HHsearch alignment for GI: 254780787 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=99.68 E-value=2.9e-16 Score=129.17 Aligned_cols=142 Identities=29% Similarity=0.367 Sum_probs=106.0
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHH-CCCCCCEECCCEEEEECCCCEEEEEECCCHHHHHHH--------HHHHHHCCCC
Q ss_conf 8986236850446777886422210-012310001214999517843888851661578999--------8666420680
Q gi|254780787|r 386 VTIMGHVDHGKTSLLDAIRKADVAK-GEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFYEM--------RARGARVTDI 456 (884)
Q Consensus 386 v~v~ghvd~GKt~lld~~r~~~~~~-~e~ggitq~iga~~~~~~~~~~~~iDtPGh~~f~~~--------r~rg~~~~d~ 456 (884)
T Consensus 4 ValvG~pN~GKStL~N~l~g~~~~ivs~~pgtTrd~~~~~~~~~~~~i~l~DTpG~~~~~~~~e~~~~~~~~~~i~~aDl 83 (157)
T cd04164 4 VVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIRETEDEIEKIGIERAREAIEEADL 83 (157)
T ss_pred EEEECCCCCCHHHHHHHHHCCCCEEECCCCCEEEECCEEEEEECCEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCE
T ss_conf 99988999989999999968973343288984786326789539988999726775444578999999999863015767
Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf 59999836674023577789899709941561233124433200022100001320001234740363110024774112
Q gi|254780787|r 457 AVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKL 536 (884)
Q Consensus 457 ~ilvv~~~~g~~~qt~e~~~~~~~~~~p~iva~nk~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 536 (884)
T Consensus 84 il~vvD~~~~~~~~~~~~~~~~--~~~p~i~v~NKiDl~~~~~~------~~~-------~~~~~vi~ISA~~g~Gi~~L 148 (157)
T cd04164 84 VLFVIDASRGLDEEDLEILELP--ADKPIIVVLNKSDLLPDSEL------LSL-------LAGKPIIAISAKTGEGLDEL 148 (157)
T ss_pred EEEEEECCCCCCHHHHHHHHHH--CCCCEEEEEECCCCCCCHHH------HHH-------CCCCCEEEEECCCCCCHHHH
T ss_conf 9999889877888899999851--47998999967601486667------985-------28997799985279599999
Q ss_pred CCCHHC
Q ss_conf 210000
Q gi|254780787|r 537 LDAILL 542 (884)
Q Consensus 537 ~~~~~~ 542 (884)
T Consensus 149 ~~~I~e 154 (157)
T cd04164 149 KEALLE 154 (157)
T ss_pred HHHHHH
T ss_conf 999999