gnl|CDD|5373, cd00140, POL3Bc, DNA polymerase III beta subunit; the processivity factor of the holoenzyme forms a ring shaped dimer that encircles dsDNA (sliding clamp)

             CD-Length = 364 residues, 100.0% aligned
             Score =  417 bits (1074), Expect = 1e-117

Query:  1    MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE  60
Sbjct:  1    MKFTIEREALLKALSKVARVISSRPTIPILSNVLLEAEEDGLTLTGTDLEISIESSIAAE  60

Query:  61   DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVE  120
Sbjct:  61   IIEEEGSVLVPARKLSDIVRALPDK-DVTLSFEEDKLLITTGKSRFSLPTLDAEDYPHLP  119

Query:  121  EGPGSLNFSIAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMC  180
Sbjct:  120  EIEEGSELTLPQKLLKEGIEQTAFAASTDETRPVLNGVNLETSGDELRLVATDGHRLAVR  179

Query:  181  SLDAQIPSQDRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDG  240
Sbjct:  180  ELKLEIPDED-FNVIVPRKTLNELKKLLTDGEELVSIFISSNQILFELGNFKFTSRLIEG  238

Query:  241  KFPDYERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQ  300
Sbjct:  239  EFPDYKRLIPTEFETKVTIDRKELKKALKRVALLANEKNRGVRLTVSEGQLKLTSNAPEV  298

Query:  301  EEAEEEVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAY  360
Sbjct:  299  GEAEEEVDVDYEGEDLEIAFNPKYLLDALKALKSEEIELKFTDSNKPFLLSPNEDEDLKY  358

Query:  361  VVMPMR  366
Sbjct:  359  LIMPMR  364

gnl|CDD|3918, smart00480, POL3Bc, DNA polymerase III beta subunit;

             CD-Length = 346 residues, 100.0% aligned
             Score =  385 bits (991), Expect = 4e-108

Query:  17   VAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLEDAAEPGEITVPARKLM  76
Sbjct:  1    VSRVISSRPTIPILSNILLEAKDDGLTLTATDLEISIKSSIAAEVESEEGSVTVPAKKFL  60

Query:  77   DICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVEEGPGSLNFSIAQSKLR  136
Sbjct:  61   DIVRKLPDA-EITLSFKEDKLLITSGKSRFNLPTLPAEEFPELPEIEEGVTFELPTSLLK  119

Query:  137  RLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMCSLDAQIPSQDRHQVIV  196
Sbjct:  120  EGIEKTAFAVSTDETRYVLNGVNLEISNDELRLVATDGHRLAVREIKLEKEEDDSFSVII  179

Query:  197  PRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDGKFPDYERVLPRGGDKL  256
Sbjct:  180  PRKSLNELNKLLTDNEELVNIFISSNQILFELGNVIFTSRLIDGEFPDYKRVIPKEFETK  239

Query:  257  VVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQEEAEEEVQVEYNGGNL  316
Sbjct:  240  LTVNRKELKEALKRVALLADEKNRSVKLTLSEGQLKLTANSPEVGEAEEEIDVDYEGEDL  299

Query:  317  EIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAYVVM  363
Sbjct:  300  EIAFNPKYLLDALKALKSEEIELKFTDSSSPFLISPPDDEDLKYLIM  346

gnl|CDD|3918, smart00480, POL3Bc, DNA polymerase III beta subunit;

             CD-Length = 346 residues, only  41.9% aligned
             Score = 43.6 bits (103), Expect = 4e-05

Query:  3    FTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTD---LEVELVGRVVL  59
Sbjct:  111  FELPTSLLKEGIEKTAFAVSTDETRYVLNGVNLEISNDELRLVATDGHRLAVREIKLEKE  170

Query:  60   EDAAEPGEITVPARKLMDICKSLP-NDVLIDIRVEEQKLLVKAGRSRFTLSTLPAN--DF  116
Sbjct:  171  ED--DSFSVIIPRKSLNELNKLLTDNEELVNIFISSNQILFELGNVIFTSRLIDGEFPDY  228

Query:  117  PTVEEGPGSLNFSIAQSKLRRLIDRTS  143
Sbjct:  229  KRVIPKEFETKLTVNRKELKEALKRVA  255

gnl|CDD|25954, pfam02767, DNA_pol3_beta_2, 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.

             CD-Length = 116 residues,  99.1% aligned
             Score =  147 bits (372), Expect = 2e-36

Query:  130  IAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMCSLDAQIPSQ  189
Sbjct:  2    LPSKVLKELIEQTAFAMGRDETRPVLTGVNLETEGNELRLVATDGHRLAVRKLELSVENN  61

Query:  190  DRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDGKFPD  244
Sbjct:  62   DIFSVIVPRKTLLELAKLLTDNGEMVKIQIGEGQIRFEFGNVIFTSRLIDGKYPD  116

gnl|CDD|25954, pfam02767, DNA_pol3_beta_2, 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.

             CD-Length = 116 residues,  99.1% aligned
             Score = 37.1 bits (86), Expect = 0.003

Query:  4    TIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTD-LEVELVGRVVLEDA  62
Sbjct:  1    QLPSKVLKELIEQTAFAMGRDETRPVLTGVNLETEGNELRLVATDGHRLAVRKLELSVEN  60

Query:  63   AEPGEITVPARKLMDICKSLP-NDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFP  117
Sbjct:  61   NDIFSVIVPRKTLLELAKLLTDNGEMVKIQIGEGQIRFEFGNVIFTSRLIDGK-YP  115

gnl|CDD|1268, pfam00712, DNA_pol3_beta, 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.

             CD-Length = 119 residues, 100.0% aligned
             Score =  141 bits (357), Expect = 1e-34

Query:  1    MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE  60
Sbjct:  1    MKFTIERDVLLKALSKVARVVSNRPTIPILSGILLNVKDDRLSLTGTDLEISIESSIAAE  60

Query:  61   DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVE  120
Sbjct:  61   ISSEPGSVLIPARLLLDIVRALPDK-DVKLSVNEDRLLIISGNSRFSLPTLPAEDYPNLP  119

gnl|CDD|4799, pfam02768, DNA_pol3_beta_3, 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.

             CD-Length = 121 residues, 100.0% aligned
             Score =  139 bits (353), Expect = 4e-34

Query:  246  ERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQEEAEE  305
Sbjct:  1    KRVIPKEFKTKITVDNKELKKALARVALLADERNRGVRLSFEEGQLKLTAGNPEIGRAEE  60

Query:  306  EVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAYVVMPM  365
Sbjct:  61   EVDVDYIGEPLEIAFNPSYLLDALKALKSEEIELQFTDSTKPALISPPGDDSLKYVIMPM  120

Query:  366  R  366
Sbjct:  121  R  121

gnl|CDD|10462, COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]

             CD-Length = 364 residues, 100.0% aligned
             Score =  349 bits (897), Expect = 3e-97

Query:  1    MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE  60
Sbjct:  1    MKFSIERENLLKALQLVSRIVESRPTIPILSNVLIEAKENGLTLTGTDLEISLEARIPAE  60

Query:  61   DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLL-VKAGRSRFTLSTLPANDFPTV  119
Sbjct:  61   VEAE-GEVAVPAKKLLDIISKLPDEAVFLVTEDGISLLAVDSGKSAFVLLTLPAEDFPEY  119

Query:  120  EEGPGSLNFSIAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAM  179
Sbjct:  120  PVDEEEVEFGLPTELLKKIIKRTKFADSLLETRYELNGVLLEIEGTKLRLVATDGHRLAV  179

Query:  180  CSLDAQIPSQDRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVD  239
Sbjct:  180  EELEIPELEED-ASVIIPAKTLKELIKLLK--DADVEIFLVSDQIRFKAGETILFSKLIE  236

Query:  240  GKFPDYERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPE  299
Sbjct:  237  GEFPDYERVIPKEFEKELTLDRLELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDE  296

Query:  300  QEEAEEEVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSA  359
Sbjct:  297  PGKAEEEIDVGYTGEELKIGFNLAYLLDVLKALDSEEVQFGFNDSSSPFLIRPEENDDFK  356

Query:  360  YVVMPMRL  367
Sbjct:  357  YLIMPMRL  364