HHsearch alignment for GI: 254780814 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=98.55  E-value=1.8e-07  Score=77.17  Aligned_cols=99  Identities=29%  Similarity=0.492  Sum_probs=78.0

Q ss_pred             HHHHHHHCCCCCCCCCCCEEEEEEEEEEEEEEEEEECCC---CCCEEEEEECCCCCCCCCCEEHHHHHHHHHHHHHHHHH
Q ss_conf             577653003565568852036420036999733453177---54121222246216667721035688899999999986
Q gi|254780814|r  230 EAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDG---YHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEK  306 (803)
Q Consensus       230 ~~fv~~l~~~~~~~~~~~i~~~~~~~~~~veval~~~~~---~~e~i~SfvN~I~T~~GGtHv~gf~~al~~~i~~y~~~  306 (803)
T Consensus         2 ~~~i~~i~g~~~--~~~l~~v~~~~~~~~i~g~i~~~~~~~~~~~~q~~fVN~R~v~~~~~~~~ai~~~y~~~~~-----   74 (107)
T cd00329           2 KDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN-----   74 (107)
T ss_pred             HHHHHHHHCHHH--HHHCEEEEEECCCEEEEEEEECCCCCCCCCCCEEEEECCEEECCCHHHHHHHHHHHHHHHH-----
T ss_conf             779998819898--9717799875499899999957853567785479999784860776999999999999861-----


Q ss_pred             CCCCCCCCCCCCHHHHHCCCEEEEEEECCC--CCCC-CCCHHHH
Q ss_conf             242000123576134305721566652137--6335-7210020
Q gi|254780814|r  307 SFGSKKDKRSVIGDDCREGFTSVLSIKMPD--PRFS-SQTKEKL  347 (803)
Q Consensus       307 ~~~~Kk~k~~~~~~Diregl~~visvki~n--P~F~-gQTK~kL  347 (803)
T Consensus        75 ------------~~~~~~~p~~vl~i~~~~~~vDvNvhP~K~ev  106 (107)
T cd00329          75 ------------GDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEV  106 (107)
T ss_pred             ------------CCCCCCCCEEEEEEEECCHHEEECCCCCCCCC
T ss_conf             ------------46789887899999848153872749983413