HHsearch alignment for GI: 254780263 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=99.72  E-value=4.6e-17  Score=124.84  Aligned_cols=145  Identities=23%  Similarity=0.280  Sum_probs=99.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCEEEEEEEEEECCCEEEEEEECCCCHHH--------
Q ss_conf             799999046898878999999876444200131268686986292063789998219908999847873024--------
Q gi|254780263|r   13 LGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPGHADY--------   84 (392)
Q Consensus        13 ~ni~~iGhvd~GKSTL~~~L~~~~~~~~~~~~~~D~~~~E~~rGiTi~~~~~~~~~~~~~i~iiD~PGH~~f--------   84 (392)
T Consensus         2 ~~ValvG~pN~GKStL~N~l~g~~~------~ivs~-----~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~~~~~e~~~   70 (157)
T cd04164           2 IKVVIVGKPNVGKSSLLNALAGRDR------AIVSD-----IAGTTRDVIEESIDIGGIPVRLIDTAGIRETEDEIEKIG   70 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCC------EEECC-----CCCEEEECCEEEEEECCEEEEEEECCCCCCCCCHHHHHH
T ss_conf             7999988999989999999968973------34328-----898478632678953998899972677544457899999


Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCEEEEEEEEEEEEE
Q ss_conf             67798774002331452012344332106778888631876023310023335612221101232100111014532210
Q gi|254780263|r   85 VKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTP  164 (392)
Q Consensus        85 ~~~mi~g~~~~D~ailvVda~~G~~~QT~eh~~l~~~lgi~~iIv~iNKmD~v~~~~~~~~i~~~i~~~l~~~~~~~~~p  164 (392)
T Consensus        71 ~~~~~~~i~~aDlil~vvD~~~~~~~~~~~--~~~~~~~~p-~i~v~NKiDl~~~~~~~~~~--------------~~~~  133 (157)
T cd04164          71 IERAREAIEEADLVLFVIDASRGLDEEDLE--ILELPADKP-IIVVLNKSDLLPDSELLSLL--------------AGKP  133 (157)
T ss_pred             HHHHHHHCCCCCEEEEEEECCCCCCHHHHH--HHHHHCCCC-EEEEEECCCCCCCHHHHHHC--------------CCCC
T ss_conf             999986301576799998898778888999--998514799-89999676014866679852--------------8997


Q ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHC
Q ss_conf             2331146764114445652123320344310
Q gi|254780263|r  165 IIRGSALCALQGTNKELGEDSIHALMKAVDT  195 (392)
Q Consensus       165 ii~~sa~~g~~~~n~~~~~~~~~~Ll~~i~~  195 (392)
T Consensus       134 vi~ISA~~g~----------Gi~~L~~~I~e  154 (157)
T cd04164         134 IIAISAKTGE----------GLDELKEALLE  154 (157)
T ss_pred             EEEEECCCCC----------CHHHHHHHHHH
T ss_conf             7999852795----------99999999999