Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate 6936591 Sama_0779 glutamyl-tRNA synthetase domain-containing protein (RefSeq)
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__SB2B:6936591 Length = 290 Score = 135 bits (339), Expect = 2e-36 Identities = 97/299 (32%), Positives = 139/299 (46%), Gaps = 29/299 (9%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSP+G+LH G+ A+ ++L AR +GG++++RIED D R P ++IL L G Sbjct: 9 RFAPSPSGSLHFGSLIAALGSFLRARSQGGQWLVRIEDIDPPREVPGAADDILRTLDAFG 68 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125 L WD +QS R + Y+ I LL G AY+C CT ++++A+ YD R Sbjct: 69 LHWDGKLMYQSQRTEAYQAKIDVLLASGEAYFCQCTRKQIQAIGGV---------YDGRC 119 Query: 126 RHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPRG 185 R L + A R V F D + G V+ + D +I R+ Sbjct: 120 RQL-GHQSGAIRIVNRARVNHF----------HDGLMGEVAVPDSFAAEDFIIKRSD--- 165 Query: 186 EIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNST 245 G Y L VV+DD GIT+V+RG D I + +Q+ L+ G P + H PL Sbjct: 166 --GLYAYQLAVVMDDAKTGITEVVRGADLIEASCRQLSLFNQFGYQAPAWMHLPLACAEA 223 Query: 246 GQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFSFERI 304 G KLSK++ T + + PAL + LG P+ L A FS I Sbjct: 224 GFKLSKQNHATPVDKANPL----PALKAALAFLGQPIPDAHSVESLLAQAVADFSVASI 278 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: 312 Number of extensions: 15 Number of successful extensions: 2 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: 290 Length adjustment: 30 Effective length of query: 455 Effective length of database: 260 Effective search space: 118300 Effective search space used: 118300 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: 50 (23.9 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