HHsearch alignment for GI: 254780601 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=90.39  E-value=1.3  Score=23.21  Aligned_cols=120  Identities=18%  Similarity=0.262  Sum_probs=60.1

Q ss_pred             CCEEEECCCCCCHHH-HHHHHHHHHHHCCCCC-------------CCCCCCCEEEEECCCHHH----HHHHHHHHHHHHH
Q ss_conf             969999289874689-9999999986104212-------------255688279998499899----9999999999854
Q gi|254780601|r   38 KDVLVSAQTGSGKTV-AFGLALASTLLAENDR-------------FSPASAPLALAIAPTREL----AVQVGRELEWLYA   99 (573)
Q Consensus        38 ~d~i~~a~TGsGKT~-af~lp~l~~l~~~~~~-------------~~~~~~~~~lil~PTrEL----a~Qv~~~~~~l~~   99 (573)
T Consensus        15 HA~LF~G~~G~Gk~~~A~~--~A~~l~C~~~~~~~~Cg~C~~C~~~~~G~HPD~~~~~P~~~~~~~~~de~-~~-~~~g~   90 (216)
T TIGR00678        15 HAYLFTGPEGVGKELLALA--LAKALLCEPRGGGEPCGECHSCRLIEAGNHPDLHRLEPEGQSKSLTADEA-AE-GEEGS   90 (216)
T ss_pred             CCEEEECCCCCCHHHHHHH--HHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCHHHH-HH-HHCCC
T ss_conf             6125444888748999999--99998077857788888588899987079982378742347777776458-97-62564


Q ss_pred             -----HCCCEEEEEECCCCHHHHHHHHCCCCEEEEECCCCHHHHHHCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHH
Q ss_conf             -----469879999889987999996128975998223101332100012246431899961311001001235788875
Q gi|254780601|r  100 -----KTGVVVAVCIGGVSVHRERRDLQNGAHIVVGTPGRLCDHIRGKGLNISHLKAVVLDEADEMLDLGFRDDIEFILD  174 (573)
Q Consensus       100 -----~~~~~v~~~~gg~~~~~q~~~l~~~~~iiv~TPgrl~d~~~~~~l~l~~v~~lVlDEaD~ml~~gf~~~i~~i~~  174 (573)
T Consensus        91 a~~~~~~~Ik----------~dq~R~l~--------------~~~~~~~-~~~~~rVviI~~Ae~mn~----~AANALLK  141 (216)
T TIGR00678        91 AKRRALPQIK----------VDQVRELV--------------EFLSLTP-QESGRRVVIIEDAERMNE----AAANALLK  141 (216)
T ss_pred             CCCCCCCCCC----------HHHHHHHH--------------HHHHHCC-CCCCCEEEEECCHHHCCH----HHHHHHHH
T ss_conf             2113678787----------27899999--------------9986064-214751799767323258----98986510


Q ss_pred             HC--CCCCCEEEEECCCC
Q ss_conf             21--43342256311112
Q gi|254780601|r  175 SS--PKKRRMLMFSATIS  190 (573)
Q Consensus       175 ~~--p~~~q~~l~SAT~~  190 (573)
T Consensus       142 tLEEPp~~t~fiL~~~~~  159 (216)
T TIGR00678       142 TLEEPPPNTLFILITHSP  159 (216)
T ss_pred             HEECCCCCEEEEEECCCC
T ss_conf             101279870798850888