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_086510078.1 BZY95_RS11575 hydroxyectoine utilization dehydratase EutB
Query= SwissProt::Q9WYJ1 (401 letters) >NCBI__GCF_002151265.1:WP_086510078.1 Length = 334 Score = 230 bits (587), Expect = 4e-65 Identities = 131/318 (41%), Positives = 193/318 (60%), Gaps = 7/318 (2%) Query: 2 ITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAH 61 +TL I +A+R + RT L S LSE +I LK+E LQ +G+FK+RGA N IA Sbjct: 8 VTLASIYQARRRIAGQALRTPLVRSHALSERFDADILLKLETLQPSGAFKLRGAANMIAA 67 Query: 62 LSE----EERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQV 117 L E + + GVV AS GNH + VA AA G+PATI + R P +K+ LGA+V Sbjct: 68 LIERHGCDALEAGVVTASTGNHGRAVAYAAARLGVPATICLSRLVPANKVAAIEALGAEV 127 Query: 118 ILEGNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVG 177 G DEA+ R+ + G + PF+DP + AGQGTIGLE+MED PD++ V+V + Sbjct: 128 RRVGESQDEAFGEVERLIRERGMTLIPPFDDPLIAAGQGTIGLELMEDAPDLDRVIVGLS 187 Query: 178 GGGLISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLAD--GIAVKK 235 GGGL+ G+ A+K++ PE ++ GV +M SL+ GR VE +LAD G + Sbjct: 188 GGGLLGGIGAAVKAIRPEARITGVSLSRGAAMWQSLQAGRPVAVEEVESLADSLGGGIGL 247 Query: 236 PGDLTFELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDVKGK 294 TF LV++ +DE V+E IA A++ +LE K++ EGA AVG+AA+ + ++V+G+ Sbjct: 248 DNRCTFSLVREVMDEHYQVSEAAIAQAMVDILEHEKLLVEGAAAVGLAALAEHGIEVRGQ 307 Query: 295 KVAIVISGGNIDVNMIDR 312 +VA+++SG + + +DR Sbjct: 308 RVALILSGNGVALETLDR 325 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: 256 Number of extensions: 9 Number of successful extensions: 4 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 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