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_011882283.1 serine/threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >NCBI__GCF_000016205.1:WP_011882283.1 Length = 325 Score = 229 bits (583), Expect = 1e-64 Identities = 112/306 (36%), Positives = 187/306 (61%), Gaps = 1/306 (0%) Query: 3 TLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHL 62 T +D+ A L+ HRT + SS L + G +++ K ENLQ+ G+FK RGA+N ++ Sbjct: 8 TYDDVAAAAARLQGHAHRTPVMTSSTLDDALGAQVFFKCENLQRMGAFKFRGAFNALSRF 67 Query: 63 SEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGN 122 +R+ GVV S+GNHAQ +AL+A++ GIPATIVMP+ AP +K+ TR G V+ Sbjct: 68 DATQRRNGVVTFSSGNHAQAIALSARMLGIPATIVMPQDAPAAKMAATRGYGGNVVTYDR 127 Query: 123 IFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLI 182 ++ + + EK G + P++ VIAGQGT E+ +++ ++ V P+GGGGL+ Sbjct: 128 YTEDREQIGRELAEKHGLTLIPPYDHADVIAGQGTAAKELFDEVGPLDAVFAPLGGGGLL 187 Query: 183 SGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFE 242 SG ++A ++++P+ K+ GV+ E S R G ++ T+ADG + G+LTF+ Sbjct: 188 SGTALATRALSPQAKLYGVEPEAGNDGQQSFRSGAIVHIDTPRTIADGAQTQHLGNLTFQ 247 Query: 243 LVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLN-KLDVKGKKVAIVIS 301 ++++ VD+++ + E+ D++ F + K++ E G + +AA K ++ GK+V IVIS Sbjct: 248 ILRRDVDDILTATDAELVDSMRFFATRMKLIVEPTGCLSLAAARKMKDELAGKRVGIVIS 307 Query: 302 GGNIDV 307 GGN+D+ Sbjct: 308 GGNVDL 313 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: 237 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: 325 Length adjustment: 29 Effective length of query: 372 Effective length of database: 296 Effective search space: 110112 Effective search space used: 110112 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