HHsearch alignment for GI: 254780484 and conserved domain: cd04164

>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=99.96  E-value=2.1e-28  Score=182.42  Aligned_cols=155  Identities=24%  Similarity=0.318  Sum_probs=114.4

Q ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCEEEECCEEEEEEEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             68999748998898999997389737987388841452120266555678508964999976001011122447898888
Q gi|254780484|r   30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGG  109 (212)
Q Consensus        30 p~VaivG~~NvGKSSLiNaL~g~~~~a~~~~~p~tt~~~~~~~~~~~~~~~~~~~~~~~~DtpG~~~~~~~~~~~~~~~~  109 (212)
T Consensus         2 ~~ValvG~pN~GKStL~N~l~g~~-~~ivs~~pgtTrd~------~~~~~~~~~~~i~l~DTpG~~~~~~~~e~~~~---   71 (157)
T cd04164           2 IKVVIVGKPNVGKSSLLNALAGRD-RAIVSDIAGTTRDV------IEESIDIGGIPVRLIDTAGIRETEDEIEKIGI---   71 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCC-CEEECCCCCEEEEC------CEEEEEECCEEEEEEECCCCCCCCCHHHHHHH---
T ss_conf             799998899998999999996897-33432889847863------26789539988999726775444578999999---


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             99877776642000001122357887545455432102575322122221111024689999999999753136898689
Q gi|254780484|r  110 LIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVI  189 (212)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  189 (212)
T Consensus        72 --~~~~~~i~~aDlil~vvD~~~~~~~~~~~~~~~~--~~~p~i~v~NKiDl~~~~~~~~~------------~~~~~vi  135 (157)
T cd04164          72 --ERAREAIEEADLVLFVIDASRGLDEEDLEILELP--ADKPIIVVLNKSDLLPDSELLSL------------LAGKPII  135 (157)
T ss_pred             --HHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHH--CCCCEEEEEECCCCCCCHHHHHH------------CCCCCEE
T ss_conf             --9998630157679999889877888899999851--47998999967601486667985------------2899779


Q ss_pred             EEECCCCCCHHHHHHHHHHHH
Q ss_conf             998888899899999999872
Q gi|254780484|r  190 PTSSVKRKGIEVLRKAILETI  210 (212)
Q Consensus       190 ~vSA~~g~Gi~eL~~~I~~~l  210 (212)
T Consensus       136 ~ISA~~g~Gi~~L~~~I~e~a  156 (157)
T cd04164         136 AISAKTGEGLDELKEALLELA  156 (157)
T ss_pred             EEECCCCCCHHHHHHHHHHHC
T ss_conf             998527959999999999972