Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate 3607475 Dshi_0888 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Dino:3607475 Length = 324 Score = 205 bits (521), Expect = 1e-57 Identities = 118/314 (37%), Positives = 178/314 (56%), Gaps = 3/314 (0%) Query: 12 DDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTD 71 DD++ A +R+ I++T + S+YF++ E+F K EN Q+ G+FK+RGA N + L+D Sbjct: 14 DDVVAAHERIKPHIHRTPVLTSSYFNDLVGAELFFKCENFQKAGAFKVRGACNAVFGLSD 73 Query: 72 AEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNF 131 A +GV S+GNHA +S + GI VVMP+ AP++K AA Y + + Sbjct: 74 ALAERGVATHSSGNHALSLSYAAGRRGIPCNVVMPRTAPEAKKAAVRGYGGIITECEPST 133 Query: 132 NDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAG 191 A +E+ E G F+ PY+DP+V+AGQGT E ME +D +I PIGGGG+I+G Sbjct: 134 TSREAVFAEVQERTGAEFVHPYNDPRVVAGQGTCSREFMEQTDGLDMMIAPIGGGGMISG 193 Query: 192 IAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYEIV 251 + + +I P +++I + E SF +G I T+ADG V +LT+ V Sbjct: 194 CCLTLSNIAPEVQIIAAEPEQADDAYRSFKAGHIIADDAPVTIADGLKVPLK-DLTWHFV 252 Query: 252 RELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKTVSIIS 311 V DI+ SE EI ++M QR K+V E + A+ A +L K D++ R V I++ Sbjct: 253 SNHVSDILTASEQEIIDAMKLTWQRMKIVMEPSCAVPLATILKNK-DKFAGKRVGV-IVT 310 Query: 312 GGNIDLSRVSQITG 325 GGN+DL ++ ITG Sbjct: 311 GGNVDLDKLPWITG 324 Lambda K H 0.318 0.136 0.386 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: 233 Number of extensions: 7 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: 329 Length of database: 324 Length adjustment: 28 Effective length of query: 301 Effective length of database: 296 Effective search space: 89096 Effective search space used: 89096 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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