|
Name |
Accession |
Description |
Interval |
E-value |
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
5-1442 |
0e+00 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 2336.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 5 LVKERKLSELFPEV-INNENERELFDTARIQNINVYKKSRKLEIFIVSDTLIPAKTLDSVEQSFKKLFE-LEQVHLRVSF 82
Cdd:PRK00448 1 NEMQEKFKKLLDQInIPDDLQSEALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFShIADIKVTFSI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 83 NVELSI--EEALEKYWDSILYIVKKNIALCRGILSGCKWKIEDKKLYIYLKTKG-TEILKCKSCDTLIENIIKECFGLEI 159
Cdd:PRK00448 81 EVENITftEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIeRDHLKKKHLPKLIKQYEKFGFGILK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 160 KVEFKDFEidEDKINEYIEFKENEEAKIVTDTVIKNNEKTQKTEKSEKtsgesksnvsSAGGEKSEVIFGKNF-NDSVMN 238
Cdd:PRK00448 161 IDFEIDDS--KEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSK----------NFDPKEGPVQIGKKIdKEEITP 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 239 MSEVTQDSGRVVVKGEIIRTEARELKSGKLLYVFDVTDFTNSLTVKIFLDKDKSGSVIERLKEKANVKIRGEAQYDKFSR 318
Cdd:PRK00448 229 MKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTR 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 319 ELSILASDIVEVPVQVRTDNAA-EKRVELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKN 397
Cdd:PRK00448 309 DLVMNAQDINEIKHPERKDTAEeEKRVELHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKA 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 398 KIKVIYGIEAYLLDDSVPIVYH-ANGHPVDGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEF 476
Cdd:PRK00448 389 GIKVIYGVEANLVDDGVPIVYNeVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAF 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 477 VVKLTGITDDMVSDAPTIDKVLPEFLEFVGTSPLVAHNAVFDTGFIRHNARLINR-NVDNPVIDTLELSRQMFPELKKHK 555
Cdd:PRK00448 469 TTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLeKIKNPVIDTLELSRFLYPELKSHR 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 556 LDVVAKHLGVSLENHHRALDDAKACGEIFIKCLEILAEKNVKTIDDIQNVFEGCWNYQKANSYHAIILVKNYVGLRNLYK 635
Cdd:PRK00448 549 LNTLAKKFGVELEHHHRADYDAEATAYLLIKFLKDLKEKGITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFK 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 636 IVSKTHLEYFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILEnKDEDEISRIVKFYDYLEIQPLGNNRFLVESGKVN 715
Cdd:PRK00448 629 LVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQ-KGDEELEEIAKFYDYIEIQPPANYQHLIERELVK 707
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 716 SEEDLKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMAGQGFSDADNQA---PLYFRTTDEMLEEFEYLGREK 792
Cdd:PRK00448 708 DEEELKEIIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRKILVASQGGGNPLNRHplpELHFRTTDEMLDEFAFLGEEL 787
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 793 CYEVVVTNTNLIADMCEDILPIPEGTFPPKIEGAEEEIRMLAENKAREIYGDPLPEIVEKRMEKELNSIIKNGFSVMYII 872
Cdd:PRK00448 788 AKEIVVENTNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIYGEPLPEIVEKRIEKELNSIIGNGFAVIYLI 867
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 873 AQKLVWKSLSDGYLVGSRGSVGSSFVAYLIGITEVNSLPPHYICENCKYSEFIEDGSYGCGFDMPEKECPRCGKILKKDG 952
Cdd:PRK00448 868 SQKLVKKSLEDGYLVGSRGSVGSSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDG 947
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 953 YDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGVGHVYRAGTIGTIAEKTAYGFVKNYLDERGIVATNAEINR 1032
Cdd:PRK00448 948 HDIPFETFLGFKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTAYGYVKKYEEDTGKFYRNAEIDR 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1033 LVKGCTGVKRTTGQHPGGVMIVPQDREIYEFCPIQYPADDPDSGTITTHFDYHSISGRLLKLDILGHDDPTVIKMLEDLT 1112
Cdd:PRK00448 1028 LAQGCTGVKRTTGQHPGGIIVVPKYMDIYDFTPIQYPADDVNSEWKTTHFDFHSIHDNLLKLDILGHDDPTMIRMLQDLT 1107
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1113 GVNARTIPIGEKRTMGIFSSTEPLGIRPEDINCPVGTFAIPEFGTKFVRQMLVDTKPKTFSELIRISGLSHGTDVWLNNA 1192
Cdd:PRK00448 1108 GIDPKTIPMDDPKVMKLFSSTEALGVTPEQIGCETGTLGIPEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNA 1187
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1193 QDLVRNNIASLSEVICTRDDIMLNLIHYGLPNKTAFKIMEDVRKGKGLKEEYEQIMREKKVPDWYIESCKKIKYMFPKAH 1272
Cdd:PRK00448 1188 QELIKEGIATLSDVIGCRDDIMVYLIHKGLEPKLAFKIMESVRKGKGLTEEEEELMKENNVPDWYIESCKKIKYMFPKAH 1267
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1273 AAAYVMMAFRIAWFKVYYPEAFYATYFTVRADEFDASMMCHGKEKVKNKIKEYELKGNNMTQKEKNTLTILEVANEMYAR 1352
Cdd:PRK00448 1268 AAAYVLMAWRIAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEIKSKGNDASNKEKDLLTVLEIALEMLER 1347
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1353 GIKFLPIDIYKSDAVKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQGEFLSVDDLRIRAKVSKTVIEILQQNGCLDGL 1432
Cdd:PRK00448 1348 GFKFQKVDLYKSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIEKLDELGVLDDL 1427
|
1450
....*....|
gi 316940249 1433 PESNQISLFG 1442
Cdd:PRK00448 1428 PETNQLSLFD 1437
|
|
| polC_Gram_pos |
TIGR01405 |
DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain ... |
240-1441 |
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: 1793.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 240 SEVTQDSGRVVVKGEIIRTEARELKSGKLLYVFDVTDFTNSLTVKIFLDKDKSGSVIERLKEKANVKIRGEAQYDKFSRE 319
Cdd:TIGR01405 1 EKINEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 320 LSILASDIVEVPVQVRTDNAAEKRVELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKI 399
Cdd:TIGR01405 81 LQMIIKDIEEIPYAERKDNAKEKRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 400 KVIYGIEAYLLDDSVPIVYHANGHPV--DGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFV 477
Cdd:TIGR01405 161 KIIYGMEANLVDDRVPIVYNPDDQKLldDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 478 VKLTGITDDMVSDAPTIDKVLPEFLEFVGTSPLVAHNAVFDTGFIRHN-ARLINRNVDNPVIDTLELSRQMFPELKKHKL 556
Cdd:TIGR01405 241 TELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNfEKVGLEPLENPVIDTLELARALNPEYKSHRL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 557 DVVAKHLGVSLENHHRALDDAKACGEIFIKCLEILAEKNVKTIDDIQNVFEGCWNYQKANSYHAIILVKNYVGLRNLYKI 636
Cdd:TIGR01405 321 GNICKKLGVDLDDHHRADYDAEATAKVFKVMVEQLKEKGITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYKL 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 637 VSKTHLEYFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILEnKDEDEISRIVKFYDYLEIQPLGNNRFLVESGKVNS 716
Cdd:TIGR01405 401 VSISLTKYFYTRPRILRSLLKKYREGLLIGSACSEGELFDALLS-KPDDELEEIAKRYDFIEIQPPGNYAHLIEREQVKD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 717 EEDLKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMAGQGFSDADNQAP-------LYFRTTDEMLEEFEYLG 789
Cdd:TIGR01405 480 KEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYRKILVASQGLGNPLNRHFnpkevpeLHFRTTNEMLDEFSFLG 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 790 REKCYEVVVTNTNLIADMCEDILPIPEGTFPPKIEGAEEEIRMLAENKAREIYGDPLPEIVEKRMEKELNSIIKNGFSVM 869
Cdd:TIGR01405 560 EEKAYEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIYGDPLPEIVEQRIEKELKSIIGNGFAVI 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 870 YIIAQKLVWKSLSDGYLVGSRGSVGSSFVAYLIGITEVNSLPPHYICENCKYSEFIEDGSYGCGFDMPEKECPRCGKILK 949
Cdd:TIGR01405 640 YLISQLLVQKSLQDGYLVGSRGSVGSSLVATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 950 KDGYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGVGHVYRAGTIGTIAEKTAYGFVKNYLDERGIVATNAE 1029
Cdd:TIGR01405 720 KDGQDIPFETFLGFKGDKVPDIDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAYGYVKKYFEDQGKHYRDAE 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1030 INRLVKGCTGVKRTTGQHPGGVMIVPQDREIYEFCPIQYPADDPDSGTITTHFDYHSISGRLLKLDILGHDDPTVIKMLE 1109
Cdd:TIGR01405 800 IERLVQGCTGVKRTTGQHPGGIIIVPKYMDVYDFTPVQYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHDDPTMIKMLQ 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1110 DLTGVNARTIPIGEKRTMGIFSSTEPLGIRPEDINCPVGTFAIPEFGTKFVRQMLVDTKPKTFSELIRISGLSHGTDVWL 1189
Cdd:TIGR01405 880 DLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFGTKFVRGMLEETKPKTFADLVRISGLSHGTDVWL 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1190 NNAQDLVRNNIASLSEVICTRDDIMLNLIHYGLPNKTAFKIMEDVRKGKGLKEEYEQIMREKKVPDWYIESCKKIKYMFP 1269
Cdd:TIGR01405 960 GNAQDLIKSGIKTLSDVIGCRDDIMVYLIHKGLEPKLAFKIMEKVRKGKGLKAEYIELMKENKVPEWYIESCLKIKYMFP 1039
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1270 KAHAAAYVMMAFRIAWFKVYYPEAFYATYFTVRADEFDASMMCHGKEKVKNKIKEYELKGNNM--TQKEKNTLTILEVAN 1347
Cdd:TIGR01405 1040 KAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKAFDLETMIKGKEFIKQKLEEINTRRKINkaSPKEKDLLTVLEIVL 1119
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1348 EMYARGIKFLPIDIYKSDAVKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQGEFLSVDDLRIRAKVSKTVIEILQQNG 1427
Cdd:TIGR01405 1120 EMMARGFKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTKISKTHIEKLDSMG 1199
|
1210
....*....|....
gi 316940249 1428 CLDGLPESNQISLF 1441
Cdd:TIGR01405 1200 VLDNLPETNQLSLF 1213
|
|
| PHP_PolIIIA_POLC |
cd07435 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
343-813 |
8.86e-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: 358.71 E-value: 8.86e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 343 RVELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAvtdhgvvqaypeaceaakknkikviygieayllddsvpivyhang 422
Cdd:cd07435 1 RVELHAHTKMSAMDGVTSVKELVKRAAEWGHKAIA--------------------------------------------- 35
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 423 hpvdgefvvfdiettglsadkdkiteigavkikegkivdtfstfvnpeipipefvvkltgITDdmvsdaptidkvlpefl 502
Cdd:cd07435 36 ------------------------------------------------------------ITD----------------- 38
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 503 efvgtsplvaHNAVfdtgfirhnarlinrnvdnpvidtlelsrQMFPEL----KKHKLDVVakhLGVslenhhralddak 578
Cdd:cd07435 39 ----------HGVV-----------------------------QAFPEAyeaaKKNGIKVI---YGV------------- 63
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 579 acgeifikcleilaEKNVktiddiqnvfegcwnyqkANSYHAIILVKNYVGLRNLYKIVSKTHLEYFHKRPRLPRKLLMM 658
Cdd:cd07435 64 --------------EAYL------------------VDPYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEK 111
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 659 HREGLILGSACEAGELYRAILENKDEDEISRIVKFYDYLEIQPLGNNRFLVESGKVNSEEDLKNINRKIVALGEKYNKPV 738
Cdd:cd07435 112 YREGLLIGSACENGELFEAALNKKSDEELEEIASFYDYIEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPV 191
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 739 VATCDVHFMDPQDEVFRRILMAGQGFSD--ADNQAPLYFRTTDEMLEEFEYLGREKCYEVVVTNTNLIADMCEDILP 813
Cdd:cd07435 192 VATGDVHYLDPEDKIYREILLAGQGGGDgrADEQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIEDIKP 268
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
426-599 |
5.44e-91 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 292.05 E-value: 5.44e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 426 DGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFV 505
Cdd:COG2176 7 DLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 506 GTSPLVAHNAVFDTGFIRHNARLINRNVDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFI 585
Cdd:COG2176 87 GDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELFL 166
|
170
....*....|....
gi 316940249 586 KCLEILAEKNVKTI 599
Cdd:COG2176 167 KLLEKLEEKGITTL 180
|
|
| DNA_pol3_alpha |
pfam07733 |
Bacterial DNA polymerase III alpha NTPase domain; |
828-1098 |
2.41e-78 |
|
Bacterial DNA polymerase III alpha NTPase domain;
Pssm-ID: 400196 [Multi-domain] Cd Length: 259 Bit Score: 259.36 E-value: 2.41e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 828 EEIRMLAENKAREIYGDPLPEIVEKRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVGS-RGSVGSSFVAYLIGITE 906
Cdd:pfam07733 1 EYLRKLVEEGLKERYGEGLPEEYQERLEYELNVIIKMGFAGYFLIVWDLVKWAKDNGILVGPgRGSAAGSLVAYLLGITE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 907 VNSLPphyicenckysefiedgsygcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKY 986
Cdd:pfam07733 81 VDPLK-----------------------------------------HDLLFERFLNPERVSMPDIDIDFEDERREEVIDY 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 987 TEELFGVGHVYRAGTIGTIAEKTA-------------------------YGFVKNYLDE----RGIVATNAEINRLV--- 1034
Cdd:pfam07733 120 VKEKYGRDRVAQIATFGTYAAKSAirdvgralglpydeidrlaklipfeLGILEKALEEepelKELIESDPEVKRLIela 199
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 316940249 1035 KGCTGVKRTTGQHPGGVMIVPQDreIYEFCPIQYPADDpdsGTITTHFDYHSI-SGRLLKLDILG 1098
Cdd:pfam07733 200 KKLEGLPRHTGQHAGGVVISPDP--LTDFVPLYKADDD---DRPVTQFDKDDLeDLGLLKMDFLG 259
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
618-1432 |
1.01e-75 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 273.87 E-value: 1.01e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 618 YHAIILVKNYVGLRNLYKIVSKTHLEYFHK-RPRLPRKLLMMHREGLILGSACEAGELYRAILENkDEDEISRIVKFYD- 695
Cdd:COG0587 81 YHLVLLAKNREGYRNLCRLLSRAYLEGFYKgKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAG-QYDEAEAALARLKd 159
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 696 ------YLEIQPLGnnrflvesgkvnSEEDlKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA---GQGFSD 766
Cdd:COG0587 160 ifgdrfYLELQRHG------------LPED-RRVNAALLELARELGLPLVATNDVHYLNPEDAEAHDVLLCirtGKTLDD 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 767 ADNQAP----LYFRTTDEMLEEFEYlgrekcYEVVVTNTNLIADMCE-------DILP---IPEGtfppkiEGAEEEIRM 832
Cdd:COG0587 227 PGRRRFanaeRYLKSPEEMAELFAD------LPEALANTLEIAERCNfsldlgkYQLPkfpVPEG------ETEEEYLRK 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 833 LAENKAREIYGDPLPEIVEKRMEKELNSIIKNGFS-----VMYIIAqklvW-KSLsdGYLVGS-RGSVGSSFVAYLIGIT 905
Cdd:COG0587 295 LAEEGLERRYPEGIPEEYRERLEYELDVIEKMGFPgyfliVWDFIR----WaRSN--GIPVGPgRGSAAGSLVAYALGIT 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 906 EVNslpphyicenckysefiedgsygcgfdmPEKecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGE-----YQ 980
Cdd:COG0587 369 DVD----------------------------PIR-------------YDLLFERFLNPERVSMPDIDIDFCHErreevIQ 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 981 PIAHKYteelfGVGHVYRAGTIGTIAEKTA-----------YGFV---------------KNYLDE----RGIVATNAEI 1030
Cdd:COG0587 408 YVYEKY-----GRDRVAQIATFGTMRARAAirdvgrvlglpYGEVdrlaklipndpgitlEKALEEepelRELYDSDPEV 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1031 NRLVKGCT---GVKRTTGQHPGGVMIVPqdREIYEFCPIQYpadDPDSGTITTHFDYHSI--SGrLLKLDILGhddpTVI 1105
Cdd:COG0587 483 RRLLDLARkleGLPRHLSTHAGGVVISD--DPLTDLVPLER---AAMGGRPVTQFDKDDVeaLG-LLKFDFLGlrtlTVI 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1106 ----KMLEDLTG--VNARTIPIGEKRTMGIFSSTEPLGIrpedincpvgtfaipefgtkF------VRQMLVDTKPKTFS 1173
Cdd:COG0587 557 rdalDLIKENRGidIDLADIPLDDPKTYELLQRGDTIGV--------------------FqlesrgMRSLLKRLKPDCFE 616
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1174 ELI------R---ISGLSHgtDVWLNNaqdlvRNNIASlsevictrddimlnlIHYGLPnktafkIMEDVrkgkgLKEEY 1244
Cdd:COG0587 617 DLValvalyRpgpMQGGMV--PPYIRR-----KHGREP---------------VEYPHP------ELEPI-----LKETY 663
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1245 ------EQIMR-----------E---------KKVP-------DWYIESCKK--------------IK----YMFPKAHA 1273
Cdd:COG0587 664 gvivyqEQVMQiaqvlagfslgEadllrramgKKKKeemakqrEKFVEGAVAngydeefaeeifdqIEkfagYGFNKSHA 743
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1274 AAYVMMAFRIAWFKVYYPEAFYAtyftvradefdASMMC--HGKEKVKnkikeyelkgnnmtqkekntlTILEVANEMya 1351
Cdd:COG0587 744 AAYALLAYQTAYLKAHYPAEFMA-----------ALLNSqpMGFYKPA---------------------QYVQEARRH-- 789
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1352 rGIKFLPIDIYKSDAvKFKIEKDG-LRPPLNALQGLGVSAAHSIAEARNQ-GEFLSVDDLRIRA---KVSKTVIEILQQN 1426
Cdd:COG0587 790 -GIEVLPPDVNESDW-DFTVEPGGaIRLGLGAIKGVGEAAAEAIVAAREEnGPFTSLFDFCRRVdlrKLNKRVLEALIKA 867
|
....*.
gi 316940249 1427 GCLDGL 1432
Cdd:COG0587 868 GAFDSL 873
|
|
| polc |
TIGR00594 |
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
617-1432 |
1.16e-73 |
|
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: 267.32 E-value: 1.16e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 617 SYHAIILVKNYVGLRNLYKIVSKTHLEYFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILENkDEDEISRIVKFYD- 695
Cdd:TIGR00594 84 AYHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLG-EERLAEEAALKYQe 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 696 ------YLEIQPLGnnrflvesgkvnSEEDLKnINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA-GQGFSDAD 768
Cdd:TIGR00594 163 ifgddyYLELQDHG------------IPEQRV-VNEALLEISEELGIPLVATNDVHYINPEDAHAHEILLCiQTGKTLSD 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 769 NQAP------LYFRTTDEMLEEFEYlgrekcYEVVVTNTNLIADMCED---ILP---IPEGTFPPKIEGAEEEIRMLAEN 836
Cdd:TIGR00594 230 PKRLkfysdeFYLKSPEEMAELFAD------IPEALANTVEIAERCNLvdvKLGpprLPSYQIPPDFTSQEDYLRHLADE 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 837 KAREIYGDPLPEI-----VEKRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVG-SRGSVGSSFVAYLIGITEVNSL 910
Cdd:TIGR00594 304 GLRERLAAGPPGYkrraqYKERLEYELDVINSMGFPGYFLIVWDFIKWAKDHGIPVGpGRGSAAGSLVAYALKITDIDPI 383
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 911 PphyicenckysefiedgsygcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEEL 990
Cdd:TIGR00594 384 K-----------------------------------------HGLLFERFLNPERISMPDIDIDFCDERRDEVIEYVADK 422
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 991 FGVGHVYRAGTIGTIAEKTA-----------YGFV-----------KNYLDE--------RGIVATNAEINRLV---KGC 1037
Cdd:TIGR00594 423 YGHDNVAQIITFGTMKAKAAlrdvarvldipYAEAdriaklipprpGKTLKEaleaspqlRQLYEEDPEVKQLIdmaRKL 502
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1038 TGVKRTTGQHPGGVMIVPQdrEIYEFCPIQYpadDPDSGTITTHFDYHSI-SGRLLKLDILGHDDPTVIKMLEDL----- 1111
Cdd:TIGR00594 503 EGLNRNAGVHAAGVVISSE--PLTDYVPLYK---DKEGGAISTQYDMDDLeAVGLLKMDFLGLKTLTLIQDATELirkrr 577
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1112 -TGVNARTIPIGEKRTMGIFSSTEPLGIrpedincpvgtFAIPEFGtkfVRQMLVDTKPKTFSELIRIsglshgtdvwln 1190
Cdd:TIGR00594 578 gIDLDIASIPLDDKKTFSLLQEGDTTGV-----------FQLESRG---MQDLLKRLKPDGFEDIIAV------------ 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1191 NAqdLVRNNIASLSEVictrdDIMLNLIHYGLPNKTAFKIMEDVrkgkgLKEEY------EQIMR--------------- 1249
Cdd:TIGR00594 632 NA--LYRPGPMESGMI-----PDFIDRKHGREPIEYPHPLLEPI-----LKETYgvivyqEQVMQiaqrlagfslgeadl 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1250 -----EKKVPDW-------YIESCKK---------------IK---YMFPKAHAAAYVMMAFRIAWFKVYYPEAFYATYF 1299
Cdd:TIGR00594 700 lrramGKKKAEEmakerekFVEGAEKngydpeiaenlfdliEKfagYGFNKSHAAAYGMISYQTAYLKANYPAEFMAALL 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1300 TVRADEfdasmmchgKEKVKNKIKEYElkgnnmtqkekntltilevanemyARGIKFLPIDIYKSDaVKFKIEKDGLRPP 1379
Cdd:TIGR00594 780 TSEIND---------IEKVAVYIAEAK------------------------KMGIEVLPPDINESG-QDFAVEDKGIRYG 825
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 1380 LNALQGLGVSAAHSIAEARNQ-GEFLSVDDLRIRA---KVSKTVIEILQQNGCLDGL 1432
Cdd:TIGR00594 826 LGAIKGVGESVVKSIIEERNKnGPFKSLFDFINRVdfkKLNKKVLEALIKAGAFDSL 882
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
428-589 |
4.33e-68 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 226.21 E-value: 4.33e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 428 EFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:COG0847 1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRNVD-NPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFIK 586
Cdd:COG0847 81 AVLVAHNAAFDLGFLNAELRRAGLPLPpFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFLA 160
|
...
gi 316940249 587 CLE 589
Cdd:COG0847 161 LLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
430-585 |
6.15e-63 |
|
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: 211.39 E-value: 6.15e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGLSADKDKITEIGAVKIKEG-KIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGTS 508
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 316940249 509 PLVAHNAVFDTGFIRHNA-RLINRNVDNPVIDTLELSRQMFPELKKHKL-DVVAKHLGVSLENHHRALDDAKACGEIFI 585
Cdd:cd06127 81 VLVAHNASFDLRFLNRELrRLGGPPLPNPWIDTLRLARRLLPGLRSHRLgLLLAERYGIPLEGAHRALADALATAELLL 159
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
429-603 |
2.67e-61 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 220.56 E-value: 2.67e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGTS 508
Cdd:PRK07883 17 FVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 509 PLVAHNAVFDTGFIRHNA-RLINRNVDNPVIDTLELSRQMFP--ELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFI 585
Cdd:PRK07883 97 VLVAHNAPFDIGFLRAAAaRCGYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTPTHRALDDARATVDVLH 176
|
170
....*....|....*...
gi 316940249 586 KCLEILAEKNVKTIDDIQ 603
Cdd:PRK07883 177 GLIERLGNLGVHTLEELL 194
|
|
| dnaE |
PRK06826 |
DNA polymerase III DnaE; Reviewed |
618-1442 |
1.29e-52 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 202.81 E-value: 1.29e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 618 YHAIILVKNYVGLRNLYKIVSKTHLEYFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILENkDEDEISRIVKFYD-- 695
Cdd:PRK06826 88 YHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKG-NYEKAKEAALFYKdi 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 696 ------YLEIQPLGnnrfLVESGKVNSEedlkninrkIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA---GQGFSD 766
Cdd:PRK06826 167 fgkenfYLELQDHG----IPEQRKVNEE---------LIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCiqtGKTVDD 233
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 767 AD----NQAPLYFRTTDEMLEEFEYLGRekcyevVVTNTNLIADMCE-DI------LP---IPEGtfppkiEGAEEEIRM 832
Cdd:PRK06826 234 ENrmrfPSDEFYLKSPEEMYELFSYVPE------ALENTVKIAERCNvEFefgkskLPkfpLPEG------YDPYEYLRE 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 833 LAENKAREIYGDPLPEIVEkRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVG-SRGSVGSSFVAYLIGITEVNslp 911
Cdd:PRK06826 302 LCYEGLKKRYPNPSEELIE-RLEYELSVIKQMGYVDYFLIVWDFIRFARENGIMVGpGRGSAAGSLVAYTLGITKID--- 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 912 phyicenckysefiedgsygcgfdmPEKecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELF 991
Cdd:PRK06826 378 -------------------------PIK-------------YNLLFERFLNPERVSMPDIDIDFCYERRQEVIDYVVEKY 419
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 992 GVGHVYRAGTIGTIAEKTA-----------YGFVKNY-----------LDE--------RGIVATNAEINRLV---KGCT 1038
Cdd:PRK06826 420 GKDRVAQIITFGTMAARAAirdvgralnypYAEVDRIakmiptelgitIDKalelnpelKEAYENDERVRELIdtaRALE 499
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1039 GVKRTTGQHPGGVMIVPQDreIYEFCPIQyPADDPdsgtITTHFDYHSIS--GrLLKLDILGHDDPTVI----KMLEDLT 1112
Cdd:PRK06826 500 GLPRHASTHAAGVVISSEP--LVEYVPLQ-KNDGS----IVTQFTMTTLEelG-LLKMDFLGLRTLTVIrdavDLIKKNR 571
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1113 G--VNARTIP---------IGEKRTMGIFsSTEPLGIRpedincpvgtfaipefgtKFVRQMlvdtKPKTFSELIR-IS- 1179
Cdd:PRK06826 572 GieIDLDKIDyddkkvykmIGEGKTVGVF-QLESAGMR------------------SFMKEL----KPDSLEDIIAgISl 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1180 ---GLSHGTDVWLNNAQDlvRNNIASLSE-----------VICTRDDIML---NLIHYGLP---------NKTAFKIMED 1233
Cdd:PRK06826 629 yrpGPMDSIPRYIKNKNN--PEKIEYLHPklepilkvtygCIVYQEQVMQivrDLAGYSMGrsdlvrramSKKKHDVMEE 706
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1234 VRKG--KGLKEEYEQIMREKKVPDwyiESCKKI--------KYMFPKAHAAAYVMMAFRIAWFKVYYPEAFYATYFTVRA 1303
Cdd:PRK06826 707 ERKNfiYGIVDEGGPGCIRNGIDE---ETANKIfdsmmdfaSYAFNKSHAAAYAVVAYQTAYLKRYYPVEFMAALLNSVM 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1304 DEFDasmmchgkekvknKIKEYelkgnnmtqkekntltiLEVANEMyarGIKFLPIDIYKSDAvKFKIEKDGLRPPLNAL 1383
Cdd:PRK06826 784 GNSD-------------KVAFY-----------------IEECRRL---GIEVLPPDINESYS-KFTVEGDKIRFGLAAV 829
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1384 QGLGVSAAHSIAEARNQ-GEFLSVDDL--RIRAK-VSKTVIEILQQNGCLDGLP------------------------ES 1435
Cdd:PRK06826 830 KNVGENAIDSIVEEREKkGKFKSLVDFceRVDTSqINKRAVESLIKAGAFDSLGvyrsqllavyekildsiskqrkknIE 909
|
....*..
gi 316940249 1436 NQISLFG 1442
Cdd:PRK06826 910 GQISLFD 916
|
|
| dnaE |
PRK05673 |
DNA polymerase III subunit alpha; Validated |
618-1432 |
4.30e-52 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 201.10 E-value: 4.30e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 618 YHAIILVKNYVGLRNLYKIVSKTHLE-YFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILENKdEDEISRIVKFY-- 694
Cdd:PRK05673 83 THLTLLAKNETGYRNLFKLSSRAYLEgQYGYKPRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQ-YDEAEEAAAEYqe 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 695 ---D--YLEIQPLGnnrflvesgkvNSEEdlKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA---GQGFSD 766
Cdd:PRK05673 162 ifgDrfYLELMRHG-----------LPIE--RRVEHALLELAKELGLPLVATNDVHYLTPEDAEAHEALLCiaeGKTLDD 228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 767 ADNQAPL----YFRTTDEMLEEFEYLgREKCyevvvTNTNLIADMC-------EDILPIpegtFP-PKIEGAEEEIRMLA 834
Cdd:PRK05673 229 PDRFRFYspeqYLKSAEEMRELFADL-PEAL-----DNTVEIAERCnvevrlgKPFLPR----FPtPDGETEEDYLRKEA 298
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 835 EN--KAR--EIYGDPLPEIVEKRMEKELNSIIKNGFS-----VMYIIAqklvWkSLSDGYLVG-SRGSVGSSFVAYLIGI 904
Cdd:PRK05673 299 KEglEERlaFLFPDEERPEYVERLEYELDVIIQMGFPgyfliVADFIQ----W-AKDNGIPVGpGRGSGAGSLVAYALGI 373
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 905 TEVNSLPphyicenckysefiedgsygcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFS----GEYq 980
Cdd:PRK05673 374 TDLDPLR-----------------------------------------FGLLFERFLNPERVSMPDFDIDFCqdrrDEV- 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 981 pIahKYTEELFGVGHVYRAGTIGTIAEKTA-----------YGFV----------------KNYLDE---RGIVATNAEI 1030
Cdd:PRK05673 412 -I--RYVAEKYGRDAVAQIITFGTMKAKAVirdvgrvlgmpYGFVdritklippdpgitlaKAYEEEpelRELYESDPEV 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1031 NRLV---KGCTGVKRTTGQHPGGVMIvpQDREIYEFCPIqYpaDDPDSGTITTHFDYHSIS--GrLLKLDILGHDDPTVI 1105
Cdd:PRK05673 489 KRLIdmaRKLEGLTRNAGVHAAGVVI--SPTPLTDFVPL-Y--RDPDSGMPVTQFDMKDVEaaG-LVKFDFLGLRTLTII 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1106 KMLEDLtgVNAR--------TIPIGEKRTMGIFSSTEPLGIrpedincpvgtFAIPEFGtkfVRQMLVDTKPKTFSELIR 1177
Cdd:PRK05673 563 DDALKL--IKKRrgidvdleAIPLDDPKTYELLQRGETLGV-----------FQLESRG---MRDLLKRLKPDCFEDIIA 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1178 ISGL-----------------SHGtdvwlnnaqdlvRNNIASLSEVIctrDDIMlnlihyglpnKTAFKIM---EDV--- 1234
Cdd:PRK05673 627 LVALyrpgpmesgmipnfidrKHG------------REEIEYPHPEL---EPIL----------KETYGIIvyqEQVmqi 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1235 ---------------RK--GKGLKEE-------YEQIMREKKVPDwyiESCKKI-----K---YMFPKAHAAAYVMMAFR 1282
Cdd:PRK05673 682 aqvlagyslggadllRRamGKKKPEEmakqreiFVEGAKKNGIDE---EAADAIfdlleKfagYGFNKSHAAAYALVSYQ 758
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1283 IAWFKVYYPEAFYAtyftvradefdASMMChgkekvknkikeyelkgnNMTQKEKntltileVA---NEMYARGIKFLPI 1359
Cdd:PRK05673 759 TAYLKAHYPAEFMA-----------ALLTS------------------DMDNTDK-------VAvylDECRRMGIKVLPP 802
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 1360 DIYKSDAvKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQ-GEFLSVDDL--RI-RAKVSKTVIEILQQNGCLDGL 1432
Cdd:PRK05673 803 DVNESLY-DFTVVDGDIRYGLGAIKGVGEGAVEAIVEAREEgGPFKDLFDFcaRVdLKKVNKRVLESLIKAGAFDSL 878
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
428-587 |
9.00e-52 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 185.40 E-value: 9.00e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 428 EFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:PRK06807 9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRN-VDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLeNHHRALDDAKACGEIFIK 586
Cdd:PRK06807 89 NVIVAHNASFDMRFLKSNVNMLGLPePKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL-SSHNAFDDCITCAAVYQK 167
|
.
gi 316940249 587 C 587
Cdd:PRK06807 168 C 168
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
428-592 |
1.03e-51 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 179.42 E-value: 1.03e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 428 EFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAV-FDTGFIR--HNARLINRNVDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLE-NHHRALDDAKACGEI 583
Cdd:smart00479 81 RILVAGNSAhFDLRFLKleHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARATAKL 160
|
....*....
gi 316940249 584 FIKCLEILA 592
Cdd:smart00479 161 FKKLLERLE 169
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
429-585 |
1.65e-46 |
|
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: 164.22 E-value: 1.65e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTglSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGTS 508
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 316940249 509 PLVAHNAVFDTGFIRHNARLINRNV-DNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLeNHHRALDDAKACGEIFI 585
Cdd:cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPpPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILL 155
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
429-591 |
4.08e-46 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 180.92 E-value: 4.08e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADK-DKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:PRK08074 5 FVVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRN-VDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFIK 586
Cdd:PRK08074 85 AYFVAHNVHFDLNFLNEELERAGYTeIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAELFLQ 164
|
....*
gi 316940249 587 CLEIL 591
Cdd:PRK08074 165 LLNKL 169
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
426-602 |
1.04e-41 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 154.02 E-value: 1.04e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 426 DGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEiPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFV 505
Cdd:PRK08517 67 DQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRLFL 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 506 GTSPLVAHNAVFDTGFIRHNARLINRNV-DNPVIDTLELSRQMFpELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIF 584
Cdd:PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGLGPlLNRKLCTIDLAKRTI-ESPRYGLSFLKELLGIEIEVHHRAYADALAAYEIF 224
|
170
....*....|....*...
gi 316940249 585 IKCLEILAEkNVKTIDDI 602
Cdd:PRK08517 225 KICLLNLPS-YIKTTEDL 241
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
430-584 |
2.89e-41 |
|
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: 149.42 E-value: 2.89e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGLSADKDKITEIGAVKIK--EGKIVDTFSTFVNPEIP--IPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFV 505
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDggENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 506 GT-SPLVAHNAVFDTGFIRHN-ARLINRNV--DNPVIDTLELSRQMFPELKKHKLDVVAKHLGVS-LENHHRALDDAKAC 580
Cdd:pfam00929 81 RKgNLLVAHNASFDVGFLRYDdKRFLKKPMpkLNPVIDTLILDKATYKELPGRSLDALAEKLGLEhIGRAHRALDDARAT 160
|
....
gi 316940249 581 GEIF 584
Cdd:pfam00929 161 AKLF 164
|
|
| dnaE |
PRK06920 |
DNA polymerase III subunit alpha; |
613-1435 |
7.13e-40 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 161.50 E-value: 7.13e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 613 QKANSYHAIILVKNYVGLRNLYKIVSKTHLEyfhKRPRLPRKLLMMHREGLILGSACEAGELYRAILENKDED--EISRI 690
Cdd:PRK06920 73 EEEKSYPLVLLAENEIGYQNLLKISSSIMTK---SKEGIPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQaeEVARA 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 691 VK-----FYDYLEIQPLGNNRFLVEsgkvnseedlkninrKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILM---AGQ 762
Cdd:PRK06920 150 YQnmfgnFYMSLQHHAIQDELLLQE---------------KLPEFSNRVNIPVVATNDVRYINQSDALVHECLLsveSGT 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 763 GFSDADNQA----PLYFRTTDEMLEEFEYlgrekcYEVVVTNTNLIADMCEDILPIPEGTFP----PKIEGAEEEIRMLA 834
Cdd:PRK06920 215 KMTDPDRPRlktdQYYLKSSDEMEALFSH------VPEAIYNTVEIAERCRVEIPFHVNQLPkfpvPSNETADMYLRRVC 288
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 835 ENKAREIYGDPlPEIVEKRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVG-SRGSVGSSFVAYLIGITEVNSLpph 913
Cdd:PRK06920 289 EEGLQKRYGTP-KEVHINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHILTGpGRGSAAGSLVSYVLEITDIDPI--- 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 914 yicenckysefiedgsygcgfdmpekecprcgkilkkdGYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGV 993
Cdd:PRK06920 365 --------------------------------------EYDLLFERFLNPERVTLPDIDIDFPDTRRDEMIRYVKDKYGQ 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 994 GHVYRAGTIGTIAEKTA-------YG--------FVKNYLDERGIVATNA-----EINRLVKGCT-------------GV 1040
Cdd:PRK06920 407 LRVAQIVTFGTLAAKAAirdiarvMGlpprdidiFSKLIPSKLGITLKDAyeesqSLREFIQGNLlhervfeiakrveGL 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1041 KRTTGQHPGGVmiVPQDREIYEFCPIQypadDPDSGTITTHF--DYHSISGrLLKLDILGHDDPTVI----KMLEDLTGV 1114
Cdd:PRK06920 487 PRHTSIHAAGV--IMSQEPLTGSVAIQ----EGHNDVYVTQYpaDALEELG-LLKMDFLGLRNLTLLeniiKFIEQKTGK 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1115 --NARTIPIGEKRTMGIFSSTEPLGIrpedincpvgtFAIPEFGtkfVRQMLVDTKPKTFSELIRISGL----------- 1181
Cdd:PRK06920 560 eiDIRNLPLQDEKTFQLLGRGDTTGV-----------FQLESSG---MRNVLRGLKPNEFEDIVAVNSLyrpgpmeqipt 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1182 ----SHGTdVWLNNAQDLVRNNIASLSEVICTRDDIML-------------NLIHYGLPNKTAfKIMEDVRKG--KG-LK 1241
Cdd:PRK06920 626 fiesKHGK-RKIEYLHPDLKPILERTYGVIVYQEQIMQiasklagfslgeaDLLRRAVSKKNR-DILDQERKHfvQGcLQ 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1242 EEYEQIMREkKVPDWYIescKKIKYMFPKAHAAAYVMMAFRIAWFKVYYPEAFYATYFTvradefdaSMMchGKEkvkNK 1321
Cdd:PRK06920 704 NGYDETSAE-KIYDLIV---RFANYGFNRSHAVAYSMIGYQLAYLKANYTLEFMTALLS--------SAI--GNE---DK 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1322 IKEY--ELKGnnmtqkekntltilevanemyaRGIKFLPIDIYKSdAVKFKIEKDGLRPPLNALQGLGVSAAHSIAEARN 1399
Cdd:PRK06920 767 IVQYirETKR----------------------KGFHVLPPSLQRS-GYNFQIEGNAIRYSLLSIRNIGMATVTALYEERE 823
|
890 900 910
....*....|....*....|....*....|....*....
gi 316940249 1400 QGEFLSVDD--LRIRAK-VSKTVIEILQQNGCLDGLPES 1435
Cdd:PRK06920 824 KKMFEDLFEfcLRMPSKfVTERNLEAFVWSGCFDDFGVS 862
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
429-589 |
3.32e-39 |
|
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: 158.43 E-value: 3.32e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGTS 508
Cdd:TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 509 PLVAHNAVFDTGFIRHNarLINRNVD---NPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFI 585
Cdd:TIGR01407 82 IFVAHNVHFDLNFLAKA--LKDCGYEplpKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELLL 159
|
....
gi 316940249 586 KCLE 589
Cdd:TIGR01407 160 LLFE 163
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
428-602 |
2.02e-38 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 144.43 E-value: 2.02e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 428 EFVVFDIETTGLSADK-DKITEIGAVKIKEGKIV-DTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFV 505
Cdd:PRK07740 60 PFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFI 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 506 GTSPLVAHNAVFDTGFIRHNA-RLINRNVDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIF 584
Cdd:PRK07740 140 GAGVLVAHHAGHDKAFLRHALwRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKLW 219
|
170
....*....|....*...
gi 316940249 585 IKCLEILAEKNVKTIDDI 602
Cdd:PRK07740 220 AILLVEAQQRGITTLHDL 237
|
|
| dnaE |
PRK07374 |
DNA polymerase III subunit alpha; Validated |
560-1441 |
9.26e-38 |
|
DNA polymerase III subunit alpha; Validated
Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 154.88 E-value: 9.26e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 560 AKHLG---VSLENH---HRALDDAKACGEIFIKCLeILAEKNV--KTIDDIQNvfegcwnyQKANSYHAIILVKNYVGLR 631
Cdd:PRK07374 28 AKELGmpaIALTDHgvmYGAIELLKLCKGKGIKPI-IGNEMYVinGSIDDPQP--------KKEKRYHLVVLAKNATGYK 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 632 NLYKIVSKTHLEYFH-----KRPRLPRKLLMMHREGLILGSACEAGELYRAILenKDEDEISRIVK------FYD--YLE 698
Cdd:PRK07374 99 NLVKLTTISHLNGMRgrgifSRPCIDKELLKQYSEGLIVSTACLGGEIPQAIL--RGRPDVARDVAawykevFGDdfYLE 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 699 IQPLGnnrflvesgkvnSEEDlKNINRKIVALGEKYNKPVVATCDVHFMDPQD-EVFRRIL--MAGQGFSDADN---QAP 772
Cdd:PRK07374 177 IQDHG------------SIED-RIVNVELVRIAKELGIKLIATNDAHYLSKNDvEAHDALLcvLTGKLISDEKRlryTGT 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 773 LYFRTTDEMLEEF-EYLGREKCYEvVVTNTNLIADMCE--DIL--------PIPEGTFPpkiegaEEEIRMLAENKAREI 841
Cdd:PRK07374 244 EYIKSEEEMLRLFrDHLDPEVIQE-AIANTVEVAEKVEeyDILgtyrmprfPIPEGHTA------VSYLTEVTEQGLLKR 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 842 YG----DPLPEIVEKRMEKELNSIIKNGFSVMYIIaqklVWKSL----SDGYLVG-SRGSVGSSFVAYLIGITEVNSLpp 912
Cdd:PRK07374 317 LKlnslDEIDENYKERLSYELKIIEQMGFPTYFLV----VWDYIrfarEQGIPVGpGRGSAAGSLVAYALGITNIDPV-- 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 913 hyicenckysefiedgSYGcgfdmpekecprcgkilkkdgydIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFG 992
Cdd:PRK07374 391 ----------------KNG-----------------------LLFERFLNPERKSMPDIDTDFCIERRGEVIDYVTRRYG 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 993 VGHVYRAGTIGTIAEKTAYGFVKNYLD---------------ERGIVAT----------NAEINRLVKGCTGVKR----- 1042
Cdd:PRK07374 432 EDKVAQIITFNRMTSKAVLKDVARVLDipygeadrlaklipvVRGKPAKlkamigkespSPEFREKYEKDPRVKKwvdma 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1043 --------TTGQHPGGVMI--VPQDreiyEFCPIQYpadDPDSGTITTHF--DYHSISgrLLKLDILGHDDPTVI----K 1106
Cdd:PRK07374 512 mriegtnkTFGVHAAGVVIasDPLD----ELVPLQR---NNDGQVITQYFmeDIESLG--LLKMDFLGLKNLTMIektlE 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1107 MLEDLTG--VNARTIPIGEKRTMGIFSSTEPLGIrpedincpvgtFAIPEFGtkfVRQMLVDTKPKTFSELIRI------ 1178
Cdd:PRK07374 583 LVEQSTGerIDPDNLPLDDEKTFELLARGDLEGI-----------FQLESSG---MRQVVRDLKPSSLEDISSIlalyrp 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1179 ----SGL-------SHGtdvwlNNAQDLVRNNIAS-LSE---VICTRDDIMlnlihyglpnktafKIMEDVrKGKGLKEE 1243
Cdd:PRK07374 649 gpldAGLipkfinrKHG-----REAIDFAHPLLEPiLTEtygIMVYQEQIM--------------KIAQDL-AGYSLGQA 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1244 --YEQIMREKKVPDW------YIESCKK------------------IKYMFPKAHAAAYVMMAFRIAWFKVYYPEAFYAT 1297
Cdd:PRK07374 709 dlLRRAMGKKKVSEMqkhrgiFVEGASKrgvdekvadelfdqmvlfAEYCFNKSHSTAYGAVTYQTAYLKAHYPVAYMAA 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1298 YFTVRADEFDasmmchgkekvknKIKEYelkgnnmtqkekntltileVANeMYARGIKFLPIDIYKSdAVKFKIEKDGLR 1377
Cdd:PRK07374 789 LLTVNAGSSD-------------KVQRY-------------------ISN-CNSMGIEVMPPDINRS-GIDFTPKGNRIL 834
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 316940249 1378 PPLNALQGLGVSAAHSIAEAR-NQGEFLSVDDL--RIRAKV-SKTVIEILQQNGCLDGL-PESNQISLF 1441
Cdd:PRK07374 835 FGLSAVKNLGDGAIRNIIAARdSDGPFKSLADLcdRLPSNVlNRRSLESLIHCGALDAFsPNANRAQLI 903
|
|
| PHP_PolIIIA_DnaE3 |
cd12113 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
617-820 |
1.35e-37 |
|
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: 143.35 E-value: 1.35e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 617 SYHAIILVKNYVGLRNLYKIVSKTHLEYFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILENkDEDEISRIVKFYD- 695
Cdd:cd12113 85 YYHLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNG-DEEEAREAALEYRd 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 696 -------YLEIQPlgnnrflvesgkvNSEEDLKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA---GQGFS 765
Cdd:cd12113 164 ifgkdnfYLELQD-------------HGLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLCiqtGKTLD 230
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 316940249 766 DAD------NQapLYFRTTDEMLEEFEYlgrekcYEVVVTNTNLIADMCEDILPIPEGTFP 820
Cdd:cd12113 231 DPNrmrfdtDE--FYLKSPEEMRELFPD------VPEALENTLEIAERCNVELDFGKLHLP 283
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
429-644 |
2.10e-37 |
|
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: 140.28 E-value: 2.10e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDkITEIGAV-KIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:TIGR00573 9 ETTGDNETTGLYAGHD-IIEIGAVeIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRNVD--NPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFI 585
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKLYKVEPktNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILA 167
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 316940249 586 KCLEILAEKNVKTIDDIQnvfegcwnyQKANSYHAIILVKNYVGLRNLYKIVSKTHLEY 644
Cdd:TIGR00573 168 KLYLVMTGKQTKYGENEG---------QQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
430-586 |
3.80e-37 |
|
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: 137.66 E-value: 3.80e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGLSADK-DKITEIGAVKIKEGKIVD-TFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:cd06131 2 IVLDTETTGLDPREgHRIIEIGCVELINRRLTGnTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLIN-----RNVDNpVIDTLELSRQMFPeLKKHKLDVVAKHLGVSLENH--HRALDDAKAC 580
Cdd:cd06131 82 AELVIHNASFDVGFLNAELSLLGlgkkiIDFCR-VIDTLALARKKFP-GKPNSLDALCKRFGIDNSHRtlHGALLDAELL 159
|
....*.
gi 316940249 581 GEIFIK 586
Cdd:cd06131 160 AEVYLE 165
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
430-593 |
3.40e-32 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 126.13 E-value: 3.40e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGL-SADKDKITEIGAVKIKEGKIV-DTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:PRK05711 7 IVLDTETTGLnQREGHRIIEIGAVELINRRLTgRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRG 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRNVDNP-----VIDTLELSRQMFPeLKKHKLDVVAKHLGVSleNHHR----ALDDAk 578
Cdd:PRK05711 87 AELIIHNAPFDIGFMDYEFALLGRDIPKTntfckVTDTLAMARRMFP-GKRNSLDALCKRYGID--NSHRtlhgALLDA- 162
|
170
....*....|....*
gi 316940249 579 acgeifikclEILAE 593
Cdd:PRK05711 163 ----------EILAE 167
|
|
| DNA_pol3_finger |
pfam17657 |
Bacterial DNA polymerase III alpha subunit finger domain; |
1101-1251 |
4.10e-32 |
|
Bacterial DNA polymerase III alpha subunit finger domain;
Pssm-ID: 407553 [Multi-domain] Cd Length: 166 Bit Score: 123.41 E-value: 4.10e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1101 DPTVIKMLEDLT------GVNARTIPIGEKRTMGIFSSTEPLGIrpedincpvgtfaiPEFGTKFVRQMLVDTKPKTFSE 1174
Cdd:pfam17657 1 TLTIIRDALDLIkenrgiGIDLATIPLDDPKTYKLLSSGDTLGV--------------FQFESRGMRQMLKRLKPDTFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1175 LIRISGLSHGTDVWLNNAQDLV--RNNIA-------SLSEVICTRDDIML--------NLIHYGLPNKTAFKIMEDVRKG 1237
Cdd:pfam17657 67 LVALSALYRPGPMQGGNVDDYIkrKHGKEkieyphpDLEPILKETYGVIVyqeqvmqiAQILAGFSLGEADLLRRAMGKK 146
|
170
....*....|....*....
gi 316940249 1238 K-----GLKEEYEQIMREK 1251
Cdd:pfam17657 147 KpeemeKLREKFIEGAKEN 165
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
430-576 |
9.47e-28 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 112.98 E-value: 9.47e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGLSADKDKITEIGAVKIKEGKivdTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT-S 508
Cdd:PRK06309 5 IFYDTETTGTQIDKDRIIEIAAYNGVTSE---SFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTdN 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 316940249 509 PLVAHNA-VFDTGFIRHNARlinRNVDNP----VIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDD 576
Cdd:PRK06309 82 ILVAHNNdAFDFPLLRKECR---RHGLEPptlrTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
429-596 |
4.12e-27 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 113.64 E-value: 4.12e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDKITEIGAVKIK-EGKIVDTFSTFVNPEI-PIPefvVKLTGITDDMVSDAPTIDKVLPEFLEFVG 506
Cdd:PRK06063 17 WAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLNPGVdPGP---THVHGLTAEMLEGQPQFADIAGEVAELLR 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 507 TSPLVAHNAVFDTGFIRHNARLINRN--VDNpVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIF 584
Cdd:PRK06063 94 GRTLVAHNVAFDYSFLAAEAERAGAElpVDQ-VMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVLAGIL 172
|
170
....*....|..
gi 316940249 585 IKCLEILAEKNV 596
Cdd:PRK06063 173 RPSLERARERDV 184
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
429-589 |
9.46e-27 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 118.64 E-value: 9.46e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSAdKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGTS 508
Cdd:PRK07246 9 YAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 509 PLVAHNAVFDTGFIRHNARLINRNVDNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACGEIFIKCL 588
Cdd:PRK07246 88 IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAELFLKLL 167
|
.
gi 316940249 589 E 589
Cdd:PRK07246 168 Q 168
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
426-584 |
1.49e-26 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 110.30 E-value: 1.49e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 426 DGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFV 505
Cdd:PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 506 GTSP-LVAHNAVFDTGFIRHNARLINRNV---DNPVIDTLELSRqMFPELKKHKLDVVAKHLGVSLENHHRALDDAKACG 581
Cdd:PRK06310 86 KEGDyIVGHSVGFDLQVLSQESERIGETFlskHYYIIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINI 164
|
...
gi 316940249 582 EIF 584
Cdd:PRK06310 165 KVF 167
|
|
| polC_OBF |
cd04484 |
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
248-330 |
3.02e-24 |
|
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: 97.67 E-value: 3.02e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 248 RVVVKGEIIRTEARELKSGKLLYVFDVTDFTNSLTVKIFLDKDKsgSVIERLKEKAN-VKIRGEAQYDKFSRELSILASD 326
Cdd:cd04484 1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDE--KDKEELKSKGDwVRVRGKVQYDTFSKELVLMIND 78
|
....
gi 316940249 327 IVEV 330
Cdd:cd04484 79 IEEI 82
|
|
| DNA_pol3_a_NII |
pfam11490 |
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
94-208 |
3.09e-24 |
|
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: 98.96 E-value: 3.09e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 94 KYWDSILYIVKKNIALCRGILSGCKWKIEDKKLYIYLKTKGT-EILKCKSCDTLIENIIKECFG-LEIKVEFKDFEIDED 171
Cdd:pfam11490 1 DYWEEIVEELSKKSPSLKSLLKNQKPEVEGNKLIIKVPNEIEaNFLKKKNLDKLLEEYIKFGFGkLSIDVEVDEDESSEE 80
|
90 100 110
....*....|....*....|....*....|....*..
gi 316940249 172 KINEYIEFKENEEAKIVTDTVIKNNEKTQKTEKSEKT 208
Cdd:pfam11490 81 ELEEFEEQKEEEEQKAIQEAIEALEKKEAEKKSKEKE 117
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
423-586 |
6.20e-23 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 98.05 E-value: 6.20e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 423 HPVDGEFVVFDIETTGLSADKDKITEIGAVKIKEGKIV--DTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPE 500
Cdd:PRK09145 25 PPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 501 FLEFVGTSPLVAHNAVFDTGFI-RHNARLINRNVDNPVIdtlELSRQMFPELKKH--------KLDVVAKHLGVSLENHH 571
Cdd:PRK09145 105 LLAFIGNRPLVGYYLEFDVAMLnRYVRPLLGIPLPNPLI---EVSALYYDKKERHlpdayidlRFDAILKHLDLPVLGRH 181
|
170
....*....|....*
gi 316940249 572 RALDDAKACGEIFIK 586
Cdd:PRK09145 182 DALNDAIMAALIFLR 196
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
345-411 |
1.08e-22 |
|
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Pssm-ID: 197753 [Multi-domain] Cd Length: 67 Bit Score: 92.71 E-value: 1.08e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 345 ELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIEAYLLD 411
Cdd:smart00481 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
345-413 |
3.04e-22 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 95.30 E-value: 3.04e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 316940249 345 ELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIEAYLLDDS 413
Cdd:pfam02811 1 HLHVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVAPGS 69
|
|
| PRK09532 |
PRK09532 |
DNA polymerase III subunit alpha; Reviewed |
618-1143 |
1.20e-21 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 102.13 E-value: 1.20e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 618 YHAIILVKNYVGLRNLYKIVSKTHLEYFH-----KRPRLPRKLLMMHREGLILGSACEAGELYRAILENkDEDEISRIVK 692
Cdd:PRK09532 83 YHQVVLAKNTQGYKNLVKLTTISHLQGVQgkgifARPCINKELLEQYHEGLIVTSACLGGEIPQAILSG-RPDAARKVAK 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 693 FYD-------YLEIQPLGnnrflvesgkvnSEEDlKNINRKIVALGEKYNKPVVATCDVHFMDPQD-EVFRRIL--MAGQ 762
Cdd:PRK09532 162 WYKklfgddfYLEIQDHG------------SQED-RIVNVEIVKIARELGIKIIATNDSHFISCYDvEAHDALLciQTGK 228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 763 GFSDADN---QAPLYFRTTDEMLEEFEYLGREKCYEVVVTNTNLIADMCE--DIL--------PIPEGTFPpkiEGAEEE 829
Cdd:PRK09532 229 LITEDKRlrySGTEYLKSAEEMRLLFRDHLPDDVIAEAIANTLEVADKIEpyNILgepripnyPVPSGHTP---DTYVEE 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 830 IRM--LAENKAREIYGDpLPEIVEKRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVG-SRGSVGSSFVAYLIGITE 906
Cdd:PRK09532 306 VAWqgLLERLNCKSRSE-VEPVYKERLEYELKMLQQMGFSTYFLVVWDYIKYARDNNIPVGpGRGSAAGSLVAYCLKITN 384
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 907 VNslPPHyicenckysefiedgsygcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKY 986
Cdd:PRK09532 385 ID--PVH---------------------------------------HGLLFERFLNPERKSMPDIDTDFCIERRDEMIKY 423
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 987 TEELFGVGHVYRAGTIGTIAEKTAYGFVKNYLD---------------ERGIVA--------------------TNAEIN 1031
Cdd:PRK09532 424 VTEKYGEDRVAQIITFNRMTSKAVLKDVARVLDipygeadkmaklipvSRGKPTklkvmisdetpepefkekydNDPRVR 503
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1032 RLVKGCT---GVKRTTGQHPGGVMI--VPQDreiyEFCPIQypaDDPDSGTITTHF--DYHSISgrLLKLDILGHDDPTV 1104
Cdd:PRK09532 504 RWLDMAIrieGTNKTFGVHAAGVVIssEPLD----EIVPLQ---KNNDGAVITQYFmeDLESLG--LLKMDFLGLRNLTT 574
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 316940249 1105 IKMLEDLTGVNAR------TIPIGEKRTMGIFSSTEPLGIrPEDI 1143
Cdd:PRK09532 575 IQKTADLIKENRGveidldQLPLDERKALKILAKGEAKKL-PKDV 618
|
|
| PHP_PolIIIA_DnaE1 |
cd07433 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
613-808 |
5.51e-21 |
|
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: 94.47 E-value: 5.51e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 613 QKANSYHAIILVKNYVGLRNLYKIVSKTHLE-YFHKRPRLPRKLLMMHREGLILGSACEAGELYRAILENKdEDEISRIV 691
Cdd:cd07433 73 DADEPFRLTLLAQNEQGYKNLTELISRAYLEgQRNGGPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGN-PDLAEALL 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 692 KFYdyleiQPLGNNRFLVESGKVNSEEDlKNINRKIVALGEKYNKPVVATCDVHFMDPQDEVFRRILMA-GQGFSDADNQ 770
Cdd:cd07433 152 QFL-----KKIFPDRFYLELQRHGRPEE-EAYEHALIDLAYELGLPLVATNDVRFLKPEDFEAHEARVCiAEGRTLDDPR 225
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 316940249 771 APL------YFRTTDEMLEEFEYLGRekcyevVVTNTNLIADMC 808
Cdd:cd07433 226 RPRryspqqYFKSAEEMAELFADLPE------AIENTVEIAKRC 263
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
429-588 |
1.02e-20 |
|
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.
Pssm-ID: 99836 [Multi-domain] Cd Length: 176 Bit Score: 91.13 E-value: 1.02e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDK-----ITEIGAVKI--KEGKIVDTFSTFVNPEI--PIPEFVVKLTGITDDMVSDAPTIDKVLP 499
Cdd:cd06133 1 YLVIDFEATCWEGNSKPdypneIIEIGAVLVdvKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 500 EFLEFVGTSPLVAhNAVF---DTGFIRHNARLINRNVDNPV----IDTLELSRQMFPELKKHKLDVVAKHLGVSLE-NHH 571
Cdd:cd06133 81 EFLEWLGKNGKYA-FVTWgdwDLKDLLQNQCKYKIINLPPFfrqwIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEgRHH 159
|
170
....*....|....*..
gi 316940249 572 RALDDAKACGEIFIKCL 588
Cdd:cd06133 160 RGLDDARNIARILKRLL 176
|
|
| HHH_6 |
pfam14579 |
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain. |
1353-1435 |
1.38e-20 |
|
Helix-hairpin-helix motif; The HHH domain is a short DNA-binding domain.
Pssm-ID: 434050 [Multi-domain] Cd Length: 88 Bit Score: 87.53 E-value: 1.38e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1353 GIKFLPIDIYKSDAvKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQGEFLSVDDL--RIRAKVSKTVIEILQQNGCLD 1430
Cdd:pfam14579 1 GIEVLPPDINRSDW-DFTVEGGGIRLGLGAIKGLGEAAAERIVEERENGPFKSLEDFarRVDLKLNKRVLEALIKAGAFD 79
|
....*
gi 316940249 1431 GLPES 1435
Cdd:pfam14579 80 SLGGN 84
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
429-611 |
6.60e-20 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 92.15 E-value: 6.60e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTglSADKDKITEIGAVKIKEGKIVDTFSTFVNP-EIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:PRK06195 3 FVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPkEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNAVFDTGFIRHNARLINRNV-DNPVIDTLELSRQMFPELKKHKLDVVAKHLGVSLEnHHRALDDAKACGEIFIK 586
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMpSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFK-HHDALADAMACSNILLN 159
|
170 180
....*....|....*....|....*
gi 316940249 587 CLEILAEKNVKTIDDIQNVFEGCWN 611
Cdd:PRK06195 160 ISKELNSKDINEISKLLGVTLGYVN 184
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
423-522 |
1.96e-19 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 90.42 E-value: 1.96e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 423 HPVDGEFV----VFDIETTGLSADKDKITEIGAVKI---KEGKI---VDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAp 492
Cdd:PRK09182 29 PAPRGEFVrlgvILDTETTGLDPRKDEIIEIGMVAFeydDDGRIgdvLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQ- 107
|
90 100 110
....*....|....*....|....*....|..
gi 316940249 493 TIDkvlPEFLE-FVGTSPLV-AHNAVFDTGFI 522
Cdd:PRK09182 108 TID---PAAVDaLIAPADLIiAHNAGFDRPFL 136
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
428-594 |
3.85e-19 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 87.14 E-value: 3.85e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 428 EFVVFDIETTGLsADKDKITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLEFVGT 507
Cdd:PRK07247 6 TYIAFDLEFNTV-NGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 508 SPLVAHNA----------------------VFDTGFIRhnarlinRNVDNPVIDTLelsrqmfpelkkhKLDVVAKHLGV 565
Cdd:PRK07247 85 LPLIGYNAqksdlpilaengldlsdqyqvdLYDEAFER-------RSSDLNGIANL-------------KLQTVADFLGI 144
|
170 180
....*....|....*....|....*....
gi 316940249 566 SLENHHrALDDAKACGEIFIKCLEILAEK 594
Cdd:PRK07247 145 KGRGHN-SLEDARMTARVYESFLESDQNK 172
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
429-576 |
3.24e-18 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 85.16 E-value: 3.24e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADkdkITEIGAVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLefvGTS 508
Cdd:PRK07983 2 LRVIDTETCGLQGG---IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY---GSE 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 509 PLVAHNAVFDtgfirhnaRLINRNVDNPVIDTLELSRQMFPELK--------KHKLDV-VAKHLgvsleNHHRALDD 576
Cdd:PRK07983 76 WYVAHNASFD--------RRVLPEMPGEWICTMKLARRLWPGIKysnmalykSRKLNVqTPPGL-----HHHRALYD 139
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
429-588 |
4.49e-17 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 80.67 E-value: 4.49e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSADKDK-----ITEIGAVKI-KEGKIVDTFSTFVNPEI--PIPEFVVKLTGITDDMVSDAPTIDKVLPE 500
Cdd:COG5018 4 YLVIDLEATCWDGKPPPgfpmeIIEIGAVKVdENGEIIDEFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAEAIED 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 501 FLEFVGtsplvAHNAVF-------DTGFIRhNARLinRNVDNPV----IDTLELSRQMFPELKKHKLDVVAKHLGVSLE- 568
Cdd:COG5018 84 FKKWIG-----SEDYILcswgdydRKQLER-NCRF--HGVPYPFgdrhINLKKLFALYFGLKKRIGLKKALELLGLEFEg 155
|
170 180
....*....|....*....|
gi 316940249 569 NHHRALDDAKACGEIFIKCL 588
Cdd:COG5018 156 THHRALDDARNTAKLFKKIL 175
|
|
| dnaE2 |
PRK05672 |
error-prone DNA polymerase; Validated |
724-1432 |
3.62e-16 |
|
error-prone DNA polymerase; Validated
Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 84.52 E-value: 3.62e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 724 NRKIVALGEKYNKPVVATCDVHFMDPQDevfRRILMA------GQGFSDAD-NQAPL---YFRTTDEMLEEFeylgreKC 793
Cdd:PRK05672 181 NARLAALAARAGVPLVATGDVHMHHRSR---RRLQDAmtairaRRSLAEAGgWLAPNgerHLRSGAEMARLF------PD 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 794 YEVVVTNTNLIADMCE---DIL-------PIPEGtfppkiEGAEEEIRMLAENKAREIYGDPLPEIVEKRMEKELNSIIK 863
Cdd:PRK05672 252 YPEALAETVELAERCAfdlDLLayeypdePVPAG------HTPASWLRQLTEAGAARRYGPGIPPKARAQIEHELALIAE 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 864 NGFSVMYIIAQKLVWKSLSDGYLVGSRGSVGSSFVAYLIGITEVNslpphyicenckysefiedgsygcgfdmPEKecpr 943
Cdd:PRK05672 326 LGYEGYFLTVHDIVRFARSQGILCQGRGSAANSAVCYALGITEVD----------------------------PVQ---- 373
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 944 cgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSgeyqpiaHKYTEELfgVGHVYR----------AGTIG---------- 1003
Cdd:PRK05672 374 ---------SGLLFERFLSPERDEPPDIDVDFE-------HDRREEV--IQYVYRrygrdraaqvANVITyrprsavrdv 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1004 ----------------TIAEKTAYGFVKNYLDERGIVATNAEINR---LVKGCTGVKRTTGQHPGGVMIVpqDREIYEFC 1064
Cdd:PRK05672 436 akalglspgqvdawakQVSRWSGSADDLQRLRQAGLDPESPIPRRvveLAAQLIGFPRHLSQHSGGFVIC--DRPLARLV 513
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1065 P-----------IQYPADDPDsgtitthfdyhsiSGRLLKLDILGhddptvIKMLE------DL----TGVNAR--TIPI 1121
Cdd:PRK05672 514 PvenaamegrsvIQWDKDDCA-------------AVGLVKVDVLA------LGMLSalhrafDLiaehRGRRLTlaSIPL 574
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1122 GEKRTMGIFSSTEplgirpedincPVGTFAIPEfgtkfvR-QM--LVDTKPKTFSEL------IR---ISGlshgtdvwl 1189
Cdd:PRK05672 575 DDPAVYDMLCRAD-----------SVGVFQVES------RaQMamLPRLRPRTFYDLvvevaiVRpgpIQG--------- 628
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1190 nnaqDLV------RNNIaslsEVICTRDDIMLNLIH--YGLP--------------------------NKTAFKIMEDVR 1235
Cdd:PRK05672 629 ----GMVhpylrrRNGQ----EPVTYPHPELEKVLErtLGVPlfqeqvmqiaidaagftpgeadqlrrAMAAWRRKGRLE 700
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1236 KgkgLKEEYEQIMREKKVPDWYIESC-KKIK----YMFPKAHAAAYVMMAFRIAWFKVYYPEAFYATYftvradefdasm 1310
Cdd:PRK05672 701 R---LRERLYDGMLARGYTGEFADRIfEQIKgfgeYGFPESHAASFAKLVYASSWLKCHHPAAFCAAL------------ 765
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1311 mchgkekvknkikeyeLKGNNMTQKEKNTLtileVANemyAR--GIKFLPIDIYKSDAvKFKIEKDGLRPP-----LNAL 1383
Cdd:PRK05672 766 ----------------LNSQPMGFYSPQQL----VQD---ARrhGVEVLPVDVNASGW-DATLEPLPDGGPavrlgLRLV 821
|
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 316940249 1384 QGLGVSAAHSIAEARNQGEFLSVDDLRIRAKVSKTVIEILQQNGCLDGL 1432
Cdd:PRK05672 822 RGLGEEAAERIVAARARGPFTSVEDLARRAGLDRRQLEALADAGALRSL 870
|
|
| PHP_PolIIIA |
cd07431 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
344-416 |
4.79e-16 |
|
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: 77.63 E-value: 4.79e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 316940249 344 VELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIEAYLLDDSVPI 416
Cdd:cd07431 1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPY 73
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
344-423 |
7.61e-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: 74.00 E-value: 7.61e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 344 VELHLHTQMSAMDgVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEAC--------EAAKKNKIKVIYGIEAYLLDDSVP 415
Cdd:cd07309 1 VDLHTHTVFSDGD-HAKLTELVDKAKELGPDALAITDHGNLRGLAEFNtagk*nhiKAAEAAGIKIIIGSEVNLTVLAHP 79
|
....*...
gi 316940249 416 IVYHANGH 423
Cdd:cd07309 80 VVATSDSH 87
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
785-1423 |
1.03e-15 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 82.81 E-value: 1.03e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 785 FEYLGREKCY----EVVVTNTNLIADMCEDILPIPEGTFPPKIEGAEEE--------IRMLAENKAREIYGDPLpeiVEK 852
Cdd:PRK07135 178 FKFFDFEKWFedidEKILKRTNYLVENINIEFPKKEFNLPDFDNNLGLEsdlflkkiLKESVINKKAELKYYPN---VKE 254
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 853 RMEKELNSIIKNGFSVMY-IIAQKLVWKSlSDGYLVG-SRGSVGSSFVAYLIGITEVNSLPphyicenckysefiedgsy 930
Cdd:PRK07135 255 RINYEYSVIKKLKFSNYFlIIWDFIKWAR-KNKISIGpGRGSASGSLVSYLLNITSVNPLK------------------- 314
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 931 gcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGVGHVYRAGTIGTIAEKTA 1010
Cdd:PRK07135 315 ----------------------YDLLFERFLNPDRITMPDIDIDIQDDRRDEVIDYIFEKYGYEHCATISTFQTLGAKSA 372
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1011 YGFVKNYLDergivATNAEINR--------------------------------------LVKGCTGVKRTTGQHPGGVM 1052
Cdd:PRK07135 373 IRDVGRMLG-----IPESDVNAisklipnnqsleeaydknksffreliskgdpiykklykIAKKLEGLPRQSGTHAAGII 447
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1053 IvpQDREIYEFCPIQYPADDPDSGTITTHF--DYHsisgrLLKLDILGHDDPTVIKMLEDLTG--------VNARTIPIG 1122
Cdd:PRK07135 448 I--SNKPITNYVPTFESKDNYNQVQYSMEFleDFG-----LLKIDLLGLKNLTIIKNIEEKINkellfdhlINFNDLPII 520
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1123 EKRTMGIFSSTEPLGIrpedincpvgtFAIPEFG-TKFVRQMLVDTkpktFSELIRI-----SGLSHGTDVWLNNaqdlv 1196
Cdd:PRK07135 521 DKKTNNLLSNGKTEGI-----------FQLESPGmKSTIKKVGIDS----FEDIVAIislyrPGPIQYIPIYAKN----- 580
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1197 RNNIASLSEVICTRDDIM---LNLIHYglpnktAFKIMEDVRKGKGLKEEYEQIMRE----------KKVPDWYIES--- 1260
Cdd:PRK07135 581 KKNPKNIEKIHPEYDEIVaptYGIIIY------QEQIMQIAQKVAGFSFAQADLLRRaiskkdetklDKIKDKFIEGgik 654
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1261 -------CKKI--------KYMFPKAHAAAYVMMAFRIAWFKVYYPEAFYatyftvradefdaSMMCHGKEKVKNKIKEY 1325
Cdd:PRK07135 655 ngyskkvLEKIysliekfaDYGFNKSHAVAYATLAYKMAYYKANYPLVFY-------------SALISNSNGSQENIKKY 721
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1326 ELKGNNMtqkekntltilevanemyarGIKFLPIDIYKSDAVKFkIEKDGLRPPLNALQGLGVSAAHSIAEARNQ-GEFL 1404
Cdd:PRK07135 722 VKEAKNN--------------------GIKVYSPDINFSTENAV-FDNGKIFLPLIMIKGLGSVAIKKIIDERNKnGKYK 780
|
730 740
....*....|....*....|..
gi 316940249 1405 SVDDLRIRAK---VSKTVIEIL 1423
Cdd:PRK07135 781 NFFDFILRLKfigISKSIIEKL 802
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
343-437 |
1.57e-15 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 76.49 E-value: 1.57e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 343 RVELHLHTQMSamDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIE-------------AYL 409
Cdd:COG0613 3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEistrwegrevhilGYG 80
|
90 100
....*....|....*....|....*....
gi 316940249 410 LDDSVPIVYHANGHPVD-GEFVVFDIETT 437
Cdd:COG0613 81 IDPEDPALEALLGIPVEkAEREWLSLEEA 109
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
429-586 |
2.95e-15 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 77.79 E-value: 2.95e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGL---SADKDKITEIGAVKIKEG--KIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVLPEFLE 503
Cdd:PRK06722 7 FIVFDIERNFRpykSEDPSEIVDIGAVKIEAStmKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQ 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 504 FVGTSPLVAHNAVFDTGFIRHNARLinRNVDNPV------IDTLELSRQMFPELKKH--KLDVVAKHLGVSLE-NHHRAL 574
Cdd:PRK06722 87 FIGEDSIFVTWGKEDYRFLSHDCTL--HSVECPCmekerrIDLQKFVFQAYEELFEHtpSLQSAVEQLGLIWEgKQHRAL 164
|
170
....*....|..
gi 316940249 575 DDAKACGEIFIK 586
Cdd:PRK06722 165 ADAENTANILLK 176
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
426-583 |
6.70e-15 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 75.78 E-value: 6.70e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 426 DGEFVVFDIETTGLSADKDKITEIGAVKIKE-GKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSD-----APTIDKVLP 499
Cdd:PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDAdGEVVESREWLADPGVEIPEEASAVHGITTEYARAhgrpaAEVLAEIAD 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 500 EFLEFVGTS-PLVAHNAVFD-TGFIRHNARL-INRNVDNPVIDTLELSRQMFPELK-KHKLDVVAKHLGVSLENHHRALD 575
Cdd:PRK07942 85 ALREAWARGvPVVVFNAPYDlTVLDRELRRHgLPSLVPGPVIDPYVIDKAVDRYRKgKRTLTALCEHYGVRLDNAHEATA 164
|
....*...
gi 316940249 576 DAKACGEI 583
Cdd:PRK07942 165 DALAAARV 172
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
426-584 |
4.61e-14 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 73.42 E-value: 4.61e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 426 DGEFVVFDIETTGLSADKDKITEIGAV-------KIKEGKivdtfSTFVNPEIPIPEFVVKLTGITDDMVSDAPTIDKVL 498
Cdd:PRK09146 46 EVPFVALDFETTGLDAEQDAIVSIGLVpftlqriRCRQAR-----HWVVKPRRPLEEESVVIHGITHSELQDAPDLERIL 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 499 PEFLEFVGTSPLVAHNAVFDTGFIRHNAR-LINRNVDNPVIDTLELSRQMFPE--------LKKHKLDVVakHLGVSLE- 568
Cdd:PRK09146 121 DELLEALAGKVVVVHYRRIERDFLDQALRnRIGEGIEFPVIDTMEIEARIQRKqagglwnrLKGKKPESI--RLADSRLr 198
|
170 180
....*....|....*....|...
gi 316940249 569 -------NHHrALDDAKACGEIF 584
Cdd:PRK09146 199 yglpaysPHH-ALTDAIATAELL 220
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
344-406 |
1.09e-13 |
|
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: 70.11 E-value: 1.09e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 316940249 344 VELHLHTQMSamDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIE 406
Cdd:cd07438 1 IDLHTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVE 61
|
|
| dnaE |
PRK05898 |
DNA polymerase III subunit alpha; |
852-1431 |
1.92e-13 |
|
DNA polymerase III subunit alpha;
Pssm-ID: 135648 [Multi-domain] Cd Length: 971 Bit Score: 75.65 E-value: 1.92e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 852 KRMEKELNSIIKNGFSVMYIIAQKLVWKSLSDGYLVG-SRGSVGSSFVAYLIGITEVNSLPphyicenckysefiedgsy 930
Cdd:PRK05898 256 KRLKYELDIINEKQFDDYFLIVYDFINFAKSNGIIIGpGRGSAAGSLIAYLLHITDIDPIK------------------- 316
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 931 gcgfdmpekecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGVGHVYRAGTIGTIAEKTA 1010
Cdd:PRK05898 317 ----------------------YNLIFERFLNPTRKSMPDIDTDIMDERRDEVVEYLFEKYGNDHVAHIITFQRIKAKMA 374
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1011 Y------------------GFVKNYLDERGIVATNA------------EINRLVKGCTGVKRTTGQHPGGVMIvpQDREI 1060
Cdd:PRK05898 375 IrdvgrilgidlkvidkicKNIKPDYEEDLDLAIKKntilkemyvlhkELFDLAKKIINAPRQIGTHAAGVVL--SNSLL 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1061 YEFCPIQYPADDpdsgTITTHF--DYHSISGrLLKLDILGHDDPTVI----KMLEDLTG--VNARTIPIGEK-------- 1124
Cdd:PRK05898 453 TNIIPIQLGIND----RPLSQYsmEYLERFG-LIKMDLLGLKNLTIIdnvlKLIKENQNkkIDLFNINLNDKnvfedlak 527
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1125 -RTMGIFSSTEP------LGIRP---EDINCPVGTFAI-PEFGTK-FVRQMLVDTKPKTFSE-LIRISGLSHGTDVWLNN 1191
Cdd:PRK05898 528 gRTNGIFQLESPgmkkvlKKVKPqniEDISIVSALFRPgPQQNIKtFVERRFKREEFSYWNEaTKKILEPTHGIIVYQEQ 607
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1192 AQDLVRNnIA--SLSEVICTRDDIMLNLIHYGLPNKTAFkiMEDVRKGKGLKEEYEQIMRekkvpdwYIESCKKikYMFP 1269
Cdd:PRK05898 608 VINLVKT-IAnfDIATADNFRRAISKKDEKILIQLKKDF--IEGALKNNYKQPLVNQIFE-------YIFSFAD--YGFN 675
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1270 KAHAAAYVMMAFRIAWFKVYYPEAFYATYFTVRADEfdasmmchgkekvKNKIKEYelkgnnmtqkekntltilevANEM 1349
Cdd:PRK05898 676 HSHSLAYSYISYWMAYLKHYYPLEFLSILLSHTSAS-------------KDKLLSY--------------------LNEA 722
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1350 YARGIKFLPIDI-YKSDAVKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQGE---FLSVDDLRIRAKVSKTVIEILQQ 1425
Cdd:PRK05898 723 KEFNISIKKPDInYSSNSFVLDTQKQIIRFGFNTIKGFGDELLKKIKSALQNKTfsdFISYIDALKKNNVSLSNIEILIN 802
|
....*.
gi 316940249 1426 NGCLDG 1431
Cdd:PRK05898 803 VGTFDS 808
|
|
| dnaE |
PRK07279 |
DNA polymerase III DnaE; Reviewed |
783-1295 |
2.01e-13 |
|
DNA polymerase III DnaE; Reviewed
Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 75.45 E-value: 2.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 783 EEFEYLGREKCYEVVVTNTNLIADMCEDI---LPIPEgtFPPKIEgAEEEIRMLAEN--KAREIYGDPLPEivekRMEKE 857
Cdd:PRK07279 195 QSLETLFQERFPQALDNLEKLVSGISYDFdtdLKLPR--FNRDRP-AVEELRELAELglKEKGLWSSPYQE----RLDKE 267
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 858 LNSIIKNGFSVMYIIaqklVWKSL----SDGYLVG-SRGSVGSSFVAYLIGITevnslpphyicenckysefiedgsygc 932
Cdd:PRK07279 268 LSVIHDMGFDDYFLI----VWDLLrfgrSQGYYMGmGRGSAAGSLVAYALDIT--------------------------- 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 933 GFDmPEKecprcgkilkkdgYDIPFETFLGFEGDKEPDIDLNFSGEYQPIAHKYTEELFGVGHVYRAGTIGTIAEKTAY- 1011
Cdd:PRK07279 317 GID-PVK-------------HNLLFERFLNKERYSMPDIDIDLPDIYRSEFLRYVRNRYGSDHSAQIVTFSTFGAKQAIr 382
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1012 --------------------GFVKNYLDE-------RGIVATNAEINR---LVKGCTGVKRTTGQHPGGvmIVPQDREIY 1061
Cdd:PRK07279 383 dvfkrfgvpeyelsnltkkiSFRDSLASVyeknisfRQIINSKLEYQKafeIAKRIEGNPRQTSIHAAG--VVMSDDDLT 460
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1062 EFCPIQYPADDPdsgtiTTHFDYHSI-SGRLLKLDILGHDDPTVI-KMLEDLTGVNARTIPIGE--------------KR 1125
Cdd:PRK07279 461 NHIPLKYGDDMM-----ITQYDAHAVeANGLLKMDFLGLRNLTFVqKMQEKVAKDYGIHIDIEAidledketlalfaaGD 535
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1126 TMGIFSSTEPLGIR------P---EDIncpVGTFAI-----PEFGTKFVR----QMLVDTKPKTFSELI----------- 1176
Cdd:PRK07279 536 TKGIFQFEQPGAINllkrikPvcfEDI---VATTSLnrpgaSDYTDNFVKrrhgQEKVDLIDPVIAPILeptygimlyqe 612
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1177 -------RISGLSHGTdvwlnnaQDLVRNNIA--SLSEVICTRDDIMLNLIHYGLPNKTA---FKIMEdvrkgkglkeey 1244
Cdd:PRK07279 613 qvmqiaqVFAGFSLGK-------ADLLRRAMSkkNASEMQKMEEDFLQGALELGHSEEKArelFDRME------------ 673
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|.
gi 316940249 1245 eqimrekkvpdwyiescKKIKYMFPKAHAAAYVMMAFRIAWFKVYYPEAFY 1295
Cdd:PRK07279 674 -----------------KFAGYGFNRSHAFAYSALAFQLAYFKAHYPAVFY 707
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
344-406 |
5.47e-13 |
|
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: 67.26 E-value: 5.47e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 316940249 344 VELHLHTQMSAmDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIE 406
Cdd:cd07432 1 ADLHIHSVFSP-DSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVE 62
|
|
| DNA_pol3_a_NI |
pfam14480 |
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
10-72 |
5.22e-10 |
|
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: 56.78 E-value: 5.22e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 316940249 10 KLSELFPEVINNENERELFDTARIQNINVYKKSRKLEIFIVSDTLIPAKTLDSVEQSFKKLFE 72
Cdd:pfam14480 1 RFFELFPQLKLPDELEELFEDAEIEKVTVHKKSKKWRFYISSPHLLPKEVIYKFEQRLKEQFF 63
|
|
| PRK07373 |
PRK07373 |
DNA polymerase III subunit alpha; Reviewed |
1268-1436 |
7.12e-07 |
|
DNA polymerase III subunit alpha; Reviewed
Pssm-ID: 236003 [Multi-domain] Cd Length: 449 Bit Score: 53.53 E-value: 7.12e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1268 FPKAHAAAYVMMAFRIAWFKVYYPEAFYATYFTVRADEFDasmmchgkekvknKIKEYelkgnnmtqkekntltiLEVAN 1347
Cdd:PRK07373 38 FNKSHSTAYAYVTYQTAYLKANYPVEYMAALLTANSGNQD-------------KVQKY-----------------RENCQ 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 1348 EMyarGIKFLPIDIYKSDaVKFKIEKDGLRPPLNALQGLGVSAAHSIAEARNQ-GEFLSVD------DLRIrakVSKTVI 1420
Cdd:PRK07373 88 KM---GIEVEPPDINRSG-KDFTPVGEKILFGLSAVRNLGEGAIESILKAREEgGEFKSLAdfcdrvDLRV---VNRRAL 160
|
170
....*....|....*.
gi 316940249 1421 EILQQNGCLDGLpESN 1436
Cdd:PRK07373 161 ETLIYCGAFDKI-EPN 175
|
|
| PHP_PolIIIA_DnaE2 |
cd07434 |
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
344-417 |
7.64e-07 |
|
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity.
Pssm-ID: 213989 [Multi-domain] Cd Length: 260 Bit Score: 52.07 E-value: 7.64e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 316940249 344 VELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDH----GVVQAYpeacEAAKKNKIKVIYGieAYL-LDDSVPIV 417
Cdd:cd07434 2 AELHCLSNFSFLRGASHPEELVARAAELGYRALAITDEcslaGVVRAH----AAAKELGLKLIVG--SELvLADGTRLV 74
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
343-413 |
1.07e-06 |
|
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis
Pssm-ID: 440997 [Multi-domain] Cd Length: 232 Bit Score: 51.31 E-value: 1.07e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 343 RVELHLHTQMSamDGVTSVGELIKRAAQWGHKAIAVTDHGV------------VQAYPEACEAAKKN--KIKVIYGIEA- 407
Cdd:COG1387 2 RGDLHTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDHSPslfvanglseerLLEYLEEIEELNEKypDIKILKGIEVd 79
|
....*.
gi 316940249 408 YLLDDS 413
Cdd:COG1387 80 ILPDGS 85
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
430-475 |
5.50e-06 |
|
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: 50.48 E-value: 5.50e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 316940249 430 VVFDIETTGLSADKDKITEIGAVKI-KEGKIVDTFSTFVNPEIPIPE 475
Cdd:pfam13361 189 VVFDVETTGLDTTEDEIIQIAAIKLnKKGVVIESFERFLRLKKPVGD 235
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
416-565 |
1.18e-05 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 47.63 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 416 IVYHANGHPVDgEFVVFDIETTGLSADKDKITEIGAVKIKEGK-IVDTFstfvnpeipipefvvkltgITDDMVSDAPTI 494
Cdd:COG3359 5 AYFFAELLPSE-DLLFFDIETTGLSGGGTVIFLIGLADGEGDGfVVRQY-------------------FGEDPGEEAALL 64
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 316940249 495 DKVLPEFLEFvgtSPLVAHN-AVFDTGFIRHNARLINRNVDNPV---IDTLELSRQMFPE-LKKHKLDVVAKHLGV 565
Cdd:COG3359 65 EAFLEWLADY---KLLVTYNgKSFDLPFLKTRFTLHRLPPPLPEfphLDLLHPARRLWKNrLPSGGLKTVEELLGI 137
|
|
| Orn |
COG1949 |
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]; |
433-576 |
2.62e-05 |
|
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
Pssm-ID: 441552 Cd Length: 177 Bit Score: 46.25 E-value: 2.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 433 DIETTGLSADKDKITEIGAVkI--KEGKIVDtfstfVNPEIPI----------PEFVVKL---TGITDDMVSDAPTIDKV 497
Cdd:COG1949 8 DLEMTGLDPETDRIIEIATI-VtdSDLNILA-----EGPVLVIhqsdealdgmDDWNRRMhtkSGLIDRVRASTVTEAEA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 498 LPEFLEFV------GTSPLvAHNAV-FDTGFI-RHNARLIN----RNVDnpvIDTL-ELSRQMFPELKKHkldvVAKHLG 564
Cdd:COG1949 82 EAQTLAFLkqhvpaGKSPL-CGNSIgQDRRFLaRYMPELEAyfhyRNLD---VSTLkELARRWYPEVLAG----PKKKGG 153
|
170
....*....|..
gi 316940249 565 vslenhHRALDD 576
Cdd:COG1949 154 ------HRALAD 159
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
429-514 |
3.70e-05 |
|
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.
Pssm-ID: 99839 [Multi-domain] Cd Length: 177 Bit Score: 45.79 E-value: 3.70e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 429 FVVFDIETTGLSA-DKDKITEIGAV-------------KIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDMVSDAPTI 494
Cdd:cd06136 1 FVFLDLETTGLPKhNRPEITELCLVavhrdhllntsrdKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80
|
90 100
....*....|....*....|....*.
gi 316940249 495 DK----VLPEFLEfVGTSP--LVAHN 514
Cdd:cd06136 81 DSdtanLIKLFLR-RQPKPicLVAHN 105
|
|
| Orn |
cd06135 |
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ... |
433-576 |
5.36e-05 |
|
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Pssm-ID: 99838 [Multi-domain] Cd Length: 173 Bit Score: 45.23 E-value: 5.36e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 433 DIETTGLSADKDKITEIGAVkIKEGK---IVDTFSTFVNPE----IPIPEFVVKL---TGITDDMVSDAPTIDKVLPEFL 502
Cdd:cd06135 5 DLEMTGLDPEKDRILEIACI-ITDGDlniIAEGPELVIHQPdevlDGMDEWCTEMhtkSGLTERVRASTVTLAQAEAELL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 503 EFV------GTSPLvAHNAV-FDTGFI-----RHNARLINRNVDnpvIDTL-ELSRQMFPELKKHKLdvvaKHLGVslen 569
Cdd:cd06135 84 EFIkkyvpkGKSPL-AGNSVhQDRRFLdkympELEEYLHYRILD---VSSIkELARRWYPEIYRKAP----KKKGT---- 151
|
....*..
gi 316940249 570 hHRALDD 576
Cdd:cd06135 152 -HRALDD 157
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
432-577 |
8.83e-05 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 44.51 E-value: 8.83e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 432 FDIETTGLSADKDKITEIGAVKIKEGKIVdTFSTFVNPEIPIPEFVVKLtgitddmvsdaptidkvlpeFLEFVGTSPLV 511
Cdd:pfam13482 3 FDIETTGLSPGKNTIYLIGVYDVDGDKVR-TFVQYLAEGPTEEAAILQL--------------------FELLADYPLLV 61
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 512 AHN-AVFDTGFIRHNARLINRNVDNPVIDtleLSRQMFPELKKHKLDVVAKHLGVslenhHRALDDA 577
Cdd:pfam13482 62 TFNgKSFDVPFIKRRFKRYDLDELFRHID---LLHPLRKLGLESGLKSVERELGI-----ERRDDDL 120
|
|
| PRK06361 |
PRK06361 |
histidinol phosphate phosphatase domain-containing protein; |
349-406 |
2.76e-04 |
|
histidinol phosphate phosphatase domain-containing protein;
Pssm-ID: 180543 [Multi-domain] Cd Length: 212 Bit Score: 43.79 E-value: 2.76e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 316940249 349 HTQMSamDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNK--------IKVIYGIE 406
Cdd:PRK06361 2 HTIFS--DGELIPSELVRRARVLGYRAIAITDHADASNLEEILEKLVRAAeelelywdIEVIPGVE 65
|
|
| CehA_McbA_metalo |
NF038032 |
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
343-406 |
2.78e-04 |
|
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.
Pssm-ID: 468321 [Multi-domain] Cd Length: 315 Bit Score: 44.62 E-value: 2.78e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 316940249 343 RVELHLHTQMSamDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEA-AKKNKIKVIYGIE 406
Cdd:NF038032 4 SGDLHIHTNHS--DGPTTPEELARAALAEGLDVIALTDHNTISGRAYFAELlASERGLLVIPGME 66
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
249-330 |
4.62e-04 |
|
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: 40.30 E-value: 4.62e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 249 VVVKGEIIRTEarelKSGKLLYVFDVTDFTNSLTVKIFldKDKSGSVIERLKEKANVKIRGEAQYDKFsRELSILASDIV 328
Cdd:pfam01336 1 VTVAGRVTSIR----RSGGKLLFLTLRDGTGSIQVVVF--KEEAEKLAKKLKEGDVVRVTGKVKKRKG-GELELVVEEIE 73
|
..
gi 316940249 329 EV 330
Cdd:pfam01336 74 LL 75
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
346-381 |
1.81e-03 |
|
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
Pssm-ID: 213991 [Multi-domain] Cd Length: 237 Bit Score: 41.64 E-value: 1.81e-03
10 20 30
....*....|....*....|....*....|....*.
gi 316940249 346 LHLHTQMSamDGVTSVGELIKRAAQWGHKAIAVTDH 381
Cdd:cd07436 9 LHVHTTWS--DGRNSIEEMAEAARALGYEYIAITDH 42
|
|
| DNA_polA_I_Ecoli_like_exo |
cd06139 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
430-564 |
3.02e-03 |
|
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: 40.58 E-value: 3.02e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 430 VVFDIETTGLSADKDKITEIG-AVKIKEGKIVDTFSTFVNPEIPIPEFVVKLTGITDDmvsdaPTIDKVlpeflefvgts 508
Cdd:cd06139 8 FAFDTETTSLDPMQAELVGISfAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLED-----PSIKKV----------- 71
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 316940249 509 plvAHNAVFDTGFIRHNarLINrnVDNPVIDTLELSRQMFPELKKHKLDVVA-KHLG 564
Cdd:cd06139 72 ---GQNLKFDLHVLANH--GIE--LRGPAFDTMLASYLLNPGRRRHGLDDLAeRYLG 121
|
|
| dnaE |
PRK07135 |
DNA polymerase III DnaE; Validated |
341-406 |
4.71e-03 |
|
DNA polymerase III DnaE; Validated
Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 41.60 E-value: 4.71e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 316940249 341 EKRVELHLHTQMSAMDGVTSVGELIKRAAQWGHKAIAVTDHGVVQAYPEACEAAKKNKIKVIYGIE 406
Cdd:PRK07135 1 MKLINLHTNTEYSFLSSTIKLDSLIKYAKENNLKTLVLTDHNNMFGVPKFYKLCKKNNIKPIIGLD 66
|
|
| REX1_like |
cd06145 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ... |
456-583 |
5.99e-03 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Pssm-ID: 99848 Cd Length: 150 Bit Score: 39.01 E-value: 5.99e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 316940249 456 EGKIVdtFSTFVNPEIPIPEFVVKLTGITDDMVSDAP-TIDKVLPEFLEFVGT-SPLVAH------NAVfdtgfirhnaR 527
Cdd:cd06145 25 NGKVV--LDELVKPDGEIVDYNTRFSGITEEMLENVTtTLEDVQKKLLSLISPdTILVGHslendlKAL----------K 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 316940249 528 LINRNvdnpVIDT--LELSRQMFPelKKHKL-DVVAKHLGVSL---ENHHRALDDAKACGEI 583
Cdd:cd06145 93 LIHPR----VIDTaiLFPHPRGPP--YKPSLkNLAKKYLGRDIqqgEGGHDSVEDARAALEL 148
|
|
| |
