HHsearch alignment for GI: 254781215 and conserved domain: TIGR02768
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA; InterPro: IPR014136 This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, IPR005053 from INTERPRO) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, IPR014129 from INTERPRO). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer ..
Probab=94.78 E-value=0.088 Score=29.84 Aligned_cols=119 Identities=20% Similarity=0.103 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf 58999999999998740565554210124650257-65978999999999998089966999808589999999999999
Q gi|254781215|r 52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK 130 (511)
Q Consensus 52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k 130 (511)
T Consensus 416 s~EQ~~Av~hvt~s------------~~iavVvG~AGtGKSt~L~aAR~AWe~~--Gy~V~GAA-LsGKAAegL------ 474 (888)
T TIGR02768 416 SEEQKEAVRHVTGS------------GDIAVVVGRAGTGKSTMLKAAREAWEAA--GYRVIGAA-LSGKAAEGL------ 474 (888)
T ss_pred HHHHHHHHHHHCCC------------CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEHH-HHHHHHHHH------
T ss_conf 58999998753289------------9648997489987667899999999873--97787154-555898873------
Q ss_pred HHHHCHHCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH
Q ss_conf 998550001344432222--223334443211123578616985303575561002120267614999711102997889
Q gi|254781215|r 131 WLSLLPNKHWFEMQSLSL--HPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN 208 (511)
Q Consensus 131 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~ 208 (511)
T Consensus 475 --e~~-----sGI~SRTLASle~aW~~---------------------------G~d~L~~~d--vLviDEAGMV~S~Qm 518 (888)
T TIGR02768 475 --EAE-----SGIESRTLASLEYAWAN---------------------------GRDLLEDKD--VLVIDEAGMVGSRQM 518 (888)
T ss_pred --HCC-----CCCCHHHHHHHHHHHHC---------------------------CCCCCCCCC--EEEEECCCCHHHHHH
T ss_conf --002-----68750478879999873---------------------------875224776--689851544146778
Q ss_pred -HHHHHHHCCCCCCEEEEEECCC
Q ss_conf -8888885079981389982389
Q gi|254781215|r 209 -LGILGFLTERNANRFWIMTSNP 230 (511)
Q Consensus 209 -e~i~~~Lt~~g~~~~~i~~~nP 230 (511)
T Consensus 519 ~r~l~~A~-~AGaKv--VLvGD~ 538 (888)
T TIGR02768 519 ARVLKEAE-EAGAKV--VLVGDP 538 (888)
T ss_pred HHHHHHHH-HCCCCE--EEECCH
T ss_conf 89999998-727605--984885