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