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