|
Name |
Accession |
Description |
Interval |
E-value |
| PolX |
COG1796 |
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair]; |
1-557 |
1.55e-152 |
|
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
Pssm-ID: 441401 [Multi-domain] Cd Length: 567 Bit Score: 449.26 E-value: 1.55e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLASLS-LAELEKQEGIGKSIAAKITELSLTGKLAELE 79
Cdd:COG1796 1 MDNKEIARILEEIADLLELKGENPFKIRAYRRAARAIENLPEDIEELVaEGDLTEIPGIGKAIAAKIEELLETGRLEELE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 80 ALLQKTPEGVIELLQIKGIGPKKVKSLWKELEITTKEELLEACHNNTVANLKGFGEKTQDNIIQVLQFVIKQSDKFLYGD 159
Cdd:COG1796 81 ELREEVPPGLLELLRIPGLGPKKVKKLYEELGITSLEELEAAAEEGRIRELPGFGEKTEENILKGIELLRKRGGRFLLGE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 160 VEATAFELEKKLQS-DLNSSVRLCGEMRRMMETVDRISFIVAATDASKLFANIKTLDYLEEI----PTQSGLYRWYGlyk 234
Cdd:COG1796 161 ALPLAEEILAYLRAlPGVERVEVAGSLRRRKETVGDIDILVASDDPEAVMDAFVKLPEVKEVlakgDTKASVRLKSG--- 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 235 tfkIPVEIYMTDAAHLGSELIkHSSGA---N-HLR--------------LTDANGKtflQIAhatpFASEEEFYQRVQLP 296
Cdd:COG1796 238 ---LQVDLRVVPPESFGAALQ-YFTGSkehNvALRqlakerglklneygLFDVGGE---RIA----GETEEEVYAALGLP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 297 FIPSELREGYRELKLVEENRLADLITDAAIQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEE 376
Cdd:COG1796 307 YIPPELREDRGEIEAAEEGRLPELVELDDIRGDLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDHSSSLVVAGGLDEE 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 377 TVAKQQLEIDTLNATYNTIKIFKGIESDILNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLG 456
Cdd:COG1796 387 RLLQQEEEIDALNERLDGIILLLGGEEDILDDGGLDDDDDLLLEDDDVVAAVHHSFLLQDEEMTRRRLAAANEPVVVIIH 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 457 HPTGRLLLKREGYPIDHKKIIDACAANNVIIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVAR 536
Cdd:COG1796 467 HPTGRLLLRRRPYYVDDEAIIAAAAAAGALEEENNAPRRLLLLDDLARAAAEGGVVIIIIDDAHHTDLLLDLMGGGVAAR 546
|
570 580
....*....|....*....|.
gi 2543367238 537 KAGLCVDQTFNAWPLEKVSAW 557
Cdd:COG1796 547 RRWWLEKDVNNNTLLLELLLL 567
|
|
| PRK08609 |
PRK08609 |
DNA polymerase/3'-5' exonuclease PolX; |
1-561 |
1.51e-142 |
|
DNA polymerase/3'-5' exonuclease PolX;
Pssm-ID: 236311 [Multi-domain] Cd Length: 570 Bit Score: 423.60 E-value: 1.51e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEiplasLSLAELE---KQEGIGKSIAAKITELSLTGKLAE 77
Cdd:PRK08609 1 MNKKDVIKLLETIATYMELKGENPFKISAFRKAAQALELDE-----RSLSEIDdftKLKGIGKGTAEVIQEYRETGESSV 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 78 LEALLQKTPEGVIELLQIKGIGPKKVKSLWKELEITTKEELLEACHNNTVANLKGFGEKTQDNIIQVLQFVIKQSDKFLY 157
Cdd:PRK08609 76 LQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKRPERLPI 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 158 GDVEATAFELEKKLQsDLNSSVR--LCGEMRRMMETVDRISFIVAATDASKLFANIKTLDYLEEI----PTQSGLYrwyg 231
Cdd:PRK08609 156 AQVLPIAQEIEEYLA-TIDEIIRfsRAGSLRRARETVKDLDFIIATDEPEAVREQLLQLPNIVEViaagDTKVSVE---- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 232 LYKTFKIPVEIYMTDAAHLGSELiKHSSGANhlrltDANGKtFLQIAHA------------------TPFASEEEFYQRV 293
Cdd:PRK08609 231 LEYEYTISVDFRLVEPEAFATTL-HHFTGSK-----DHNVR-MRQLAKErgekiseygveqadtgevKTFESEEAFFAHF 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 294 QLPFIPSELREGYRELKLVEEnrLADLITDAAIQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGL 373
Cdd:PRK08609 304 GLPFIPPEVREDGSEFERYKD--LSNLITLSDIQGDLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDHSQYLKVANGL 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 374 NEETVAKQQLEIDTLNATYNTIKIFKGIESDILNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTT 453
Cdd:PRK08609 382 TEERLLEQAEEIKALNEKYPEIDILSGIEMDILPDGSLDYDDEVLAELDYVIAAIHSSFSQSEEEIMKRLENACRNPYVR 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 454 MLGHPTGRLLLKREGYPIDHKKIIDACAANNVIIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGIC 533
Cdd:PRK08609 462 LIAHPTGRLIGRRDGYDVNIDQLIELAKETNTALELNANPNRLDLSAEHLKKAQEAGVKLAINTDAHHTEMLDDMKYGVA 541
|
570 580
....*....|....*....|....*...
gi 2543367238 534 VARKAGLCVDQTFNAWPLEKVSAWLKTK 561
Cdd:PRK08609 542 TARKGWIQKDRVINTWSREEFKDFIKRN 569
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
326-558 |
9.88e-134 |
|
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: 388.70 E-value: 9.88e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 326 IQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEETVAKQQLEIDTLNATYNTIKIFKGIESDI 405
Cdd:cd07436 5 IRGDLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDHSKSLRVANGLSEERLREQIEEIDALNEKLPGIRILKGIEVDI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 406 LNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLGHPTGRLLLKREGYPIDHKKIIDACAANNV 485
Cdd:cd07436 85 LPDGSLDYPDEVLAELDVVVASVHSGFNQSEEEMTERLLKAIENPHVDILGHPTGRLLGRREGYEVDMERVIEAAAETGT 164
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2543367238 486 IIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVARKAGLCVDQTFNAWPLEKVSAWL 558
Cdd:cd07436 165 ALEINANPDRLDLDDRHARRAKEAGVKIAINTDAHSTDGLDNMRYGVGTARRGWLEKEDVLNTLPLEELLKFL 237
|
|
| HHH_8 |
pfam14716 |
Helix-hairpin-helix domain; |
3-69 |
5.90e-17 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434152 [Multi-domain] Cd Length: 67 Bit Score: 75.23 E-value: 5.90e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2543367238 3 NQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLAslSLAELEKQEGIGKSIAAKITEL 69
Cdd:pfam14716 1 NQEIADALEELADLLELKGEDPFRVRAYRRAARALEALPEEIT--SLEELTKLPGIGKKIAAKIEEI 65
|
|
| POLXc |
smart00483 |
DNA polymerase X family; includes vertebrate polymerase beta and terminal ... |
1-220 |
4.27e-13 |
|
DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Pssm-ID: 214688 Cd Length: 334 Bit Score: 70.47 E-value: 4.27e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLASLslAELEKQEGIGKSIAAKITELSLTGKLAELEA 80
Cdd:smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSM--KDLKGLPGIGDKIKKKIEEIIETGKSSKVLE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 81 LLQK-TPEGVIELLQIKGIGPKKVKsLWKELEITTKEELLEACHNN-TVANLKGFgeKTQDNIIQvlqfVIKQSDKFLYG 158
Cdd:smart00483 79 ILNDeVYKSLKLFTNVFGVGPKTAA-KWYRKGIRTLEELKKNKELKlTKQQKAGL--KYYEDILK----KVSRAEAFAVE 151
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2543367238 159 DVEATAFELEKKlqsdlNSSVRLCGEMRRMMETVDRISFIVAAT-DASKLFANIKTLDYLEEI 220
Cdd:smart00483 152 YIVKRAVRKILP-----DAIVTLTGSFRRGKETGHDVDFLITSPhPAKEKELEVLDLLLLEST 209
|
|
| hisJ_fam |
TIGR01856 |
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate ... |
329-429 |
9.68e-06 |
|
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Pssm-ID: 273837 [Multi-domain] Cd Length: 253 Bit Score: 47.39 E-value: 9.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 329 SFHNHSTYS-DGQHSLEEMTKACVALGYTYFGISDHSKSAFYASG-------LNEETVAKQQLEIDTLNATY-NTIKIFK 399
Cdd:TIGR01856 2 DSHSHSPFCaHGTDTLREVVQEAIQLGFEEICFTEHAPRPFYYPEedflkkeMLFLSLPEYFQEINQLKQEYaDKIKILI 81
|
90 100 110
....*....|....*....|....*....|..
gi 2543367238 400 GIESDILnDGSLDYSDDVLKSF--DFIVASIH 429
Cdd:TIGR01856 82 GLEVDYI-PGFEEEIKDFLDSYnlDFVIGSVH 112
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolX |
COG1796 |
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair]; |
1-557 |
1.55e-152 |
|
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
Pssm-ID: 441401 [Multi-domain] Cd Length: 567 Bit Score: 449.26 E-value: 1.55e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLASLS-LAELEKQEGIGKSIAAKITELSLTGKLAELE 79
Cdd:COG1796 1 MDNKEIARILEEIADLLELKGENPFKIRAYRRAARAIENLPEDIEELVaEGDLTEIPGIGKAIAAKIEELLETGRLEELE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 80 ALLQKTPEGVIELLQIKGIGPKKVKSLWKELEITTKEELLEACHNNTVANLKGFGEKTQDNIIQVLQFVIKQSDKFLYGD 159
Cdd:COG1796 81 ELREEVPPGLLELLRIPGLGPKKVKKLYEELGITSLEELEAAAEEGRIRELPGFGEKTEENILKGIELLRKRGGRFLLGE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 160 VEATAFELEKKLQS-DLNSSVRLCGEMRRMMETVDRISFIVAATDASKLFANIKTLDYLEEI----PTQSGLYRWYGlyk 234
Cdd:COG1796 161 ALPLAEEILAYLRAlPGVERVEVAGSLRRRKETVGDIDILVASDDPEAVMDAFVKLPEVKEVlakgDTKASVRLKSG--- 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 235 tfkIPVEIYMTDAAHLGSELIkHSSGA---N-HLR--------------LTDANGKtflQIAhatpFASEEEFYQRVQLP 296
Cdd:COG1796 238 ---LQVDLRVVPPESFGAALQ-YFTGSkehNvALRqlakerglklneygLFDVGGE---RIA----GETEEEVYAALGLP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 297 FIPSELREGYRELKLVEENRLADLITDAAIQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEE 376
Cdd:COG1796 307 YIPPELREDRGEIEAAEEGRLPELVELDDIRGDLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDHSSSLVVAGGLDEE 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 377 TVAKQQLEIDTLNATYNTIKIFKGIESDILNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLG 456
Cdd:COG1796 387 RLLQQEEEIDALNERLDGIILLLGGEEDILDDGGLDDDDDLLLEDDDVVAAVHHSFLLQDEEMTRRRLAAANEPVVVIIH 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 457 HPTGRLLLKREGYPIDHKKIIDACAANNVIIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVAR 536
Cdd:COG1796 467 HPTGRLLLRRRPYYVDDEAIIAAAAAAGALEEENNAPRRLLLLDDLARAAAEGGVVIIIIDDAHHTDLLLDLMGGGVAAR 546
|
570 580
....*....|....*....|.
gi 2543367238 537 KAGLCVDQTFNAWPLEKVSAW 557
Cdd:COG1796 547 RRWWLEKDVNNNTLLLELLLL 567
|
|
| PRK08609 |
PRK08609 |
DNA polymerase/3'-5' exonuclease PolX; |
1-561 |
1.51e-142 |
|
DNA polymerase/3'-5' exonuclease PolX;
Pssm-ID: 236311 [Multi-domain] Cd Length: 570 Bit Score: 423.60 E-value: 1.51e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEiplasLSLAELE---KQEGIGKSIAAKITELSLTGKLAE 77
Cdd:PRK08609 1 MNKKDVIKLLETIATYMELKGENPFKISAFRKAAQALELDE-----RSLSEIDdftKLKGIGKGTAEVIQEYRETGESSV 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 78 LEALLQKTPEGVIELLQIKGIGPKKVKSLWKELEITTKEELLEACHNNTVANLKGFGEKTQDNIIQVLQFVIKQSDKFLY 157
Cdd:PRK08609 76 LQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKRPERLPI 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 158 GDVEATAFELEKKLQsDLNSSVR--LCGEMRRMMETVDRISFIVAATDASKLFANIKTLDYLEEI----PTQSGLYrwyg 231
Cdd:PRK08609 156 AQVLPIAQEIEEYLA-TIDEIIRfsRAGSLRRARETVKDLDFIIATDEPEAVREQLLQLPNIVEViaagDTKVSVE---- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 232 LYKTFKIPVEIYMTDAAHLGSELiKHSSGANhlrltDANGKtFLQIAHA------------------TPFASEEEFYQRV 293
Cdd:PRK08609 231 LEYEYTISVDFRLVEPEAFATTL-HHFTGSK-----DHNVR-MRQLAKErgekiseygveqadtgevKTFESEEAFFAHF 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 294 QLPFIPSELREGYRELKLVEEnrLADLITDAAIQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGL 373
Cdd:PRK08609 304 GLPFIPPEVREDGSEFERYKD--LSNLITLSDIQGDLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDHSQYLKVANGL 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 374 NEETVAKQQLEIDTLNATYNTIKIFKGIESDILNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTT 453
Cdd:PRK08609 382 TEERLLEQAEEIKALNEKYPEIDILSGIEMDILPDGSLDYDDEVLAELDYVIAAIHSSFSQSEEEIMKRLENACRNPYVR 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 454 MLGHPTGRLLLKREGYPIDHKKIIDACAANNVIIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGIC 533
Cdd:PRK08609 462 LIAHPTGRLIGRRDGYDVNIDQLIELAKETNTALELNANPNRLDLSAEHLKKAQEAGVKLAINTDAHHTEMLDDMKYGVA 541
|
570 580
....*....|....*....|....*...
gi 2543367238 534 VARKAGLCVDQTFNAWPLEKVSAWLKTK 561
Cdd:PRK08609 542 TARKGWIQKDRVINTWSREEFKDFIKRN 569
|
|
| PHP_PolX |
cd07436 |
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
326-558 |
9.88e-134 |
|
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: 388.70 E-value: 9.88e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 326 IQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEETVAKQQLEIDTLNATYNTIKIFKGIESDI 405
Cdd:cd07436 5 IRGDLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDHSKSLRVANGLSEERLREQIEEIDALNEKLPGIRILKGIEVDI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 406 LNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLGHPTGRLLLKREGYPIDHKKIIDACAANNV 485
Cdd:cd07436 85 LPDGSLDYPDEVLAELDVVVASVHSGFNQSEEEMTERLLKAIENPHVDILGHPTGRLLGRREGYEVDMERVIEAAAETGT 164
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2543367238 486 IIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVARKAGLCVDQTFNAWPLEKVSAWL 558
Cdd:cd07436 165 ALEINANPDRLDLDDRHARRAKEAGVKIAINTDAHSTDGLDNMRYGVGTARRGWLEKEDVLNTLPLEELLKFL 237
|
|
| HIS2 |
COG1387 |
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
326-557 |
8.45e-104 |
|
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: 312.09 E-value: 8.45e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 326 IQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEETVAKQQLEIDTLNATYNTIKIFKGIESDI 405
Cdd:COG1387 1 MRGDLHTHTTYSDGEGTIEEMVEAAIELGLEYIAITDHSPSLFVANGLSEERLLEYLEEIEELNEKYPDIKILKGIEVDI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 406 LNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLGHPTGRLLLKREGYPIDHKKIIDACAANNV 485
Cdd:COG1387 81 LPDGSLDYPDELLAPLDYVIGSVHSILEEDYEEYTERLLKAIENPLVDILGHPDGRLLGGRPGYEVDIEEVLEAAAENGV 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2543367238 486 IIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVARKAGLCVDQTFNAWPLEKVSAW 557
Cdd:COG1387 161 ALEINTRPLRLDPSDELLKLAKELGVKITIGSDAHSPEDLGDLEYGVALARRAGLTKEDVFNTLRKEELLKL 232
|
|
| PRK07945 |
PRK07945 |
PHP domain-containing protein; |
324-557 |
6.17e-62 |
|
PHP domain-containing protein;
Pssm-ID: 236135 [Multi-domain] Cd Length: 335 Bit Score: 207.14 E-value: 6.17e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 324 AAIQGSFHNHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEETVAKQQLEIDTLNATYNTIKIFKGIES 403
Cdd:PRK07945 94 AALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDHSPRLTVANGLSAERLRKQLDVVAELNEELAPFRILTGIEV 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 404 DILNDGSLDYSDDVLKSFDFIVASIHSNLKMNEEKATQRLITAIENPFTTMLGHPTGRLLL-KREGYP---IDHKKIIDA 479
Cdd:PRK07945 174 DILDDGSLDQEPELLDRLDVVVASVHSKLRMDAAAMTRRMLAAVANPHTDVLGHCTGRLVTgNRGTRPeskFDAEAVFAA 253
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2543367238 480 CAANNVIIEINAHPWRLDMDWRHIGYALDKGCIISINPDAHEKIGLADVHFGICVARKAGLCVDQTFNAWPLEKVSAW 557
Cdd:PRK07945 254 CREHGTAVEINSRPERRDPPTRLLRLALDAGCLFSIDTDAHAPGQLDWLGYGCERAEEAGVPADRIVNTWPADRLLAW 331
|
|
| NT_POLXc |
cd00141 |
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ... |
4-303 |
3.27e-40 |
|
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 148.11 E-value: 3.27e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 4 QEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLASLslAELEKQEGIGKSIAAKITELSLTGKLAELEALLQ 83
Cdd:cd00141 1 QEIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESL--EEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 84 KTPEGVIELLQIKGIGPKKVKSLWkELEITTKEELLEAChnntvanlkgfGEKTQDNIIQVLQFVIKQSDKFLYGDVEAT 163
Cdd:cd00141 79 DVPPGLLLLLRVPGVGPKTARKLY-ELGIRTLEDLRKAA-----------GAKLEQNILIGLEYYEDFQQRIPREEALAI 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 164 AFELEKKLQS-DLNSSVRLCGEMRRMMETVDRISFIVAATDA------SKLFANIKTLDYLEEIpTQSGLYRWYGLYKTF 236
Cdd:cd00141 147 AEIIKEALREvDPVLQVEIAGSYRRGKETVGDIDILVTHPDAtsrgllEKVVDALVELGFVTEV-LSKGDTKASGILKLP 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 237 K----IPVEIYMTDAAHLGSELIkHSSGANH----LR--------------LTDANGKTFLqiahatPFASEEEFYQRVQ 294
Cdd:cd00141 226 GgwkgRRVDLRVVPPEEFGAALL-YFTGSKQfnraLRrlakekglklneygLFDGVDGERL------PGETEEEIFEALG 298
|
....*....
gi 2543367238 295 LPFIPSELR 303
Cdd:cd00141 299 LPYIEPELR 307
|
|
| PHP_HisPPase_Ycdx_like |
cd07437 |
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
331-530 |
6.73e-28 |
|
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. YcdX may be involved in swarming.
Pssm-ID: 213992 [Multi-domain] Cd Length: 233 Bit Score: 111.77 E-value: 6.73e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 331 HNHSTYSDgqH---SLEEMTKACVALGYTYFGISDH------SKSAFYASGLneetvakqqleiDTLNATYNTIKIFKGI 401
Cdd:cd07437 6 HTHTIASG--HaysTIEEMARAAAEKGLKLLGITDHgpampgAPHPWYFGNL------------KVIPREIYGVRILRGV 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 402 ESDILN-DGSLDYSDDVLKSFDFIVASIHSN--LKMNEEKATQRLITAIENPFTTMLGHPTgrlllkREGYPIDHKKIID 478
Cdd:cd07437 72 EANIIDyDGNLDLPERVLKRLDYVIASLHEPcfAPGTKEENTRAYINAMENPYVDIIGHPG------NPRYPIDYEAVVK 145
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2543367238 479 ACAANNVIIEINAH---PWRLDMDWRHIG---YALDKGCIISINPDAH--EKIG--------LADVHF 530
Cdd:cd07437 146 AAKEYNVLLEINNSslsPSRKGSRENCREiaeLCKKYGVPVIVGSDAHiaYDIGnfdealelLEEIGF 213
|
|
| PRK09248 |
PRK09248 |
putative hydrolase; Validated |
329-490 |
3.12e-18 |
|
putative hydrolase; Validated
Pssm-ID: 236429 [Multi-domain] Cd Length: 246 Bit Score: 84.12 E-value: 3.12e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 329 SFHNHSTysdgqhsLEEMTKACVALGYTYFGISDHSKSA--------FYasglNEETVAKqqlEIDTlnatyntIKIFKG 400
Cdd:PRK09248 14 SGHAYST-------LHENAAEAKQKGLKLFAITDHGPDMpgaphywhFG----NLRVLPR---KVDG-------VGILRG 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 401 IESDILN-DGSLDYSDDVLKSFDFIVASIH------SNLKMNeekaTQRLITAIENPFTTMLGHPtgrlllkreG---YP 470
Cdd:PRK09248 73 IEANIKNyDGEIDLPGDMLKKLDIVIAGFHepvfapGDKETN----TQALINAIKNGRVDIIGHP---------GnpkYP 139
|
170 180
....*....|....*....|
gi 2543367238 471 IDHKKIIDACAANNVIIEIN 490
Cdd:PRK09248 140 IDIEAVVKAAKEHNVALEIN 159
|
|
| HHH_8 |
pfam14716 |
Helix-hairpin-helix domain; |
3-69 |
5.90e-17 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434152 [Multi-domain] Cd Length: 67 Bit Score: 75.23 E-value: 5.90e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2543367238 3 NQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLAslSLAELEKQEGIGKSIAAKITEL 69
Cdd:pfam14716 1 NQEIADALEELADLLELKGEDPFRVRAYRRAARALEALPEEIT--SLEELTKLPGIGKKIAAKIEEI 65
|
|
| PHP_HisPPase_Hisj_like |
cd12110 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; ... |
329-521 |
3.86e-13 |
|
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Bacillus subtilis YtvP HisJ has strong histidinol phosphate phosphatase (HisPPase) 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. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce 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 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: 213994 [Multi-domain] Cd Length: 244 Bit Score: 69.13 E-value: 3.86e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 329 SFHNHSTYSD-GQHSLEEMTKACVALGYTYFGISDHSKSAFYASGLNEETVAKQQL-----EIDTLNATY-NTIKIFKGI 401
Cdd:cd12110 2 DYHTHTPRCDhASGTLEEYVEAAIELGFTEIGFSEHAPLPFEFDDYPESRMAEEELedyveEIRRLKEKYaDQIEIKLGL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 402 ESDILNDGSLDYSDDVLK-SFDFIVASIH---------------SNLKMNEEKATQR----LITAIENPFTTMLGHPTgr 461
Cdd:cd12110 82 EVDYFPGYEEELRELLYGyPLDYVIGSVHflggwgfdfpedgiaEYFEGDIDELYERyfdlVEKAIESGLFDIIGHPD-- 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2543367238 462 lLLKREGYPIDHKK--------IIDACAANNVIIEINA----HPWRlDM--DWRHIGYALDKGCIISINPDAHE 521
Cdd:cd12110 160 -LIKKFGKNDEPDEdyeelierILRAIAEAGVALEINTaglrKPVG-EPypSPEFLELAKELGIPVTLGSDAHS 231
|
|
| POLXc |
smart00483 |
DNA polymerase X family; includes vertebrate polymerase beta and terminal ... |
1-220 |
4.27e-13 |
|
DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Pssm-ID: 214688 Cd Length: 334 Bit Score: 70.47 E-value: 4.27e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 1 MTNQEIADVLAQTASLMELHDENSFKVRSIQNAGFQIEKIEIPLASLslAELEKQEGIGKSIAAKITELSLTGKLAELEA 80
Cdd:smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSM--KDLKGLPGIGDKIKKKIEEIIETGKSSKVLE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 81 LLQK-TPEGVIELLQIKGIGPKKVKsLWKELEITTKEELLEACHNN-TVANLKGFgeKTQDNIIQvlqfVIKQSDKFLYG 158
Cdd:smart00483 79 ILNDeVYKSLKLFTNVFGVGPKTAA-KWYRKGIRTLEELKKNKELKlTKQQKAGL--KYYEDILK----KVSRAEAFAVE 151
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2543367238 159 DVEATAFELEKKlqsdlNSSVRLCGEMRRMMETVDRISFIVAAT-DASKLFANIKTLDYLEEI 220
Cdd:smart00483 152 YIVKRAVRKILP-----DAIVTLTGSFRRGKETGHDVDFLITSPhPAKEKELEVLDLLLLEST 209
|
|
| PRK08392 |
PRK08392 |
hypothetical protein; Provisional |
331-539 |
4.06e-12 |
|
hypothetical protein; Provisional
Pssm-ID: 169423 [Multi-domain] Cd Length: 215 Bit Score: 65.58 E-value: 4.06e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 331 HNHSTYSDGQHSLEEMTKACVALGYTYFGISDHS----KSAFYASgLNEETVAKQQLEIDTLnatyntikifKGIESDIL 406
Cdd:PRK08392 4 HTHTVYSDGIGSVRDNIAEAERKGLRLVGISDHIhyftPSKFNAY-INEIRQWGEESEIVVL----------AGIEANIT 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 407 NDGsLDYSDDVLKSFDFIVASIHSNLKMNE-EKATQRLITAIENPFTTMLGHPTGrlLLKREGYPI--DHKKIIDACAAN 483
Cdd:PRK08392 73 PNG-VDITDDFAKKLDYVIASVHEWFGRPEhHEYIELVKLALMDENVDIIGHFGN--SFPYIGYPSeeELKEILDLAEAY 149
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 2543367238 484 NVIIEINAHPWRLDMDWrhIGYALDKGCIISINPDAHEKIGLADVHFGICVARKAG 539
Cdd:PRK08392 150 GKAFEISSRYRVPDLEF--IRECIKRGIKLTFASDAHRPEDVGNVSWSLKVFKKAG 203
|
|
| PHP |
pfam02811 |
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
330-492 |
6.27e-10 |
|
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.
Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 58.32 E-value: 6.27e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 330 FHNHSTYS--DGQHSLEEMTKACVALGYTYFGISDHskSAFYasGLNE--ETVAKQQleidtlnatyntIKIFKGIESDI 405
Cdd:pfam02811 2 LHVHSEYSllDGAARIEELVKRAKELGMPAIAITDH--GNLF--GAVEfyKAAKKAG------------IKPIIGCEVYV 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 406 LNDGSLDYSDDVLKSFDFIVASIH----------SNLKMNEEKATQRLITAIENPFTTML-------GHPtGRLLLKREG 468
Cdd:pfam02811 66 APGSREETEKLLAKYFDLVLLAVHevgyknliklSSRAYLEGFKPRIDKELLEEYFEGLIalsgcvlGHL-DLILLAPGD 144
|
170 180
....*....|....*....|....*...
gi 2543367238 469 YPiDHKKIIDAC----AANNVIIEINAH 492
Cdd:pfam02811 145 YE-EAEELAEEYleifGEDGFYLEINTH 171
|
|
| YciV |
COG0613 |
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
330-363 |
6.06e-06 |
|
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];
Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 47.21 E-value: 6.06e-06
10 20 30
....*....|....*....|....*....|....
gi 2543367238 330 FHNHSTYSDGQHSLEEMTKACVALGYTYFGISDH 363
Cdd:COG0613 6 LHVHTTASDGSLSPEELVARAKAAGLDVLAITDH 39
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
91-146 |
8.14e-06 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 43.25 E-value: 8.14e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 2543367238 91 ELLQIKGIGPKKVKSLWKELeITTKEELLEACHnNTVANLKGFGEKTQDNIIQVLQ 146
Cdd:pfam14520 3 ELLSISGIGPKTALALLSAG-IGTVEDLAEADV-DELAEIPGIGEKTAQRIILELR 56
|
|
| hisJ_fam |
TIGR01856 |
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate ... |
329-429 |
9.68e-06 |
|
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Pssm-ID: 273837 [Multi-domain] Cd Length: 253 Bit Score: 47.39 E-value: 9.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 329 SFHNHSTYS-DGQHSLEEMTKACVALGYTYFGISDHSKSAFYASG-------LNEETVAKQQLEIDTLNATY-NTIKIFK 399
Cdd:TIGR01856 2 DSHSHSPFCaHGTDTLREVVQEAIQLGFEEICFTEHAPRPFYYPEedflkkeMLFLSLPEYFQEINQLKQEYaDKIKILI 81
|
90 100 110
....*....|....*....|....*....|..
gi 2543367238 400 GIESDILnDGSLDYSDDVLKSF--DFIVASIH 429
Cdd:TIGR01856 82 GLEVDYI-PGFEEEIKDFLDSYnlDFVIGSVH 112
|
|
| PHP_HisPPase_AMP |
cd07438 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
330-363 |
1.41e-04 |
|
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: 42.38 E-value: 1.41e-04
10 20 30
....*....|....*....|....*....|....
gi 2543367238 330 FHNHSTYSDGQHSLEEMTKACVALGYTYFGISDH 363
Cdd:cd07438 3 LHTHSTASDGTLSPEELVELAKEAGLKVLAITDH 36
|
|
| PHP_HisPPase |
cd07432 |
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
330-520 |
1.44e-04 |
|
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: 41.84 E-value: 1.44e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 330 FHNHSTYS-DGQHSLEEMTKACVALGYTYFGISDHsksafyASGLNEETVAKQQLEIDtlnatyntIKIFKGIEsdilnd 408
Cdd:cd07432 3 LHIHSVFSpDSDMTPEEIVERAIELGLDGIAITDH------NTIDGAEEALKEAYKDG--------LLVIPGVE------ 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 409 gsldysddvlksFDFIVasihsnlkmneekatqrlitaienpfttmLGHPTGRLllkregYPIDHKKIIDACAANNVIIE 488
Cdd:cd07432 63 ------------VTLVV-----------------------------LAHPDRPS------RYGLSDLILKPLIKNGDAIE 95
|
170 180 190
....*....|....*....|....*....|...
gi 2543367238 489 INAHPWRLDMDWRHIG-YALDKGCIISINPDAH 520
Cdd:cd07432 96 VNNSRLRYGLNNLAAKrYAELGGLPITGGSDAH 128
|
|
| POLIIIAc |
smart00481 |
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
330-364 |
1.90e-04 |
|
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: 39.94 E-value: 1.90e-04
10 20 30
....*....|....*....|....*....|....*..
gi 2543367238 330 FHNHSTYS--DGQHSLEEMTKACVALGYTYFGISDHS 364
Cdd:smart00481 2 LHVHSDYSllDGALSPEELVKRAKELGLKAIAITDHG 38
|
|
| RNase_P_p30 |
pfam01876 |
RNase P subunit p30; This protein is part of the RNase P complex that is involved in tRNA ... |
332-490 |
2.00e-04 |
|
RNase P subunit p30; This protein is part of the RNase P complex that is involved in tRNA maturation.
Pssm-ID: 396447 [Multi-domain] Cd Length: 214 Bit Score: 43.01 E-value: 2.00e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 332 NHSTYSDGQHSLEEMTKACVALGYTYFGISDHSKsafyASGLNEETVAKQQLEIDTLNATYNTIKIFKGIESDILNDGSL 411
Cdd:pfam01876 4 NIPWPPDGSKLPSRTILTLAELGYTGVAINFTVE----AEDGKIPDASEIAERLDELRPELYGLKVYSRVTLVVSDPSKL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2543367238 412 DYSDDVLKSFDFIVAsihsnlKMNEEKATQRlitAIENPFTTMLGHP-TGRLllkreGYPIDHkKIIDACAANNVIIEIN 490
Cdd:pfam01876 80 QLLSKFRQKYDLLAV------RPGDEKANRA---ACENLDVDIISFPyTSRL-----PFGLKH-KLARLAVERGVAFEIN 144
|
|
| PHP |
cd07309 |
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
330-405 |
2.10e-03 |
|
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: 37.41 E-value: 2.10e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2543367238 330 FHNHSTYSDGQH-SLEEMTKACVALGYTYFGISDHSKsafyASGLNEETVAKQQLEIDTlnATYNTIKIFKGIESDI 405
Cdd:cd07309 3 LHTHTVFSDGDHaKLTELVDKAKELGPDALAITDHGN----LRGLAEFNTAGK*NHIKA--AEAAGIKIIIGSEVNL 73
|
|
| DnaE |
COG0587 |
DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
331-363 |
9.81e-03 |
|
DNA polymerase III, alpha subunit [Replication, recombination and repair];
Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 38.90 E-value: 9.81e-03
10 20 30
....*....|....*....|....*....|....*
gi 2543367238 331 HNHSTYS--DGQHSLEEMTKACVALGYTYFGISDH 363
Cdd:COG0587 9 HVHSEYSllDGASRPEELVARAAELGMPALAITDH 43
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|
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