Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate Echvi_1189 Echvi_1189 Threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Cola:Echvi_1189 Length = 319 Score = 178 bits (452), Expect = 2e-49 Identities = 108/310 (34%), Positives = 176/310 (56%), Gaps = 6/310 (1%) Query: 4 LEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLS 63 L DIK+A + + +H T + ++++ ++Y K EN QK G+FK RGA N I L Sbjct: 10 LIDIKQAYQRIMAYIHHTPILTCEAINKMADCQLYFKCENFQKVGAFKARGATNAILKLP 69 Query: 64 EEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVI-LEGN 122 +K GV S+GNHA +A AA+ G A IVMP A K R G ++I E N Sbjct: 70 PGLKKNGVATHSSGNHAAALARAAKETGTKAYIVMPSTAAAIKKAAVRTYGGEIIECEPN 129 Query: 123 IFDEAYEAAL-RIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGL 181 + +A E L ++ E+TGA F+ P++ VI GQ T LE+ ++ + ++ PVGGGGL Sbjct: 130 L--KARETTLEKVVEETGAAFIPPYDYMDVIEGQATCALEMWDEGIPFDAIITPVGGGGL 187 Query: 182 ISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTF 241 ++G ++ ++ + V G + + SL+ + +E T+ADG+ + G F Sbjct: 188 LAGTALTTHYLSRKTPVYGAEPKGADDAYRSLKANKIIPMENPNTIADGL-LTSLGKRNF 246 Query: 242 ELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDVKGKKVAIVI 300 ++ K V +++ V++++I A+ + E+ K+V E + AV +AA+L NK + K+V IVI Sbjct: 247 TIISKNVADILTVSDDQIIAAMRLVFERMKLVIEPSSAVPLAAILANKPLFQNKRVGIVI 306 Query: 301 SGGNIDVNMI 310 SGGN+DV+ + Sbjct: 307 SGGNVDVSKL 316 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: 218 Number of extensions: 8 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: 319 Length adjustment: 29 Effective length of query: 372 Effective length of database: 290 Effective search space: 107880 Effective search space used: 107880 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