Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate Dsui_1040 Dsui_1040 glutamyl-queuosine tRNA(Asp) synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__PS:Dsui_1040 Length = 303 Score = 152 bits (383), Expect = 2e-41 Identities = 101/280 (36%), Positives = 143/280 (51%), Gaps = 18/280 (6%) Query: 4 RVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQW 63 R R APSP+G LH G+ A+ + L AR R G++++R+ED D R+ P + IL L+ Sbjct: 9 RGRFAPSPSGPLHFGSLVAALGSCLEARCRQGEWLVRMEDVDGPRTVPGAADAILRSLEA 68 Query: 64 LGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDN 123 G WD +QS R + Y A+ L GLAY C C+ +E+ + G APRY Sbjct: 69 YGFVWDGPVLWQSQRHEAYAAALARLQAAGLAYPCACSRKEIAEGHGGRSIDG-APRYAG 127 Query: 124 RHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAP 183 R Q+ R P DR++ ++D + GRV GD+V+ RA Sbjct: 128 TCRSGLQPGQSPRAWRLRLP--------DREVSFEDGLLGRVGHNLERDVGDIVLLRAD- 178 Query: 184 RGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILN 243 G Y L VVVDD G+T V+RG D + +TP+QI L + LG P + H PL N Sbjct: 179 ----GQYAYQLAVVVDDAFQGVTHVVRGADLLDSTPRQIWLQQCLGVPTPAYVHLPLATN 234 Query: 244 STGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPP 283 + G+KLSK+ ++ D R + PAL + + LG PP Sbjct: 235 ARGEKLSKQTRALALDDDRPV----PALVDALEFLGQRPP 270 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: 404 Number of extensions: 26 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: 303 Length adjustment: 30 Effective length of query: 455 Effective length of database: 273 Effective search space: 124215 Effective search space used: 124215 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