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