HHsearch alignment for GI: 254780709 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=97.71  E-value=0.00091  Score=46.75  Aligned_cols=144  Identities=20%  Similarity=0.259  Sum_probs=80.7

Q ss_pred             EECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             31135444442478999999985226742677434512456889999975303532122358661245422899996514
Q gi|254780709|r  114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQAKK  193 (321)
Q Consensus       114 il~vG~nG~GKTTT~aKLA~~~~~~g~kV~lva~DtfR~aA~eQL~~~a~~~~v~~~~~~~~~dp~~v~~~a~~~a~~~~  193 (321)
T Consensus         4 ValvG~pN~GKStL~N~l~------g~~~~ivs~-------------------~pgtT----rd~~~~~------~~~~~   48 (157)
T cd04164           4 VVIVGKPNVGKSSLLNALA------GRDRAIVSD-------------------IAGTT----RDVIEES------IDIGG   48 (157)
T ss_pred             EEEECCCCCCHHHHHHHHH------CCCCEEECC-------------------CCCEE----EECCEEE------EEECC
T ss_conf             9998899998999999996------897334328-------------------89847----8632678------95399


Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHH-HHHHHHCCCCEEEEECCCCCCCH
Q ss_conf             87599865433321157789999899876302223430112310233522577899-98764358976999654578706
Q gi|254780709|r  194 VDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQV-EMFHAVAGTTGLIMTKMDGTARG  272 (321)
Q Consensus       194 ~DvvliDTAGR~~~~~~lm~EL~ki~~v~~~~~~~~p~~~~lVlda~~gq~~~~~a-~~F~~~~~~~g~I~TKlD~ta~~  272 (321)
T Consensus        49 ~~i~l~DTpG~-~~~~~~~e-~~~~~~~~~~i--~~aDlil~vvD~~~~~~~~~~~~~~~~~~~p-~i~v~NKiDl~~~~  123 (157)
T cd04164          49 IPVRLIDTAGI-RETEDEIE-KIGIERAREAI--EEADLVLFVIDASRGLDEEDLEILELPADKP-IIVVLNKSDLLPDS  123 (157)
T ss_pred             EEEEEEECCCC-CCCCCHHH-HHHHHHHHHHC--CCCCEEEEEEECCCCCCHHHHHHHHHHCCCC-EEEEEECCCCCCCH
T ss_conf             88999726775-44457899-99999998630--1576799998898778888999998514799-89999676014866


Q ss_pred             HHHHHHHHHHCCCEEEEEC--CCCCCCCCC
Q ss_conf             9999999997698899975--898132555
Q gi|254780709|r  273 GGLIPIVVTHKIPVYFLGV--GEGINDLEP  300 (321)
Q Consensus       273 G~~ls~~~~~~~Pi~fig~--Ge~i~Dl~~  300 (321)
T Consensus       124 ~~---~~~~~~~~vi~ISA~~g~Gi~~L~~  150 (157)
T cd04164         124 EL---LSLLAGKPIIAISAKTGEGLDELKE  150 (157)
T ss_pred             HH---HHHCCCCCEEEEECCCCCCHHHHHH
T ss_conf             67---9852899779998527959999999