HHsearch alignment for GI: 254780809 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=8.9e-36  Score=268.08  Aligned_cols=144  Identities=44%  Similarity=0.627  Sum_probs=129.6

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHCCHHCCCCCCCCCCEEECCCCCCCCCEEEEEEECCHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             23024311466318889999855200023454687211000124568358999508100024103566667888998503
Q gi|254780809|r  219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVEN  298 (440)
Q Consensus       219 g~~v~i~G~pN~GKSSL~N~L~~~~~aIVs~~~GTTRD~i~~~~~i~g~~~~l~DTaGir~t~d~IE~~GI~ra~~~i~~  298 (440)
T Consensus         1 ~~~ValvG~pN~GKStL~N~l~g~~~~ivs~~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~~~~~e~~~~~~~~~~i~~   80 (157)
T cd04164           1 GIKVVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIRETEDEIEKIGIERAREAIEE   80 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEECCCCCEEEECCEEEEEECCEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             97999988999989999999968973343288984786326789539988999726775444578999999999863015


Q ss_pred             HCCEEECCCCCCHH------HHHHHCCCCCCCCCCCCCCCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             01102013589856------634312898532222333446542------00000133332323589999999996
Q gi|254780809|r  299 ADLILLLKEINSKK------EISFPKNIDFIFIGTKSDLYSTYT------EEYDHLISSFTGEGLEELINKIKSIL  362 (440)
Q Consensus       299 aDlil~v~D~~~~~------~~~~~~~~~~i~V~NK~Dl~~~~~------~~~~~~ISaktg~Gi~~L~~~I~~~l  362 (440)
T Consensus        81 aDlil~vvD~~~~~~~~~~~~~~~~~~~p~i~v~NKiDl~~~~~~~~~~~~~~vi~ISA~~g~Gi~~L~~~I~e~a  156 (157)
T cd04164          81 ADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLLPDSELLSLLAGKPIIAISAKTGEGLDELKEALLELA  156 (157)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             7679999889877888899999851479989999676014866679852899779998527959999999999972