Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_085770076.1 B1812_RS01795 tRNA glutamyl-Q(34) synthetase GluQRS
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_002117405.1:WP_085770076.1 Length = 305 Score = 137 bits (344), Expect = 7e-37 Identities = 96/278 (34%), Positives = 133/278 (47%), Gaps = 21/278 (7%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSP G LH+G A +A+ N+ AR GG+F+LR ED D R+RP+Y I E L WLG Sbjct: 18 RFAPSPNGFLHLGHAYSALLNFELARTCGGRFLLRTEDIDLARARPDYEAAIYEDLAWLG 77 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQ--APRYDN 123 L W+ QS+ Y A++ L GL Y C CT E+ + AP Y Sbjct: 78 LDWERPVRRQSEHFADYAAALERLDAMGLVYPCACTRSEIAKAAGPDPLRDPDGAPLYPG 137 Query: 124 RHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLG---------G 174 R E AG + +++ + + G +SW+ G G Sbjct: 138 TCRGNRRESLREILKAGG---VALRLDMAKAMNVLGAEAGALSWREHRRGDIPAHPERWG 194 Query: 175 DMVIARA-APRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPP 233 D+V+AR P Y+L VVVDD G+T+V+RG D + T LL LG P Sbjct: 195 DVVLARKDTPTS------YHLAVVVDDALQGVTNVVRGADLLPATGLHRLLQGLLGLPAP 248 Query: 234 NFAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPAL 271 ++ H L+L + G+KLSK ++ D RA G A A+ Sbjct: 249 SYRHHALLLCAEGEKLSKSKSSKTLRDLRAEGMSAAAV 286 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: 382 Number of extensions: 23 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: 305 Length adjustment: 30 Effective length of query: 455 Effective length of database: 275 Effective search space: 125125 Effective search space used: 125125 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 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