>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.

Probab=97.90 E-value=0.00011 Score=54.36 Aligned_cols=144 Identities=23% Similarity=0.317 Sum_probs=90.9 Q ss_pred HHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC------------------------EEEEECCCCC-----CHH-- Q ss_conf 984244467359986056565027999999770882------------------------4998618888-----888-- Q gi|254780270|r 358 QMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQ------------------------YVRMSLGGVY-----DEA-- 406 (820) Q Consensus 358 ~~~~~~~~g~il~l~gppgvGKts~~~sia~al~r~------------------------f~~islgg~~-----d~~-- 406 (820) T Consensus 6 ~~~~~~r~~HA~LF~G~~G~Gk~~~A~~~A~~l~C~~~~~~~~Cg~C~~C~~~~~G~HPD~~~~~P~~~~~~~~~de~~~ 85 (216) T TIGR00678 6 RALEKGRLAHAYLFTGPEGVGKELLALALAKALLCEPRGGGEPCGECHSCRLIEAGNHPDLHRLEPEGQSKSLTADEAAE 85 (216) T ss_pred HHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHH T ss_conf 89860678861254448887489999999999807785778888858889998707998237874234777777645897 Q ss_pred -HHCC----CCCCCCCCCCH-HHHHHHHHCC--CCCEEEEEECHHHHHHHCCCCHHHHHHHHCCCCCCCCEEEEECCCCC Q ss_conf -8356----32001456712-8999998327--88739999331554231177115566554060016813320103523 Q gi|254780270|r 407 -DIRG----HRRTYIGSMPG-RIIQSLKRAK--RSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEY 478 (820) Q Consensus 407 -~i~g----h~~ty~ga~pg-~ii~~l~~~~--~~npv~~ldeidk~~~~~~gdp~~allevldp~qn~~f~d~y~~~~~ 478 (820) T Consensus 86 ~~~-g~a~~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~----AANALLKtL-------------EEPp 147 (216) T TIGR00678 86 GEE-GSAKRRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEA----AANALLKTL-------------EEPP 147 (216) T ss_pred HHC-CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHH----HHHHHHHHE-------------ECCC T ss_conf 625-6421136787872789999999860642147517997673232589----898651010-------------1279 Q ss_pred CCCCEEEEEECCCC--C-CCHHHCCCEEEEEECCCCHHHHHHHHHH Q ss_conf 64427999934865--5-4413117247998258786899989998 Q gi|254780270|r 479 DLSDVMFIMTANTL--N-IPLPLMDRMEIIRIAGYTEEEKLQIAKN 521 (820) Q Consensus 479 dls~v~fi~tan~~--~-i~~~l~drme~i~~~~y~~~ek~~i~~~ 521 (820) T Consensus 148 --~~t~fiL~~~~~DP~~lLpTI~SRCq~~~f~~l~~~~~~~~L~~ 191 (216) T TIGR00678 148 --PNTLFILITHSPDPERLLPTIRSRCQVLPFPPLSEEALLQWLIE 191 (216) T ss_pred --CCEEEEEECCCCCHHHHCCCCCCCEEEEEECCCCHHHHHHHHHH T ss_conf --87079885088884332211103201586259988999999997

HHsearch alignment for GI: 254780270 and conserved domain: TIGR00678