HHsearch alignment for GI: 254780321 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=99.66  E-value=1.8e-15  Score=123.30  Aligned_cols=146  Identities=29%  Similarity=0.423  Sum_probs=100.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHCCEEEEEEEEEEEECCCCCEEEEEEEECCCCCHHH
Q ss_conf             79998013898778899999982980544443113058677987195052327999974378843899996178730027
Q gi|254780321|r   13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFT   92 (606)
Q Consensus        13 N~~IiaHvDhGKTTL~d~lL~~tg~i~~~~~~~~vlD~~~~EreRGITIka~~~~~~~~~~~~~~y~iNlIDTPGH~DF~   92 (606)
T Consensus         3 ~ValvG~pN~GKStL~N~l---~g~--~~~i---vs~------~pgtTrd~~~~~~-----~~~~~~i~l~DTpG~~~~~   63 (157)
T cd04164           3 KVVIVGKPNVGKSSLLNAL---AGR--DRAI---VSD------IAGTTRDVIEESI-----DIGGIPVRLIDTAGIRETE   63 (157)
T ss_pred             EEEEECCCCCCHHHHHHHH---HCC--CCEE---ECC------CCCEEEECCEEEE-----EECCEEEEEEECCCCCCCC
T ss_conf             9999889999899999999---689--7334---328------8984786326789-----5399889997267754445


Q ss_pred             HHH-----HHHHH---HCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             999-----99997---3026899998687886558999999997099679983267887532113388877555322321
Q gi|254780321|r   93 YEV-----SRSLS---ACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTED  164 (606)
Q Consensus        93 ~EV-----~r~l~---a~dgaiLvVdA~~Gvq~QT~~~~~~A~~~~l~~I~viNKiD~~~A~~e~v~~ei~~~~g~~~~~  164 (606)
T Consensus        64 ~~~e~~~~~~~~~~i~~aDlil~vvD~~~~~~~~~~~~~--~~~~~~p~i~v~NKiDl~~~--~~----~~~~--~~~~~  133 (157)
T cd04164          64 DEIEKIGIERAREAIEEADLVLFVIDASRGLDEEDLEIL--ELPADKPIIVVLNKSDLLPD--SE----LLSL--LAGKP  133 (157)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHH--HHHCCCCEEEEEECCCCCCC--HH----HHHH--CCCCC
T ss_conf             789999999998630157679999889877888899999--85147998999967601486--66----7985--28997


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             00011100223200678776321
Q gi|254780321|r  165 ALLVSAKTGEGIPLLLERIVQQL  187 (606)
Q Consensus       165 ii~vSAktG~GV~~LLd~Iv~~i  187 (606)
T Consensus       134 vi~ISA~~g~Gi~~L~~~I~e~a  156 (157)
T cd04164         134 IIAISAKTGEGLDELKEALLELA  156 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC
T ss_conf             79998527959999999999972