Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate 3607475 Dshi_0888 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Dino:3607475 Length = 324 Score = 221 bits (564), Expect = 2e-62 Identities = 118/310 (38%), Positives = 185/310 (59%), Gaps = 4/310 (1%) Query: 3 TLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHL 62 T +D+ A +K +HRT + SS +++ G E++ K EN QK G+FK+RGA N + L Sbjct: 12 TYDDVVAAHERIKPHIHRTPVLTSSYFNDLVGAELFFKCENFQKAGAFKVRGACNAVFGL 71 Query: 63 SEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGN 122 S+ +RGV S+GNHA ++ AA GIP +VMPR AP +K R G +I E Sbjct: 72 SDALAERGVATHSSGNHALSLSYAAGRRGIPCNVVMPRTAPEAKKAAVRGYGG-IITECE 130 Query: 123 IFDEAYEAAL-RIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGL 181 + EA +QE+TGA FVHP+NDP V+AGQGT E ME +++++ P+GGGG+ Sbjct: 131 PSTTSREAVFAEVQERTGAEFVHPYNDPRVVAGQGTCSREFMEQTDGLDMMIAPIGGGGM 190 Query: 182 ISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTF 241 ISG + + ++ PEV++I + E S + G + T+ADG+ V DLT+ Sbjct: 191 ISGCCLTLSNIAPEVQIIAAEPEQADDAYRSFKAGHIIADDAPVTIADGLKVPLK-DLTW 249 Query: 242 ELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDVKGKKVAIVI 300 V +V +++ +E+EI DA+ ++ K+V E + AV +A +L NK GK+V +++ Sbjct: 250 HFVSNHVSDILTASEQEIIDAMKLTWQRMKIVMEPSCAVPLATILKNKDKFAGKRVGVIV 309 Query: 301 SGGNIDVNMI 310 +GGN+D++ + Sbjct: 310 TGGNVDLDKL 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: 251 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: 324 Length adjustment: 29 Effective length of query: 372 Effective length of database: 295 Effective search space: 109740 Effective search space used: 109740 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