Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate GFF5498 PS417_28140 asparaginase
Query= curated2:Q8TV84 (458 letters) >FitnessBrowser__WCS417:GFF5498 Length = 325 Score = 137 bits (344), Expect = 7e-37 Identities = 111/356 (31%), Positives = 167/356 (46%), Gaps = 51/356 (14%) Query: 98 NVSVMSTGGTIACRVDYETGAVKPAFTAE--ELVGAVPELLDVINIVDARAVLDLLSENM 155 NV V+ TGGTI + A F A E + +P + ++D S NM Sbjct: 6 NVMVLYTGGTIGMQASTHGLAPASGFEARMREQLAHLPA--PAWRFQEMAPLID--SANM 61 Query: 156 EPKHWMKIAEEVVDALSDPDVEGVVIGHGTDTMAFTAAALSFVIEGLNGPVVLVGAQRSS 215 P +W ++ VV+A+ D + V+I HGTDT+A++AAA+SF + GL PVV G+ + Sbjct: 62 TPAYWQRLRTAVVEAVDD-GCDAVLILHGTDTLAYSAAAMSFQLLGLPAPVVFTGSMLPA 120 Query: 216 DRPSSDAASNLIAACAFAGDGEVGEVTVCMHGWTSDEVCLVHRGVRVRKMHTSRRDAFRS 275 P SDA N+ A A G G V + HG + R K+ + R+ F + Sbjct: 121 GVPDSDAWENVSGALAALGKGIAPGVHLYFHG-------ALMAPTRCAKIRSFGRNPFAA 173 Query: 276 V---------ESIPIAKVDVKDLRNPKIEFLRSDYRRPEDGEPEISGGFEEKVALVKFAP 326 + ESIP A DYR+P+ V ++ P Sbjct: 174 LNRQGGAARAESIPQAL----------------DYRQPKA---------LASVGVLPLVP 208 Query: 327 GMDPEVLDFYVDRGYRGIVLE--GTGLGHVSE-QWLESIERAVDDGIAVVMTSQCLYGRV 383 G+ LD + G + ++LE G+G G ++L S++RA D G+ VV +QC G V Sbjct: 209 GIGAAQLDAVIGSGIQALILECFGSGTGPSDNPEFLASLQRAQDQGVVVVAITQCHEGGV 268 Query: 384 NMNVYRTGRLLRAVGVIPGEDMLPEVAYVKLMYVLDRTDDIKEVERLMRTNIAGEI 439 ++VY G LR VGV+ G M E A+ KL ++ D +EV RL+ ++ GE+ Sbjct: 269 ELDVYEAGSRLRGVGVLSGGGMTREAAFGKLNALIGAGLDTQEVRRLVELDLCGEL 324 Lambda K H 0.318 0.139 0.404 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: 343 Number of extensions: 26 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: 458 Length of database: 325 Length adjustment: 30 Effective length of query: 428 Effective length of database: 295 Effective search space: 126260 Effective search space used: 126260 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 (21.7 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