Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate 207152 DVU1693 glutamyl-tRNA synthetase
Query= metacyc::MONOMER-13959 (483 letters) >MicrobesOnline__882:207152 Length = 324 Score = 179 bits (454), Expect = 1e-49 Identities = 102/258 (39%), Positives = 147/258 (56%), Gaps = 4/258 (1%) Query: 5 VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64 +R R APSPTG++H+GNA + +L AR GGK ++R+ED D R + + L+ Sbjct: 2 IRGRLAPSPTGNIHLGNAWAFMLAWLAARQAGGKVLLRMEDIDPDRARPEYAEGIMADLR 61 Query: 65 WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124 WLG+DWDE D+GG GPY QS R Y + L G Y CYCT +EL Sbjct: 62 WLGLDWDEGPDIGGPCGPYVQSRRVQDYARVLDVLATLGAVYPCYCTRKELRTLAGAPHP 121 Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKG--EISFESDGI 182 Y G R+LT EE + EGR+P++R R P+G V AF+D + G + ES G Sbjct: 122 GDLGAPYPGTCRNLTIEECSRKEKEGRRPAMRLRWPDG-VFAFDDGLFGPQQAGGESCG- 179 Query: 183 GDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHM 242 GDF + + DG Y AV +DD M +T V+RG D +S TP+Q+ +Y G P + H+ Sbjct: 180 GDFALRRSDGVFAYQLAVVVDDIAMGVTQVVRGADLLSCTPRQLALYSLLGAQPPAYLHV 239 Query: 243 TLIVNESRKKLSKRDESI 260 L+++ + ++L+KR +S+ Sbjct: 240 PLLLDATGERLAKRHQSL 257 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: 354 Number of extensions: 13 Number of successful extensions: 4 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: 324 Length adjustment: 31 Effective length of query: 452 Effective length of database: 293 Effective search space: 132436 Effective search space used: 132436 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