HHsearch alignment for GI: 254780163 and conserved domain: TIGR00678

>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=97.60  E-value=0.00021  Score=50.85  Aligned_cols=143  Identities=25%  Similarity=0.365  Sum_probs=88.2

Q ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHHC-CCCEEEEEHHHHHC-CCCCCH-HCCCCCHHCCCC----CCC----------
Q ss_conf             7874068861432003889999987304-77337720688612-465301-104780002564----443----------
Q gi|254780163|r  504 NKPIGCYVFSGPTGVGKTEISKQLAFAL-GVQLLRFDMSEYME-RHAVSR-LIGAPPGYVGFG----QGG----------  566 (798)
Q Consensus       504 ~rP~g~flf~GptGvGKTelak~la~~~-~~~lir~dmsey~e-~~~vs~-LiGappGYvG~~----egg----------  566 (798)
T Consensus        11 ~r~~HA~LF~G~~G~Gk~~~A~~~A~~l~C~~---~~~~~~Cg~C~~C~~~~~G~HPD~~~~~P~~~~~~~~~de~~~~~   87 (216)
T TIGR00678        11 GRLAHAYLFTGPEGVGKELLALALAKALLCEP---RGGGEPCGECHSCRLIEAGNHPDLHRLEPEGQSKSLTADEAAEGE   87 (216)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC---CCCCCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHH
T ss_conf             67886125444888748999999999980778---577888885888999870799823787423477777764589762


Q ss_pred             -----------CCCHHHHH-----------CCCEEEEECCHHHCCHHHHHHHHHHHHHHHCCCCCCCEECCCCEEEEEEC
Q ss_conf             -----------10035551-----------58517774044550289999999987775021779977612542999942
Q gi|254780163|r  567 -----------ILADSVDQ-----------NPYSVVLLDEIEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILIMTT  624 (798)
Q Consensus       567 -----------~Lte~vr~-----------~P~sVvl~DEiEKAh~~v~~~llqild~G~ltd~~Gr~vdf~n~iii~Ts  624 (798)
T Consensus        88 ~g~a~~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~AANALLKtLEEPp-----------~~t~fiL~~  156 (216)
T TIGR00678        88 EGSAKRRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEAAANALLKTLEEPP-----------PNTLFILIT  156 (216)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHHHHEECCC-----------CCEEEEEEC
T ss_conf             564211367878727899999998606421475179976732325898986510101279-----------870798850


Q ss_pred             CCCHHHHHHCCCCCCCCCCHHHHHHHHHHHCCHHHHCCCCEEEECCCCCHHHHHHHHHHH
Q ss_conf             421455330368988211148899999872887881776828962889999999999999
Q gi|254780163|r  625 NAGALEMSKARIGFGSSRNDDADKEALRNFLSPEFLNRLDSIIPFFPLSSDIIRQVVHKF  684 (798)
Q Consensus       625 N~G~~~~~~~~~g~~~~~~~~~~~~~l~~~f~peflnRid~ii~F~~l~~~~~~~i~~~~  684 (798)
T Consensus       157 ~~~---------------DP~~lLpTI~--------SRC-q~~~f~~l~~~~~~~~L~~~  192 (216)
T TIGR00678       157 HSP---------------DPERLLPTIR--------SRC-QVLPFPPLSEEALLQWLIEQ  192 (216)
T ss_pred             CCC---------------CHHHHCCCCC--------CCE-EEEEECCCCHHHHHHHHHHC
T ss_conf             888---------------8433221110--------320-15862599889999999970