Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate PP_0495 PP_0495 type 1 L-asparaginase
Query= curated2:O26802 (435 letters) >FitnessBrowser__Putida:PP_0495 Length = 329 Score = 102 bits (253), Expect = 2e-26 Identities = 87/288 (30%), Positives = 133/288 (46%), Gaps = 30/288 (10%) Query: 145 SENMKPEYWVETARAVYGEIK-DGADGVVVAHGTDTMHYTSAALSFMLRT-PVPVVFTGA 202 S NM+ W+ A+ + G DGV+V HGTD+M Y++AALSF+L P PVV TG+ Sbjct: 61 SANMQQHNWLAMRDAIVAAVDVAGHDGVLVLHGTDSMAYSAAALSFLLLDLPAPVVLTGS 120 Query: 203 QRSSDRPSSDASLNIQCSVRAATSEIAEVTVCMHATMDDLSCHLH----RGVKVRKMHTS 258 + P SDA N+ ++R H D + + H G + K+ + Sbjct: 121 MLPAGVPDSDAWDNLCGALRQFE----------HGLEDGVQLYFHGQLLHGCRASKLRSE 170 Query: 259 RRDTFRSMNALPLAEVTPDGIKILEENYRKRGSDELELSDRVEERVAFIKSYPGISPDII 318 D F ++ AE D I E Y++ R +A + +PG+ + Sbjct: 171 AFDAFAALPRHRDAE-RADTIPA-ELGYKQ---------PRKPVNLAVVPVFPGLQAGHL 219 Query: 319 KWHLDEGYRGIVIE--GTGLGHCPD-TLIPVIGEAHDMGVPVAMTSQCLNGRVNMNVYST 375 + +D G +G+++E G+G G D L+ V+ A GV +A SQC G V + Y+ Sbjct: 220 QALIDSGVQGLLLECYGSGTGPSDDQALLNVLSTARQRGVMLAAISQCPEGSVVFDTYAA 279 Query: 376 GRRLLQAGVIPCDDMLPEVAYVKMCWVLGQTDDPEMAREMMRENIAGE 423 G RL AG++ M E A KM +LG D + A ++ GE Sbjct: 280 GNRLRGAGLVSGGGMTREAALGKMVALLGAGLDADAADRWFVLDLCGE 327 Lambda K H 0.318 0.135 0.395 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: 335 Number of extensions: 20 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: 435 Length of database: 329 Length adjustment: 30 Effective length of query: 405 Effective length of database: 299 Effective search space: 121095 Effective search space used: 121095 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