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=4.6e-36  Score=261.94  Aligned_cols=155  Identities=35%  Similarity=0.488  Sum_probs=114.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCEEEEEEEEEEECCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             08999718988788899998588501025898530223899999899899999658842076368999999999999987
Q gi|255764471|r    3 YTIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADGKNCSIAKQMNDQTELAINE   82 (470)
Q Consensus         3 ~~iaivG~pNvGKStL~N~l~~~~~aiv~~~~g~Trd~~~~~~~~~~~~~~liDT~G~~~~~~~~~~~~i~~~~~~ai~~   82 (470)
T Consensus         2 ~~ValvG~pN~GKStL~N~l~g~~~~ivs~~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~-~~~~e~~~~~~~~~~i~~   80 (157)
T cd04164           2 IKVVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIRET-EDEIEKIGIERAREAIEE   80 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCEEECCCCCEEEECCEEEEEECCEEEEEEECCCCCCC-CCHHHHHHHHHHHHHCCC
T ss_conf             7999988999989999999968973343288984786326789539988999726775444-578999999999863015


Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHCCCHHHHHHHHHHHHCCCCCEEEHHHCCCCCHHHHHHHHHH
Q ss_conf             79899997598877623445553321023322220565223012100124553122220100111022201479999998
Q gi|255764471|r   83 AHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDTRIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKI  162 (470)
Q Consensus        83 aD~il~vvD~~~g~~~~D~~i~~~lr~~~~~~ilv~NK~D~~~~~~~~~e~~~lg~~~~i~iSA~~g~Gi~~L~~~i~~~  162 (470)
T Consensus        81 aDlil~vvD~~~~~~~~~~~~~~~~--~~~p~i~v~NKiDl~~~~~~~---~~~~~~~vi~ISA~~g~Gi~~L~~~I~e~  155 (157)
T cd04164          81 ADLVLFVIDASRGLDEEDLEILELP--ADKPIIVVLNKSDLLPDSELL---SLLAGKPIIAISAKTGEGLDELKEALLEL  155 (157)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHH--CCCCEEEEEECCCCCCCHHHH---HHCCCCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             7679999889877888899999851--479989999676014866679---85289977999852795999999999997


Q ss_pred             H
Q ss_conf             6
Q gi|255764471|r  163 F  163 (470)
Q Consensus       163 ~  163 (470)
T Consensus       156 a  156 (157)
T cd04164         156 A  156 (157)
T ss_pred             C
T ss_conf             2