Align L-threonine dehydratase catabolic TdcB; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate N515DRAFT_0537 N515DRAFT_0537 threonine dehydratase
Query= curated2:Q99U50 (346 letters) >FitnessBrowser__Dyella79:N515DRAFT_0537 Length = 315 Score = 170 bits (430), Expect = 5e-47 Identities = 106/309 (34%), Positives = 161/309 (52%), Gaps = 5/309 (1%) Query: 16 LGDIEEAKASIKPFIRRTPLIKSMYLSQNITKGNVYLKLENMQFTGSFKFRGASNKINHL 75 L I +A A I P+ TP+++S L + ++ K EN+Q G+FKFRGA N + L Sbjct: 7 LDQIRDAAARIAPYAAVTPVLRSARLDA-LAGAQLHFKCENLQRGGAFKFRGACNAVWSL 65 Query: 76 SDEQKAKGIIGASAGNHAQGVALTAKLLGIDATIVMPETAPIAKQNATKGYGAKVILKGK 135 D Q A+G++ S+GNH +A+ A GI A +V+PE A AK A + GA + Sbjct: 66 DDAQAARGVVTHSSGNHGNALAMAAATRGIAAHVVVPEGAVRAKLEAIEQAGAVLHRCAP 125 Query: 136 NFNETRLYMEELAKENGMTIVHPYDDKFVMAGQGTIGLEILDDIWNVNTVIVPVGGGGLI 195 EL ++ G +VHPY D VMAGQGT+ LE++ + ++ +I PVGGGGL Sbjct: 126 TTAAREAMTAELQRQTGAELVHPYADARVMAGQGTLVLELMRQVEGLDALITPVGGGGLA 185 Query: 196 AGIATALKSFNPSIHIIGVQAENVHGMAESFYKRALTEHREDSTIADGCDVKVPGEKTYE 255 AG A A P + + G + A S + A E + T+ DG + G ++ Sbjct: 186 AGCAIAAHGLKPELAMYGAEPTGADDAARSLAQGARVEPFQADTLCDGLRTLI-GAPNFD 244 Query: 256 VVKHLVDEFILVSEEEIEHAMQDLMQRAKIITEGAGALPTAAILSGKIDKKWLEGKNVVA 315 ++ + I VS+EE AM+ L + K++ E + A AA+L + G+ V Sbjct: 245 ALRTHRTQVITVSDEETIAAMKLLWRELKLVVEVSSATVLAAVLK---QAEHFAGRRVGL 301 Query: 316 LVSGGNVDL 324 +++GGNVDL Sbjct: 302 VLTGGNVDL 310 Lambda K H 0.315 0.133 0.373 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: 234 Number of extensions: 8 Number of successful extensions: 4 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: 346 Length of database: 315 Length adjustment: 28 Effective length of query: 318 Effective length of database: 287 Effective search space: 91266 Effective search space used: 91266 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 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