HHsearch alignment for GI: 254780711 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=97.15  E-value=0.0036  Score=44.42  Aligned_cols=141  Identities=23%  Similarity=0.333  Sum_probs=73.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89962344333468899999999861489507820542210047799998510347422233210368999999999974
Q gi|254780711|r  102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARD  181 (461)
Q Consensus       102 vIllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~Dt~R~aA~eQL~~~a~~~~v~~~~~~~~~dp~~i~~~a~~~a~~  181 (461)
T Consensus         3 ~ValvG~pN~GKStL~N~l~-------g~~~~ivs~-~--pg-------------tT-------rd~~~~------~~~~   46 (157)
T cd04164           3 KVVIVGKPNVGKSSLLNALA-------GRDRAIVSD-I--AG-------------TT-------RDVIEE------SIDI   46 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHH-------CCCCEEECC-C--CC-------------EE-------EECCEE------EEEE
T ss_conf             99998899998999999996-------897334328-8--98-------------47-------863267------8953


Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHH--H-HHHHHCCCCCCCCCCCHHCCHHHHHHH-HHHHHHCCCCCEEEEECCCCCCCC
Q ss_conf             158869983344222112468999--9-998513851100031011122568888-988763584407764115766330
Q gi|254780711|r  182 GGYDAVILDTAGRNHINDSLMQEI--S-EIKSLTNPHEILLVADALTGQDAVHLA-RNFDKIVDLTGIILTRMDGDGRGG  257 (461)
Q Consensus       182 ~~~D~iiiDTaGR~~~d~~lm~El--~-~i~~~~~p~e~~lV~da~~Gq~a~~~a-~~F~~~~~i~giIlTKlD~~akgG  257 (461)
T Consensus        47 ~~~~i~l~DTpG~~~~-~~~~e~~~~~~~~~~i~~aDlil~vvD~~~~~~~~~~~~~~~~~~~p-~i~v~NKiDl~~~~~  124 (157)
T cd04164          47 GGIPVRLIDTAGIRET-EDEIEKIGIERAREAIEEADLVLFVIDASRGLDEEDLEILELPADKP-IIVVLNKSDLLPDSE  124 (157)
T ss_pred             CCEEEEEEECCCCCCC-CCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHCCCC-EEEEEECCCCCCCHH
T ss_conf             9988999726775444-57899999999986301576799998898778888999998514799-899996760148666


Q ss_pred             HHHHHHHHHCCCHHHEE--CCCCCCCCC
Q ss_conf             36777888478730261--586723210
Q gi|254780711|r  258 AALSMRTVTGKPIKAIG--TGEKINDLE  283 (461)
Q Consensus       258 ~als~~~~~~~PI~fig--~GE~~~dle  283 (461)
T Consensus       125 ---~~~~~~~~~vi~ISA~~g~Gi~~L~  149 (157)
T cd04164         125 ---LLSLLAGKPIIAISAKTGEGLDELK  149 (157)
T ss_pred             ---HHHHCCCCCEEEEECCCCCCHHHHH
T ss_conf             ---7985289977999852795999999