HHsearch alignment for GI: 254780648 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=100.00  E-value=1.3e-34  Score=229.75  Aligned_cols=150  Identities=23%  Similarity=0.269  Sum_probs=123.3

Q ss_pred             EEEEECCCCCCCEEEEEECCCCCH-HHHHHHCCCEECCEEEEECCEEEEEECCCCCCCCCCCCCCCH-HHHHHHHHHHHH
Q ss_conf             124421677753035410145401-212110000001026632986899822642124731167751-234433333578
Q gi|254780648|r  162 IGIIGLPNAGKSTFLASVTRAKPK-IADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQGAGIG-DRFLKHTERTHV  239 (335)
Q Consensus       162 VglVG~PNaGKSTLln~ls~ak~k-Ia~ypFTT~~P~lGvv~~~~~~~~i~D~PGlIegA~~~~glG-~~FLrhIer~~v  239 (335)
T Consensus         4 ValvG~pN~GKStL~N~l~g~~~~ivs~~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~~~~~e~~~~~~~~~~i~~aDl   83 (157)
T cd04164           4 VVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIRETEDEIEKIGIERAREAIEEADL   83 (157)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCEEECCCCCEEEECCEEEEEECCEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCE
T ss_conf             99988999989999999968973343288984786326789539988999726775444578999999999863015767


Q ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf             87520222211013466678998777667505988999974658998899999999998629948999888788999999
Q gi|254780648|r  240 LLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQIL  319 (335)
Q Consensus       240 Ll~VVD~s~~d~~~~~~~I~~EL~~y~~~L~~Kp~IIVlNKiDl~~~e~~~~~~~~l~~~~~~~vi~ISA~tg~GI~eL~  319 (335)
T Consensus        84 il~vvD~~~~~~~~~~~~~~--------~~~~~p~i~v~NKiDl~~~~~~~------~~~~~~~vi~ISA~~g~Gi~~L~  149 (157)
T cd04164          84 VLFVIDASRGLDEEDLEILE--------LPADKPIIVVLNKSDLLPDSELL------SLLAGKPIIAISAKTGEGLDELK  149 (157)
T ss_pred             EEEEEECCCCCCHHHHHHHH--------HHCCCCEEEEEECCCCCCCHHHH------HHCCCCCEEEEECCCCCCHHHHH
T ss_conf             99998898778888999998--------51479989999676014866679------85289977999852795999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780648|r  320 ECLHDK  325 (335)
Q Consensus       320 ~~I~e~  325 (335)
T Consensus       150 ~~I~e~  155 (157)
T cd04164         150 EALLEL  155 (157)
T ss_pred             HHHHHH
T ss_conf             999997