Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__azobra:AZOBR_RS06795 Length = 331 Score = 228 bits (581), Expect = 2e-64 Identities = 128/308 (41%), Positives = 184/308 (59%), Gaps = 6/308 (1%) Query: 5 EDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSE 64 +DI EA L RT L +++L+E GG + LK E LQ++GSFK RGA+N+++ L+ Sbjct: 12 QDIVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLTP 71 Query: 65 EERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNIF 124 EER+ GVVA S+GNHAQGVA AA + G+PA IVMP AP KI TR GA+V+L Sbjct: 72 EERRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRWT 131 Query: 125 DEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDV----EVVVVPVGGGG 180 + A I E+ GA V P++ P ++AGQGT+GLEI + + V+ P GGG Sbjct: 132 ESREAIATAIAEERGAATVPPYDHPQIMAGQGTVGLEIAAQAQAIGAVPDDVIAPCSGGG 191 Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRG-RAERVEGKPTLADGIAVKKPGDL 239 L+SGV+ A++ P+ ++ + + SL G R E G+ ++ D + PG L Sbjct: 192 LMSGVATAVRHSFPDARLWAAEPAGFDDVARSLAAGERVENAAGQRSICDALLTPTPGAL 251 Query: 240 TFELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDVKGKKVAI 298 TF ++K + +AV + E+ A+ + K+V E GAVG+AAVL KL G+ VA+ Sbjct: 252 TFPVMKDLLSGSLAVTDAEVKAAMAYAFTVLKLVVEPGGAVGLAAVLTGKLPAAGRTVAV 311 Query: 299 VISGGNID 306 V+SGGN+D Sbjct: 312 VLSGGNVD 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: 243 Number of extensions: 7 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: 331 Length adjustment: 29 Effective length of query: 372 Effective length of database: 302 Effective search space: 112344 Effective search space used: 112344 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