HHsearch alignment for GI: 254780332 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=99.33  E-value=8.4e-11  Score=101.71  Aligned_cols=221  Identities=16%  Similarity=0.167  Sum_probs=139.1

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             72677621310027699999999998510111233333212479758999585217999878999987410110001213
Q gi|254780332|r  219 SDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGEL  298 (504)
Q Consensus       219 G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEMs~~el~~R~is~~s~I~~~~i~~g~l  298 (504)
T Consensus         1 G~v~~l~g~gG~GKS~lal~lAl~vA~G~~~~g---~~~~~~~~G~Vly~~~Ed~~~~l~rRl~a~~~~~~~~~~~~rl~   77 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFG---GGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLF   77 (239)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCC---CCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEE
T ss_conf             938999808998889999999999975996568---98546877619999788998999999999998638665554166


Q ss_pred             CHHHHHHHHHHHHHHHHCCEEEECC-CCCCHHHHHHHHHHHCCCCCCCEEEECCHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             7688998999999986278078258-998899999988640224447467767135325664432113788999999999
Q gi|254780332|r  299 TRPDYEKIVACSQVMQKLPLYIDQT-GGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALK  377 (504)
Q Consensus       299 ~~~e~~~i~~a~~~l~~~~l~I~d~-~~~ti~~I~~~~r~~~~~~gi~~vvIDYLqli~~~~~~~~~r~~~i~~is~~lK  377 (504)
T Consensus        78 ~-----------~~~~~~~l~~~~~~~~~~~~~~~~i~~~~-~~~~~~LVViDpL~~~~~---~dENd~~~m~~~i~~l~  142 (239)
T cd01125          78 I-----------DSGRIQPISIAREGRIIVVPEFERIIEQL-LIRRIDLVVIDPLVSFHG---VSENDNGAMDAVIKALR  142 (239)
T ss_pred             E-----------CCCCCCCCCCCCCCCCCCHHHHHHHHHHH-HCCCCCEEEECCCHHHCC---CCCCCHHHHHHHHHHHH
T ss_conf             4-----------15566644133577210148999999997-458998999838177489---99788999999999999


Q ss_pred             HHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHCCEEEEEECHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99988279199977138220168999984010143242233138788972556616442333322211100000011233
Q gi|254780332|r  378 ALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNKDDILAYTKWQEDLKRV  457 (504)
Q Consensus       378 ~lA~e~~ipvi~lsQLnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~R~~~y~~~~~~~~~~~~~~~~~~~~~~~~~  457 (504)
T Consensus       143 ~ia~~tg~aVl~vHHt~K~~~~~~---~~~~a~RGaSaLvd~aR~~~~l~~m~~----~ea~~---------~gi~~~~~  206 (239)
T cd01125         143 RIAAQTGAAILLVHHVRKGSAKDG---DTQEAARGASALVDGARWVRALTRMTS----EEAEK---------MGVGKAQP  206 (239)
T ss_pred             HHHHHCCCEEEEEECCCCCCCCCC---HHHHCCCCHHHHHHHHHHHHHHHCCCH----HHHHH---------CCCCHHCC
T ss_conf             999971999999706887678871---044346648774323547667737999----99998---------29980106


Q ss_pred             CCEEEEEEEECCCCCC
Q ss_conf             8838999974089972
Q gi|254780332|r  458 KGIADIIIAKQRHGPT  473 (504)
Q Consensus       458 ~~~~elivaKnR~G~~  473 (504)
T Consensus       207 ~~~~r~~~~k~n~~~~  222 (239)
T cd01125         207 GLFFRFGVSKKNNAAA  222 (239)
T ss_pred             CCEEEECCCCCCCCCC
T ss_conf             8769963431026999