|
Name |
Accession |
Description |
Interval |
E-value |
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
3-1437 |
0e+00 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 2609.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 3 LNQQEMFEKLLEQIEMP---TGPEFTEAAIDKLTVHQASKVWEFHLHFQHVLPYTQFMTFQNKLQIAFKEIA--RVTFTI 77
Cdd:PRK00448 1 NEMQEKFKKLLDQINIPddlQSEALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFSHIAdiKVTFSI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 78 VTDDTEVNGRELAEYWEWIVQHSGIKSPLVQSLCNSNVPTYEDGRVILLAENEVIQNFLTNQALGPIESTYHRLGFPKFS 157
Cdd:PRK00448 81 EVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 158 VHTMIDESASqaKIKEFHEQKAKSDQALAQKAEAAIKKANEKRQKQADAPAPIDGPVQLGKQINPQEPaKQMVQITEEER 237
Cdd:PRK00448 161 IDFEIDDSKE--ELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEI-TPMKEINEEER 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 238 SVVVEGYVFDMEVRTLRSQRQLLILKVTDYSSSMVVKKFSRNADDEAQFAALKPGMWVRVRGSVQEDSFMRDLTINAYDI 317
Cdd:PRK00448 238 RVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQDI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 318 NETSHASRQDTAPaDEKRVELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGV 397
Cdd:PRK00448 318 NEIKHPERKDTAE-EEKRVELHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGV 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 398 EANMVDDGVPIAYNDAHVDLKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSIT 477
Cdd:PRK00448 397 EANLVDDGVPIVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGIT 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 478 DDMVRGSKSEEEVFKLFREFYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKF 557
Cdd:PRK00448 477 DDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKF 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 558 NVNLEHHHRAIYDAETTGHLNHLFLKDAEDRyQVQFHDQLNDHMNENAAYRHARPFHATLYAQTQAGLKNLFRIISLSNV 637
Cdd:PRK00448 557 GVELEHHHRADYDAEATAYLLIKFLKDLKEK-GITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNT 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 638 EYYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYYDFLEVQPKPAYSALIESGLIADTDHLEEI 717
Cdd:PRK00448 636 KYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKEI 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 718 ISNMVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQP-GNPLNRTERPDVHFRSTDEMLKDFDFLGTETAHEVVVDT 796
Cdd:PRK00448 716 IKNLIELGKKLNKPVVATGDVHYLDPEDKIYRKILVASQGgGNPLNRHPLPELHFRTTDEMLDEFAFLGEELAKEIVVEN 795
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 797 PRALADQFEIVRPVKDKLYTPRMKGAEAEIEKLTMDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKS 876
Cdd:PRK00448 796 TNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIYGEPLPEIVEKRIEKELNSIIGNGFAVIYLISQKLVKKS 875
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 877 NKDGYLVGSRGSVGSSIVATLSGITEVNPMPPHYRCPNCQYSHFYTNNEYGSGYDLPPKDCPECGTDMVRDGQNIPFETF 956
Cdd:PRK00448 876 LEDGYLVGSRGSVGSSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDGHDIPFETF 955
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 957 LGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGEKNVYRAGTIGTVADKTGYGYVKAYERDTNQTLRSAEVDRLAKGTTGV 1036
Cdd:PRK00448 956 LGFKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTAYGYVKKYEEDTGKFYRNAEIDRLAQGCTGV 1035
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1037 KRTTGQHPAGIIVVPDYMDIYDFTPVQYPADDQSAAWQTTHFDFHSIHDNILKIDILGHDDPTMIRMLQDLSGVQPESIP 1116
Cdd:PRK00448 1036 KRTTGQHPGGIIVVPKYMDIYDFTPIQYPADDVNSEWKTTHFDFHSIHDNLLKLDILGHDDPTMIRMLQDLTGIDPKTIP 1115
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1117 PVDPHVMKIFSSPEVLGVTEDQIFSKTGTLGIPEFGTRFVRGMLEETHPSTFNELLQISGLSHGTDVWLGNAEELIKDGT 1196
Cdd:PRK00448 1116 MDDPKVMKLFSSTEALGVTPEQIGCETGTLGIPEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNAQELIKEGI 1195
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1197 VTLAEVIGCRDNIMTDLIHYGMESDMSFQIMEHVRKGRGIPDEWQQAMKDANVPDWYIESCLKIKYMFPRAHAAAYILMA 1276
Cdd:PRK00448 1196 ATLSDVIGCRDDIMVYLIHKGLEPKLAFKIMESVRKGKGLTEEEEELMKENNVPDWYIESCKKIKYMFPKAHAAAYVLMA 1275
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1277 LRVAYFKVYFPLIYYTAYFSVRADDFDLVAMAHGKDAVKASMKAITDKGMDASAKEKNLLTVLELANEMLERGFKFSMVD 1356
Cdd:PRK00448 1276 WRIAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEIKSKGNDASNKEKDLLTVLEIALEMLERGFKFQKVD 1355
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1357 LDKSDASDWLIDGDTLIAPFRAVPGLGLNVAKQIVAARADKPFLSKEDLSKRGKVSKSLIDFMTENGVLSDLPDENQLSL 1436
Cdd:PRK00448 1356 LYKSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIEKLDELGVLDDLPETNQLSL 1435
|
.
gi 489736634 1437 F 1437
Cdd:PRK00448 1436 F 1436
|
|
| polC_Gram_pos |
TIGR01405 |
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain ... |
232-1437 |
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: 1837.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 232 ITEEERSVVVEGYVFDMEVRTLRSQRQLLILKVTDYSSSMVVKKFSRNADDEAQFAALKPGMWVRVRGSVQEDSFMRDLT 311
Cdd:TIGR01405 3 INEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRDLQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 312 INAYDINETSHASRQDTAPadEKRVELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNI 391
Cdd:TIGR01405 83 MIIKDIEEIPYAERKDNAK--EKRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 392 KILYGVEANMVDDGVPIAYNDAHVDL-KESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETT 470
Cdd:TIGR01405 161 KIIYGMEANLVDDRVPIVYNPDDQKLlDDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 471 TNLTSITDDMVRGSKSEEEVFKLFREFYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRL 550
Cdd:TIGR01405 241 TELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 551 NTLAKKFNVNLEHHHRAIYDAETTGHLNHLFLKDAEDRYqVQFHDQLNDHMNENAAYRHARPFHATLYAQTQAGLKNLFR 630
Cdd:TIGR01405 321 GNICKKLGVDLDDHHRADYDAEATAKVFKVMVEQLKEKG-ITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 631 IISLSNVEYYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYYDFLEVQPKPAYSALIESGLIAD 710
Cdd:TIGR01405 400 LVSISLTKYFYTRPRILRSLLKKYREGLLIGSACSEGELFDALLSKPDDELEEIAKRYDFIEIQPPGNYAHLIEREQVKD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 711 TDHLEEIISNMVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQP-GNPLNRT----ERPDVHFRSTDEMLKDFDFLG 785
Cdd:TIGR01405 480 KEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYRKILVASQGlGNPLNRHfnpkEVPELHFRTTNEMLDEFSFLG 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 786 TETAHEVVVDTPRALADQFEIVRPVKDKLYTPRMKGAEAEIEKLTMDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVI 865
Cdd:TIGR01405 560 EEKAYEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIYGDPLPEIVEQRIEKELKSIIGNGFAVI 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 866 YLIAQRLVFKSNKDGYLVGSRGSVGSSIVATLSGITEVNPMPPHYRCPNCQYSHFYTNNEYGSGYDLPPKDCPECGTDMV 945
Cdd:TIGR01405 640 YLISQLLVQKSLQDGYLVGSRGSVGSSLVATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 946 RDGQNIPFETFLGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGEKNVYRAGTIGTVADKTGYGYVKAYERDTNQTLRSAE 1025
Cdd:TIGR01405 720 KDGQDIPFETFLGFKGDKVPDIDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAYGYVKKYFEDQGKHYRDAE 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1026 VDRLAKGTTGVKRTTGQHPAGIIVVPDYMDIYDFTPVQYPADDQSAAWQTTHFDFHSIHDNILKIDILGHDDPTMIRMLQ 1105
Cdd:TIGR01405 800 IERLVQGCTGVKRTTGQHPGGIIIVPKYMDVYDFTPVQYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHDDPTMIKMLQ 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1106 DLSGVQPESIPPVDPHVMKIFSSPEVLGVTEDQIFSKTGTLGIPEFGTRFVRGMLEETHPSTFNELLQISGLSHGTDVWL 1185
Cdd:TIGR01405 880 DLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFGTKFVRGMLEETKPKTFADLVRISGLSHGTDVWL 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1186 GNAEELIKDGTVTLAEVIGCRDNIMTDLIHYGMESDMSFQIMEHVRKGRGIPDEWQQAMKDANVPDWYIESCLKIKYMFP 1265
Cdd:TIGR01405 960 GNAQDLIKSGIKTLSDVIGCRDDIMVYLIHKGLEPKLAFKIMEKVRKGKGLKAEYIELMKENKVPEWYIESCLKIKYMFP 1039
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1266 RAHAAAYILMALRVAYFKVYFPLIYYTAYFSVRADDFDLVAMAHGKDAVKASMKAITDKG--MDASAKEKNLLTVLELAN 1343
Cdd:TIGR01405 1040 KAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKAFDLETMIKGKEFIKQKLEEINTRRkiNKASPKEKDLLTVLEIVL 1119
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1344 EMLERGFKFSMVDLDKSDASDWLIDGDTLIAPFRAVPGLGLNVAKQIVAARADKPFLSKEDLSKRGKVSKSLIDFMTENG 1423
Cdd:TIGR01405 1120 EMMARGFKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTKISKTHIEKLDSMG 1199
|
1210
....*....|....
gi 489736634 1424 VLSDLPDENQLSLF 1437
Cdd:TIGR01405 1200 VLDNLPETNQLSLF 1213
|
|
| PHP_PolIIIA_POLC |
cd07435 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
335-809 |
1.22e-114 |
|
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: 361.02 E-value: 1.22e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 335 RVELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNnikilygveanmvddgvpiayndah 414
Cdd:cd07435 1 RVELHAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKN------------------------- 55
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 415 vdlkestyvifdtettGLSAIYDrvielsavkmVKGNVVDqfeefidpgfhlsetttnltsitddmvrgskseeevfklf 494
Cdd:cd07435 56 ----------------GIKVIYG----------VEAYLVD---------------------------------------- 69
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 495 refygdaivvghnvtfdigfmntgyarhhmgpitnpiidtltlarwlypnlrgyrlntlakkfnvnlehhhraiydaett 574
Cdd:cd07435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 575 ghlnhlflkdaedryqvqfhdqlndhmnenaayrharPFHATLYAQTQAGLKNLFRIISLSNVEYYYRVPRVPRSVLNKY 654
Cdd:cd07435 70 -------------------------------------PYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKY 112
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 655 RDGILVGSACSSGEVFTAMMQKG-KEEARQKAGYYDFLEVQPKPAYSALIESGLIADTDHLEEIISNMVELGHEMNIPVA 733
Cdd:cd07435 113 REGLLIGSACENGELFEAALNKKsDEELEEIASFYDYIEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVV 192
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489736634 734 ATGDVHYLNPEDKIYRKILIHSQPGNPLNRTERPDVHFRSTDEMLKDFDFLGTETAHEVVVDTPRALADQFEIVRP 809
Cdd:cd07435 193 ATGDVHYLDPEDKIYREILLAGQGGGDGRADEQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIEDIKP 268
|
|
| DNA_pol3_alpha |
pfam07733 |
Bacterial DNA polymerase III alpha NTPase domain; |
824-1094 |
1.03e-75 |
|
Bacterial DNA polymerase III alpha NTPase domain;
Pssm-ID: 400196 [Multi-domain] Cd Length: 259 Bit Score: 252.04 E-value: 1.03e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 824 AEIEKLTMDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVGS-RGSVGSSIVATLSGITE 902
Cdd:pfam07733 1 EYLRKLVEEGLKERYGEGLPEEYQERLEYELNVIIKMGFAGYFLIVWDLVKWAKDNGILVGPgRGSAAGSLVAYLLGITE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 903 VNPMPphyrcpncqyshfytnneygsgydlppkdcpecgtdmvrdgQNIPFETFLGFYGNKVPDIDLNFSGDYQPIAHNY 982
Cdd:pfam07733 81 VDPLK-----------------------------------------HDLLFERFLNPERVSMPDIDIDFEDERREEVIDY 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 983 TKVLFGEKNVYRAGTIGTVADKT-------GYGYV-------------------KAYERDTNQ---TLRSAEVDRL---A 1030
Cdd:pfam07733 120 VKEKYGRDRVAQIATFGTYAAKSairdvgrALGLPydeidrlaklipfelgileKALEEEPELkelIESDPEVKRLielA 199
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489736634 1031 KGTTGVKRTTGQHPAGIIVVPDymDIYDFTPVQYPADDQSaawQTTHFDFHSIHD-NILKIDILG 1094
Cdd:pfam07733 200 KKLEGLPRHTGQHAGGVVISPD--PLTDFVPLYKADDDDR---PVTQFDKDDLEDlGLLKMDFLG 259
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
416-588 |
2.67e-75 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 247.36 E-value: 2.67e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 416 DLKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFR 495
Cdd:COG2176 4 DLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 496 EFYGDAIVVGHNVTFDIGFMNTGYARHHMgPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDAETTG 575
Cdd:COG2176 84 EFLGDAVLVAHNASFDLGFLNAALKRLGL-PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATA 162
|
170
....*....|...
gi 489736634 576 HLNHLFLKDAEDR 588
Cdd:COG2176 163 ELFLKLLEKLEEK 175
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
423-577 |
4.23e-55 |
|
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Pssm-ID: 176648 [Multi-domain] Cd Length: 159 Bit Score: 189.05 E-value: 4.23e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAVKMVKG-NVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGDA 501
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 502 IVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTL-AKKFNVNLEHHHRAIYDAETTGHL 577
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAEL 157
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
608-1416 |
7.56e-54 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 206.07 E-value: 7.56e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 608 RHARPFHATLYAQTQAGLKNLFRIISLSNVE-YYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAG 686
Cdd:COG0587 76 RDDAGYHLVLLAKNREGYRNLCRLLSRAYLEgFYKGKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALA 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 687 YYD-------FLEVQPkpaysalieSGLIADTDHLEEiisnMVELGHEMNIPVAATGDVHYLNPEDKIYRKIL--IH--- 754
Cdd:COG0587 156 RLKdifgdrfYLELQR---------HGLPEDRRVNAA----LLELARELGLPLVATNDVHYLNPEDAEAHDVLlcIRtgk 222
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 755 --SQPGNPLNRTerPDVHFRSTDEMLKDFDflgtetahevvvDTPRALADQFEIVR-------PVKDKL---YTPRMKGA 822
Cdd:COG0587 223 tlDDPGRRRFAN--AERYLKSPEEMAELFA------------DLPEALANTLEIAErcnfsldLGKYQLpkfPVPEGETE 288
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 823 EAEIEKLTMDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLV-F-KSNkdGYLVGS-RGSVGSSIVATLSG 899
Cdd:COG0587 289 EEYLRKLAEEGLERRYPEGIPEEYRERLEYELDVIEKMGFPGYFLIVWDFIrWaRSN--GIPVGPgRGSAAGSLVAYALG 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 900 ITEVNPMPphyrcpncqyshfytnneygsgYDLppkdcpecgtdmvrdgqniPFETFLgfygNK----VPDIDLNFSGD- 974
Cdd:COG0587 367 ITDVDPIR----------------------YDL-------------------LFERFL----NPervsMPDIDIDFCHEr 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 975 ----YQPIAHNYtkvlfGEKNVYRAGTIGTVADK-----TG------YGYV----KAYERDTNQTLRSA----------- 1024
Cdd:COG0587 402 reevIQYVYEKY-----GRDRVAQIATFGTMRARaairdVGrvlglpYGEVdrlaKLIPNDPGITLEKAleeepelrely 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1025 ----EVDRL---AKGTTGVKRTTGQHPAGIIVVPDymDIYDFTPVQYPADDQSaawQTTHFDFHSIHD-NILKIDILG-- 1094
Cdd:COG0587 477 dsdpEVRRLldlARKLEGLPRHLSTHAGGVVISDD--PLTDLVPLERAAMGGR---PVTQFDKDDVEAlGLLKFDFLGlr 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1095 -----HDdptMIRMLQDLSGVQ--PESIPPVDPHVMKIFSSPEVLGVTedQIFSktgtlgipefgtrfvRGM---LEETH 1164
Cdd:COG0587 552 tltviRD---ALDLIKENRGIDidLADIPLDDPKTYELLQRGDTIGVF--QLES---------------RGMrslLKRLK 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1165 PSTFNELlqISGLShgtdvwlgnaeeL-----IKDGTVT--------LAEVigcrdnimtDLIH----------YG---- 1217
Cdd:COG0587 612 PDCFEDL--VALVA------------LyrpgpMQGGMVPpyirrkhgREPV---------EYPHpelepilketYGvivy 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1218 ----M------------ESDM--------SFQIMEHVR-------KGRGIPDE-----WQQAMKDANvpdwyiesclkik 1261
Cdd:COG0587 669 qeqvMqiaqvlagfslgEADLlrramgkkKKEEMAKQRekfvegaVANGYDEEfaeeiFDQIEKFAG------------- 735
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1262 YMFPRAHAAAYILMALRVAYFKVYFPLIYYTAYFSVRADDFDLVAmahgkdavkasmkaitdkgmdasakeknlltvlEL 1341
Cdd:COG0587 736 YGFNKSHAAAYALLAYQTAYLKAHYPAEFMAALLNSQPMGFYKPA---------------------------------QY 782
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1342 ANEMLERGFKFSMVDLDKSDASDWLIDGDTLIAPFRAVPGLGLNVAKQIVAARADK-PFLSKEDLSKR---GKVSK---- 1413
Cdd:COG0587 783 VQEARRHGIEVLPPDVNESDWDFTVEPGGAIRLGLGAIKGVGEAAAEAIVAAREENgPFTSLFDFCRRvdlRKLNKrvle 862
|
...
gi 489736634 1414 SLI 1416
Cdd:COG0587 863 ALI 865
|
|
| polc |
TIGR00594 |
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
613-1431 |
1.38e-53 |
|
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: 205.31 E-value: 1.38e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 613 FHATLYAQTQAGLKNLFRIISLSNVEYYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYYDflE 692
Cdd:TIGR00594 85 YHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALKYQ--E 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 693 VQPKPAYSALIESGLIADtdhlEEIISNMVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQPGNPLNRTER-----P 767
Cdd:TIGR00594 163 IFGDDYYLELQDHGIPEQ----RVVNEALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKTLSDPKRlkfysD 238
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 768 DVHFRSTDEMLKDFDflgtetahevvvDTPRALADQFEI---VRPVKDKLYTPRM---------KGAEAEIEKLTMDRAH 835
Cdd:TIGR00594 239 EFYLKSPEEMAELFA------------DIPEALANTVEIaerCNLVDVKLGPPRLpsyqippdfTSQEDYLRHLADEGLR 306
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 836 AWYGNPLPEI-----VQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGITEVNPMPph 909
Cdd:TIGR00594 307 ERLAAGPPGYkrraqYKERLEYELDVINSMGFPGYFLIVWDFIKWAKDHGIPVGpGRGSAAGSLVAYALKITDIDPIK-- 384
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 910 yrcpncqyshfytnneygsgYDLppkdcpecgtdmvrdgqniPFETFLGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGE 989
Cdd:TIGR00594 385 --------------------HGL-------------------LFERFLNPERISMPDIDIDFCDERRDEVIEYVADKYGH 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 990 KNVYRAGTIGTVAdktgygyVKAYERDTNQTLRS--AEVDRLAK------GTT--------------------------- 1034
Cdd:TIGR00594 426 DNVAQIITFGTMK-------AKAALRDVARVLDIpyAEADRIAKlipprpGKTlkealeaspqlrqlyeedpevkqlidm 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1035 -----GVKRTTGQHPAGIIVVPDYMDiyDFTPVQYPADDQSAAwqtTHFDFHSIHD-NILKIDILGHDDPTMIRMLQDL- 1107
Cdd:TIGR00594 499 arkleGLNRNAGVHAAGVVISSEPLT--DYVPLYKDKEGGAIS---TQYDMDDLEAvGLLKMDFLGLKTLTLIQDATELi 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1108 -----SGVQPESIPPVDPHVMKIFSSPEvlgvtedqifsktgTLGIPEFGTRFVRGMLEETHPSTFNELLQISGL----- 1177
Cdd:TIGR00594 574 rkrrgIDLDIASIPLDDKKTFSLLQEGD--------------TTGVFQLESRGMQDLLKRLKPDGFEDIIAVNALyrpgp 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1178 ------------SHGTDVwLGNAEELIKDgtvTLAE---VIGCRDNIM---TDLIHYGM-ESDM--------SFQIMEHV 1230
Cdd:TIGR00594 640 mesgmipdfidrKHGREP-IEYPHPLLEP---ILKEtygVIVYQEQVMqiaQRLAGFSLgEADLlrramgkkKAEEMAKE 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1231 RKG-------RGIPDE-----WQQAMKDANvpdwyiesclkikYMFPRAHAAAYILMALRVAYFKVYFPliyytAYFsvr 1298
Cdd:TIGR00594 716 REKfvegaekNGYDPEiaenlFDLIEKFAG-------------YGFNKSHAAAYGMISYQTAYLKANYP-----AEF--- 774
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1299 addfdlvaMAhgkdavkASMKAITDKgmdasaKEKnlltVLELANEMLERGFKFSMVDLDKSDaSDWLIDGDTLIAPFRA 1378
Cdd:TIGR00594 775 --------MA-------ALLTSEIND------IEK----VAVYIAEAKKMGIEVLPPDINESG-QDFAVEDKGIRYGLGA 828
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 489736634 1379 VPGLGLNVAKQIVAARADK-PFLSKEDLSKRGKvSKSLIDFMTENGVLSDLPDE 1431
Cdd:TIGR00594 829 IKGVGESVVKSIIEERNKNgPFKSLFDFINRVD-FKKLNKKVLEALIKAGAFDS 881
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
422-577 |
2.19e-53 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 184.23 E-value: 2.19e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGDA 501
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489736634 502 IVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDAETTGHL 577
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAEL 157
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
416-579 |
1.30e-39 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 156.23 E-value: 1.30e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 416 DLKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFR 495
Cdd:PRK07883 11 PLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFL 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 496 EFYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPN--LRGYRLNTLAKKFNVNLEHHHRAIYDAET 573
Cdd:PRK07883 91 EFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRdeAPNVRLSTLARLFGATTTPTHRALDDARA 170
|
....*.
gi 489736634 574 TGHLNH 579
Cdd:PRK07883 171 TVDVLH 176
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
421-574 |
1.49e-37 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 138.97 E-value: 1.49e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 421 TYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFY-G 499
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLrG 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 500 DAIVVGHNVTFDIGFMNTGYARHHMG-PITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLE-HHHRAIYDAETT 574
Cdd:smart00479 81 RILVAGNSAHFDLRFLKLEHPRLGIKqPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARAT 157
|
|
| dnaE |
PRK06826 |
DNA polymerase III DnaE; Reviewed |
611-1408 |
3.38e-36 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 150.04 E-value: 3.38e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 611 RPFHATLYAQTQAGLKNLFRIISLSNVE-YYYRvPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYYD 689
Cdd:PRK06826 86 ETYHLVLLAKNETGYKNLMKIVSKAFTEgFYYK-PRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYK 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 690 --------FLEVQpkpaysaliesgliadtDH--LEEIISN--MVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQP 757
Cdd:PRK06826 165 difgkenfYLELQ-----------------DHgiPEQRKVNeeLIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCIQT 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 758 GNPLNRTER-----PDVHFRSTDEMLKDFDFLgtetahevvvdtPRALADQFEI-----VRPVKDKLYTPRM-----KGA 822
Cdd:PRK06826 228 GKTVDDENRmrfpsDEFYLKSPEEMYELFSYV------------PEALENTVKIaercnVEFEFGKSKLPKFplpegYDP 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 823 EAEIEKLTMDRAHAWYGNPLPEIVQkRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGIT 901
Cdd:PRK06826 296 YEYLRELCYEGLKKRYPNPSEELIE-RLEYELSVIKQMGYVDYFLIVWDFIRFARENGIMVGpGRGSAAGSLVAYTLGIT 374
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 902 EVNPMPphyrcpncqyshfytnneygsgYDLppkdcpecgtdmvrdgqniPFETFLgfygN----KVPDIDLNF--SGDY 975
Cdd:PRK06826 375 KIDPIK----------------------YNL-------------------LFERFL----NpervSMPDIDIDFcyERRQ 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 976 QPIahNYTKVLFGEKNVYRAGTIGTVADKT---------GYGYV------------------KAYErdTNQTLRSA---- 1024
Cdd:PRK06826 410 EVI--DYVVEKYGKDRVAQIITFGTMAARAairdvgralNYPYAevdriakmiptelgitidKALE--LNPELKEAyend 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1025 -EVDRL---AKGTTGVKRTTGQHPAGIIVVPDymDIYDFTPVQyPADDQSaawqTTHFDFHSIHD-NILKIDILGHDDPT 1099
Cdd:PRK06826 486 eRVRELidtARALEGLPRHASTHAAGVVISSE--PLVEYVPLQ-KNDGSI----VTQFTMTTLEElGLLKMDFLGLRTLT 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1100 MIR----MLQDLSGVQP--ESIPPVDPHVMKIFSSPEVLGVTedQIFSKtgtlgipefgtrfvrGM---LEETHPSTFNE 1170
Cdd:PRK06826 559 VIRdavdLIKKNRGIEIdlDKIDYDDKKVYKMIGEGKTVGVF--QLESA---------------GMrsfMKELKPDSLED 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1171 LlqISGLS---HGTdvwLGNAEELIKD----GTVT---------LAEVIGC---RDNIM---TDLIHYGM-ESD-----M 1222
Cdd:PRK06826 622 I--IAGISlyrPGP---MDSIPRYIKNknnpEKIEylhpklepiLKVTYGCivyQEQVMqivRDLAGYSMgRSDlvrraM 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1223 S---FQIMEHVRKG--RGIPDEWQQAMKDANVPDwyiESCLKI--------KYMFPRAHAAAYILMALRVAYFKVYFPLI 1289
Cdd:PRK06826 697 SkkkHDVMEEERKNfiYGIVDEGGPGCIRNGIDE---ETANKIfdsmmdfaSYAFNKSHAAAYAVVAYQTAYLKRYYPVE 773
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1290 YytayfsvraddfdlvaMAhgkdavkASMKAItdkgMDASAKeknlltVLELANEMLERGFKFSMVDLDKSDaSDWLIDG 1369
Cdd:PRK06826 774 F----------------MA-------ALLNSV----MGNSDK------VAFYIEECRRLGIEVLPPDINESY-SKFTVEG 819
|
890 900 910 920
....*....|....*....|....*....|....*....|
gi 489736634 1370 DTLIAPFRAVPGLGLNVAKQIVAARADK-PFLSKEDLSKR 1408
Cdd:PRK06826 820 DKIRFGLAAVKNVGENAIDSIVEEREKKgKFKSLVDFCER 859
|
|
| dnaE |
PRK05673 |
DNA polymerase III subunit alpha; Validated |
610-1134 |
8.75e-34 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 142.16 E-value: 8.75e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 610 ARPFHATLYAQTQAGLKNLFRIISLSNVE-YYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYY 688
Cdd:PRK05673 80 GAYTHLTLLAKNETGYRNLFKLSSRAYLEgQYGYKPRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQYDEAEEAAAEY 159
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 689 -----D--FLEVQpkpaysaliesgliaDTDHLEE--IISNMVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQPGN 759
Cdd:PRK05673 160 qeifgDrfYLELM---------------RHGLPIErrVEHALLELAKELGLPLVATNDVHYLTPEDAEAHEALLCIAEGK 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 760 PLNRTERP--DVH---FRSTDEMLKDFDflgtetahevvvDTPRALADQFEIVR--PVKDKLYTPRM------------- 819
Cdd:PRK05673 225 TLDDPDRFrfYSPeqyLKSAEEMRELFA------------DLPEALDNTVEIAErcNVEVRLGKPFLprfptpdgeteed 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 820 -------KGAEAEIEKLTMDRAHAWYgnplpeivQKRVDKELKSIIGNGFSVIYLIaqrlV--F----KSNkdGYLVG-S 885
Cdd:PRK05673 293 ylrkeakEGLEERLAFLFPDEERPEY--------VERLEYELDVIIQMGFPGYFLI----VadFiqwaKDN--GIPVGpG 358
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 886 RGSVGSSIVATLSGITEVNPMPphyrcpncqyshfytnneygsgYDLppkdcpecgtdmvrdgqniPFETFLgfygN--K 963
Cdd:PRK05673 359 RGSGAGSLVAYALGITDLDPLR----------------------FGL-------------------LFERFL----NpeR 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 964 V--PDIDLNFSGD-------YqpIAHNYtkvlfGEKNVYRAGTIGTVADK-----------TGYGYV------------- 1010
Cdd:PRK05673 394 VsmPDFDIDFCQDrrdevirY--VAEKY-----GRDAVAQIITFGTMKAKavirdvgrvlgMPYGFVdritklippdpgi 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1011 ---KAYE--------RDTNqtlrsAEVDRL---AKGTTGVKRTTGQHPAGIIVVPDymDIYDFTPVQYPADDQSAAwqtT 1076
Cdd:PRK05673 467 tlaKAYEeepelrelYESD-----PEVKRLidmARKLEGLTRNAGVHAAGVVISPT--PLTDFVPLYRDPDSGMPV---T 536
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489736634 1077 HFDFHSIHD-NILKIDILG-------HDDPTMIRMlQDLSGVQPESIPPVDPHVMKIFSSPEVLGV 1134
Cdd:PRK05673 537 QFDMKDVEAaGLVKFDFLGlrtltiiDDALKLIKK-RRGIDVDLEAIPLDDPKTYELLQRGETLGV 601
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
423-574 |
2.75e-33 |
|
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: 126.70 E-value: 2.75e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAVKMVKG--NVVDQFEEFIDP--GFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFY 498
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGenEIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 499 G-DAIVVGHNVTFDIGFMNTGYARH---HMgPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNV-NLEHHHRAIYDAET 573
Cdd:pfam00929 81 RkGNLLVAHNASFDVGFLRYDDKRFlkkPM-PKLNPVIDTLILDKATYKELPGRSLDALAEKLGLeHIGRAHRALDDARA 159
|
.
gi 489736634 574 T 574
Cdd:pfam00929 160 T 160
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
417-635 |
3.28e-33 |
|
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: 128.34 E-value: 3.28e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 417 LKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFRE 496
Cdd:TIGR00573 4 LVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 497 FYGDAIVVGHNVTFDIGFMNTGYAR-HHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDAETTG 575
Cdd:TIGR00573 84 YIRGAELVIHNASFDVGFLNYEFSKlYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADA 163
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 576 HLnhlflkdAEDRYQVQFHDQLNdhMNENAAYRHaRPFHATLYAQTQAGLKNLFRIISLS 635
Cdd:TIGR00573 164 FI-------LAKLYLVMTGKQTK--YGENEGQQS-RPYHAIKSIVKKDMLLKLIKAVSTE 213
|
|
| DNA_pol3_finger |
pfam17657 |
Bacterial DNA polymerase III alpha subunit finger domain; |
1097-1248 |
5.25e-33 |
|
Bacterial DNA polymerase III alpha subunit finger domain;
Pssm-ID: 407553 [Multi-domain] Cd Length: 166 Bit Score: 125.72 E-value: 5.25e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1097 DPTMIRMLQDLS------GVQPESIPPVDPHVMKIFSSPEvlgvtedqifsktgTLGIPEFGTRFVRGMLEETHPSTFNE 1170
Cdd:pfam17657 1 TLTIIRDALDLIkenrgiGIDLATIPLDDPKTYKLLSSGD--------------TLGVFQFESRGMRQMLKRLKPDTFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1171 LLQISGLSHGTDVWLGNAEELIKD---------GTVTLAEVIGCRDNIMTD--------LIHYGMESDMSFQIMEHVRKG 1233
Cdd:pfam17657 67 LVALSALYRPGPMQGGNVDDYIKRkhgkekieyPHPDLEPILKETYGVIVYqeqvmqiaQILAGFSLGEADLLRRAMGKK 146
|
170 180
....*....|....*....|
gi 489736634 1234 R-----GIPDEWQQAMKDAN 1248
Cdd:pfam17657 147 KpeemeKLREKFIEGAKENG 166
|
|
| DNA_pol3_a_NII |
pfam11490 |
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
91-206 |
1.09e-32 |
|
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: 123.23 E-value: 1.09e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 91 EYWEWIVQHSGIKSPLVQSLCNSNVPTYEDGRVILLAENEVIQNFLTNQALGPIESTYHRLGFPKFSVHTMIDE-SASQA 169
Cdd:pfam11490 1 DYWEEIVEELSKKSPSLKSLLKNQKPEVEGNKLIIKVPNEIEANFLKKKNLDKLLEEYIKFGFGKLSIDVEVDEdESSEE 80
|
90 100 110
....*....|....*....|....*....|....*..
gi 489736634 170 KIKEFHEQKAKSDQALAQKAEAAIKKANEKRQKQADA 206
Cdd:pfam11490 81 ELEEFEEQKEEEEQKAIQEAIEALEKKEAEKKSKEKE 117
|
|
| PHP_PolIIIA_DnaE3 |
cd12113 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
598-781 |
4.84e-32 |
|
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: 127.17 E-value: 4.84e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 598 NDHMNENAAYRHARPFHATLYAQTQAGLKNLFRIISLSNVE-YYYRvPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQK 676
Cdd:cd12113 71 GSRFDKKDKKGDKRYYHLVLLAKNEEGYRNLMKLVSLAYLEgFYYK-PRIDKELLAKYSEGLIALSACLAGEIPQLLLNG 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 677 GKEEARQKAGYYD--------FLEVQpkpaysaliesgliadtDH-LEE---IISNMVELGHEMNIPVAATGDVHYLNPE 744
Cdd:cd12113 150 DEEEAREAALEYRdifgkdnfYLELQ-----------------DHgLPEqkkVNEGLIELAKELGIPLVATNDVHYLNKE 212
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 489736634 745 DKIYRKILIHSQPGNPLNRTER-----PDVHFRSTDEMLKDF 781
Cdd:cd12113 213 DAEAHDVLLCIQTGKTLDDPNRmrfdtDEFYLKSPEEMRELF 254
|
|
| polC_OBF |
cd04484 |
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
239-320 |
6.42e-30 |
|
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Pssm-ID: 239930 [Multi-domain] Cd Length: 82 Bit Score: 113.85 E-value: 6.42e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 239 VVVEGYVFDMEVRTLRSQRQLLILKVTDYSSSMVVKKFSRNadDEAQFAALK-PGMWVRVRGSVQEDSFMRDLTINAYDI 317
Cdd:cd04484 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRK--DEKDKEELKsKGDWVRVRGKVQYDTFSKELVLMINDI 79
|
...
gi 489736634 318 NET 320
Cdd:cd04484 80 EEI 82
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
413-574 |
1.48e-29 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 118.97 E-value: 1.48e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 413 AHVDLKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFhLSETTTNLTSITDDMVRGSKSEEEVFK 492
Cdd:PRK08517 61 RFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKE-VPEYITELTGITYEDLENAPSLKEVLE 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 493 LFREFYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRgYRLNTLAKKFNVNLEHHHRAIYDAE 572
Cdd:PRK08517 140 EFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPR-YGLSFLKELLGIEIEVHHRAYADAL 218
|
..
gi 489736634 573 TT 574
Cdd:PRK08517 219 AA 220
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
422-575 |
4.32e-29 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 119.53 E-value: 4.32e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGDA 501
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489736634 502 IVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEhHHRAIYDAETTG 575
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCA 162
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
422-572 |
8.49e-29 |
|
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: 113.78 E-value: 8.49e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLS-AIYDRVIELSAVKMV----KGNVvdqFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFRE 496
Cdd:cd06131 1 QIVLDTETTGLDpREGHRIIEIGCVELInrrlTGNT---FHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 497 FYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNP---IIDTLTLARWLYPNLRgYRLNTLAKKFNVNLEHH--HRAIYDA 571
Cdd:cd06131 78 FIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARKKFPGKP-NSLDALCKRFGIDNSHRtlHGALLDA 156
|
.
gi 489736634 572 E 572
Cdd:cd06131 157 E 157
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
412-588 |
6.00e-28 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 114.00 E-value: 6.00e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 412 DAHVDLKESTYVIFDTETTGLSAIY-DRVIELSAVKMvKGNVV--DQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEE 488
Cdd:PRK07740 51 VLDIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKT-KGGEVetDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLA 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 489 EVFKLFREFYGDAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAI 568
Cdd:PRK07740 130 EVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHAL 209
|
170 180
....*....|....*....|
gi 489736634 569 YDAETTGHLNHLFLKDAEDR 588
Cdd:PRK07740 210 GDALMTAKLWAILLVEAQQR 229
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
421-583 |
6.68e-28 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 122.37 E-value: 6.68e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 421 TYVIFDTETTGLSAIY-DRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYG 499
Cdd:PRK08074 4 RFVVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 500 DAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNvnLEHH--HRAIYDAETTGhl 577
Cdd:PRK08074 84 GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELG--LEHDqpHRADSDAEVTA-- 159
|
....*.
gi 489736634 578 nHLFLK 583
Cdd:PRK08074 160 -ELFLQ 164
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
422-577 |
6.07e-27 |
|
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: 107.98 E-value: 6.07e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETtglsAIYDR--VIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYG 499
Cdd:cd06130 1 FVAIDFET----ANADRasACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489736634 500 DAIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHrAIYDAETTGHL 577
Cdd:cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHD-ALEDARACAEI 153
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
415-572 |
9.41e-27 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 110.69 E-value: 9.41e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 415 VDLKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLF 494
Cdd:PRK06310 2 SLLKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 495 REFYGDA-IVVGHNVTFDIGFMNTGYARHHMG--PITNPIIDTLTLARwLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDA 571
Cdd:PRK06310 82 KGFFKEGdYIVGHSVGFDLQVLSQESERIGETflSKHYYIIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDV 160
|
.
gi 489736634 572 E 572
Cdd:PRK06310 161 E 161
|
|
| dnaE |
PRK07374 |
DNA polymerase III subunit alpha; Validated |
608-1408 |
1.08e-26 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 119.06 E-value: 1.08e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 608 RHARPFHATLYAQTQAGLKNLFRIISLSNVE------YYYRvPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEA 681
Cdd:PRK07374 80 KKEKRYHLVVLAKNATGYKNLVKLTTISHLNgmrgrgIFSR-PCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPDVA 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 682 RQKAGYY------DF-LEVQpkpaysaliesgliadtDH--LEEIISN--MVELGHEMNIPVAATGDVHYLNPEDKIYRK 750
Cdd:PRK07374 159 RDVAAWYkevfgdDFyLEIQ-----------------DHgsIEDRIVNveLVRIAKELGIKLIATNDAHYLSKNDVEAHD 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 751 ILIHSQPGNPL---NR-----TErpdvHFRSTDEMLKDF-DFLGTETAHEVVVDTpRALADQFEivrpVKDKLYTPRM-- 819
Cdd:PRK07374 222 ALLCVLTGKLIsdeKRlrytgTE----YIKSEEEMLRLFrDHLDPEVIQEAIANT-VEVAEKVE----EYDILGTYRMpr 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 820 ------KGAEAEIEKLT----MDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGS 888
Cdd:PRK07374 293 fpipegHTAVSYLTEVTeqglLKRLKLNSLDEIDENYKERLSYELKIIEQMGFPTYFLVVWDYIRFAREQGIPVGpGRGS 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 889 VGSSIVATLSGITEVNPmpphyrcpncqyshfytnneygsgydlppkdcpecgtdmVRDGqnIPFETFLGFYGNKVPDID 968
Cdd:PRK07374 373 AAGSLVAYALGITNIDP---------------------------------------VKNG--LLFERFLNPERKSMPDID 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 969 LNFSGDYQPIAHNYTKVLFGEKNVyraGTIGTVADKTGygyvKAYERDTNQTLR--SAEVDRLAK--------------- 1031
Cdd:PRK07374 412 TDFCIERRGEVIDYVTRRYGEDKV---AQIITFNRMTS----KAVLKDVARVLDipYGEADRLAKlipvvrgkpaklkam 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1032 ---------------GTTGVKR-------------TTGQHPAGIIVVPDYMDiyDFTPVQYPADDQSAawqTTHF--DFH 1081
Cdd:PRK07374 485 igkespspefrekyeKDPRVKKwvdmamriegtnkTFGVHAAGVVIASDPLD--ELVPLQRNNDGQVI---TQYFmeDIE 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1082 SIhdNILKIDILGHDDPTMIRMLQDL----SGVQ--PESIPPVDPHVMKIFSSPEVLGvtedqIFS--KTGtlgipefgt 1153
Cdd:PRK07374 560 SL--GLLKMDFLGLKNLTMIEKTLELveqsTGERidPDNLPLDDEKTFELLARGDLEG-----IFQleSSG--------- 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1154 rfVRGMLEETHPSTFNELLQI----------SGL-------SHGTDVwLGNAEELIKDgtvTLAEVIGC---RDNIM--- 1210
Cdd:PRK07374 624 --MRQVVRDLKPSSLEDISSIlalyrpgpldAGLipkfinrKHGREA-IDFAHPLLEP---ILTETYGImvyQEQIMkia 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1211 TDLIHYGM-ESDMSFQIM-----EHVRKGRGIPDEwqQAMK---DANVPDWYIES-CLKIKYMFPRAHAAAYILMALRVA 1280
Cdd:PRK07374 698 QDLAGYSLgQADLLRRAMgkkkvSEMQKHRGIFVE--GASKrgvDEKVADELFDQmVLFAEYCFNKSHSTAYGAVTYQTA 775
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1281 YFKVYFPLIYYTAYFSVRADDFDLVamahgkdavkasMKAITDkgmdasakeknlltvlelANEMlerGFKFSMVDLDKS 1360
Cdd:PRK07374 776 YLKAHYPVAYMAALLTVNAGSSDKV------------QRYISN------------------CNSM---GIEVMPPDINRS 822
|
890 900 910 920
....*....|....*....|....*....|....*....|....*....
gi 489736634 1361 dASDWLIDGDTLIAPFRAVPGLGLNVAKQIVAAR-ADKPFLSKEDLSKR 1408
Cdd:PRK07374 823 -GIDFTPKGNRILFGLSAVKNLGDGAIRNIIAARdSDGPFKSLADLCDR 870
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
421-577 |
2.19e-25 |
|
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: 114.13 E-value: 2.19e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 421 TYVIFDTETTGLSAIYDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGD 500
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 501 AIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDAETTGHL 577
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAEL 157
|
|
| dnaE |
PRK06920 |
DNA polymerase III subunit alpha; |
617-1405 |
7.69e-25 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 112.97 E-value: 7.69e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 617 LYAQTQAGLKNLFRIislSNVEYYYRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKA--------GYY 688
Cdd:PRK06920 82 LLAENEIGYQNLLKI---SSSIMTKSKEGIPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQAEEVArayqnmfgNFY 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 689 DFLEVQPkpaysaliesglIADTDHLEEIIsnmVELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQPGNPLNRTERP- 767
Cdd:PRK06920 159 MSLQHHA------------IQDELLLQEKL---PEFSNRVNIPVVATNDVRYINQSDALVHECLLSVESGTKMTDPDRPr 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 768 ----DVHFRSTDEMLKDFdflgteTAHEVVVDTPRALADQFEIVRPVKD----KLYTPRMKGAEAEIEKLTMDRAHAWYG 839
Cdd:PRK06920 224 lktdQYYLKSSDEMEALF------SHVPEAIYNTVEIAERCRVEIPFHVnqlpKFPVPSNETADMYLRRVCEEGLQKRYG 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 840 NPlPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGITEVNPMpphyrcpncqys 918
Cdd:PRK06920 298 TP-KEVHINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHILTGpGRGSAAGSLVSYVLEITDIDPI------------ 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 919 hfytnneygsgydlppkdcpecgtdmvrdGQNIPFETFLGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGEKNVYRAGTI 998
Cdd:PRK06920 365 -----------------------------EYDLLFERFLNPERVTLPDIDIDFPDTRRDEMIRYVKDKYGQLRVAQIVTF 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 999 GTVAdktgygyVKAYERDTNQT--LRSAEVDRLAK------GTT--------------------------------GVKR 1038
Cdd:PRK06920 416 GTLA-------AKAAIRDIARVmgLPPRDIDIFSKlipsklGITlkdayeesqslrefiqgnllhervfeiakrveGLPR 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1039 TTGQHPAGII--------VVP---DYMDIYdftPVQYPADdqsaawqtthfdfHSIHDNILKIDILGHDDPTMI----RM 1103
Cdd:PRK06920 489 HTSIHAAGVImsqepltgSVAiqeGHNDVY---VTQYPAD-------------ALEELGLLKMDFLGLRNLTLLeniiKF 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1104 LQDLSGVQPE--SIPPVDPhvmKIFsspevlgvtedQIFSKTGTLGIPEFGTRFVRGMLEETHPSTFNELLQISGL---- 1177
Cdd:PRK06920 553 IEQKTGKEIDirNLPLQDE---KTF-----------QLLGRGDTTGVFQLESSGMRNVLRGLKPNEFEDIVAVNSLyrpg 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1178 -----------SHGTdVWLGNAEELIKDGTVTLAEVIGCRDNIMTdlihygMESDMS-FQIMEH-------VRKGRGIPD 1238
Cdd:PRK06920 619 pmeqiptfiesKHGK-RKIEYLHPDLKPILERTYGVIVYQEQIMQ------IASKLAgFSLGEAdllrravSKKNRDILD 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1239 EWQQAmkdanvpdwYIESCLK------------------IKYMFPRAHAAAYILMALRVAYFKVYFPLIYYTAyfsvrad 1300
Cdd:PRK06920 692 QERKH---------FVQGCLQngydetsaekiydlivrfANYGFNRSHAVAYSMIGYQLAYLKANYTLEFMTA------- 755
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1301 dfdLVAMAHGKDavkasmkaitDKgmdasakeknlltVLELANEMLERGFKFSMVDLDKSdASDWLIDGDTLIAPFRAVP 1380
Cdd:PRK06920 756 ---LLSSAIGNE----------DK-------------IVQYIRETKRKGFHVLPPSLQRS-GYNFQIEGNAIRYSLLSIR 808
|
890 900
....*....|....*....|....*
gi 489736634 1381 GLGLNVAKQIVAARADKPFlskEDL 1405
Cdd:PRK06920 809 NIGMATVTALYEEREKKMF---EDL 830
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
423-572 |
2.85e-22 |
|
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130473 [Multi-domain] Cd Length: 225 Bit Score: 97.08 E-value: 2.85e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIY-DRVIELSAVKMV----KGnvvDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREF 497
Cdd:TIGR01406 3 IILDTETTGLDPKGgHRIVEIGAVELVnrmlTG---DNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 498 YGDAIVVGHNVTFDIGFMNTGYARhhMGPITNPI------IDTLTLARWLYPNLRgYRLNTLAKKFNVNLEHH--HRAIY 569
Cdd:TIGR01406 80 IGGSELVIHNAAFDVGFLNYELER--LGPTIKKIgefcrvIDTLAMARERFPGQR-NSLDALCKRFKVDNSHRtlHGALL 156
|
...
gi 489736634 570 DAE 572
Cdd:TIGR01406 157 DAH 159
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
337-403 |
2.60e-21 |
|
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: 88.86 E-value: 2.60e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 337 ELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVEANMVD 403
Cdd:smart00481 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
423-572 |
3.01e-20 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 91.46 E-value: 3.01e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIY-DRVIELSAVKMVK----GNvvdQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREF 497
Cdd:PRK05711 7 IVLDTETTGLNQREgHRIIEIGAVELINrrltGR---NFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 498 YGDAIVVGHNVTFDIGFMNTGYARH--HMGPITN--PIIDTLTLARWLYPNLRgYRLNTLAKKFNVNLEHH--HRAIYDA 571
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLgrDIPKTNTfcKVTDTLAMARRMFPGKR-NSLDALCKRYGIDNSHRtlHGALLDA 162
|
.
gi 489736634 572 E 572
Cdd:PRK05711 163 E 163
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
337-404 |
7.24e-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: 88.37 E-value: 7.24e-20
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489736634 337 ELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVEANMVDD 404
Cdd:pfam02811 1 HLHVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVAPG 68
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
423-570 |
1.44e-19 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 89.48 E-value: 1.44e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAVKMVKGnvvDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYG-DA 501
Cdd:PRK06309 5 IFYDTETTGTQIDKDRIIEIAAYNGVTS---ESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGtDN 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 502 IVVGHNV-TFDIGFMNTGYARHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYD 570
Cdd:PRK06309 82 ILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
|
|
| DNA_pol3_a_NI |
pfam14480 |
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
8-77 |
8.01e-19 |
|
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: 81.82 E-value: 8.01e-19
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489736634 8 MFEKLLEQIEMPTG--PEFTEAAIDKLTVHQASKVWEFHLHFQHVLPYTQFMTFQNKLQIAFKEIARVTFTI 77
Cdd:pfam14480 1 RFFELFPQLKLPDEleELFEDAEIEKVTVHKKSKKWRFYISSPHLLPKEVIYKFEQRLKEQFFHIAKVKVKI 72
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
610-818 |
3.05e-17 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes.
Pssm-ID: 213988 [Multi-domain] Cd Length: 277 Bit Score: 83.68 E-value: 3.05e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 610 ARPFHATLYAQTQAGLKNLFRIISLSNVEYYYRV-PRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAGYY 688
Cdd:cd07433 75 DEPFRLTLLAQNEQGYKNLTELISRAYLEGQRNGgPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGNPDLAEALLQFL 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 689 dfLEVQPKPAYSALIESGLIADtdhlEEIISNMVELGHEMNIPVAATGDVHYLNPEDkiYR----KILIHSqpGNPLNRT 764
Cdd:cd07433 155 --KKIFPDRFYLELQRHGRPEE----EAYEHALIDLAYELGLPLVATNDVRFLKPED--FEaheaRVCIAE--GRTLDDP 224
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489736634 765 ER-----PDVHFRSTDEMLKDFdflgtetahevvVDTPRALADQFEI-----VRPVKDKLYTPR 818
Cdd:cd07433 225 RRprrysPQQYFKSAEEMAELF------------ADLPEAIENTVEIakrcnVRIELGKPFLPD 276
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
336-415 |
2.27e-16 |
|
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213985 [Multi-domain] Cd Length: 88 Bit Score: 75.54 E-value: 2.27e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 336 VELHLHSNMSQMDATnSVSDYVKQAAKWGHPAIAITDHSGAQAFPEA--------FAAGEKNNIKILYGVEANMVDDGVP 407
Cdd:cd07309 1 VDLHTHTVFSDGDHA-KLTELVDKAKELGPDALAITDHGNLRGLAEFntagk*nhIKAAEAAGIKIIIGSEVNLTVLAHP 79
|
....*....
gi 489736634 408 IAYN-DAHV 415
Cdd:cd07309 80 VVATsDSHY 88
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
418-584 |
2.35e-16 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 84.74 E-value: 2.35e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 418 KESTYVIFDTETTGLSAIYdRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREF 497
Cdd:PRK07246 5 KLRKYAVVDLEATGAGPNA-SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 498 YGDAIVVGHNVTFDIG------FMNtGYArhhmgpITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHRAIYDA 571
Cdd:PRK07246 84 IEDCIFVAHNVKFDANllaealFLE-GYE------LRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADA 156
|
170
....*....|...
gi 489736634 572 ETTGHLnHLFLKD 584
Cdd:PRK07246 157 RATAEL-FLKLLQ 168
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
422-586 |
3.88e-16 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 77.98 E-value: 3.88e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDR-----VIELSAVKM-VKGNVVDQFEEFIDPGFH--LSETTTNLTSITDDMVRGSKSEEEVFKL 493
Cdd:COG5018 4 YLVIDLEATCWDGKPPPgfpmeIIEIGAVKVdENGEIIDEFSSFVKPVRRpkLSPFCTELTGITQEDVDSAPSFAEAIED 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 494 FREFYG--DAIVV--GHnvtFDIGFMNTGYARHHM-GPITNPIIDTLTLARWLYPNLRGYRLNTLAKKFNVNLE-HHHRA 567
Cdd:COG5018 84 FKKWIGseDYILCswGD---YDRKQLERNCRFHGVpYPFGDRHINLKKLFALYFGLKKRIGLKKALELLGLEFEgTHHRA 160
|
170
....*....|....*....
gi 489736634 568 IYDAETTGHLNHLFLKDAE 586
Cdd:COG5018 161 LDDARNTAKLFKKILGDKR 179
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
424-577 |
4.66e-16 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 78.61 E-value: 4.66e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 424 IFDTETTGLSAiydRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVfklFREFYGDAIV 503
Cdd:PRK07983 4 VIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDV---IPHYYGSEWY 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489736634 504 VGHNVTFDigfmntgyaRHHMGPITNPIIDTLTLARWLYPNLRgYRLNTLAKKFNVNLE-----HHHRAIYDAETTGHL 577
Cdd:PRK07983 78 VAHNASFD---------RRVLPEMPGEWICTMKLARRLWPGIK-YSNMALYKSRKLNVQtppglHHHRALYDCYITAAL 146
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
336-413 |
1.74e-14 |
|
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: 73.01 E-value: 1.74e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 336 VELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVEANMVDDGVP-----IAY 410
Cdd:cd07431 1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPyplllLAK 80
|
...
gi 489736634 411 NDA 413
Cdd:cd07431 81 NNE 83
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
611-906 |
1.01e-13 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 76.32 E-value: 1.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 611 RPFHATLYAQTQAGLKNLFRIISLSNVEYY-----YRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKA 685
Cdd:PRK09532 81 RKYHQVVLAKNTQGYKNLVKLTTISHLQGVqgkgiFARPCINKELLEQYHEGLIVTSACLGGEIPQAILSGRPDAARKVA 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 686 GYY------DF-LEVQpkpaysaliesgliadtDH--LEEIISN--MVELGHEMNIPVAATGDVHYLNPEDKIYRKILIH 754
Cdd:PRK09532 161 KWYkklfgdDFyLEIQ-----------------DHgsQEDRIVNveIVKIARELGIKIIATNDSHFISCYDVEAHDALLC 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 755 SQPGNPLNRTERPDV----HFRSTDEMLKDF-DFLGTETAHEVVVDTpRALADQFE---IVRPVKDKLY-TPRMKGAEAE 825
Cdd:PRK09532 224 IQTGKLITEDKRLRYsgteYLKSAEEMRLLFrDHLPDDVIAEAIANT-LEVADKIEpynILGEPRIPNYpVPSGHTPDTY 302
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 826 IEKLT----MDRAHAWYGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGI 900
Cdd:PRK09532 303 VEEVAwqglLERLNCKSRSEVEPVYKERLEYELKMLQQMGFSTYFLVVWDYIKYARDNNIPVGpGRGSAAGSLVAYCLKI 382
|
....*.
gi 489736634 901 TEVNPM 906
Cdd:PRK09532 383 TNIDPV 388
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
595-694 |
2.42e-13 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 69.49 E-value: 2.42e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 595 DQLNDHMNENAAYRhARPFHATLYAQTQAGLKNLFRIISLSNVEYyyRVPRVPRSVLNKYRDGILVGSACSSGEVFTAMM 674
Cdd:pfam02811 64 YVAPGSREETEKLL-AKYFDLVLLAVHEVGYKNLIKLSSRAYLEG--FKPRIDKELLEEYFEGLIALSGCVLGHLDLILL 140
|
90 100
....*....|....*....|....*....
gi 489736634 675 QKGK-EEARQKAGYYD--------FLEVQ 694
Cdd:pfam02811 141 APGDyEEAEELAEEYLeifgedgfYLEIN 169
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
422-589 |
7.89e-13 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 71.27 E-value: 7.89e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDRVIELSAVKM-VKGNVVDQFEEFIDPGfhLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGD 500
Cdd:PRK06063 17 WAVVDVETSGFRPGQARIISLAVLGLdADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 501 AIVVGHNVTFDIGFMNTGYARHHMGPITNPIIDTLTLARWL---YPNLrgyRLNTLAKKFNVNLEHHHRAIYDAETTGHL 577
Cdd:PRK06063 95 RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLglgLPNL---RLETLAAHWGVPQQRPHDALDDARVLAGI 171
|
170
....*....|..
gi 489736634 578 NHLFLKDAEDRY 589
Cdd:PRK06063 172 LRPSLERARERD 183
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
422-577 |
8.68e-13 |
|
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: 68.02 E-value: 8.68e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDR-----VIELSAVKM-VKGN-VVDQFEEFIDPGFH--LSETTTNLTSITDDMVRGSKSEEEVFK 492
Cdd:cd06133 1 YLVIDFEATCWEGNSKPdypneIIEIGAVLVdVKTKeIIDTFSSYVKPVINpkLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 493 LFREFYGDAIVVGhNVTF---DIGFMNTG---YARHHMGPITNPIIDtltLARWlYPNLRGYR----LNTLAKKFNVNLE 562
Cdd:cd06133 81 EFLEWLGKNGKYA-FVTWgdwDLKDLLQNqckYKIINLPPFFRQWID---LKKE-FAKFYGLKkrtgLSKALEYLGLEFE 155
|
170
....*....|....*.
gi 489736634 563 -HHHRAIYDAETTGHL 577
Cdd:cd06133 156 gRHHRGLDDARNIARI 171
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
846-1434 |
2.02e-11 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 68.95 E-value: 2.02e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 846 VQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGITEVNPMPphyrcpncqyshfytnn 924
Cdd:PRK07135 252 VKERINYEYSVIKKLKFSNYFLIIWDFIKWARKNKISIGpGRGSASGSLVSYLLNITSVNPLK----------------- 314
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 925 eygsgYDLppkdcpecgtdmvrdgqniPFETFLGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGEKNVYRAGTIGTVADK 1004
Cdd:PRK07135 315 -----YDL-------------------LFERFLNPDRITMPDIDIDIQDDRRDEVIDYIFEKYGYEHCATISTFQTLGAK 370
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1005 TGYGYVKAY-----------------------ERDTNQTLRSAEVDR----------LAKGTTGVKRTTGQHPAGIIV-- 1049
Cdd:PRK07135 371 SAIRDVGRMlgipesdvnaisklipnnqsleeAYDKNKSFFRELISKgdpiykklykIAKKLEGLPRQSGTHAAGIIIsn 450
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1050 ------VPDYMDIYDFTPVQYPADDQSaawqtthfDFhsihdNILKIDILGhddptmirmLQDLSGVQ--PESIPPvDPH 1121
Cdd:PRK07135 451 kpitnyVPTFESKDNYNQVQYSMEFLE--------DF-----GLLKIDLLG---------LKNLTIIKniEEKINK-ELL 507
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1122 VMKIFSSpEVLGVTEDQIF---SKTGTLGIPEFGTRFVRGMLEETHPSTFNELLQI-----SGLSHGTDVWLGNaeeliK 1193
Cdd:PRK07135 508 FDHLINF-NDLPIIDKKTNnllSNGKTEGIFQLESPGMKSTIKKVGIDSFEDIVAIislyrPGPIQYIPIYAKN-----K 581
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1194 DGTVTLAEVIGCRDNIMTD---LIHYG---ME-----SDMSFQIMEHVRKGRGIPDEWQ-QAMKDA--------NVPDWY 1253
Cdd:PRK07135 582 KNPKNIEKIHPEYDEIVAPtygIIIYQeqiMQiaqkvAGFSFAQADLLRRAISKKDETKlDKIKDKfieggiknGYSKKV 661
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1254 IESC-LKI----KYMFPRAHAAAYILMALRVAYFKVYFPLIYYTAyfsvraddfdLVAMAHGkdavkasmkaitdkgmda 1328
Cdd:PRK07135 662 LEKIySLIekfaDYGFNKSHAVAYATLAYKMAYYKANYPLVFYSA----------LISNSNG------------------ 713
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1329 sakekNLLTVLELANEMLERGFKFSMVDLDKSDASDWLIDGDtLIAPFRAVPGLGLNVAKQIVAARAD----KPFLskeD 1404
Cdd:PRK07135 714 -----SQENIKKYVKEAKNNGIKVYSPDINFSTENAVFDNGK-IFLPLIMIKGLGSVAIKKIIDERNKngkyKNFF---D 784
|
650 660 670
....*....|....*....|....*....|...
gi 489736634 1405 LSKRGK---VSKSLIDFMTENGVLSDLPDENQL 1434
Cdd:PRK07135 785 FILRLKfigISKSIIEKLIKANTLRSFGNQDTL 817
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
612-906 |
2.49e-11 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 68.73 E-value: 2.49e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 612 PFHATLYAQTQAGLKNLFRIISLSNV-----EYYYRvprvPRSVLNKYRDGILVGSACSSGEVFTAMMQKGKEEARQKAG 686
Cdd:PRK05672 79 GPHLLVLARDREGYGRLSRLITRARLragkgEYRLD----LDDLAEPAGGHWAILTGCRKGFVILALPYGGDAAALAALA 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 687 YYdFLEVQPKPAYSALIESGLIADTDHLEEIIsnmvELGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQPGNPLNRTER 766
Cdd:PRK05672 155 AL-LDAFFADRVWLELTLHGRPDDDRRNARLA----ALAARAGVPLVATGDVHMHHRSRRRLQDAMTAIRARRSLAEAGG 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 767 -----PDVHFRSTDEMLKDFDflgtetAHEVVVDTPRALADQ----FEIVRPVKDKLYTPRMKGAEAEIEKLTMDRAHAW 837
Cdd:PRK05672 230 wlapnGERHLRSGAEMARLFP------DYPEALAETVELAERcafdLDLLAYEYPDEPVPAGHTPASWLRQLTEAGAARR 303
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489736634 838 YGNPLPEIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVGSRGSVGSSIVATLSGITEVNPM 906
Cdd:PRK05672 304 YGPGIPPKARAQIEHELALIAELGYEGYFLTVHDIVRFARSQGILCQGRGSAANSAVCYALGITEVDPV 372
|
|
| dnaE |
PRK05898 |
DNA polymerase III subunit alpha; |
844-1437 |
7.37e-11 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 135648 [Multi-domain] Cd Length: 971 Bit Score: 67.17 E-value: 7.37e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 844 EIVQKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGITEVNPMpphyrcpncqySHfyt 922
Cdd:PRK05898 252 KIYVKRLKYELDIINEKQFDDYFLIVYDFINFAKSNGIIIGpGRGSAAGSLIAYLLHITDIDPI-----------KY--- 317
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 923 nneygsgydlppkdcpecgtdmvrdgqNIPFETFLGFYGNKVPDIDLNFSGD--------------YQPIAHNYT----K 984
Cdd:PRK05898 318 ---------------------------NLIFERFLNPTRKSMPDIDTDIMDErrdevveylfekygNDHVAHIITfqriK 370
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 985 VLFGEKNVYRAGTIGT-VADKTGYGYVKAYERD------TNQTLRSA-----EVDRLAKGTTGVKRTTGQHPAGIIVVPD 1052
Cdd:PRK05898 371 AKMAIRDVGRILGIDLkVIDKICKNIKPDYEEDldlaikKNTILKEMyvlhkELFDLAKKIINAPRQIGTHAAGVVLSNS 450
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1053 YmdIYDFTPVQYPADDQSaawqTTHFDFHSIHD-NILKIDILGHDDPT-------MIRMLQDLSgVQPESIPPVDPHVMK 1124
Cdd:PRK05898 451 L--LTNIIPIQLGINDRP----LSQYSMEYLERfGLIKMDLLGLKNLTiidnvlkLIKENQNKK-IDLFNINLNDKNVFE 523
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1125 IFSSPEVLGV-------------------TED-QIFSKTGTLGIPEFGTRFVRGMLEETHPSTFNE-LLQISGLSHGTDV 1183
Cdd:PRK05898 524 DLAKGRTNGIfqlespgmkkvlkkvkpqnIEDiSIVSALFRPGPQQNIKTFVERRFKREEFSYWNEaTKKILEPTHGIIV 603
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1184 WlgnAEELIKdgtvtLAEVIGCRDnimtdlihyGMESDMSFQIMEhvRKGRGIPDEWQQAMKDANVPDWYIESCLK---- 1259
Cdd:PRK05898 604 Y---QEQVIN-----LVKTIANFD---------IATADNFRRAIS--KKDEKILIQLKKDFIEGALKNNYKQPLVNqife 664
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1260 -----IKYMFPRAHAAAYILMALRVAYFKVYFPLiyytayfsvradDFDLVAMAHGKDavkasmkaitdkgmdasAKEKN 1334
Cdd:PRK05898 665 yifsfADYGFNHSHSLAYSYISYWMAYLKHYYPL------------EFLSILLSHTSA-----------------SKDKL 715
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1335 LLTVlelaNEMLERGFKFSMVDLDKSDaSDWLIDGD--TLIAPFRAVPGLGLNVAKQIVAARADKP---FLSKEDLSKRG 1409
Cdd:PRK05898 716 LSYL----NEAKEFNISIKKPDINYSS-NSFVLDTQkqIIRFGFNTIKGFGDELLKKIKSALQNKTfsdFISYIDALKKN 790
|
650 660
....*....|....*....|....*...
gi 489736634 1410 KVSKSLIDFMTENGVLsdlpDENQLSLF 1437
Cdd:PRK05898 791 NVSLSNIEILINVGTF----DSFKLSRL 814
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
423-514 |
8.72e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 64.61 E-value: 8.72e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAVKMVK------GNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSE-EEVfklfR 495
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFEYdddgriGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDpAAV----D 115
|
90 100
....*....|....*....|
gi 489736634 496 EFYGDA-IVVGHNVTFDIGF 514
Cdd:PRK09182 116 ALIAPAdLIIAHNAGFDRPF 135
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
336-418 |
1.05e-10 |
|
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213987 [Multi-domain] Cd Length: 129 Bit Score: 60.72 E-value: 1.05e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 336 VELHLHSNMSQmDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVEANMVddgVPiayndAHV 415
Cdd:cd07432 1 ADLHIHSVFSP-DSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEVTLV---VL-----AHP 71
|
...
gi 489736634 416 DLK 418
Cdd:cd07432 72 DRP 74
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
422-575 |
2.34e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 61.84 E-value: 2.34e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 422 YVIFDTETTGLSAIYDRVIELSAVKmVKGNVVD---QFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFY 498
Cdd:PRK09145 31 WVALDCETTGLDPRRAEIVSIAAVK-IRGNRILtseRLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 499 GDAIVVGHNVTFDIGFMNTgYARHHMG-PITNPIIDTLTL-ARWLYPNLRG----YRLNTLAKKFNVNLEHHHRAIYDAE 572
Cdd:PRK09145 110 GNRPLVGYYLEFDVAMLNR-YVRPLLGiPLPNPLIEVSALyYDKKERHLPDayidLRFDAILKHLDLPVLGRHDALNDAI 188
|
...
gi 489736634 573 TTG 575
Cdd:PRK09145 189 MAA 191
|
|
| dnaE |
PRK07279 |
DNA polymerase III DnaE; Reviewed |
847-1324 |
2.43e-10 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 65.44 E-value: 2.43e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 847 QKRVDKELKSIIGNGFSVIYLIAQRLVFKSNKDGYLVG-SRGSVGSSIVATLSGITEVNPMPphyrcpncqyshfytnne 925
Cdd:PRK07279 261 QERLDKELSVIHDMGFDDYFLIVWDLLRFGRSQGYYMGmGRGSAAGSLVAYALDITGIDPVK------------------ 322
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 926 ygsgydlppkdcpecgtdmvrdgQNIPFETFLGFYGNKVPDIDLNFSGDYQPIAHNYTKVLFGEKNVYRAGTIGTVADKT 1005
Cdd:PRK07279 323 -----------------------HNLLFERFLNKERYSMPDIDIDLPDIYRSEFLRYVRNRYGSDHSAQIVTFSTFGAKQ 379
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1006 G-------YGyVKAYE----------RDT-------NQTLRSAEVDRL--------AKGTTGVKRTTGQHPAGIIVVPDy 1053
Cdd:PRK07279 380 AirdvfkrFG-VPEYElsnltkkisfRDSlasvyekNISFRQIINSKLeyqkafeiAKRIEGNPRQTSIHAAGVVMSDD- 457
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1054 mDIYDFTPVQYPADdqsaaWQTTHFDFHSIHDN-ILKIDILGHDDPTMIRMLQDL------SGVQPESIPPVDPHVMKIF 1126
Cdd:PRK07279 458 -DLTNHIPLKYGDD-----MMITQYDAHAVEANgLLKMDFLGLRNLTFVQKMQEKvakdygIHIDIEAIDLEDKETLALF 531
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1127 SSPEvlgvtedqifsktgTLGIPEFGTRFVRGMLEETHPSTFNEL-----LQISGLSHGTDVWLGNaeeliKDGTvtlaE 1201
Cdd:PRK07279 532 AAGD--------------TKGIFQFEQPGAINLLKRIKPVCFEDIvattsLNRPGASDYTDNFVKR-----RHGQ----E 588
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1202 VIGCRDNIMTDLIH--YGMesdMSF--QIME--HVRKG--RGIPDEWQQAM--KDAN----VPDWYIESCLKI------- 1260
Cdd:PRK07279 589 KVDLIDPVIAPILEptYGI---MLYqeQVMQiaQVFAGfsLGKADLLRRAMskKNASemqkMEEDFLQGALELghseeka 665
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 1261 -----------KYMFPRAHAAAYILMALRVAYFKVYFPLIYYTAYFSVRADDFDLVAMAHGKDAVKASMKAI--TDK 1324
Cdd:PRK07279 666 relfdrmekfaGYGFNRSHAFAYSALAFQLAYFKAHYPAVFYDIMLNYSSSDYITDALEFGFEVAKLSINTIpyHDK 742
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
335-424 |
2.06e-09 |
|
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: 59.40 E-value: 2.06e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 335 RVELHLHSNMSqmDATNSVSDYVKQAAKWGHPAIAITDHSgaQAFPEAFAAGEKN----------------NIKILYGVE 398
Cdd:COG1387 2 RGDLHTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDHS--PSLFVANGLSEERlleyleeieelnekypDIKILKGIE 77
|
90 100
....*....|....*....|....*.
gi 489736634 399 ANMVDDGVpIAYNDAhvDLKESTYVI 424
Cdd:COG1387 78 VDILPDGS-LDYPDE--LLAPLDYVI 100
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
425-577 |
2.19e-09 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 59.60 E-value: 2.19e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 425 FDTETTGLSAIYDRVIElSAVKMVK--GNVVDQFEEFIDPGFHLSETTTNLTSITDDMVR--GSKSEE---EVFKLFREF 497
Cdd:PRK07942 11 FDLETTGVDPETARIVT-AALVVVDadGEVVESREWLADPGVEIPEEASAVHGITTEYARahGRPAAEvlaEIADALREA 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 498 YGDAI-VVGHNVTFDIGFMNTGYARHHMGPITN-PIIDTLTLARWLYPNLRGYR-LNTLAKKFNVNLEHHHRAIYDAETT 574
Cdd:PRK07942 90 WARGVpVVVFNAPYDLTVLDRELRRHGLPSLVPgPVIDPYVIDKAVDRYRKGKRtLTALCEHYGVRLDNAHEATADALAA 169
|
...
gi 489736634 575 GHL 577
Cdd:PRK07942 170 ARV 172
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
423-577 |
1.24e-08 |
|
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: 56.15 E-value: 1.24e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAV--KMVKGNVVDQFEEF---IDP--GFHLSETTTNLTSIT-DDMVRGSKSEEEVFK-L 493
Cdd:cd06134 8 VVVDVETGGFNPQTDALLEIAAVtlEMDEQGNLYPDETFhfhILPfeGANLDPAALEFNGIDpFHPFRFAVDEKEALKeI 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 494 FREFYGD--------AIVVGHNVTFDIGFMNTGYARhhMGPITNP-----IIDTLTLARWLYPNlrgyrlNTLAK----- 555
Cdd:cd06134 88 FKPIRKAlkaqgctrAILVGHNAHFDLGFLNAAVAR--CKIKRNPfhpfsTFDTATLAGLAYGQ------TVLAKacqaa 159
|
170 180
....*....|....*....|..
gi 489736634 556 KFNVNLEHHHRAIYDAETTGHL 577
Cdd:cd06134 160 GIEFDNKEAHSALYDTQKTAEL 181
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
336-398 |
1.26e-08 |
|
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: 55.48 E-value: 1.26e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489736634 336 VELHLHSNMSqmDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVE 398
Cdd:cd07438 1 IDLHTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVE 61
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
335-398 |
1.63e-08 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 56.07 E-value: 1.63e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489736634 335 RVELHLHSNMSqmDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVE 398
Cdd:COG0613 3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVE 64
|
|
| HHH_6 |
pfam14579 |
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain. |
1362-1417 |
2.22e-08 |
|
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain.
Pssm-ID: 434050 [Multi-domain] Cd Length: 88 Bit Score: 52.86 E-value: 2.22e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 1362 ASDWL--IDGDTLIAPFRAVPGLGLNVAKQIVAARADKPFLSKEDLSKR--GKVSKSLID 1417
Cdd:pfam14579 11 RSDWDftVEGGGIRLGLGAIKGLGEAAAERIVEERENGPFKSLEDFARRvdLKLNKRVLE 70
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
239-317 |
4.94e-08 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 51.47 E-value: 4.94e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489736634 239 VVVEGYVFDMEvrtlRSQRQLLILKVTDYSSSMVVKKFsrNADDEAQFAALKPGMWVRVRGSVQEDSFmRDLTINAYDI 317
Cdd:pfam01336 1 VTVAGRVTSIR----RSGGKLLFLTLRDGTGSIQVVVF--KEEAEKLAKKLKEGDVVRVTGKVKKRKG-GELELVVEEI 72
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
442-571 |
9.57e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 55.56 E-value: 9.57e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 442 LSAVKMVKGNVVDQFEEFIDPG-FHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYGDAIVVGHNVTFDIG-FMNTGY 519
Cdd:PRK06195 21 IGIVVVKDGEIVEKVHYLIKPKeMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISvLRKTLE 100
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 489736634 520 ARHHMGPITNPIIdTLTLARWLYPNLRGYRLNTLAKKFNVNLEHHHrAIYDA 571
Cdd:PRK06195 101 LYNIPMPSFEYIC-TMKLAKNFYSNIDNARLNTVNNFLGYEFKHHD-ALADA 150
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
420-507 |
2.75e-07 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 52.48 E-value: 2.75e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 420 STYVIFDTETTGLSAIyDRVIELSAVKMVKGNVVDQFEEFIDPGFHLSETTTNLTSITDDMVRGSKSEEEVFKLFREFYG 499
Cdd:PRK07247 5 ETYIAFDLEFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVG 83
|
....*...
gi 489736634 500 DAIVVGHN 507
Cdd:PRK07247 84 ELPLIGYN 91
|
|
| PHP_HisPPase_Ycdx_like |
cd07437 |
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
336-424 |
1.17e-06 |
|
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: 51.29 E-value: 1.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 336 VELHLHSNMSQmDATNSVSDYVKQAAKWGHPAIAITDHsgAQAFPEA----------FAAGEKNNIKILYGVEANMVDDg 405
Cdd:cd07437 3 ADLHTHTIASG-HAYSTIEEMARAAAEKGLKLLGITDH--GPAMPGAphpwyfgnlkVIPREIYGVRILRGVEANIIDY- 78
|
90 100
....*....|....*....|....
gi 489736634 406 vpiaynDAHVDLKEST-----YVI 424
Cdd:cd07437 79 ------DGNLDLPERVlkrldYVI 96
|
|
| DNA_polA_I_Ecoli_like_exo |
cd06139 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
416-557 |
1.02e-05 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Pssm-ID: 176651 [Multi-domain] Cd Length: 193 Bit Score: 47.90 E-value: 1.02e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 416 DLKESTYVIFDTETTGLSAIYDRVIELS-AVKmvKGNVVdqfeeFIDpgfhlsetttnltsITDDMVRGSKSEEEVFKLF 494
Cdd:cd06139 1 ELEKAKVFAFDTETTSLDPMQAELVGISfAVE--PGEAY-----YIP--------------LGHDYGGEQLPREEVLAAL 59
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489736634 495 REFYGDAIV--VGHNVTFDIGFMntgyaRHHMGPITNPIIDTLTLARWLYPNLRGYRLNTLAKKF 557
Cdd:cd06139 60 KPLLEDPSIkkVGQNLKFDLHVL-----ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERY 119
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
338-405 |
1.52e-05 |
|
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213991 [Multi-domain] Cd Length: 237 Bit Score: 47.80 E-value: 1.52e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 338 LHLHSNMSqmDATNSVSDYVKQAAKWGHPAIAITDHSGAQAF-----PEAFAA---------GEKNNIKILYGVEANMVD 403
Cdd:cd07436 9 LHVHTTWS--DGRNSIEEMAEAARALGYEYIAITDHSKSLRVanglsEERLREqieeidalnEKLPGIRILKGIEVDILP 86
|
..
gi 489736634 404 DG 405
Cdd:cd07436 87 DG 88
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
611-756 |
2.28e-05 |
|
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: 46.43 E-value: 2.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 611 RPFHATLYAQTQAGLKNLFRIISLSN-VEYYYRVPRVPRSVLNKYRDGILVgsacssgevftammqkgkeearqkagyyd 689
Cdd:cd07431 71 EPYPLLLLAKNNEGYQNLLRLSTAAMlGEEKDGVPYLDLEELAEAASGLLV----------------------------- 121
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489736634 690 flevqpkpaysaLIESGLIADtdhleeiisnmveLGHEMNIPVAATGDVHYLNPEDKIYRKILIHSQ 756
Cdd:cd07431 122 ------------VLLGPLLLL-------------LAAEQGLPLVATNDVHYLNPEDAFAADVLTAFL 163
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
337-398 |
2.95e-05 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 48.70 E-value: 2.95e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489736634 337 ELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVE 398
Cdd:PRK05672 7 ELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAE 68
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
417-501 |
4.58e-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: 47.40 E-value: 4.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 417 LKESTYVIFDTETTGLSAIYDRVIELSAVKMVKGNVV-DQFEEFIDP--------GFH------LSETTTNLTSITDDMV 481
Cdd:pfam13361 183 LEQDNIVVFDVETTGLDTTEDEIIQIAAIKLNKKGVViESFERFLRLkkpvgdslQVHgfsdefLQENGETPAEALRDFL 262
|
90 100
....*....|....*....|
gi 489736634 482 RGSKSEEEVFKLFREFYGDA 501
Cdd:pfam13361 263 EKLENLRELYSILREYDDIE 282
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
423-577 |
8.00e-05 |
|
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 44.95 E-value: 8.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIELSAVKMVKG-NVVDQFEEFIDPGFHL--SETTTNLTSIT-DDMVRGSKSEEEVFKLFREFY 498
Cdd:cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENfNEIEPFNIFCRLPPDVlpSPEALIVTGITpQQLLKEGLSEYEFIAKIHRLF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 499 G--DAIVVGHN-VTFDIGFMNTGYARHHMGPIT----NP-----IIDTLTLARWLYPN----------LRGYRLNTLAKK 556
Cdd:cd06138 81 NtpGTCIVGYNnIRFDDEFLRFAFYRNLYDPYTwewkNGnsrwdLLDVVRAYYALRPDgivwpknddgKPSFKLEDLAQA 160
|
170 180
....*....|....*....|.
gi 489736634 557 FNVNLEHHHRAIYDAETTGHL 577
Cdd:cd06138 161 NGIEHSNAHDALSDVEATIAL 181
|
|
| RPA2_OBF_family |
cd03524 |
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ... |
241-315 |
9.61e-04 |
|
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).
Pssm-ID: 239601 [Multi-domain] Cd Length: 75 Bit Score: 39.27 E-value: 9.61e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489736634 241 VEGYVFDmeVRTLRSQRQLLILKVTDYSS-SMVVKKFsrNADDEAQFAALKPGMWVRVRGSVQEDSFMRDLTINAY 315
Cdd:cd03524 2 IVGIVVA--VEEIRTEGKVLIFTLTDGTGgTIRVTLF--GELAEELENLLKEGQVVYIKGKVKKFRGRLQLIVESI 73
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
336-398 |
2.45e-03 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 42.42 E-value: 2.45e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489736634 336 VELHLHSNMSQMDATNSVSDYVKQAAKWGHPAIAITDHSGAQAFPEAFAAGEKNNIKILYGVE 398
Cdd:PRK09532 4 VGLHIHSDYSLLDGASQLPALVDRAIELGMPAIALTDHGVMYGAIELLKVCRNKGIKPIIGNE 66
|
|
| PRK09248 |
PRK09248 |
putative hydrolase; Validated |
336-403 |
2.61e-03 |
|
putative hydrolase; Validated
Pssm-ID: 236429 [Multi-domain] Cd Length: 246 Bit Score: 41.36 E-value: 2.61e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489736634 336 VELHLHSNMSQmDATNSVSDYVKQAAKWGHPAIAITDHsgAQAFPEA-----FAA-----GEKNNIKILYGVEANMVD 403
Cdd:PRK09248 5 VDTHTHTIASG-HAYSTLHENAAEAKQKGLKLFAITDH--GPDMPGAphywhFGNlrvlpRKVDGVGILRGIEANIKN 79
|
|
| AcrA |
COG0845 |
Multidrug efflux pump subunit AcrA (membrane-fusion protein) [Cell wall/membrane/envelope ... |
172-298 |
3.03e-03 |
|
Multidrug efflux pump subunit AcrA (membrane-fusion protein) [Cell wall/membrane/envelope biogenesis, Defense mechanisms];
Pssm-ID: 440606 [Multi-domain] Cd Length: 324 Bit Score: 41.47 E-value: 3.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 172 KEFHEQKAKSDQALAQ--KAEAAIKKAnekRQKQADAP--APIDG-----PVQLGKQINPQEPakqMVQITEEERsVVVE 242
Cdd:COG0845 99 QELDQAKAALDQAQAAlaAAQAALEQA---RANLAYTTirAPFDGvvgerNVEPGQLVSAGTP---LFTIADLDP-LEVE 171
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489736634 243 GYVFDMEVRTLRSQR--QLLILKVTDYSSSMVVKKFSRNADD-------EAQFA----ALKPGMWVRVR 298
Cdd:COG0845 172 FDVPESDLARLKVGQpvTVTLDAGPGKTFEGKVTFIDPAVDPatrtvrvRAELPnpdgLLRPGMFVRVR 240
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
423-560 |
8.28e-03 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 38.73 E-value: 8.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 423 VIFDTETTGLSAIYDRVIeLSAVKMVKGNVVDQFEEFIDPGFHLsetttnltsitddmvrgSKSEEEVFKLFREFygDAI 502
Cdd:pfam13482 1 LFFDIETTGLSPGKNTIY-LIGVYDVDGDKVRTFVQYLAEGPTE-----------------EAAILQLFELLADY--PLL 60
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 489736634 503 VVGHNVTFDIGFMNTGYARHHMgPITNPIIDtltLARWLYPNLRGYRLNTLAKKFNVN 560
Cdd:pfam13482 61 VTFNGKSFDVPFIKRRFKRYDL-DELFRHID---LLHPLRKLGLESGLKSVERELGIE 114
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
439-586 |
8.42e-03 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 39.29 E-value: 8.42e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 439 VIELSAVKMVKGNVVDQFEEFIDPGF--HLSETTTNLTSITDDMVRGSKSEEEVFKLFREF----------YGDA--IVV 504
Cdd:PRK07748 29 IIEVGLVSVVGCEVEDTFSSYVKPKTfpSLTERCKSFLGITQEDVDKGISFEELVEKLAEYdkrckptivtWGNMdmKVL 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489736634 505 GHNVTFD-IGFmntgyarhhmgPITNPIIDtLTLArwlYPNLRGYRLNTLAKKF-----NVNLEHHHRAIYDAETTGHLN 578
Cdd:PRK07748 109 KHNCEKAgVPF-----------PFKGQCRD-LSLE---YKKFFGERNQTGLWKAieeygKEGTGKHHCALDDAMTTYNIF 173
|
....*...
gi 489736634 579 HLFLKDAE 586
Cdd:PRK07748 174 KLVEKDKE 181
|
|
| |
