Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate GFF2535 PS417_12925 serine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__WCS417:GFF2535 Length = 321 Score = 240 bits (613), Expect = 4e-68 Identities = 113/315 (35%), Positives = 201/315 (63%), Gaps = 1/315 (0%) Query: 3 TLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHL 62 T +D+ +A + L+ V H T + S L +TG ++++K E+LQ+ GSFK RGA+N ++ Sbjct: 5 TYQDVIDAAQRLEGVAHATPVFTSRTLDALTGAQVFIKCEHLQRAGSFKFRGAFNALSQF 64 Query: 63 SEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGN 122 + ++RK GVVA S+GNHAQG+ALAAQ+ GIPATIVMP AP +K+ TR GA V+L Sbjct: 65 NPQQRKAGVVAFSSGNHAQGIALAAQLLGIPATIVMPTDAPAAKVAATREYGASVVLYDR 124 Query: 123 IFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLI 182 ++ + + + G + P++ PH++AGQGT E++E ++ + V +GGGG++ Sbjct: 125 FTEDREQIGRNLATEQGLTLIPPYDHPHILAGQGTAAKELLESTGPLDALFVGLGGGGML 184 Query: 183 SGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFE 242 SG +++ ++++P+ + GV+ E S R G ++ T+ADG + G+ TF Sbjct: 185 SGTALSTRALSPDCLLYGVEPEAGNDGQRSFRSGSIVHIDTPKTIADGAQTQHLGNYTFP 244 Query: 243 LVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIVIS 301 +++ V++++ V++ E+ A+ F +++ K+V E G +G+AA+LN+ KG++V I+++ Sbjct: 245 IIRDNVNDILTVSDAELVAAMKFFMQRMKMVVEPTGCLGLAALLNEAGRFKGQRVGIIVT 304 Query: 302 GGNIDVNMIDRIINK 316 GGN+D+ ++++ Sbjct: 305 GGNVDIEKYAALLSE 319 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: 267 Number of extensions: 14 Number of successful extensions: 2 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: 321 Length adjustment: 29 Effective length of query: 372 Effective length of database: 292 Effective search space: 108624 Effective search space used: 108624 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