Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011386660.1 AMB_RS21810 tRNA glutamyl-Q(34) synthetase GluQRS
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000009985.1:WP_011386660.1 Length = 277 Score = 155 bits (392), Expect = 2e-42 Identities = 99/275 (36%), Positives = 140/275 (50%), Gaps = 20/275 (7%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MT+ R APSPTG LH+G A +A+F + A+ GG+F+LRIED DR R RPE+T+ I Sbjct: 1 MTI-TRFAPSPTGELHLGHAHSALFAFAAAKAAGGRFLLRIEDIDRTRCRPEFTQGIFTD 59 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLGL W+ QS+ D YR A+ L GL Y C+CT ++ + E + G AP Sbjct: 60 LGWLGLDWERPVRVQSEHFDEYRAALDRLEGMGLLYPCFCTRKD---IAREVEGAGHAPH 116 Query: 121 ------YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDR----QIEWQDLVRGRVSWQGA 170 Y RHL+ E+ AG+ +R + + W D +G + Q Sbjct: 117 GPDGPLYPGHCRHLSVAERRERREAGQAFALRLDVAAAAARVGPLAWHDRAQGEQTAQ-P 175 Query: 171 DLGGDMVIARAAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGA 230 +L GD+V+AR Y+L V VDD G+T V RG+D T LL LG Sbjct: 176 ELFGDVVLARKDIPAS-----YHLAVTVDDALQGVTLVTRGQDLFEATHVHRLLQALLGL 230 Query: 231 TPPNFAHTPLILNSTGQKLSKRDGVTSISDFRAMG 265 P + H L+ + +G++ +KRD ++ R G Sbjct: 231 PVPGYLHHRLLTDPSGRRYAKRDRSLTLRALREAG 265 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: 392 Number of extensions: 17 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: 277 Length adjustment: 30 Effective length of query: 455 Effective length of database: 247 Effective search space: 112385 Effective search space used: 112385 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 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