Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate SMc00735 SMc00735 glutamyl-Q tRNA(Asp) synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Smeli:SMc00735 Length = 298 Score = 163 bits (413), Expect = 6e-45 Identities = 114/297 (38%), Positives = 148/297 (49%), Gaps = 38/297 (12%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSP G LH+G A +A+ N A GG+F+LRIED DR R RPE+ I E L WLG Sbjct: 12 RFAPSPNGLLHLGHALSAILNHDMAAAMGGRFLLRIEDIDRTRCRPEFEAAIFEDLAWLG 71 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQA------- 118 L W+E QS+ L +Y A++ L GL Y T E+ A A +AKGQA Sbjct: 72 LDWEEPVRRQSEHLGVYAAALERLKAMGLVYPAVMTRGEIRAAVAAAEAKGQAWPRDPDG 131 Query: 119 -PRYDNRHRHLTPEEQAAFEAAGRTPVIRFKIED-----DRQIEWQD-----------LV 161 P Y R R TP+EQAA A+GR R + + + W++ +V Sbjct: 132 TPLYPGRERGFTPDEQAALLASGRPYAWRLDMGEAVRCAGEPLTWRETGLSQSGEATSIV 191 Query: 162 RGRVSWQGADLGGDMVIARA-APRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPK 220 +W GD++++R+ AP Y+L VVVDD GIT V+RG D T Sbjct: 192 ADPAAW------GDVILSRSDAPSS------YHLSVVVDDALQGITHVVRGRDLYHATSV 239 Query: 221 QILLYEALGATPPNFAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTL 277 LL L P + H L+L G+KLSK D T I+ FRA G+ PA M L Sbjct: 240 HRLLQRLLDLPQPVYHHHRLVLGPDGRKLSKSDSDTGIAAFRAAGH-RPADVRAMVL 295 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: 410 Number of extensions: 26 Number of successful extensions: 3 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: 298 Length adjustment: 30 Effective length of query: 455 Effective length of database: 268 Effective search space: 121940 Effective search space used: 121940 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