Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate SM_b20432 SM_b20432 threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Smeli:SM_b20432 Length = 334 Score = 231 bits (589), Expect = 2e-65 Identities = 128/317 (40%), Positives = 198/317 (62%), Gaps = 3/317 (0%) Query: 2 ITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAH 61 +T++DI+ A R + V T LA S LSE+ G + LK+E+ Q TGSFK+RGA N + Sbjct: 7 VTIDDIEVAARRISGRVLTTPLAMSGSLSELCGVPVGLKLEHHQTTGSFKLRGATNAVLS 66 Query: 62 LSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEG 121 LS +R GV+AAS GNH + +A AA+ G ATI M P++K+++ R LGA V + G Sbjct: 67 LSAGDRALGVIAASTGNHGRALAHAAKAEGSVATICMSHLVPVNKVSEIRRLGANVRIVG 126 Query: 122 NIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGL 181 N DEA E R+ + G V V PF+ ++AGQGT+GLE++ +PDV +V+VPV GGGL Sbjct: 127 NSQDEAQEEVERLVAENGLVMVPPFDHRAIVAGQGTLGLEVVAQMPDVAMVLVPVSGGGL 186 Query: 182 ISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLAD--GIAVKKPGDL 239 +GV+ A+K+ P +VIG+ E +M AS G V+ +P+LAD G + + Sbjct: 187 AAGVAAAVKARRPATRVIGLTMERGAAMKASFAAGGPALVDEQPSLADSLGGGIGLDNRV 246 Query: 240 TFELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDVKGKKVAI 298 TF + ++ +D+++ + E EIA + + + + EGAGAVG++A+L K+ +A+ Sbjct: 247 TFRMCRELLDDIILLTEAEIAAGMRHAYAEEREIVEGAGAVGISALLAGKIKDIDGPIAV 306 Query: 299 VISGGNIDVNMIDRIIN 315 +ISG N+D+++ R++N Sbjct: 307 IISGRNVDMDLHLRVMN 323 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: 286 Number of extensions: 11 Number of successful extensions: 3 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: 334 Length adjustment: 30 Effective length of query: 371 Effective length of database: 304 Effective search space: 112784 Effective search space used: 112784 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