Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PfGW456L13_3185 Threonine dehydratase (EC 4.3.1.19)
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3185 Length = 318 Score = 167 bits (423), Expect = 4e-46 Identities = 106/288 (36%), Positives = 154/288 (53%), Gaps = 4/288 (1%) Query: 30 SEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREAL-AKGVITASAGNHAQGVAFSAD 88 +++LG ++ K EN TGAFK+RG + FM RE AKG+++A+ GNH Q +A +A Sbjct: 32 AQRLGCTVWVKHENHTPTGAFKVRGGITFMHWLKREHPGAKGIVSATRGNHGQSLALAAR 91 Query: 89 LLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERGALFVHPFDD 148 LG+ + + +PE +K A R +GAEVV GR+FD+A A + + V PF Sbjct: 92 TLGLQALIVVPEGNSVEKNNAMRGFGAEVVEYGRDFDDAREEAARLAHAQDLFLVPPFHT 151 Query: 149 PLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAIRETHPHVRIIGVETAAAPS 208 LV G T LE+ PD+ + VPIG G I G+ A ++GV + A + Sbjct: 152 ELVK-GVATYALELFNAAPDLDTVYVPIGCGSGICGVIAARDALDLETEVVGVVSTQAAA 210 Query: 209 AHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEEIALAIVALLE 268 A S G I + T ADG+AV+KP F + +V V +++IA A+ Sbjct: 211 AQLSFDAGAICETASANTFADGLAVRKPIPEAFAVYAAGAARIVSVSDDQIAEAMRVYYT 270 Query: 269 RTKLLVEGAGAVPLAALLNRRVTDLSGKTV-CVLSGGNIDVKTISVVV 315 T L EGAGA LAAL++ R +SG+ V +LSGGN+D + V+ Sbjct: 271 DTHNLAEGAGASALAALISEREA-MSGRRVGVILSGGNVDRSVYAQVI 317 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: 269 Number of extensions: 12 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: 318 Length adjustment: 29 Effective length of query: 373 Effective length of database: 289 Effective search space: 107797 Effective search space used: 107797 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