Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate H281DRAFT_05256 H281DRAFT_05256 threonine ammonia-lyase, biosynthetic, long form
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Burk376:H281DRAFT_05256 Length = 341 Score = 215 bits (548), Expect = 1e-60 Identities = 120/269 (44%), Positives = 169/269 (62%), Gaps = 4/269 (1%) Query: 19 RRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGN 78 R TEL + S +L P+Y K E+ Q +FK+RGA N M P EAL +GVITASAGN Sbjct: 58 RETELERAPQLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIPAEALTRGVITASAGN 117 Query: 79 HAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYG---AEVVLTGRNFDEAYAAAVQAQ 135 HAQGVA SA +GV + + +P +TP KV A R +G EVV G ++ +AY AVQ Q Sbjct: 118 HAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQFGESYSDAYGHAVQLQ 177 Query: 136 EERGALFVHPFDDPLVMAGQGTIGLEVL-QELPDVANILVPIGGGGLIAGIATAIRETHP 194 EERG FVHPFDDP V+AGQGT+ +E+L Q + I VPIGGGGL AG+A ++ P Sbjct: 178 EERGLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAYVKSVRP 237 Query: 195 HVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLV 254 +++IGV+T + + SL+ G+ V + +DG AVK G TF + + +D+V+LV Sbjct: 238 EIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLV 297 Query: 255 EEEEIALAIVALLERTKLLVEGAGAVPLA 283 + + AI + + T+ ++E AG++ +A Sbjct: 298 NTDALCAAIKDVFQDTRSVLEPAGSLAVA 326 Lambda K H 0.319 0.137 0.383 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: 268 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: 402 Length of database: 341 Length adjustment: 30 Effective length of query: 372 Effective length of database: 311 Effective search space: 115692 Effective search space used: 115692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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