HHsearch alignment for GI: 254780810 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=95.11  E-value=0.22  Score=28.26  Aligned_cols=99  Identities=19%  Similarity=0.204  Sum_probs=50.0

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHCCCC----------CEEEEEECCCCHHH-HHHHHHHH---------CCEEE-E
Q ss_conf             2312220487787899999999998611886----------46999950878789-99999840---------34278-2
Q gi|254780810|r  174 GQRSLIVAPPRTGKTILLQNIAHSIKKNHPE----------CYLIVLLIDERPEE-VTDMQRSV---------QGEVI-S  232 (423)
Q Consensus       174 gqr~~i~~~~~~gkt~ll~~ia~~~~~~~~~----------v~~i~~ligEr~~e-v~e~~~~~---------~~~vv-~  232 (423)
T Consensus         1 G~v~~l~g~gG~GKS~lal~lAl~vA~G~~~~g~~~~~~~~G~Vly-~~~Ed~~~~l~rRl~a~~~~~~~~~~~~rl~~~   79 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVY-LSAEDPREEIHRRLEAILQHLEPDDAGDRLFID   79 (239)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE-EECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEC
T ss_conf             9389998089988899999999999759965689854687761999-978899899999999999863866555416641


Q ss_pred             CCCCCCHHHH----HHHHHHHHHHHHHHHHCCCCEEEEEECHHHHH
Q ss_conf             3667888899----99999999999999977992899981638987
Q gi|254780810|r  233 STFDESAARH----VQVAEMVIAKAKCLVEYGLDVVILLDSITRLC  274 (423)
Q Consensus       233 st~d~~~~~~----~~~a~~a~~~a~~~~e~G~dVll~~DslTR~A  274 (423)
T Consensus        80 ~~~~~~l~~~~~~~~~~~~~~~~i~~~~~-~~~~~LVViDpL~~~~  124 (239)
T cd01125          80 SGRIQPISIAREGRIIVVPEFERIIEQLL-IRRIDLVVIDPLVSFH  124 (239)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHH-CCCCCEEEECCCHHHC
T ss_conf             55666441335772101489999999974-5899899983817748