Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate AZOBR_RS12675 AZOBR_RS12675 glutamyl-tRNA synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__azobra:AZOBR_RS12675 Length = 283 Score = 179 bits (454), Expect = 1e-49 Identities = 112/278 (40%), Positives = 151/278 (54%), Gaps = 20/278 (7%) Query: 3 VRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQ 62 V R APSPTG+LH+G A +A+F W AR GG+F+LRIED D +R RPE+ ++ E L Sbjct: 4 VVTRFAPSPTGHLHLGHAHSALFGWTTARKAGGRFLLRIEDIDPQRCRPEFDRDLREDLA 63 Query: 63 WLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEEL--EALRAEQKAKG-QAP 119 WLGLTW+E QS+ LD YR A+ L D G+ Y C+CT +++ E RA G P Sbjct: 64 WLGLTWEEPVRRQSEHLDDYRAALARLADLGVVYPCFCTRKDIAAEIARAGHAPHGPDGP 123 Query: 120 RYDNRHRHLTPEEQAAFEAAGRTPVIRFKIED----DRQIEWQDLVRGRVSWQGA--DLG 173 Y R L+ E+ AAG +R + + W D RG WQ A L Sbjct: 124 LYPGTCRGLSDMERQDRIAAGAAYAVRLDVGKAMAMTGPLRWHDRRRG---WQDAMPSLL 180 Query: 174 GDMVIARA-APRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATP 232 GD+V+AR P Y+L V +DD G+T V RG+D T LL E L P Sbjct: 181 GDIVLARKDVPTS------YHLAVTLDDHLQGVTLVTRGDDLFFATNAHRLLQELLRVVP 234 Query: 233 PNFAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPA 270 P++ H PL++N G++L+KRD ++ R +G L PA Sbjct: 235 PDYDHHPLLVNERGERLAKRDNAKTLRSLRELG-LTPA 271 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: 416 Number of extensions: 27 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 283 Length adjustment: 30 Effective length of query: 455 Effective length of database: 253 Effective search space: 115115 Effective search space used: 115115 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