Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011444212.1 SARO_RS02745 tRNA glutamyl-Q synthetase
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000013325.1:WP_011444212.1 Length = 281 Score = 115 bits (287), Expect = 2e-30 Identities = 97/278 (34%), Positives = 127/278 (45%), Gaps = 25/278 (8%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MTV R APSP G LH+G A +A+ A+ G+F+LRIED D RSRP+ + Sbjct: 1 MTV-TRFAPSPNGPLHLGHAYSAIVAHDRAKRDNGEFLLRIEDIDGARSRPDLADEFRAD 59 Query: 61 LQWLGLTWDE-GPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAP 119 LQWL L + E P QS R+ YR A L G+ Y C CT E+ A Q G P Sbjct: 60 LQWLRLDYREVAP--QSQRIASYRTAANELRAMGILYPCTCTRAEIAAAAVAQGPDG--P 115 Query: 120 RYDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQI----EWQDLVRGRVSWQGADLGGD 175 Y P G R +E I EW D G V ++ GD Sbjct: 116 LYPGTCLRRGP-------VPGPDVAWRLDMEQATLIAGPLEWTDERHG-VQQARPEMFGD 167 Query: 176 MVIARA-APRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPN 234 +V+ R AP Y+L +DD GIT V RG D T LL LG P Sbjct: 168 VVLWRKDAPAS------YHLAATLDDATDGITHVTRGVDLFRATHVHRLLQHLLGLPVPV 221 Query: 235 FAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPALA 272 + H P+++ + G+KL+KR +++D R G A+A Sbjct: 222 WYHHPVLVEADGRKLAKRRDAPALADRRRAGEDGRAVA 259 Lambda K H 0.320 0.136 0.418 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: 369 Number of extensions: 26 Number of successful extensions: 3 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: 485 Length of database: 281 Length adjustment: 30 Effective length of query: 455 Effective length of database: 251 Effective search space: 114205 Effective search space used: 114205 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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