Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate PfGW456L13_3185 Threonine dehydratase (EC 4.3.1.19)
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3185 Length = 318 Score = 169 bits (428), Expect = 1e-46 Identities = 103/315 (32%), Positives = 174/315 (55%), Gaps = 3/315 (0%) Query: 2 ITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAH 61 +T +DI++A R + V+ TA +L++ G +++K EN TG+FK+RG + Sbjct: 4 LTRDDIEQAARHVYQVMPATAQYPWPLLAQRLGCTVWVKHENHTPTGAFKVRGGITFMHW 63 Query: 62 LSEEER-KRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120 L E +G+V+A+ GNH Q +ALAA+ G+ A IV+P + K R GA+V+ Sbjct: 64 LKREHPGAKGIVSATRGNHGQSLALAARTLGLQALIVVPEGNSVEKNNAMRGFGAEVVEY 123 Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGG 180 G FD+A E A R+ V PF+ ++ G T LE+ PD++ V VP+G G Sbjct: 124 GRDFDDAREEAARLAHAQDLFLVPPFHT-ELVKGVATYALELFNAAPDLDTVYVPIGCGS 182 Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLT 240 I GV A +++ E +V+GV + + S G T ADG+AV+KP Sbjct: 183 GICGVIAARDALDLETEVVGVVSTQAAAAQLSFDAGAICETASANTFADGLAVRKPIPEA 242 Query: 241 FELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIV 299 F + +V+V++++IA+A+ +AEGAGA +AA++++ + + G++V ++ Sbjct: 243 FAVYAAGAARIVSVSDDQIAEAMRVYYTDTHNLAEGAGASALAALISEREAMSGRRVGVI 302 Query: 300 ISGGNIDVNMIDRII 314 +SGGN+D ++ ++I Sbjct: 303 LSGGNVDRSVYAQVI 317 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: 227 Number of extensions: 13 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: 318 Length adjustment: 29 Effective length of query: 372 Effective length of database: 289 Effective search space: 107508 Effective search space used: 107508 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