Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Echvi_1296 Echvi_1296 glutamyl-tRNA synthetase, bacterial family
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Cola:Echvi_1296 Length = 513 Score = 321 bits (822), Expect = 4e-92 Identities = 180/507 (35%), Positives = 287/507 (56%), Gaps = 33/507 (6%) Query: 1 MGNEVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQL 60 M EVRVR+APSPTG LHIG RTAL+NYLFA+ GKF++R+EDTD+ R ++G E+ Sbjct: 1 MNKEVRVRFAPSPTGALHIGGVRTALYNYLFAKKNQGKFLLRIEDTDQTRFVKGAEEYIK 60 Query: 61 NYLKWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKERE 120 L+W+GI DES G +GPYRQSER +Y Y +L+EKG AY + T EEL+ RE Sbjct: 61 EALEWIGITPDESPWKEGPHGPYRQSERKPLYMQYAMDLVEKGHAYYAFDTSEELDAMRE 120 Query: 121 E-QIARGEMPRYSGKHR-------DLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVK 172 AR P+Y+ R L ++E + + G IR +VP + I ND+++ Sbjct: 121 RLTAARVVSPQYNSITRTQMKNSLTLPEDEVKARLESGDPYVIRLKVPRKEEIRLNDMIR 180 Query: 173 GEISFESDGIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAF 232 G + S+ + D V++K DG PTY+ A +DD+LM +THV+RGE+ + + P +++Y+ Sbjct: 181 GWVMVHSNTLDDKVLMKSDGMPTYHLANIVDDHLMGITHVIRGEEWLPSAPIHVLLYRYL 240 Query: 233 GWD--IPQFGHMTLIVN-ESRKKLSKRDES---------------IIQFIEQYKELGYLP 274 GW+ +PQF H+ L++ + KLSKRD F + +++ GY P Sbjct: 241 GWEDTMPQFAHLPLLLKPDGNGKLSKRDADKNGFPIFPMDWTDPRTGDFSQGFRQAGYFP 300 Query: 275 EALFNFIGLLGWSPVGEEELFTKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDL 334 +A NF+ LGW+P +E+F+ E+ I F V R+ KS FD++K KW N QY+K Sbjct: 301 DAFVNFLAFLGWNPGDNQEIFSMEELINAFSVERIGKSGTKFDINKAKWFNEQYLKAKSN 360 Query: 335 DQVVELTLPHLQKAGKVGTELSAEEQEWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEY 394 + + + L++ G + AE+ ++++ E+ ++ +++ + E+ Sbjct: 361 HDLAQYLIEDLKQEGIEILQAKAEQ------IVAIMKERATFPSDLWKEGRFMLIAPTEF 414 Query: 395 NQEAKAVLEEEQVPEVLSTFAAKLEELE-EFTPDNIKASIKAVQKETGHKGKKLFMPIRV 453 +++ A E V VL+ + L++ E EFTP + KA +++ + K K+ +R+ Sbjct: 415 DEKVAAKKWNEDVVAVLTAYRDALDKFEGEFTPQSAKAMLESAAESQEIKLGKVMQAVRL 474 Query: 454 AVTGQTHGPELPQSIELIGKETAIQRL 480 AVTG GP+L + +IGK+ I+R+ Sbjct: 475 AVTGVGAGPDLMEIFTIIGKDELIKRI 501 Lambda K H 0.316 0.137 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 660 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 513 Length adjustment: 34 Effective length of query: 449 Effective length of database: 479 Effective search space: 215071 Effective search space used: 215071 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory