HHsearch alignment for GI: 254780399 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=99.86  E-value=4e-22  Score=178.70  Aligned_cols=103  Identities=31%  Similarity=0.636  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCHHHHHHHCCCHHH-CHHHHHHHHHHHHHHC---CCCC
Q ss_conf             89999973216665431002244203656666216110332320667751521000-7588899998755442---7999
Q gi|254780399|r  205 FPERISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGRTVQ-DKFILSTIRTAYAETI---PLGR  280 (594)
Q Consensus       205 l~~ri~~i~G~~~~~~l~~i~~~~~~~~i~G~is~P~~~r~~~~~q~ifVNgR~V~-~~~l~~AI~~aY~~~l---~~g~  280 (594)
T Consensus         1 l~~~i~~i~g~~~~~~l~~v~~~~~~~~i~g~i~~~~~~~~~~~~q~~fVN~R~v~~~~~~~~ai~~~y~~~~~~~~~~~   80 (107)
T cd00329           1 LKDRLAEILGDKVADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALNGDDVRR   80 (107)
T ss_pred             CHHHHHHHHCHHHHHHCEEEEEECCCEEEEEEEECCCCCCCCCCCEEEEECCEEECCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             97799988198989717799875499899999957853567785479999784860776999999999999861467898


Q ss_pred             CEEEEEEEEEEHHHHCCCCCCHHHHHH
Q ss_conf             807999999606571247571111255
Q gi|254780399|r  281 YPVVVLLLEIDPRQVDVNVHPAKSYIR  307 (594)
Q Consensus       281 ~P~~vL~i~i~p~~vDVNVHP~K~eVr  307 (594)
T Consensus        81 ~p~~vl~i~~~~~~vDvNvhP~K~ev~  107 (107)
T cd00329          81 YPVAVLSLKIPPSLVDVNVHPTKEEVR  107 (107)
T ss_pred             CCEEEEEEEECCHHEEECCCCCCCCCC
T ss_conf             878999998481538727499834139