Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate PfGW456L13_1527 glutamyl-Q-tRNA synthetase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1527 Length = 298 Score = 135 bits (341), Expect = 1e-36 Identities = 85/249 (34%), Positives = 129/249 (51%), Gaps = 27/249 (10%) Query: 8 RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67 R+AP+P+GHLH G+ AL +YL AR+ GG++++R+ED D R + G + + L L+ G Sbjct: 12 RFAPTPSGHLHFGSLVAALASYLDARSVGGRWLMRMEDLDPPREVPGAQAAILKALESYG 71 Query: 68 IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127 +WD G RQSER+D Y + L +GLAY C C+ ++LE Sbjct: 72 FEWDG--------GLVRQSERHDAYAEVIDRLFNQGLAYACTCSRKQLEP---------- 113 Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI-SFESDGIGDFV 186 Y G + L + +IR RVPE + F D V+G+ +GDFV Sbjct: 114 ---YHGIYPGLCRNAGH----GTDDAAIRLRVPELE-YHFIDRVQGQYRQHLGREVGDFV 165 Query: 187 IVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIV 246 I ++DG Y AV +DD +T ++RG D + +TP+Q+ + + G P++ H+ LI Sbjct: 166 IRRRDGLYAYQLAVVLDDAWQGITDIVRGADLLDSTPRQLYLQELLGLPQPRYLHIPLIT 225 Query: 247 NESRKKLSK 255 KL K Sbjct: 226 QPDGNKLGK 234 Lambda K H 0.316 0.137 0.394 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: 369 Number of extensions: 22 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: 483 Length of database: 298 Length adjustment: 30 Effective length of query: 453 Effective length of database: 268 Effective search space: 121404 Effective search space used: 121404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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