Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Pf6N2E2_5159 glutamyl-Q-tRNA synthetase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5159 Length = 293 Score = 135 bits (340), Expect = 2e-36 Identities = 85/249 (34%), Positives = 126/249 (50%), 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: 7 RFAPTPSGHLHFGSLVAALASYLDARAMGGRWLLRMEDLDPPREEPGAQAAILKALESYG 66 Query: 68 IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127 +WD + RQSER+D Y L +GLAY C C+ ++LE Sbjct: 67 FEWDGEM--------VRQSERHDAYDQVINRLFSQGLAYACTCSRKQLE----------- 107 Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI-SFESDGIGDFV 186 Y G + L + +IR RVPE + F D V+GE +GDFV Sbjct: 108 --AYQGIYPGLCRNAGH----GTEDAAIRLRVPELE-YHFTDRVQGEFRQHLGREVGDFV 160 Query: 187 IVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIV 246 I ++DG Y AV +DD +T ++RG D + +TP+Q+ + + G P++ H+ LI Sbjct: 161 IRRRDGLYAYQLAVVLDDAWQGVTDIVRGADLLDSTPRQLYLQELLGLPQPRYLHVPLIT 220 Query: 247 NESRKKLSK 255 KL K Sbjct: 221 QPDGHKLGK 229 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: 356 Number of extensions: 19 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: 293 Length adjustment: 30 Effective length of query: 453 Effective length of database: 263 Effective search space: 119139 Effective search space used: 119139 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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