HHsearch alignment for GI: 254780334 and conserved domain: cd01125

>cd01125 repA Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=99.46  E-value=4.6e-12  Score=107.56  Aligned_cols=181  Identities=24%  Similarity=0.309  Sum_probs=111.1

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHCC------------CCCEEEEECCCCHHHHHHHHHHCCC----C--CCCHHE--
Q ss_conf             7089995498751889999999998503------------9819999864630478888752015----7--751000--
Q gi|254780334|r   90 GSVILVGGDPGIGKSTLLMQTAASLAYK------------KHRITYVSGEEAIGQIRLRAQRLNT----I--NSSVYI--  149 (479)
Q Consensus        90 Gs~~Li~G~PGvGKSTL~Lqia~~~a~~------------g~~vlYvS~EEs~~Qi~~Ra~Rl~~----~--~~~i~~--  149 (479)
T Consensus         1 G~v~~l~g~gG~GKS~lal~lAl~vA~G~~~~g~~~~~~~~G~Vly~~~Ed~~~~l~rRl~a~~~~~~~~~~~~rl~~~~   80 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDS   80 (239)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEECC
T ss_conf             93899980899888999999999997599656898546877619999788998999999999998638665554166415


Q ss_pred             --------ECC------CCHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             --------034------788999999973169828997216876654204455636799999999999753079789998
Q gi|254780334|r  150 --------AIE------TNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLV  215 (479)
Q Consensus       150 --------~~e------~~l~~il~~~i~~~~~~~vVIDSIQtl~~~~~~s~~GsvsQvre~~~~L~~~AK~~~i~vili  215 (479)
T Consensus        81 ~~~~~l~~~~~~~~~~~~~~~~i~~~-~~~~~~~LVViDpL~~~~~~d----ENd~~~m~~~i~~l~~ia~~tg~aVl~v  155 (239)
T cd01125          81 GRIQPISIAREGRIIVVPEFERIIEQ-LLIRRIDLVVIDPLVSFHGVS----ENDNGAMDAVIKALRRIAAQTGAAILLV  155 (239)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHH-HHCCCCCEEEECCCHHHCCCC----CCCHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             56664413357721014899999999-745899899983817748999----7889999999999999999719999997


Q ss_pred             EEECCCCC--------CCCHHHHHHHHHEEEEE------ECCCC-----CCCCCCEEEEEEEECCC-CCCCEEEEEECCC
Q ss_conf             63036654--------33114578775302785------15556-----66544215676320256-7651279985156
Q gi|254780334|r  216 GHVTKEGQ--------IAGPRVIEHMVDAVLYF------EGGTR-----NTQYDYRILRSVKNRFG-PTDEIGVFEMSDK  275 (479)
Q Consensus       216 ghvTK~G~--------iAGp~~LeH~VD~vl~~------ege~~-----~~~~~~R~Lr~~KNRfG-~t~e~gvf~m~~~  275 (479)
T Consensus       156 HHt~K~~~~~~~~~~a~RGaSaLvd~aR~~~~l~~m~~~ea~~~gi~~~~~~~~~r~~-~~k~n~~~~~~~~~w~~r~~g  234 (239)
T cd01125         156 HHVRKGSAKDGDTQEAARGASALVDGARWVRALTRMTSEEAEKMGVGKAQPGLFFRFG-VSKKNNAAATEADRWYRRNSG  234 (239)
T ss_pred             ECCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHCCCCHHCCCCEEEEC-CCCCCCCCCCCCCCEEEECCC
T ss_conf             0688767887104434664877432354766773799999998299801068769963-431026999976614684278


Q ss_pred             C
Q ss_conf             6
Q gi|254780334|r  276 G  276 (479)
Q Consensus       276 G  276 (479)
T Consensus       235 g  235 (239)
T cd01125         235 G  235 (239)
T ss_pred             C
T ss_conf             3