 E-value: 3.76e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDS 504
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500942978 505 VMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHH 567
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSH 152
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
426-581 |
7.88e-29 |
|
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: 113.99 E-value: 7.88e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 426 VVFDVETTGLSAVNNALIQIAASKMHKG--NIIAEFDEFIDPGHP--LSQFTTDLTGITDEHVRGSKPLEQVLREFQDFC 501
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGenEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 502 Q-DSVMVAHNATFDVGFMNVNYERAG---LPIISqPVIDTLEFARNLYPDFKRHGLGPLTKRFGVA-LEHHHMANYDAEA 576
Cdd:pfam00929 81 RkGNLLVAHNASFDVGFLRYDDKRFLkkpMPKLN-PVIDTLILDKATYKELPGRSLDALAEKLGLEhIGRAHRALDDARA 159
|
....*
gi 500942978 577 TGRLL 581
Cdd:pfam00929 160 TAKLF 164
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
416-604 |
7.28e-28 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 113.61 E-value: 7.28e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 416 ADVVLSDATYVVFDVETTGLSAVN-NALIQIAASKMhKGNIIAE--FDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQ 492
Cdd:PRK07740 52 LDIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKT-KGGEVETdtFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAE 130
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 493 VLREFQDFCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANY 572
Cdd:PRK07740 131 VLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALG 210
|
170 180 190
....*....|....*....|....*....|..
gi 500942978 573 DAEATGRLLFIFLKDALEKhNLTNLNQLNTEL 604
Cdd:PRK07740 211 DALMTAKLWAILLVEAQQR-GITTLHDLYAAL 241
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
425-575 |
7.77e-28 |
|
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: 111.08 E-value: 7.77e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAVNN-ALIQIAASKMHKGNIIAE-FDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQ 502
Cdd:cd06131 1 QIVLDTETTGLDPREGhRIIEIGCVELINRRLTGNtFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500942978 503 DSVMVAHNATFDVGFMNVNYERAGLPIISQP---VIDTLEFARNLYPDfKRHGLGPLTKRFGVALEHH--HMANYDAE 575
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARKKFPG-KPNSLDALCKRFGIDNSHRtlHGALLDAE 157
|
|
| polC_OBF |
cd04484 |
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
241-323 |
9.38e-28 |
|
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Pssm-ID: 239930 [Multi-domain] Cd Length: 82 Bit Score: 107.68 E-value: 9.38e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 241 RIVFEGLVFEVEQKTTKTGRVIINFKMTDYTSSFTLQKWAKNEEEaQKFDMVKKGNWLRVRGNVETNNFTRDLTMNVQEV 320
Cdd:cd04484 1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEK-DKEELKSKGDWVRVRGKVQYDTFSKELVLMINDI 79
|
...
gi 500942978 321 QEV 323
Cdd:cd04484 80 EEI 82
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
420-586 |
1.26e-25 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 107.80 E-value: 1.26e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 420 LSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDpGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQD 499
Cdd:PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVK-AKEVPEYITELTGITYEDLENAPSLKEVLEEFRL 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 500 FCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDfKRHGLGPLTKRFGVALEHHHMANYDAEATGR 579
Cdd:PRK08517 144 FLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEIEVHHRAYADALAAYE 222
|
....*..
gi 500942978 580 LLFIFLK 586
Cdd:PRK08517 223 IFKICLL 229
|
|
| DNA_pol3_a_NII |
pfam11490 |
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
92-205 |
2.33e-25 |
|
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: 102.04 E-value: 2.33e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 92 AYYPEAFTEDLCQSAGFKALFQPLEVAYRDGVLWIKGPETIDTDHFRKNHLPNLVEQYKRFGFGNLAVDIQVCQ-EMTQQ 170
Cdd:pfam11490 1 DYWEEIVEELSKKSPSLKSLLKNQKPEVEGNKLIIKVPNEIEANFLKKKNLDKLLEEYIKFGFGKLSIDVEVDEdESSEE 80
|
90 100 110
....*....|....*....|....*....|....*
gi 500942978 171 QAEIFHAQNAEIYQQANEENLAALEQLAQMAPPPE 205
Cdd:pfam11490 81 ELEEFEEQKEEEEQKAIQEAIEALEKKEAEKKSKE 115
|
|
| dnaE |
PRK05673 |
DNA polymerase III subunit alpha; Validated |
617-1148 |
4.01e-24 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 110.58 E-value: 4.01e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 617 HATLYVINQVGLKNMFKLVSLSNTK-YFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYY---- 691
Cdd:PRK05673 84 HLTLLAKNETGYRNLFKLSSRAYLEgQYGYKPRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQYDEAEEAAAEYqeif 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 692 -D--FIEVMPPALyapmiakeqfkdmaEIEETI-KQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVrALGQGAPInw 767
Cdd:PRK05673 164 gDrfYLELMRHGL--------------PIERRVeHALLELAKELGLPLVATNDVHYLTPEDAEAHEALL-CIAEGKTL-- 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 768 tigngenAQPAPL----PKAHFRTTSEMLDEFAFLGESLA--REIV------ITNPNAMLDRFEDvqvvkTDLYTPYIEK 835
Cdd:PRK05673 227 -------DDPDRFrfysPEQYLKSAEEMRELFADLPEALDntVEIAercnveVRLGKPFLPRFPT-----PDGETEEDYL 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 836 AEETVAELTYQKAFEIYGNPLPDIIDlRIEKELTSILGNGFaviylASQMLV-----HRSNERGYLVG-SRGSVGSSFVA 909
Cdd:PRK05673 295 RKEAKEGLEERLAFLFPDEERPEYVE-RLEYELDVIIQMGF-----PGYFLIvadfiQWAKDNGIPVGpGRGSGAGSLVA 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 910 TMIGITEVNPMPphyvcpncqhsefitdgsygsgFDLpdkdcekcgtkykkdgqdiPFETFLgfDGDKV--PDIDLNFsg 987
Cdd:PRK05673 369 YALGITDLDPLR----------------------FGL-------------------LFERFL--NPERVsmPDFDIDF-- 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 988 dDQpsahlD--------VRDIFGEENAFRAGTVGTVAAKTA-----------YGFV-R-----------------GYERD 1030
Cdd:PRK05673 404 -CQ-----DrrdeviryVAEKYGRDAVAQIITFGTMKAKAVirdvgrvlgmpYGFVdRitklippdpgitlakayEEEPE 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1031 YGKFYR-DVEVERL---AAGAAGVKRTTGQHPGGIIVFPDymDVYDFTPVqY--PADDVTAswqtTHFNFHDIdENV--L 1102
Cdd:PRK05673 478 LRELYEsDPEVKRLidmARKLEGLTRNAGVHAAGVVISPT--PLTDFVPL-YrdPDSGMPV----TQFDMKDV-EAAglV 549
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|...
gi 500942978 1103 KLDILG-------HDDPTMVRKlQDLSGIDPQTIPADDKGVMALFSGTEILGV 1148
Cdd:PRK05673 550 KFDFLGlrtltiiDDALKLIKK-RRGIDVDLEAIPLDDPKTYELLQRGETLGV 601
|
|
| dnaE |
PRK06920 |
DNA polymerase III subunit alpha; |
624-1316 |
1.41e-23 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 108.73 E-value: 1.41e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 624 NQVGLKNMFKLVSLSNTKYFEGvprIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYDFIEvmppALYA 703
Cdd:PRK06920 86 NEIGYQNLLKISSSIMTKSKEG---IPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQAEEVARAYQNMF----GNFY 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 704 PMIAKEQFKDMAEIEEtikQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIvRALGQGAPINWTIGNGENaqpapLPKA 783
Cdd:PRK06920 159 MSLQHHAIQDELLLQE---KLPEFSNRVNIPVVATNDVRYINQSDALVHECL-LSVESGTKMTDPDRPRLK-----TDQY 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 784 HFRTTSEMLDEFAFLGESLAREIVITnpnamlDRFE-DVQVVKTDL---YTPYIEKAEETVAELTYQKAFEIYGNPlPDI 859
Cdd:PRK06920 230 YLKSSDEMEALFSHVPEAIYNTVEIA------ERCRvEIPFHVNQLpkfPVPSNETADMYLRRVCEEGLQKRYGTP-KEV 302
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 860 IDLRIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG-SRGSVGSSFVATMIGITEVNPMpphyvcpncqhsefitdg 938
Cdd:PRK06920 303 HINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHILTGpGRGSAAGSLVSYVLEITDIDPI------------------ 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 939 sygsgfdlpdkdcekcgtKYkkdgqDIPFETFLGFDGDKVPDIDLNFsgddqPSAHLD-----VRDIFGEENAFRAGTVG 1013
Cdd:PRK06920 365 ------------------EY-----DLLFERFLNPERVTLPDIDIDF-----PDTRRDemiryVKDKYGQLRVAQIVTFG 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1014 TVAAKTAygfVRGYERDYGKFYRDVE------------------------------------VERLAAGAAGVKRTTGQH 1057
Cdd:PRK06920 417 TLAAKAA---IRDIARVMGLPPRDIDifsklipsklgitlkdayeesqslrefiqgnllherVFEIAKRVEGLPRHTSIH 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1058 PGGIIVFPDYMDvyDFTPVQYPADDVtasWQTTHFNFHDIDENVLKLDILGHDDPTMVRKLQDL------SGIDPQTIPA 1131
Cdd:PRK06920 494 AAGVIMSQEPLT--GSVAIQEGHNDV---YVTQYPADALEELGLLKMDFLGLRNLTLLENIIKFieqktgKEIDIRNLPL 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1132 DDKGVMALFSGteilgvtpeqiGTPTGMLGIPEFGtnfVRGMVEETKPTTFSELLQLSGL---------------SHGTD 1196
Cdd:PRK06920 569 QDEKTFQLLGR-----------GDTTGVFQLESSG---MRNVLRGLKPNEFEDIVAVNSLyrpgpmeqiptfiesKHGKR 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1197 VWLGNAQDLiKAGIANLSTVIGCRDDIMVylmhagLPPKMA-FNIMER--VRKGLWLK---ISEEERNGYIQAMKDNKVP 1270
Cdd:PRK06920 635 KIEYLHPDL-KPILERTYGVIVYQEQIMQ------IASKLAgFSLGEAdlLRRAVSKKnrdILDQERKHFVQGCLQNGYD 707
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....
gi 500942978 1271 dwyIESCGKI--------KYMFPKAHAAAYVMMALRVAYFKVHHPLYYYCAYFS 1316
Cdd:PRK06920 708 ---ETSAEKIydlivrfaNYGFNRSHAVAYSMIGYQLAYLKANYTLEFMTALLS 758
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
425-629 |
3.89e-23 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 107.08 E-value: 3.89e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAvNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDS 504
Cdd:PRK07246 9 YAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 505 VMVAHNATFDVGFMNVN-----YEraglpiISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEATGR 579
Cdd:PRK07246 88 IFVAHNVKFDANLLAEAlflegYE------LRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAE 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 580 lLFIFLKD---ALEKHNLTNLNQL------NTELIAEDSYKKARVKHATLYV-INQVGLK 629
Cdd:PRK07246 162 -LFLKLLQkieSLPKECLERLLEYadsllfESYLVIEEALANAKPYSSPDYIkVQGIVLK 220
|
|
| PHP_PolIIIA_DnaE3 |
cd12113 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
617-748 |
3.43e-22 |
|
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: 98.28 E-value: 3.43e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 617 HATLYVINQVGLKNMFKLVSLSNTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAVKTAAYYD---- 692
Cdd:cd12113 87 HLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRdifg 166
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 693 ----FIEVMPpalyapmiakeqfKDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEE 748
Cdd:cd12113 167 kdnfYLELQD-------------HGLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKED 213
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
340-406 |
5.37e-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: 90.79 E-value: 5.37e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500942978 340 EFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIVE 406
Cdd:smart00481 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
|
|
| dnaE |
PRK07374 |
DNA polymerase III subunit alpha; Validated |
611-1462 |
1.29e-21 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 102.49 E-value: 1.29e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 611 KKARVKHATLYVINQVGLKNMFKLVSLSNTKYFEGV-----PRIPRTVLNAHREGLILGTACQEGEVFDDLLSKGIDEAV 685
Cdd:PRK07374 80 KKEKRYHLVVLAKNATGYKNLVKLTTISHLNGMRGRgifsrPCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPDVAR 159
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 686 KTAAYYDfiEVMPPALYApmiakeQFKDMAEIEETI--KQLIEVGRRAGLPVLATGNVHYI---DPEEE----------- 749
Cdd:PRK07374 160 DVAAWYK--EVFGDDFYL------EIQDHGSIEDRIvnVELVRIAKELGIKLIATNDAHYLsknDVEAHdallcvltgkl 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 750 IYREIIVRALGqgapinwtigngenaqpaplpKAHFRTTSEMLDEFAflgESLAREIV---ITNPNAMLDRFEDVQVVKT 826
Cdd:PRK07374 232 ISDEKRLRYTG---------------------TEYIKSEEEMLRLFR---DHLDPEVIqeaIANTVEVAEKVEEYDILGT 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 827 ----DLYTPYIEKAEETVAELTYQKAFEIYGNPLPDIIDL----RIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG 898
Cdd:PRK07374 288 yrmpRFPIPEGHTAVSYLTEVTEQGLLKRLKLNSLDEIDEnykeRLSYELKIIEQMGFPTYFLVVWDYIRFAREQGIPVG 367
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 899 -SRGSVGSSFVATMIGITEVNPMpphyvcpncqhsefitdgSYGsgfdlpdkdcekcgtkykkdgqdIPFETFLGFDGDK 977
Cdd:PRK07374 368 pGRGSAAGSLVAYALGITNIDPV------------------KNG-----------------------LLFERFLNPERKS 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 978 VPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTA-----------YG----------FVRGYE-------- 1028
Cdd:PRK07374 407 MPDIDTDFCIERRGEVIDYVTRRYGEDKVAQIITFNRMTSKAVlkdvarvldipYGeadrlaklipVVRGKPaklkamig 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1029 --------RDygKFYRDVEVER---LAAGAAGVKRTTGQHPGGIIVFPDYMDvyDFTPVQYPADDVTaswqTTHFNFHDI 1097
Cdd:PRK07374 487 kespspefRE--KYEKDPRVKKwvdMAMRIEGTNKTFGVHAAGVVIASDPLD--ELVPLQRNNDGQV----ITQYFMEDI 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1098 DE-NVLKLDILGHDDPTMVRKLQDL----SG--IDPQTIPADDKGVMALFSGTEILGVTpeQIGTpTGMlgipefgtnfv 1170
Cdd:PRK07374 559 ESlGLLKMDFLGLKNLTMIEKTLELveqsTGerIDPDNLPLDDEKTFELLARGDLEGIF--QLES-SGM----------- 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1171 RGMVEETKPTTF---SELLQL-------SGL-------SHGTDVwLGNAQDLIKAgIanLSTVIGcrddIMVY---LMH- 1229
Cdd:PRK07374 625 RQVVRDLKPSSLediSSILALyrpgpldAGLipkfinrKHGREA-IDFAHPLLEP-I--LTETYG----IMVYqeqIMKi 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1230 ----AGLPPKMAfNIMERV--RKglwlKISEEE--RNGYIQ-AMK---DNKVPDWYIESCGKI-KYMFPKAHAAAYVMMA 1296
Cdd:PRK07374 697 aqdlAGYSLGQA-DLLRRAmgKK----KVSEMQkhRGIFVEgASKrgvDEKVADELFDQMVLFaEYCFNKSHSTAYGAVT 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1297 LRVAYFKVHHPLYYYCAYFSIRAKAFDlatmsgglervkakmeeialkKKNNEASNveqdlyttlelVNEMlerGFKFGK 1376
Cdd:PRK07374 772 YQTAYLKAHYPVAYMAALLTVNAGSSD---------------------KVQRYISN-----------CNSM---GIEVMP 816
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1377 LDLYKShATDFLIEEDTLIPPFVAMDGLGENVAKQVVAAR-AEGEFLSKTELRKR---GGLSGTLVEKMDEMGILGKM-P 1451
Cdd:PRK07374 817 PDINRS-GIDFTPKGNRILFGLSAVKNLGDGAIRNIIAARdSDGPFKSLADLCDRlpsNVLNRRSLESLIHCGALDAFsP 895
|
970
....*....|.
gi 500942978 1452 EDNQLSLFDDL 1462
Cdd:PRK07374 896 NANRAQLIADL 906
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
340-408 |
1.61e-20 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 90.30 E-value: 1.61e-20
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500942978 340 EFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIVEDS 408
Cdd:pfam02811 1 HLHVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVAPGS 69
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
426-575 |
2.02e-19 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 89.15 E-value: 2.02e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 426 VVFDVETTGLSAVN-NALIQIAASKM--HK--GNiiaEFDEFIDPG---HPLSQfttDLTGITDEHVRGSKPLEQVLREF 497
Cdd:PRK05711 7 IVLDTETTGLNQREgHRIIEIGAVELinRRltGR---NFHVYIKPDrlvDPEAL---AVHGITDEFLADKPTFAEVADEF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 498 QDFCQDSVMVAHNATFDVGFMNVNYER--AGLPIISQ--PVIDTLEFARNLYPDfKRHGLGPLTKRFGVALEHH--HMAN 571
Cdd:PRK05711 81 LDFIRGAELIIHNAPFDIGFMDYEFALlgRDIPKTNTfcKVTDTLAMARRMFPG-KRNSLDALCKRYGIDNSHRtlHGAL 159
|
....
gi 500942978 572 YDAE 575
Cdd:PRK05711 160 LDAE 163
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
339-416 |
1.92e-18 |
|
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: 84.56 E-value: 1.92e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 339 VEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIVEDSVP-----IAY 413
Cdd:cd07431 1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPyplllLAK 80
|
...
gi 500942978 414 NEA 416
Cdd:cd07431 81 NNE 83
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
423-570 |
1.36e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 83.71 E-value: 1.36e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 423 ATYVVFDVETTGLSAVNNALIQIAAskmHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFC- 501
Cdd:PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCg 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 502 QDSVMVAHNA-TFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMA 570
Cdd:PRK06309 79 TDNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRA 148
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
418-575 |
3.23e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 79.87 E-value: 3.23e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 418 VVLSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREF 497
Cdd:PRK06310 2 SLLKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 498 QDFCQDS-VMVAHNATFDVGFMNVNYERAGLPIISQ--PVIDTLEFARnLYPDFKRHGLGPLTKRFGVALEHHHMANYDA 574
Cdd:PRK06310 82 KGFFKEGdYIVGHSVGFDLQVLSQESERIGETFLSKhyYIIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDV 160
|
.
gi 500942978 575 E 575
Cdd:PRK06310 161 E 161
|
|
| DNA_pol3_a_NI |
pfam14480 |
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
4-78 |
2.25e-15 |
|
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: 72.19 E-value: 2.25e-15
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500942978 4 KFQLLLQQIGMPLDarQSGAFSTATIEKVVLHKVSKLWEFTFRFETPLPLMDYQLFKARLATEFEKvGNKIQFSI 78
Cdd:pfam14480 1 RFFELFPQLKLPDE--LEELFEDAEIEKVTVHKKSKKWRFYISSPHLLPKEVIYKFEQRLKEQFFH-IAKVKVKI 72
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
339-414 |
3.20e-15 |
|
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: 72.07 E-value: 3.20e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 339 VEFHAHTNMSTMDALPaVEDLVARAAAWGHKAVAITDHGNVQSFPHG--------YHAARKAGIKPLFGMEANIVEDSVP 410
Cdd:cd07309 1 VDLHTHTVFSDGDHAK-LTELVDKAKELGPDALAITDHGNLRGLAEFntagk*nhIKAAEAAGIKIIIGSEVNLTVLAHP 79
|
....
gi 500942978 411 IAYN 414
Cdd:cd07309 80 VVAT 83
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
425-581 |
3.20e-15 |
|
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: 74.95 E-value: 3.20e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETT-----GLSAVNNALIQIAASKM--HKGNIIAEFDEFIDP--GHPLSQFTTDLTGITDEHVRGSKPLEQVLR 495
Cdd:cd06133 1 YLVIDFEATcwegnSKPDYPNEIIEIGAVLVdvKTKEIIDTFSSYVKPviNPKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 496 EFQDFCQDSVMVAhNATF---DVGFMNVN---YERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALE-HHH 568
Cdd:cd06133 81 EFLEWLGKNGKYA-FVTWgdwDLKDLLQNqckYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEgRHH 159
|
170
....*....|...
gi 500942978 569 MANYDAEATGRLL 581
Cdd:cd06133 160 RGLDDARNIARIL 172
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
427-588 |
1.17e-14 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 74.76 E-value: 1.17e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 427 VFDVETTGLSAvnnALIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDfcqDSVM 506
Cdd:PRK07983 4 VIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYG---SEWY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 507 VAHNATFDvgfmnvnyeRAGLPIISQPVIDTLEFARNLYPDFKrHGLGPLTKRFGVALE-----HHHMANYDAEATGRLL 581
Cdd:PRK07983 78 VAHNASFD---------RRVLPEMPGEWICTMKLARRLWPGIK-YSNMALYKSRKLNVQtppglHHHRALYDCYITAALL 147
|
....*..
gi 500942978 582 FIFLKDA 588
Cdd:PRK07983 148 IDIMNTS 154
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
421-590 |
6.78e-14 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 74.35 E-value: 6.78e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 421 SDATYVVFDVETTGLSAVNNALIQIAASKMH-KGNIIAEFDEFIDPGH---PlsqftTDLTGITDEHVRGSKPLEQVLRE 496
Cdd:PRK06063 13 YPRGWAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLNPGVdpgP-----THVHGLTAEMLEGQPQFADIAGE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 497 FQDFCQDSVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHMANYDAEA 576
Cdd:PRK06063 88 VAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARV 167
|
170
....*....|....
gi 500942978 577 TGRLLFIFLKDALE 590
Cdd:PRK06063 168 LAGILRPSLERARE 181
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
425-621 |
7.84e-13 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 70.96 E-value: 7.84e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTglSAVNNALIQIAASKMHKGNIIAEFDEFIDPGH-PLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQD 503
Cdd:PRK06195 3 FVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEmRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 504 SVMVAHNATFDVGFMNVNYERAGLPIISQPVIDTLEFARNLYPDFKRHGLGPLTKRFGVALEHHHmANYDAEATGRLLFI 583
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHD-ALADAMACSNILLN 159
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 500942978 584 FLKDAlekhNLTNLNQLNTEL------IAEDSYKKARVKHATLY 621
Cdd:PRK06195 160 ISKEL----NSKDINEISKLLgvtlgyVNENGYKPSSRKGRILK 199
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
423-511 |
1.03e-12 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 68.27 E-value: 1.03e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 423 ATYVVFDVETTGLSAVNNaLIQIAASKMHKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQ 502
Cdd:PRK07247 5 ETYIAFDLEFNTVNGVSH-IIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVG 83
|
....*....
gi 500942978 503 DSVMVAHNA 511
Cdd:PRK07247 84 ELPLIGYNA 92
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
421-580 |
2.47e-12 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 68.08 E-value: 2.47e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 421 SDATYVVFDVETTG---LSA--VNNALIQIAASkmhkGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGS-KPLEQVL 494
Cdd:PRK07942 4 HPGPLAAFDLETTGvdpETAriVTAALVVVDAD----GEVVESREWLADPGVEIPEEASAVHGITTEYARAHgRPAAEVL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 495 RE----FQDFCQDSV-MVAHNATFDVGFMNVNYERAGLP-IISQPVIDTLEFARNLypDFKRHG---LGPLTKRFGVALE 565
Cdd:PRK07942 80 AEiadaLREAWARGVpVVVFNAPYDLTVLDRELRRHGLPsLVPGPVIDPYVIDKAV--DRYRKGkrtLTALCEHYGVRLD 157
|
170
....*....|....*
gi 500942978 566 HHHMANYDAEATGRL 580
Cdd:PRK07942 158 NAHEATADALAAARV 172
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
602-808 |
1.02e-11 |
|
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: 67.12 E-value: 1.02e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 602 TELIAEDSYKKARVKHATLYVINQVGLKNMFKLVSLS-NTKYFEGVPRIPRTVLNAHREGLILGTACQEGEVFDDLLSKG 680
Cdd:cd07433 64 ADLNVANPDDADEPFRLTLLAQNEQGYKNLTELISRAyLEGQRNGGPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGN 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 681 IDEAVKTAAYYdfIEVMPPALYApmiakE-QFKDMAEIEETIKQLIEVGRRAGLPVLATGNVHYIDPEEEIYREIIVrAL 759
Cdd:cd07433 144 PDLAEALLQFL--KKIFPDRFYL-----ElQRHGRPEEEAYEHALIDLAYELGLPLVATNDVRFLKPEDFEAHEARV-CI 215
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 500942978 760 GQGAPINwtigngENAQPAPL-PKAHFRTTSEMLDEFAFLGESLAREIVI 808
Cdd:cd07433 216 AEGRTLD------DPRRPRRYsPQQYFKSAEEMAELFADLPEAIENTVEI 259
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
723-1148 |
1.18e-11 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 69.89 E-value: 1.18e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 723 QLIEVGRRAGLPVLATGNVHYIDPEEeiyREI--IVRALGQGAPIN----WTIGNGEnaqpaplpkAHFRTTSEMLDEFA 796
Cdd:PRK05672 183 RLAALAARAGVPLVATGDVHMHHRSR---RRLqdAMTAIRARRSLAeaggWLAPNGE---------RHLRSGAEMARLFP 250
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 797 FLGESLAREIVITNPNAmldrFeDVQVVKTDlYTPYIEKAEETVA----ELTYQKAFEIYGNPLPDIIDLRIEKELTSIL 872
Cdd:PRK05672 251 DYPEALAETVELAERCA----F-DLDLLAYE-YPDEPVPAGHTPAswlrQLTEAGAARRYGPGIPPKARAQIEHELALIA 324
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 873 GNGFAVIYLASQMLVHRSNERGYLVGSRGSVGSSFVATMIGITEVNPMpphyvcpncQHsefitdgsygsgfdlpdkdce 952
Cdd:PRK05672 325 ELGYEGYFLTVHDIVRFARSQGILCQGRGSAANSAVCYALGITEVDPV---------QS--------------------- 374
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 953 kcgtkykkdgqDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTAygfVR------G 1026
Cdd:PRK05672 375 -----------GLLFERFLSPERDEPPDIDVDFEHDRREEVIQYVYRRYGRDRAAQVANVITYRPRSA---VRdvakalG 440
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1027 Y------------------------ERDYGKFYRDVEVER---LAAGAAGVKRTTGQHPGGIIVFPDYMDVY-------- 1071
Cdd:PRK05672 441 LspgqvdawakqvsrwsgsaddlqrLRQAGLDPESPIPRRvveLAAQLIGFPRHLSQHSGGFVICDRPLARLvpvenaam 520
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1072 -DFTPVQYPADDVTASwqtthfnfhdideNVLKLDILGHDDPTMVRKLQDL----SGI--DPQTIPADDKGVMALFSGTE 1144
Cdd:PRK05672 521 eGRSVIQWDKDDCAAV-------------GLVKVDVLALGMLSALHRAFDLiaehRGRrlTLASIPLDDPAVYDMLCRAD 587
|
....
gi 500942978 1145 ILGV 1148
Cdd:PRK05672 588 SVGV 591
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
426-527 |
1.27e-10 |
|
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: 62.31 E-value: 1.27e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 426 VVFDVETTGLSAVNNALIQIAAS--KMHKGNII---------------AEFD----EF--IDPGHPLS---QFTTDLTGI 479
Cdd:cd06134 8 VVVDVETGGFNPQTDALLEIAAVtlEMDEQGNLypdetfhfhilpfegANLDpaalEFngIDPFHPFRfavDEKEALKEI 87
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 500942978 480 tdehvrgSKPLEQVLREFQdfCQDSVMVAHNATFDVGFMNVNYERAGL 527
Cdd:cd06134 88 -------FKPIRKALKAQG--CTRAILVGHNAHFDLGFLNAAVARCKI 126
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
426-517 |
4.12e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 62.69 E-value: 4.12e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 426 VVFDVETTGLSAVNNALIQIAASKM------HKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQD 499
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFeydddgRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAAVDALIA 119
|
90
....*....|....*...
gi 500942978 500 FCQdsVMVAHNATFDVGF 517
Cdd:PRK09182 120 PAD--LIIAHNAGFDRPF 135
|
|
| dnaE |
PRK07279 |
DNA polymerase III DnaE; Reviewed |
863-1311 |
1.29e-09 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 63.13 E-value: 1.29e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 863 RIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG-SRGSVGSSFVATMIGITEVNPMpphyvcpncQHsefitdgsyg 941
Cdd:PRK07279 263 RLDKELSVIHDMGFDDYFLIVWDLLRFGRSQGYYMGmGRGSAAGSLVAYALDITGIDPV---------KH---------- 323
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 942 sgfdlpdkdcekcgtkykkdgqDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTAY 1021
Cdd:PRK07279 324 ----------------------NLLFERFLNKERYSMPDIDIDLPDIYRSEFLRYVRNRYGSDHSAQIVTFSTFGAKQAI 381
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1022 gfvrgyeRDYGK-F---------------YRD-------------------VEVER---LAAGAAGVKRTTGQHPGGIIV 1063
Cdd:PRK07279 382 -------RDVFKrFgvpeyelsnltkkisFRDslasvyeknisfrqiinskLEYQKafeIAKRIEGNPRQTSIHAAGVVM 454
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1064 FPDymDVYDFTPVQYpADDVTaswqTTHFNFHDIDEN-VLKLDILGHDDPTMVRKLQDL------SGIDPQTIPADDKGV 1136
Cdd:PRK07279 455 SDD--DLTNHIPLKY-GDDMM----ITQYDAHAVEANgLLKMDFLGLRNLTFVQKMQEKvakdygIHIDIEAIDLEDKET 527
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1137 MALFSGteilGVTpeqigtptgmLGIPEFGTNFVRGMVEETKPTTFSEL-----LQLSGLSHGTDVWLGNAQ-----DLI 1206
Cdd:PRK07279 528 LALFAA----GDT----------KGIFQFEQPGAINLLKRIKPVCFEDIvattsLNRPGASDYTDNFVKRRHgqekvDLI 593
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1207 KAGIAN-LSTVIGcrddIMVY---LMH-----AGLPPKMAfNIMERV---RKGLWL-KISEEERNGYIQAMKDNKVPDWY 1273
Cdd:PRK07279 594 DPVIAPiLEPTYG----IMLYqeqVMQiaqvfAGFSLGKA-DLLRRAmskKNASEMqKMEEDFLQGALELGHSEEKAREL 668
|
490 500 510
....*....|....*....|....*....|....*....
gi 500942978 1274 IESCGKIK-YMFPKAHAAAYVMMALRVAYFKVHHPLYYY 1311
Cdd:PRK07279 669 FDRMEKFAgYGFNRSHAFAYSALAFQLAYFKAHYPAVFY 707
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
339-405 |
7.99e-09 |
|
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: 55.32 E-value: 7.99e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500942978 339 VEFHAHTNMSTMDALPaVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIV 405
Cdd:cd07432 1 ADLHIHSVFSPDSDMT-PEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEVTLV 66
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
338-401 |
9.59e-09 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 56.84 E-value: 9.59e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500942978 338 RVEFHAHTNMStmDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGME 401
Cdd:COG0613 3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVE 64
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
863-1441 |
1.03e-08 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 60.09 E-value: 1.03e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 863 RIEKELTSILGNGFAVIYLASQMLVHRSNERGYLVG-SRGSVGSSFVATMIGITEVNPMpphyvcpncqhsefitdgsyg 941
Cdd:PRK07135 255 RINYEYSVIKKLKFSNYFLIIWDFIKWARKNKISIGpGRGSASGSLVSYLLNITSVNPL--------------------- 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 942 sgfdlpdkdcekcgtKYkkdgqDIPFETFLGFDGDKVPDIDLNFSgDDQPSAHLD-VRDIFGEENAFRAGTVGTVAAKTA 1020
Cdd:PRK07135 314 ---------------KY-----DLLFERFLNPDRITMPDIDIDIQ-DDRRDEVIDyIFEKYGYEHCATISTFQTLGAKSA 372
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1021 YgfvrgyeRDYGK-------------------------------FYRDV---------EVERLAAGAAGVKRTTGQHPGG 1060
Cdd:PRK07135 373 I-------RDVGRmlgipesdvnaisklipnnqsleeaydknksFFRELiskgdpiykKLYKIAKKLEGLPRQSGTHAAG 445
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1061 IIV--------FPDYMDVYDFTPVQYPADDVTaswqtthfnfhdiDENVLKLDILGHDDPTMVRKLQDL--------SGI 1124
Cdd:PRK07135 446 IIIsnkpitnyVPTFESKDNYNQVQYSMEFLE-------------DFGLLKIDLLGLKNLTIIKNIEEKinkellfdHLI 512
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1125 DPQTIPADDKGVMALFSGTEILGVTpeQIGTPtGMlgipefgTNFVRGMveetKPTTFSEL-----LQLSGLSHGTDVWL 1199
Cdd:PRK07135 513 NFNDLPIIDKKTNNLLSNGKTEGIF--QLESP-GM-------KSTIKKV----GIDSFEDIvaiisLYRPGPIQYIPIYA 578
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1200 GNAQD--LIKAGIANLSTVIGCRDDIMVY---LMH-AGLPPKMAFNIMERVRKGLWLKISEE---ERNGYIQAMKDNKVP 1270
Cdd:PRK07135 579 KNKKNpkNIEKIHPEYDEIVAPTYGIIIYqeqIMQiAQKVAGFSFAQADLLRRAISKKDETKldkIKDKFIEGGIKNGYS 658
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1271 DWYIEscgKI--------KYMFPKAHAAAYVMMALRVAYFKVHHPLYYYCAYFsirakafdlatmsgglervkakmeeia 1342
Cdd:PRK07135 659 KKVLE---KIysliekfaDYGFNKSHAVAYATLAYKMAYYKANYPLVFYSALI--------------------------- 708
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1343 lkkknneaSNVEQDLYTTLELVNEMLERGFKFGKLDLYKSHATDFLIEEDTLIpPFVAMDGLGENVAKQVVAARAE-GEF 1421
Cdd:PRK07135 709 --------SNSNGSQENIKKYVKEAKNNGIKVYSPDINFSTENAVFDNGKIFL-PLIMIKGLGSVAIKKIIDERNKnGKY 779
|
650 660
....*....|....*....|...
gi 500942978 1422 LSKTELRKRGGLSG---TLVEKM 1441
Cdd:PRK07135 780 KNFFDFILRLKFIGiskSIIEKL 802
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
420-614 |
1.34e-08 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 57.76 E-value: 1.34e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 420 LSDAT-YVVFDVETTGL---SAVNNALIQIAASKMHKGN--IIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQV 493
Cdd:PRK06722 1 MENAThFIVFDIERNFRpykSEDPSEIVDIGAVKIEASTmkVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 494 LREFQDFC-QDSVMVAHNATfDVGFMNVNYERAGL--PIISQPV-IDTLEFARNLYPDFKRH--GLGPLTKRFGVALE-H 566
Cdd:PRK06722 81 IEKFIQFIgEDSIFVTWGKE-DYRFLSHDCTLHSVecPCMEKERrIDLQKFVFQAYEELFEHtpSLQSAVEQLGLIWEgK 159
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 500942978 567 HHMANYDAEATGRllfIFLKdALEKHNLTNLNQLNTEL-------IAEDSYKKAR 614
Cdd:PRK06722 160 QHRALADAENTAN---ILLK-AYSERDITKRYKRHGELelvkngkLTEKAKKKMR 210
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
604-1180 |
4.02e-08 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 58.21 E-value: 4.02e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 604 LIAEDSYKKARVK--HATLYVINQVGLKNMFKLVSLSNTKYFEGV-----PRIPRTVLNAHREGLILGTACQEGEVFDDL 676
Cdd:PRK09532 69 VINGDIEKQKRRRkyHQVVLAKNTQGYKNLVKLTTISHLQGVQGKgifarPCINKELLEQYHEGLIVTSACLGGEIPQAI 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 677 LSKGIDEAVKTAAYYDfiEVMPPALYApmiakeQFKDMAEIEETI--KQLIEVGRRAGLPVLATGNVHYI---DPEEE-- 749
Cdd:PRK09532 149 LSGRPDAARKVAKWYK--KLFGDDFYL------EIQDHGSQEDRIvnVEIVKIARELGIKIIATNDSHFIscyDVEAHda 220
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 750 ---------IYREIIVRALGqgapinwtigngenaqpaplpKAHFRTTSEMLDEFAflgESLAREIV---ITNPNAMLDR 817
Cdd:PRK09532 221 llciqtgklITEDKRLRYSG---------------------TEYLKSAEEMRLLFR---DHLPDDVIaeaIANTLEVADK 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 818 FEDVQVVKT----DLYTPYIEKAEETVAELTYQKAFEIYG----NPLPDIIDLRIEKELTSILGNGFAVIYLASQMLVHR 889
Cdd:PRK09532 277 IEPYNILGEpripNYPVPSGHTPDTYVEEVAWQGLLERLNcksrSEVEPVYKERLEYELKMLQQMGFSTYFLVVWDYIKY 356
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 890 SNERGYLVG-SRGSVGSSFVATMIGITEVNPMpphyvcpncQHSefitdgsygsgfdlpdkdcekcgtkykkdgqdIPFE 968
Cdd:PRK09532 357 ARDNNIPVGpGRGSAAGSLVAYCLKITNIDPV---------HHG--------------------------------LLFE 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 969 TFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEENAFRAGTVGTVAAKTA-----------YG----------FVRG- 1026
Cdd:PRK09532 396 RFLNPERKSMPDIDTDFCIERRDEMIKYVTEKYGEDRVAQIITFNRMTSKAVlkdvarvldipYGeadkmaklipVSRGk 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1027 ----------------YERDYGKfyrDVEVER---LAAGAAGVKRTTGQHPGGIIVFPDYMDvyDFTPVQYPADDVTasw 1087
Cdd:PRK09532 476 ptklkvmisdetpepeFKEKYDN---DPRVRRwldMAIRIEGTNKTFGVHAAGVVISSEPLD--EIVPLQKNNDGAV--- 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 1088 qTTHFNFHDIDE-NVLKLDILGHDDPTMVRKLQDL------SGIDPQTIPADDKGVMALFSGTEILGVtPEQIGTPTGML 1160
Cdd:PRK09532 548 -ITQYFMEDLESlGLLKMDFLGLRNLTTIQKTADLikenrgVEIDLDQLPLDERKALKILAKGEAKKL-PKDVQKTHKLL 625
|
650 660
....*....|....*....|....*.
gi 500942978 1161 ------GIPEFGTNFVRGMVEETKPT 1180
Cdd:PRK09532 626 ergdleGIFQLESSGMKQIVRDLKPS 651
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
339-413 |
2.45e-07 |
|
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: 54.02 E-value: 2.45e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500942978 339 VEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVqsfpHG----YHAARKAGIKPLFGMEANIVEDSVPIAY 413
Cdd:cd07433 3 VHLRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSNL----FGavkfYKAASKAGIKPIIGADLNVANPDDADEP 77
|
|
| HHH_6 |
pfam14579 |
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain. |
1378-1430 |
3.38e-07 |
|
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain.
Pssm-ID: 434050 [Multi-domain] Cd Length: 88 Bit Score: 49.39 E-value: 3.38e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 500942978 1378 DLYKSHAtDFLIEEDTLIPPFVAMDGLGENVAKQVVAARAEGEFLSKTELRKR 1430
Cdd:pfam14579 8 DINRSDW-DFTVEGGGIRLGLGAIKGLGEAAAERIVEERENGPFKSLEDFARR 59
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
338-427 |
2.34e-06 |
|
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: 50.54 E-value: 2.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 338 RVEFHAHTNMStmDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHG--------YHA------ARKAGIKPLFGMEAN 403
Cdd:COG1387 2 RGDLHTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDHSPSLFVANGlseerlleYLEeieelnEKYPDIKILKGIEVD 79
|
90 100
....*....|....*....|....
gi 500942978 404 IVEDSVpIAYNEAdvVLSDATYVV 427
Cdd:COG1387 80 ILPDGS-LDYPDE--LLAPLDYVI 100
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
425-587 |
3.46e-06 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 49.52 E-value: 3.46e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAVNNALIQIAASKMhKGNII---AEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFC 501
Cdd:PRK09145 31 WVALDCETTGLDPRRAEIVSIAAVKI-RGNRIltsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 502 QDSVMVAHNATFDVGFMNVNYER---AGLPiisQPVIDTlefaRNLYPDFKRHGLGP---------LTKRFGVALEHHHM 569
Cdd:PRK09145 110 GNRPLVGYYLEFDVAMLNRYVRPllgIPLP---NPLIEV----SALYYDKKERHLPDayidlrfdaILKHLDLPVLGRHD 182
|
170
....*....|....*...
gi 500942978 570 ANYDAEATGrLLFIFLKD 587
Cdd:PRK09145 183 ALNDAIMAA-LIFLRLRK 199
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
339-401 |
4.08e-06 |
|
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: 48.16 E-value: 4.08e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500942978 339 VEFHAHTNMStmDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGME 401
Cdd:cd07438 1 IDLHTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVE 61
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
340-508 |
5.54e-06 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 51.01 E-value: 5.54e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 340 EFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIVEDSVPiayNEADVV 419
Cdd:PRK05672 7 ELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAELSLGPDPDP---GGPHLL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 420 LsdatyVVFDVETTG-LSAvnnaliQIAASKMH--KGNIIAEFDEFIDP--GHPLSqfttdLTGITDEHVR-------GS 487
Cdd:PRK05672 84 V-----LARDREGYGrLSR------LITRARLRagKGEYRLDLDDLAEPagGHWAI-----LTGCRKGFVIlalpyggDA 147
|
170 180
....*....|....*....|.
gi 500942978 488 KPLEQVLREFQDFCQDSVMVA 508
Cdd:PRK05672 148 AALAALAALLDAFFADRVWLE 168
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
426-497 |
1.17e-05 |
|
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: 49.33 E-value: 1.17e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500942978 426 VVFDVETTGLSAVNNALIQIAASKM-HKGNIIAEFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREF 497
Cdd:pfam13361 189 VVFDVETTGLDTTEDEIIQIAAIKLnKKGVVIESFERFLRLKKPVGDSLQVHGFSDEFLQENGETPAEALRDF 261
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
415-581 |
1.18e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 48.38 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 415 EADVVLSDATYVVFDVETTGLSAVNNALIQIAASKMHKGNI-IAEFDE-FIDPGHPLSQFTTDLTGITDEHVRGSKPLEQ 492
Cdd:PRK09146 39 SPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIrCRQARHwVVKPRRPLEEESVVIHGITHSELQDAPDLER 118
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 493 VLREFQDFCQDSVMVAHNATFDVGFMNVNY-ERAGLPIISqPVIDTLEFARNLYPdfKRHG---------------LGPL 556
Cdd:PRK09146 119 ILDELLEALAGKVVVVHYRRIERDFLDQALrNRIGEGIEF-PVIDTMEIEARIQR--KQAGglwnrlkgkkpesirLADS 195
|
170 180
....*....|....*....|....*
gi 500942978 557 TKRFGVALEHHHMANYDAEATGRLL 581
Cdd:PRK09146 196 RLRYGLPAYSPHHALTDAIATAELL 220
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
242-323 |
6.40e-05 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 42.61 E-value: 6.40e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 242 IVFEGLVFEVEqkttKTGRVIINFKMTDYTSSFTLQKWakNEEEAQKFDMVKKGNWLRVRGNVETNNfTRDLTMNVQEVQ 321
Cdd:pfam01336 1 VTVAGRVTSIR----RSGGKLLFLTLRDGTGSIQVVVF--KEEAEKLAKKLKEGDVVRVTGKVKKRK-GGELELVVEEIE 73
|
..
gi 500942978 322 EV 323
Cdd:pfam01336 74 LL 75
|
|
| PHP_PolIIIA_DnaE2 |
cd07434 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
339-401 |
1.08e-04 |
|
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: 45.52 E-value: 1.08e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500942978 339 VEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGME 401
Cdd:cd07434 2 AELHCLSNFSFLRGASHPEELVARAAELGYRALAITDECSLAGVVRAHAAAKELGLKLIVGSE 64
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
451-509 |
3.25e-04 |
|
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: 42.50 E-value: 3.25e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 500942978 451 HKGNIIaeFDEFIDPGHPLSQFTTDLTGITDEHVRGSKPLEQVLREFQDFCQDSVMVAH 509
Cdd:cd06144 27 EDGNVV--YDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGH 83
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
339-405 |
3.97e-04 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 45.12 E-value: 3.97e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500942978 339 VEFHAHTNMSTMDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAARKAGIKPLFGMEANIV 405
Cdd:PRK09532 4 VGLHIHSDYSLLDGASQLPALVDRAIELGMPAIALTDHGVMYGAIELLKVCRNKGIKPIIGNEMYVI 70
|
|
| PHP_HisPPase_Ycdx_like |
cd07437 |
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
342-405 |
4.90e-04 |
|
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: 43.20 E-value: 4.90e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500942978 342 HAHTNMSTmDALPAVEDLVARAAAWGHKAVAITDHG-NVQSFPHGYH------AARKA-GIKPLFGMEANIV 405
Cdd:cd07437 6 HTHTIASG-HAYSTIEEMARAAAEKGLKLLGITDHGpAMPGAPHPWYfgnlkvIPREIyGVRILRGVEANII 76
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
425-562 |
8.57e-04 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 42.24 E-value: 8.57e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 425 YVVFDVETTGLSAVNNALIQIAaskmhkgniIAEFDefiDPGHPLSQFTtdLTGITDEhvrgSKPLEQVLREFQDFcqdS 504
Cdd:COG3359 17 LLFFDIETTGLSGGGTVIFLIG---------LADGE---GDGFVVRQYF--GEDPGEE----AALLEAFLEWLADY---K 75
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500942978 505 VMVAHN-ATFDVGFMNVNYERAGL--PIISQPVIDTLEFARNLYPDF-KRHGLGPLTKRFGV 562
Cdd:COG3359 76 LLVTYNgKSFDLPFLKTRFTLHRLppPLPEFPHLDLLHPARRLWKNRlPSGGLKTVEELLGI 137
|
|
| CehA_McbA_metalo |
NF038032 |
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
338-401 |
1.93e-03 |
|
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.
Pssm-ID: 468321 [Multi-domain] Cd Length: 315 Bit Score: 41.92 E-value: 1.93e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500942978 338 RVEFHAHTNMSTMDALPavEDLVARAAAWGHKAVAITDHGNVQSFPH-GYHAARKAGIKPLFGME 401
Cdd:NF038032 4 SGDLHIHTNHSDGPTTP--EELARAALAEGLDVIALTDHNTISGRAYfAELLASERGLLVIPGME 66
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
325-407 |
2.26e-03 |
|
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: 41.25 E-value: 2.26e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500942978 325 KEIRKDLmpegekrvefHAHTNMStmDALPAVEDLVARAAAWGHKAVAITDHGNVQSFPHGYHAAR-------------- 390
Cdd:cd07436 3 KDIRGDL----------HVHTTWS--DGRNSIEEMAEAARALGYEYIAITDHSKSLRVANGLSEERlreqieeidalnek 70
|
90
....*....|....*..
gi 500942978 391 KAGIKPLFGMEANIVED 407
Cdd:cd07436 71 LPGIRILKGIEVDILPD 87
|
|
| PRK09248 |
PRK09248 |
putative hydrolase; Validated |
339-405 |
3.98e-03 |
|
putative hydrolase; Validated
Pssm-ID: 236429 [Multi-domain] Cd Length: 246 Bit Score: 40.59 E-value: 3.98e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500942978 339 VEFHAHTNMSTmDALPAVEDLVARAAAWGHKAVAITDHG-NVQSFPHGYHAA------RK-AGIKPLFGMEANIV 405
Cdd:PRK09248 5 VDTHTHTIASG-HAYSTLHENAAEAKQKGLKLFAITDHGpDMPGAPHYWHFGnlrvlpRKvDGVGILRGIEANIK 78
|
|
| |
