Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate Pf1N1B4_2023 L-asparaginase (EC 3.5.1.1)
Query= curated2:Q8TV84 (458 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2023 Length = 334 Score = 139 bits (350), Expect = 1e-37 Identities = 116/352 (32%), Positives = 169/352 (48%), Gaps = 31/352 (8%) Query: 94 PKLPNVSVMSTGGTIACRVDYETGAVKPAFTAE--ELVGAVPELLDVINIVDARAVLDLL 151 P +V V+ TGGTI + A F A E + + PEL V+ R + L+ Sbjct: 7 PAAQHVMVLYTGGTIGMQASAHGLAPASGFEARMREYLHSQPEL--VVPQWRFREMAPLI 64 Query: 152 -SENMEPKHWMKIAEEVVDALSDPDVEGVVIGHGTDTMAFTAAALSFVIEGLNGPVVLVG 210 S NM P +W ++ E VVDA+ + V+I HGTDT+A++AAA+SF + GL+ VV G Sbjct: 65 DSANMTPAYWQQLREAVVDAVDVQGCDSVLILHGTDTLAYSAAAMSFQLLGLHARVVFTG 124 Query: 211 AQRSSDRPSSDAASNLIAACAFAGDGEVGEVTVCMHGWTSDEVCLVHRGVRVRKMHTSRR 270 + + SDA NL A G G V + H D R K+ + R Sbjct: 125 SMLPAGVTDSDAWENLSGALVALGQGLAPGVHLYFHSELLDP-------TRCAKVRSFGR 177 Query: 271 DAFRSVESIPIAKVDVKDLRNPKIEFLRSDYRRPEDGEPEISGGFEEKVALVKFAPGMDP 330 F+ +E VK P + +Y +P+ KVA + PG+ Sbjct: 178 HPFKRLER---QGGGVKATSVP----AQLNYNQPKQ---------LAKVAALPLFPGIGA 221 Query: 331 EVLDFYVDRGYRGIVLE--GTGLG-HVSEQWLESIERAVDDGIAVVMTSQCLYGRVNMNV 387 E LD ++ G +G+VLE G+G G + +L S+ERA D G+ VV +QC G V ++V Sbjct: 222 EQLDGLLNSGIQGLVLECYGSGTGPSDNPAFLASLERARDKGVVVVAVTQCHEGGVQLDV 281 Query: 388 YRTGRLLRAVGVIPGEDMLPEVAYVKLMYVLDRTDDIKEVERLMRTNIAGEI 439 Y G LR GV+ G M E A+ KL +L + EV RL+ ++ GE+ Sbjct: 282 YEAGSRLRDAGVLSGGGMTREAAFGKLHALLGAGLETTEVRRLVELDLCGEL 333 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: 369 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: 458 Length of database: 334 Length adjustment: 31 Effective length of query: 427 Effective length of database: 303 Effective search space: 129381 Effective search space used: 129381 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 Jul 25 2024. The underlying query database was built on Jul 25 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