Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate H281DRAFT_00878 H281DRAFT_00878 threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Burk376:H281DRAFT_00878 Length = 344 Score = 184 bits (468), Expect = 3e-51 Identities = 107/306 (34%), Positives = 165/306 (53%), Gaps = 3/306 (0%) Query: 3 TLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHL 62 TL+DI L V RT + + + G + K E LQ GSFK RGA+ + L Sbjct: 20 TLDDIAAQHFALTPWVARTPVFDRLDFASLEGTVVNFKFELLQAGGSFKARGAFTNLLAL 79 Query: 63 SEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGN 122 E +R GV S GNHA VA AA GI A +V+ R A +++ R A+++ + Sbjct: 80 DETQRSAGVTCVSGGNHAVAVAYAAMRLGISAKVVLFRAANPARVALCRQYRAEIVFAED 139 Query: 123 IFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLI 182 + EA+E RI+ + G FVHPFN + G T+G E PD+E V+VP+GGGGL Sbjct: 140 LA-EAFELVRRIEAEEGRYFVHPFNGYRTVLGSATLGYEWSTQTPDLEAVIVPIGGGGLA 198 Query: 183 SGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFE 242 +GV+ A++ NP V V GV+ E +M S ++ +AD + + ++E Sbjct: 199 AGVATAMRLANPGVHVFGVEPEGADAMGKSFAANHTVKMGHMHGIADSLMAPHTEEYSYE 258 Query: 243 LVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKL--DVKGKKVAIVI 300 L ++++DE+V V+++++ A+L L Q K+ E A A AA+L L ++GK+V +++ Sbjct: 259 LCRRHIDELVTVSDDQLCAAMLTLFGQLKLAVEPACAAATAALLGPLREKLQGKRVGVLL 318 Query: 301 SGGNID 306 G N D Sbjct: 319 CGTNTD 324 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: 223 Number of extensions: 4 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: 344 Length adjustment: 30 Effective length of query: 371 Effective length of database: 314 Effective search space: 116494 Effective search space used: 116494 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