HHsearch alignment for GI: 255764471 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=1.8e-36  Score=264.75  Aligned_cols=156  Identities=31%  Similarity=0.579  Sum_probs=135.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCEEEECCEEEEEEECHHCCCCCCCCCHHHHHHCCCCCEE
Q ss_conf             30388640356425678876520121100024566542023114203406999817110444443000111000121001
Q gi|255764471|r  203 PLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQS  282 (470)
Q Consensus       203 ~i~~~~~G~pN~GKStl~N~l~~~~r~ivs~~~GtTrD~i~~~~~~~~~~~~liDTaGirkk~~~~~~~E~~s~~~t~~~  282 (470)
T Consensus         1 ~~~ValvG~pN~GKStL~N~l~g~~~~ivs~~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~---~~~~e~~~~~~~~~~   77 (157)
T cd04164           1 GIKVVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIRET---EDEIEKIGIERAREA   77 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEECCCCCEEEECCEEEEEECCEEEEEEECCCCCCC---CCHHHHHHHHHHHHH
T ss_conf             97999988999989999999968973343288984786326789539988999726775444---578999999999863


Q ss_pred             EECCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             20120599845532122021223200000035766558944223354155566654201333200488311123453334
Q gi|255764471|r  283 VRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGE  362 (470)
Q Consensus       283 i~~advvi~viDa~~~~~~qd~~i~~~i~~~~k~~iiv~NK~Dli~~~~~~~~~~~~~~~~~~~~~~~~~i~~iSA~~g~  362 (470)
T Consensus        78 i~~aDlil~vvD~~~~~~~~~~~~~~~~--~~~p~i~v~NKiDl~~~~~~~------------~~~~~~~vi~ISA~~g~  143 (157)
T cd04164          78 IEEADLVLFVIDASRGLDEEDLEILELP--ADKPIIVVLNKSDLLPDSELL------------SLLAGKPIIAISAKTGE  143 (157)
T ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHH--CCCCEEEEEECCCCCCCHHHH------------HHCCCCCEEEEECCCCC
T ss_conf             0157679999889877888899999851--479989999676014866679------------85289977999852795


Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             8589999999999
Q gi|255764471|r  363 GLDDLMVSVLEIN  375 (470)
Q Consensus       363 gi~~l~~~i~~~~  375 (470)
T Consensus       144 Gi~~L~~~I~e~a  156 (157)
T cd04164         144 GLDELKEALLELA  156 (157)
T ss_pred             CHHHHHHHHHHHC
T ss_conf             9999999999972