Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate WP_086510351.1 BZY95_RS13015 threonine/serine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >NCBI__GCF_002151265.1:WP_086510351.1 Length = 315 Score = 221 bits (563), Expect = 2e-62 Identities = 129/307 (42%), Positives = 186/307 (60%), Gaps = 3/307 (0%) Query: 1 MITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIA 60 M+ LE I+EAQR + + + T L VLSE G I+LK E Q+TGSFK RG N + Sbjct: 1 MLPLERIQEAQRRIADSLPPTPLLLDHVLSEKFGRRIWLKGELFQRTGSFKPRGGLNWLR 60 Query: 61 HLSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120 EEE G+ A SAGNHA G+A AA +P TIVMP A K+ +R LGA+VIL Sbjct: 61 SAGEEELAGGLGAVSAGNHALGLAWAAGQADVPVTIVMPENASPFKVEGSRKLGAEVILH 120 Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGG 180 G+I +EA+E R+ + G VHP++D ++AGQGT+GLEI+E P+ ++ PVGGGG Sbjct: 121 GDI-NEAWELMHRLVAERGLTLVHPYDDERIMAGQGTVGLEILEQAPEATAILCPVGGGG 179 Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLT 240 LI+G+ A ++ P + +IGV+ SM A+ G ER+E T A + G+ T Sbjct: 180 LIAGIGSAAAALRPGLALIGVEPSGAASMAAAWSAGAPERLERVATCAKSLGAAIVGEHT 239 Query: 241 FELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLDVKGKK--VAI 298 + + ++ +++ V+++ I A+ LL QAK++AE AVGVAA+L L + V + Sbjct: 240 YPVCRETTQKLLQVDDDAIGRAMRHLLYQAKLMAEPGAAVGVAALLEDLVTLPPEGDVVV 299 Query: 299 VISGGNI 305 VI+GGN+ Sbjct: 300 VITGGNM 306 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: 255 Number of extensions: 9 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: 315 Length adjustment: 29 Effective length of query: 372 Effective length of database: 286 Effective search space: 106392 Effective search space used: 106392 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 10 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