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Conserved domains on  [gi|1490246526|gb|RKZ14106|]
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DNA polymerase III subunit beta [bacterium]

Protein Classification

DnaN family protein( domain architecture ID 11426776)

DnaN family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DnaN COG0592
DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and ...
168-538 2.56e-136

DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and repair];


:

Pssm-ID: 440357 [Multi-domain]  Cd Length: 365  Bit Score: 399.48  E-value: 2.56e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEgVKVAKAGRIAVPASRFVAFTRS 247
Cdd:COG0592     2 KFTISREELLKALQLVSRVVPSRSTLPILSNILLEAEDGGLTLTATDLEISIRTSIP-AEVEEEGSITVPAKKLLDIVRK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:COG0592    81 LPDGEVTLEVDGNKLTIKSGRSRFTLPTLPAEDFPELPEIEEENSFTLPADELKELIEKTAFAASTDETRPYLTGVLLEI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAEGS-ETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:COG0592   161 EGDKLRLVATDGHRLAVREIPLEEEAEEEFSVIIPRKTLNELAKLLDDSdEEVEIALSENQIRFEFGNTTLTSRLIDGKF 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNH 486
Cdd:COG0592   241 PDYERVIPKEFDTKVTVDRKELLEALKRVSLLANEKNRGVRLSFSDGELTLSANNPEQGEAEEELPVEYEGEDLEIGFNA 320
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1490246526 487 NYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLRL 538
Cdd:COG0592   321 KYLLDALKAIDSEEVRLEFTDPNSPALITPVDDEDY-------LYLVMPMRL 365
PHA03307 super family cl33723
transcriptional regulator ICP4; Provisional
3-157 4.52e-04

transcriptional regulator ICP4; Provisional


The actual alignment was detected with superfamily member PHA03307:

Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 4.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526    3 AAKPDKTRRVHNIPGDRSRDKPGYKRCPQPGQSPPAAGRGDEQGLLPRCCANSPRQRLAQSVPEWPSWPAKSTFWPSGIP 82
Cdd:PHA03307   812 ASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKA 891
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1490246526   83 TVPDPTPTSefllntekkksearPGPAPCDRAILGVGLRPLADDAPFGelksraaGLRLQPGRPCATTLPLDSAR 157
Cdd:PHA03307   892 AAAAPPAGA--------------PAPRPRPAPRVKLGPMPPGGPDPRG-------GFRRVPPGDLHTPAPSAAAL 945
 
Name Accession Description Interval E-value
DnaN COG0592
DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and ...
168-538 2.56e-136

DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and repair];


Pssm-ID: 440357 [Multi-domain]  Cd Length: 365  Bit Score: 399.48  E-value: 2.56e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEgVKVAKAGRIAVPASRFVAFTRS 247
Cdd:COG0592     2 KFTISREELLKALQLVSRVVPSRSTLPILSNILLEAEDGGLTLTATDLEISIRTSIP-AEVEEEGSITVPAKKLLDIVRK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:COG0592    81 LPDGEVTLEVDGNKLTIKSGRSRFTLPTLPAEDFPELPEIEEENSFTLPADELKELIEKTAFAASTDETRPYLTGVLLEI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAEGS-ETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:COG0592   161 EGDKLRLVATDGHRLAVREIPLEEEAEEEFSVIIPRKTLNELAKLLDDSdEEVEIALSENQIRFEFGNTTLTSRLIDGKF 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNH 486
Cdd:COG0592   241 PDYERVIPKEFDTKVTVDRKELLEALKRVSLLANEKNRGVRLSFSDGELTLSANNPEQGEAEEELPVEYEGEDLEIGFNA 320
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1490246526 487 NYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLRL 538
Cdd:COG0592   321 KYLLDALKAIDSEEVRLEFTDPNSPALITPVDDEDY-------LYLVMPMRL 365
PRK05643 PRK05643
DNA polymerase III subunit beta; Validated
168-538 6.34e-115

DNA polymerase III subunit beta; Validated


Pssm-ID: 235541 [Multi-domain]  Cd Length: 367  Bit Score: 344.81  E-value: 6.34e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:PRK05643    2 KFTISRNALLKALQLVQGAVERRNTIPILSNVLIEAEGGKLSLTATDLEISIETTIPAEVEVEEGSITVPAKKLLDIVRK 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LgPDKVDVK---ATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVL 324
Cdd:PRK05643   82 L-PDGAEITlelEENNRLTIKSGKSRFNLPTLPAEDFPNLPEIEEEVSFTLPQKTLKRLIEKTQFAMSTQETRYYLNGVL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 325 WELSPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAEGSETVKVFLGEHQLSFEIGETTVHTRLVDG 404
Cdd:PRK05643  161 LEIEGNELRAVATDGHRLAVRKLELEEGSLGDFSVIIPRKTLLELQKLLDDEEPVEIFISDNQILFEFGNTIFTSKLIDG 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 405 MFPAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGF 484
Cdd:PRK05643  241 KFPDYRRVIPKEFDKKLTVDRKELLQALERASILSNEKSRGVKLSLSEGQLKISANNPEQGEAEEELEVEYSGEELEIGF 320
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1490246526 485 NHNYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLRL 538
Cdd:PRK05643  321 NVKYLLDVLKALDSEEVRLSFNDANSPFLIRPPDDDSF-------LYVIMPMRL 367
beta_clamp cd00140
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
168-537 3.32e-114

Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.


Pssm-ID: 238082 [Multi-domain]  Cd Length: 365  Bit Score: 342.95  E-value: 3.32e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:cd00140     2 KFTINREALLEALQKVSRAIESRNTIPILSNVLIEASDGGLTLTATDLEISIKTTIPAEEVEEEGSVTVPAKKLLDIVRK 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:cd00140    82 LPDEEVTLETEENRLTIKSGKSRFSLNTLPAEEFPELPEIENGSSFTIPASELKELIKKTAFAVSTDETRPILNGVLLEI 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLR-LAEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:cd00140   162 EDNKLRAVATDGHRLALREIELESGAEEDFNVIVPRKTLNELLKlLEDDDEEVEISISENQILFKLGNTTFTSRLIEGEF 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNH 486
Cdd:cd00140   242 PDYERVIPKEFEKSLTVDREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSANNPEIGEAEEELEVEYEGEELEIGFNP 321
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1490246526 487 NYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLR 537
Cdd:cd00140   322 KYLLDALKAIDSEEVRLSFTDSNSPVLITPEDDDNF-------LYLIMPVR 365
POL3Bc smart00480
DNA polymerase III beta subunit;
183-534 1.32e-89

DNA polymerase III beta subunit;


Pssm-ID: 214686 [Multi-domain]  Cd Length: 345  Bit Score: 279.09  E-value: 1.32e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  183 VASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRSLGPDKVDVKATAEKV 262
Cdd:smart00480   1 VSRVISNRNTIPILSNILLEAKDDGLTLTATDLEISIKSSISAEVEDEEGSVTVPAKKFLDIVRKLPDKEITLSVEEDKL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  263 TVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWELSPGSFTMVATDGHRL 342
Cdd:smart00480  81 VITSGKSRFNLPTLDAEEFPELPFIEEGVTFELPTKLLKEGIEKTAFAVSTDETRPVLNGVNLEISNGELRLVATDGHRL 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  343 ArvRRAVNLPVKGERK-IIASSAGLQQVLRL-AEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMFPAYEQVIPKDNSQR 420
Cdd:smart00480 161 A--VREIKLESEEDDFsVIIPRKSLLELNKLlTDNEELVEIFISSNQILFETGNVIFTSRLIDGEFPDYKRVIPKEFETK 238
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  421 AVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNHNYVEDVLKHMATEN 500
Cdd:smart00480 239 LTVNRKELKEALKRVALLANEKNRSVKLTLEEGQLKLTANSPEVGEAEEEVDVDYEGEDLEIAFNPKYLLDALKALKSEE 318
                          330       340       350
                   ....*....|....*....|....*....|....
gi 1490246526  501 VVIALERSDAAAIFLPgedasagIDESDDLCLLM 534
Cdd:smart00480 319 IELKFTDSSSPFLISP-------PDDEKLKYLIM 345
dnan TIGR00663
DNA polymerase III, beta subunit; All proteins in this family for which functions are known ...
168-538 4.42e-77

DNA polymerase III, beta subunit; All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). 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: 273204 [Multi-domain]  Cd Length: 367  Bit Score: 247.25  E-value: 4.42e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:TIGR00663   2 KFTIQKDDLLKELSKVQRVLSNRPTIPILSNILLEVSDDKLTITGTDLDISIESQIPIVTIEQPGSVTINAKKFLDIVRA 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:TIGR00663  82 LPDSKIELEVKNDKLAITSGKSRFKLPTLDADEYPNLPQIEEGVSIEIPSDVLKEAINQTAFAASTDETRPVLNGVNIKQ 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRL-AEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:TIGR00663 162 EGKELLLVATDGHRLAVRKAKSEISDEEDFSVIIPGKALNELLKLlSDNGELVLISLVDTQVYFELKNYKFTSRLIDGNY 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELE-QDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFN 485
Cdd:TIGR00663 242 PDYKSVIPKEQKTSITVNRKELKEAIKRVSLLADEKRNLVLTLSEkGEKLKESSDTQEIGKAEEEIEADYDGEDLVIAFN 321
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1490246526 486 HNYVEDVLKHMATENVVIALERSDAAAIFLPgedasagidESDDLC--LLMPLRL 538
Cdd:TIGR00663 322 PKYLLDALKALKSEEIRIQFNDPSKPFLIRP---------ENDETIvyLIMPVRL 367
DNA_pol3_beta_2 pfam02767
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase ...
295-407 5.14e-21

DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.


Pssm-ID: 397061 [Multi-domain]  Cd Length: 115  Bit Score: 88.52  E-value: 5.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 295 VDSAVLCDMIRSTIYAISRDETRPALQGVLWELSPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAE 374
Cdd:pfam02767   1 LPQKVLKRLIEQTAFAASRDETRPILTGVNLEIEGDELRLVATDGHRLAVRKLEWPVENPDEANVIVPRKTLLELAKLLT 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1490246526 375 GS-ETVKVFLGEHQLSFEIGETTVHTRLVDGMFP 407
Cdd:pfam02767  81 DNgEMVDLQIGEGQIRFEFGNVRFTSRLLDGNFP 114
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
3-157 4.52e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 4.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526    3 AAKPDKTRRVHNIPGDRSRDKPGYKRCPQPGQSPPAAGRGDEQGLLPRCCANSPRQRLAQSVPEWPSWPAKSTFWPSGIP 82
Cdd:PHA03307   812 ASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKA 891
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1490246526   83 TVPDPTPTSefllntekkksearPGPAPCDRAILGVGLRPLADDAPFGelksraaGLRLQPGRPCATTLPLDSAR 157
Cdd:PHA03307   892 AAAAPPAGA--------------PAPRPRPAPRVKLGPMPPGGPDPRG-------GFRRVPPGDLHTPAPSAAAL 945
 
Name Accession Description Interval E-value
DnaN COG0592
DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and ...
168-538 2.56e-136

DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and repair];


Pssm-ID: 440357 [Multi-domain]  Cd Length: 365  Bit Score: 399.48  E-value: 2.56e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEgVKVAKAGRIAVPASRFVAFTRS 247
Cdd:COG0592     2 KFTISREELLKALQLVSRVVPSRSTLPILSNILLEAEDGGLTLTATDLEISIRTSIP-AEVEEEGSITVPAKKLLDIVRK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:COG0592    81 LPDGEVTLEVDGNKLTIKSGRSRFTLPTLPAEDFPELPEIEEENSFTLPADELKELIEKTAFAASTDETRPYLTGVLLEI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAEGS-ETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:COG0592   161 EGDKLRLVATDGHRLAVREIPLEEEAEEEFSVIIPRKTLNELAKLLDDSdEEVEIALSENQIRFEFGNTTLTSRLIDGKF 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNH 486
Cdd:COG0592   241 PDYERVIPKEFDTKVTVDRKELLEALKRVSLLANEKNRGVRLSFSDGELTLSANNPEQGEAEEELPVEYEGEDLEIGFNA 320
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1490246526 487 NYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLRL 538
Cdd:COG0592   321 KYLLDALKAIDSEEVRLEFTDPNSPALITPVDDEDY-------LYLVMPMRL 365
PRK05643 PRK05643
DNA polymerase III subunit beta; Validated
168-538 6.34e-115

DNA polymerase III subunit beta; Validated


Pssm-ID: 235541 [Multi-domain]  Cd Length: 367  Bit Score: 344.81  E-value: 6.34e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:PRK05643    2 KFTISRNALLKALQLVQGAVERRNTIPILSNVLIEAEGGKLSLTATDLEISIETTIPAEVEVEEGSITVPAKKLLDIVRK 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LgPDKVDVK---ATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVL 324
Cdd:PRK05643   82 L-PDGAEITlelEENNRLTIKSGKSRFNLPTLPAEDFPNLPEIEEEVSFTLPQKTLKRLIEKTQFAMSTQETRYYLNGVL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 325 WELSPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAEGSETVKVFLGEHQLSFEIGETTVHTRLVDG 404
Cdd:PRK05643  161 LEIEGNELRAVATDGHRLAVRKLELEEGSLGDFSVIIPRKTLLELQKLLDDEEPVEIFISDNQILFEFGNTIFTSKLIDG 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 405 MFPAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGF 484
Cdd:PRK05643  241 KFPDYRRVIPKEFDKKLTVDRKELLQALERASILSNEKSRGVKLSLSEGQLKISANNPEQGEAEEELEVEYSGEELEIGF 320
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1490246526 485 NHNYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLRL 538
Cdd:PRK05643  321 NVKYLLDVLKALDSEEVRLSFNDANSPFLIRPPDDDSF-------LYVIMPMRL 367
beta_clamp cd00140
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
168-537 3.32e-114

Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.


Pssm-ID: 238082 [Multi-domain]  Cd Length: 365  Bit Score: 342.95  E-value: 3.32e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:cd00140     2 KFTINREALLEALQKVSRAIESRNTIPILSNVLIEASDGGLTLTATDLEISIKTTIPAEEVEEEGSVTVPAKKLLDIVRK 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:cd00140    82 LPDEEVTLETEENRLTIKSGKSRFSLNTLPAEEFPELPEIENGSSFTIPASELKELIKKTAFAVSTDETRPILNGVLLEI 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLR-LAEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:cd00140   162 EDNKLRAVATDGHRLALREIELESGAEEDFNVIVPRKTLNELLKlLEDDDEEVEISISENQILFKLGNTTFTSRLIEGEF 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNH 486
Cdd:cd00140   242 PDYERVIPKEFEKSLTVDREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSANNPEIGEAEEELEVEYEGEELEIGFNP 321
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1490246526 487 NYVEDVLKHMATENVVIALERSDAAAIFLPGEDASAgidesddLCLLMPLR 537
Cdd:cd00140   322 KYLLDALKAIDSEEVRLSFTDSNSPVLITPEDDDNF-------LYLIMPVR 365
POL3Bc smart00480
DNA polymerase III beta subunit;
183-534 1.32e-89

DNA polymerase III beta subunit;


Pssm-ID: 214686 [Multi-domain]  Cd Length: 345  Bit Score: 279.09  E-value: 1.32e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  183 VASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRSLGPDKVDVKATAEKV 262
Cdd:smart00480   1 VSRVISNRNTIPILSNILLEAKDDGLTLTATDLEISIKSSISAEVEDEEGSVTVPAKKFLDIVRKLPDKEITLSVEEDKL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  263 TVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWELSPGSFTMVATDGHRL 342
Cdd:smart00480  81 VITSGKSRFNLPTLDAEEFPELPFIEEGVTFELPTKLLKEGIEKTAFAVSTDETRPVLNGVNLEISNGELRLVATDGHRL 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  343 ArvRRAVNLPVKGERK-IIASSAGLQQVLRL-AEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMFPAYEQVIPKDNSQR 420
Cdd:smart00480 161 A--VREIKLESEEDDFsVIIPRKSLLELNKLlTDNEELVEIFISSNQILFETGNVIFTSRLIDGEFPDYKRVIPKEFETK 238
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526  421 AVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNHNYVEDVLKHMATEN 500
Cdd:smart00480 239 LTVNRKELKEALKRVALLANEKNRSVKLTLEEGQLKLTANSPEVGEAEEEVDVDYEGEDLEIAFNPKYLLDALKALKSEE 318
                          330       340       350
                   ....*....|....*....|....*....|....
gi 1490246526  501 VVIALERSDAAAIFLPgedasagIDESDDLCLLM 534
Cdd:smart00480 319 IELKFTDSSSPFLISP-------PDDEKLKYLIM 345
dnan TIGR00663
DNA polymerase III, beta subunit; All proteins in this family for which functions are known ...
168-538 4.42e-77

DNA polymerase III, beta subunit; All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). 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: 273204 [Multi-domain]  Cd Length: 367  Bit Score: 247.25  E-value: 4.42e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:TIGR00663   2 KFTIQKDDLLKELSKVQRVLSNRPTIPILSNILLEVSDDKLTITGTDLDISIESQIPIVTIEQPGSVTINAKKFLDIVRA 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGVLWEL 327
Cdd:TIGR00663  82 LPDSKIELEVKNDKLAITSGKSRFKLPTLDADEYPNLPQIEEGVSIEIPSDVLKEAINQTAFAASTDETRPVLNGVNIKQ 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 328 SPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRL-AEGSETVKVFLGEHQLSFEIGETTVHTRLVDGMF 406
Cdd:TIGR00663 162 EGKELLLVATDGHRLAVRKAKSEISDEEDFSVIIPGKALNELLKLlSDNGELVLISLVDTQVYFELKNYKFTSRLIDGNY 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 407 PAYEQVIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELE-QDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFN 485
Cdd:TIGR00663 242 PDYKSVIPKEQKTSITVNRKELKEAIKRVSLLADEKRNLVLTLSEkGEKLKESSDTQEIGKAEEEIEADYDGEDLVIAFN 321
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1490246526 486 HNYVEDVLKHMATENVVIALERSDAAAIFLPgedasagidESDDLC--LLMPLRL 538
Cdd:TIGR00663 322 PKYLLDALKALKSEEIRIQFNDPSKPFLIRP---------ENDETIvyLIMPVRL 367
DNA_pol3_beta_2 pfam02767
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase ...
295-407 5.14e-21

DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.


Pssm-ID: 397061 [Multi-domain]  Cd Length: 115  Bit Score: 88.52  E-value: 5.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 295 VDSAVLCDMIRSTIYAISRDETRPALQGVLWELSPGSFTMVATDGHRLARVRRAVNLPVKGERKIIASSAGLQQVLRLAE 374
Cdd:pfam02767   1 LPQKVLKRLIEQTAFAASRDETRPILTGVNLEIEGDELRLVATDGHRLAVRKLEWPVENPDEANVIVPRKTLLELAKLLT 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1490246526 375 GS-ETVKVFLGEHQLSFEIGETTVHTRLVDGMFP 407
Cdd:pfam02767  81 DNgEMVDLQIGEGQIRFEFGNVRFTSRLLDGNFP 114
DNA_pol3_beta pfam00712
DNA polymerase III beta subunit, N-terminal domain; A dimer of the beta subunit of DNA ...
168-285 5.42e-21

DNA polymerase III beta subunit, N-terminal domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.


Pssm-ID: 395580 [Multi-domain]  Cd Length: 121  Bit Score: 88.51  E-value: 5.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 168 KIQVQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATDLDVSVVTRIEGVKVAKAGRIAVPASRFVAFTRS 247
Cdd:pfam00712   2 KFTIEREVLLKALQKVAGVIPNRPTIPILSGILLEVKDDQLSITGTDLEVSIESTVAAEIESEPGSVLLPARLFYDIVRA 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1490246526 248 LGPDK-VDVKATAEKVTVS-AGKARFEESLMAADEFPALP 285
Cdd:pfam00712  82 LPNDKdVTISFNEDRLLVIgSGRSRFSLPTLPAEDYPNLP 121
DNA_pol3_beta_3 pfam02768
DNA polymerase III beta subunit, C-terminal domain; A dimer of the beta subunit of DNA ...
412-522 1.03e-17

DNA polymerase III beta subunit, C-terminal domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.


Pssm-ID: 426968 [Multi-domain]  Cd Length: 118  Bit Score: 78.88  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 412 VIPKDNSQRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELKVEYGGEPLVIGFNHNYVED 491
Cdd:pfam02768   1 LIPKEFKKILTVDNKELLEALARVALLADEKNRVVRLSFSEGQLKLSANNPEVGEAEEIVDVNYIGEPLEIAFNVRYLLD 80
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1490246526 492 VLKHMATENVVIALERSDAAAIFLPGEDASA 522
Cdd:pfam02768  81 ALKALETEQIELQFTDSTSPALLSPPGDDDV 111
PRK14946 PRK14946
DNA polymerase III subunit beta; Provisional
167-493 2.06e-12

DNA polymerase III subunit beta; Provisional


Pssm-ID: 184910 [Multi-domain]  Cd Length: 366  Bit Score: 68.73  E-value: 2.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 167 VKIQVQQSELARALTAVASVVSNKTTLPiLSTILFDADGDAMVLAATDLDVSV---VTRIEGVKVAKAGRIAVPASRFVA 243
Cdd:PRK14946    1 MKFTIEKEIIEKQIERMQSAILNNGNSP-LSGFFLKLTRSGLFIISTNSELSYksfINKKDLIEINDVGSCLIDGVFLKN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 244 FTRSLgPDKVDVKATAEKVTVSAGKARFEESLMAADEFPALPKVSDDEAFTVDSAVLCDMIRSTIYAISRDETRPALQGV 323
Cdd:PRK14946   80 IIKKS-DNQISFELIGSELKVFWEDAQFSKTLRDSSFFPEINFEQKGIKLTVNAKNLKRAIKNTAFATTNNPNQPILSAI 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 324 LWELSPGSFTMVATDGHRLARVRRAVNLPVkgERKIIASSAGLQQVLrLAEGSETVKVFLGEHQLSFEIGETTVHTRLVD 403
Cdd:PRK14946  159 NLKSEDNFLHFSATDTIRFASEKIEISNPS--RIDISISAKNLKDFI-PPELDKDIELFIESSKISYTYDNLTIQSRIFT 235
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 404 GMFPAYEQVIPKDNS--QRAVCDRQTLADRIRRVKISADRVTNQVRFELEQDSLGLSASGTEGSHAEDELK--VEYGGEP 479
Cdd:PRK14946  236 IEYKDISNVLPKDSEilYSLTIEKKEILDLIDKATIITPGKDNVINFSLSKNELKGYISQYESGQSNVKTKnvLRFSGEL 315
                         330
                  ....*....|....
gi 1490246526 480 LVIGFNHNYVEDVL 493
Cdd:PRK14946  316 AQVNVNYKYLKDAI 329
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
3-157 4.52e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 4.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526    3 AAKPDKTRRVHNIPGDRSRDKPGYKRCPQPGQSPPAAGRGDEQGLLPRCCANSPRQRLAQSVPEWPSWPAKSTFWPSGIP 82
Cdd:PHA03307   812 ASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKA 891
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1490246526   83 TVPDPTPTSefllntekkksearPGPAPCDRAILGVGLRPLADDAPFGelksraaGLRLQPGRPCATTLPLDSAR 157
Cdd:PHA03307   892 AAAAPPAGA--------------PAPRPRPAPRVKLGPMPPGGPDPRG-------GFRRVPPGDLHTPAPSAAAL 945
DNA_pol3_beta_2 pfam02767
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase ...
171-282 9.08e-04

DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.


Pssm-ID: 397061 [Multi-domain]  Cd Length: 115  Bit Score: 39.21  E-value: 9.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490246526 171 VQQSELARALTAVASVVSNKTTLPILSTILFDADGDAMVLAATD---LDVsVVTRIEGVKVAKAGRIaVPAsRFVAFTRS 247
Cdd:pfam02767   1 LPQKVLKRLIEQTAFAASRDETRPILTGVNLEIEGDELRLVATDghrLAV-RKLEWPVENPDEANVI-VPR-KTLLELAK 77
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1490246526 248 LGPDK---VDVKATAEKVTVSAGKARFEESLMAAdEFP 282
Cdd:pfam02767  78 LLTDNgemVDLQIGEGQIRFEFGNVRFTSRLLDG-NFP 114
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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