HHsearch alignment for GI: 254780332 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=96.00  E-value=0.032  Score=36.40  Aligned_cols=149  Identities=19%  Similarity=0.265  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHHHHHHHH-CCCCCCCCCCCHHHHH----HH-HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             34336778999998741-1236644321013776----55-641677267762131002769999999999851011123
Q gi|254780332|r  179 SDAMTVAIDMAGQAFNR-DGRLAGVSTGIQTLDK----QM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQ  252 (504)
Q Consensus       179 ~~~~~~~~~~~~~~~~~-~~~~~Gi~TG~~~LD~----~~-gGl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~  252 (504)
T Consensus       384 ~~~~~~a~ER~~~~~~~~~GGmlaas~~~~rLs~EQ~~Av~hvt~s~~iavVvG~AGtGKSt~-L~aAR~A---------  453 (888)
T TIGR02768       384 PPIVDAAIERVDRILRRDSGGMLAASDQHERLSEEQKEAVRHVTGSGDIAVVVGRAGTGKSTM-LKAAREA---------  453 (888)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHH-HHHHHHH---------
T ss_conf             778888887666652278864011167877745899999875328996489974899876678-9999999---------


Q ss_pred             CCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHH-HHHHHHHHHHHCCEEEECCCCCC-HHH
Q ss_conf             3333212479758999585217999878999987410110001213768899-89999999862780782589988-999
Q gi|254780332|r  253 TDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYE-KIVACSQVMQKLPLYIDQTGGIS-MSQ  330 (504)
Q Consensus       253 ~~~~~~~~~g~~Vl~fSlEMs~~el~~R~is~~s~I~~~~i~~g~l~~~e~~-~i~~a~~~l~~~~l~I~d~~~~t-i~~  330 (504)
T Consensus       454 -----We~~Gy~V~GAAL--s--GKAAegLe~~sGI~SRTLAS-------le~aW~~G~d~L~~~dvLviDEAGMV~S~Q  517 (888)
T TIGR02768       454 -----WEAAGYRVIGAAL--S--GKAAEGLEAESGIESRTLAS-------LEYAWANGRDLLEDKDVLVIDEAGMVGSRQ  517 (888)
T ss_pred             -----HHHCCCEEEEHHH--H--HHHHHHHHCCCCCCHHHHHH-------HHHHHHCCCCCCCCCCEEEEECCCCHHHHH
T ss_conf             -----9873977871545--5--58988730026875047887-------999987387522477668985154414677


Q ss_pred             HHHHHHHHCCCCCCCEEEE-CCHHH
Q ss_conf             9998864022444746776-71353
Q gi|254780332|r  331 LATRARRLKRQRGLDLLIV-DYIQL  354 (504)
Q Consensus       331 I~~~~r~~~~~~gi~~vvI-DYLql  354 (504)
T Consensus       518 m-~r~l~~A~~AGaKvVLvGD~~QL  541 (888)
T TIGR02768       518 M-ARVLKEAEEAGAKVVLVGDPEQL  541 (888)
T ss_pred             H-HHHHHHHHHCCCCEEEECCHHHH
T ss_conf             8-89999998727605984885782