HHsearch alignment for GI: 254780222 and conserved domain: cd00329

>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch
Probab=98.33  E-value=9.2e-07  Score=65.72  Aligned_cols=74  Identities=31%  Similarity=0.360  Sum_probs=63.3

Q ss_pred             EEEEEEEEEECCC----CCCEEEEEEECCCCCCCEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEE
Q ss_conf             5589998541467----774278883000655752413046789999998763018833222332222364269999776
Q gi|254780222|r  299 RGTVEWAIAWCEE----NPEITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQNKRAISIISDDLMISAVGILSVFI  374 (686)
Q Consensus       299 ~~~veval~~~~~----~~~~~SFVN~I~T~~GGTHv~g~~~ai~k~i~~~~~~~~~kk~~~i~~~dIk~~L~~~Isv~I  374 (686)
T Consensus        26 ~~~i~g~i~~~~~~~~~~~~q~~fVN~R~v~~~~~~~~ai~~~y~~~~~---------------~~~~~~~p~~vl~i~~   90 (107)
T cd00329          26 GFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---------------GDDVRRYPVAVLSLKI   90 (107)
T ss_pred             CEEEEEEEECCCCCCCCCCCEEEEECCEEECCCHHHHHHHHHHHHHHHH---------------CCCCCCCCEEEEEEEE
T ss_conf             9899999957853567785479999784860776999999999999861---------------4678988789999984


Q ss_pred             EH--HHCC-CCCCCCC
Q ss_conf             34--5607-6446620
Q gi|254780222|r  375 RE--PEFA-GQTKTKL  387 (686)
Q Consensus       375 ~n--P~Fe-sQTKekL  387 (686)
T Consensus        91 ~~~~vDvNvhP~K~ev  106 (107)
T cd00329          91 PPSLVDVNVHPTKEEV  106 (107)
T ss_pred             CCHHEEECCCCCCCCC
T ss_conf             8153872749983413