Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate GFF448 PGA1_c04590 putative threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Phaeo:GFF448 Length = 324 Score = 196 bits (498), Expect = 8e-55 Identities = 117/322 (36%), Positives = 174/322 (54%), Gaps = 6/322 (1%) Query: 1 MITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIA 60 M + I A L T L S L E+ G + +K E LQ TGSFK RG + ++ Sbjct: 1 MTSFAAIAAAADRLSGHARETPLLSSPFLDEIAGRRVLIKAECLQHTGSFKFRGGWAALS 60 Query: 61 HLSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120 L++E+R RGV+A S+GNHAQGVA AA PA I+MP+ AP KI TR LGA+V+L Sbjct: 61 ALTDEQRHRGVLAYSSGNHAQGVAAAAAAHTTPAVILMPQDAPAIKIANTRALGAEVVLF 120 Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEV----VVVPV 176 D + E G + P++D V+AGQGT+GLEI D++V V+V Sbjct: 121 DRAKDNRDAIGAELAEARGLTLIKPYDDVEVVAGQGTVGLEIARQAADLDVTEADVLVCC 180 Query: 177 GGGGLISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKP-TLADGIAVKK 235 GGGGL +GV++A++ P++KV + E + SL G+ R E +L D I Sbjct: 181 GGGGLTAGVALALEQTAPKMKVSPCEPERFDDVTRSLVAGKICRNEASAGSLCDAILTPA 240 Query: 236 PGDLTFELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGK 294 PG++TF ++ + + V+EE+ A++ + K+V E GAV +AA L D + G Sbjct: 241 PGEITFPILARLCGSGIVVSEEDAMRAMVLAFLRLKIVLEPGGAVSLAAALFHGDQLSGP 300 Query: 295 KVAIVISGGNIDVNMIDRIINK 316 + +GGN+D + +++ Sbjct: 301 AAIAIATGGNVDAALFTEALHR 322 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: 235 Number of extensions: 9 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: 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