Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate Pf6N2E2_1562 Threonine dehydratase (EC 4.3.1.19)
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1562 Length = 318 Score = 183 bits (464), Expect = 7e-51 Identities = 110/307 (35%), Positives = 172/307 (56%), Gaps = 3/307 (0%) Query: 2 ITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAH 61 +T +DI++A R L V+ TA +L+E G +++K EN TG+FK+RG + Sbjct: 4 LTRDDIEQAARHLYEVMPATAQYAWPLLAERLGCTVWVKHENHTPTGAFKVRGGLTFVRW 63 Query: 62 LSEEERK-RGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120 L E + +G+V A+ GNH Q +ALAA G+ A IV+P+ + K R G +V+ Sbjct: 64 LKREHPEAKGIVTATRGNHGQSLALAASALGLKALIVVPQGNSVEKNNAMRGFGGEVVEY 123 Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGG 180 G FDEA E A+R+ + G V PF+ P ++ G T GLE+ +PD++ V VP+G G Sbjct: 124 GRDFDEAREEAVRLAQSHGLYLVPPFH-PELVKGVATYGLELFNAVPDLDTVYVPIGCGS 182 Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLT 240 I V A ++ + +V+GV + + S GR T ADG+AV++P Sbjct: 183 GICAVIAARDALGLKTQVVGVVSTEALAAKLSFEAGRLCETASANTFADGLAVRRPVPEA 242 Query: 241 FELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIV 299 F + +VAV++ EIA A+ +AEGAGA +AA++ + + ++GK+VA++ Sbjct: 243 FAIYGAGAARIVAVSDAEIAGAMRAYYTDTHNLAEGAGAAALAALMQERETMRGKRVAVI 302 Query: 300 ISGGNID 306 +SGGNID Sbjct: 303 LSGGNID 309 Lambda K H 0.317 0.136 0.367 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: 245 Number of extensions: 15 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: 401 Length of database: 318 Length adjustment: 29 Effective length of query: 372 Effective length of database: 289 Effective search space: 107508 Effective search space used: 107508 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: 49 (23.5 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