Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate N515DRAFT_0537 N515DRAFT_0537 threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Dyella79:N515DRAFT_0537 Length = 315 Score = 171 bits (432), Expect = 4e-47 Identities = 102/309 (33%), Positives = 170/309 (55%), Gaps = 4/309 (1%) Query: 4 LEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLS 63 L+ I++A + T + S+ L + G +++ K ENLQ+ G+FK RGA N + L Sbjct: 7 LDQIRDAAARIAPYAAVTPVLRSARLDALAGAQLHFKCENLQRGGAFKFRGACNAVWSLD 66 Query: 64 EEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNI 123 + + RGVV S+GNH +A+AA GI A +V+P A +K+ GA V+ Sbjct: 67 DAQAARGVVTHSSGNHGNALAMAAATRGIAAHVVVPEGAVRAKLEAIEQAGA-VLHRCAP 125 Query: 124 FDEAYEA-ALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLI 182 A EA +Q +TGA VHP+ D V+AGQGT+ LE+M + ++ ++ PVGGGGL Sbjct: 126 TTAAREAMTAELQRQTGAELVHPYADARVMAGQGTLVLELMRQVEGLDALITPVGGGGLA 185 Query: 183 SGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFE 242 +G ++A + PE+ + G + SL +G TL DG+ G F+ Sbjct: 186 AGCAIAAHGLKPELAMYGAEPTGADDAARSLAQGARVEPFQADTLCDGLRT-LIGAPNFD 244 Query: 243 LVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIVIS 301 ++ + +++ V++EE A+ L + K+V E + A +AAVL + + G++V +V++ Sbjct: 245 ALRTHRTQVITVSDEETIAAMKLLWRELKLVVEVSSATVLAAVLKQAEHFAGRRVGLVLT 304 Query: 302 GGNIDVNMI 310 GGN+D++ + Sbjct: 305 GGNVDLDAL 313 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: 222 Number of extensions: 10 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: 315 Length adjustment: 29 Effective length of query: 372 Effective length of database: 286 Effective search space: 106392 Effective search space used: 106392 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