Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate H281DRAFT_00878 H281DRAFT_00878 threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Burk376:H281DRAFT_00878 Length = 344 Score = 162 bits (410), Expect = 1e-44 Identities = 105/301 (34%), Positives = 153/301 (50%), Gaps = 2/301 (0%) Query: 18 VRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAG 77 V RT + F+ G + FK E LQ G+FK RGA + + + GV S G Sbjct: 35 VARTPVFDRLDFASLEGTVVNFKFELLQAGGSFKARGAFTNLLALDETQRSAGVTCVSGG 94 Query: 78 NHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEE 137 NHA VA++A LG+ + V + + P +V R Y AE+V + EA+ + + E Sbjct: 95 NHAVAVAYAAMRLGISAKVVLFRAANPARVALCRQYRAEIVFA-EDLAEAFELVRRIEAE 153 Query: 138 RGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAIRETHPHVR 197 G FVHPF+ + G T+G E + PD+ ++VPIGGGGL AG+ATA+R +P V Sbjct: 154 EGRYFVHPFNGYRTVLGSATLGYEWSTQTPDLEAVIVPIGGGGLAAGVATAMRLANPGVH 213 Query: 198 IIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEE 257 + GVE A + S V++ +AD + ++ + R +DE+V V ++ Sbjct: 214 VFGVEPEGADAMGKSFAANHTVKMGHMHGIADSLMAPHTEEYSYELCRRHIDELVTVSDD 273 Query: 258 EIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCV-LSGGNIDVKTISVVVE 316 ++ A++ L + KL VE A A AALL L GK V V L G N D T S +E Sbjct: 274 QLCAAMLTLFGQLKLAVEPACAAATAALLGPLREKLQGKRVGVLLCGTNTDPVTFSAHIE 333 Query: 317 R 317 R Sbjct: 334 R 334 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: 230 Number of extensions: 10 Number of successful extensions: 2 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: 344 Length adjustment: 30 Effective length of query: 372 Effective length of database: 314 Effective search space: 116808 Effective search space used: 116808 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 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