Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ga0059261_3754 Ga0059261_3754 Threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Korea:Ga0059261_3754 Length = 322 Score = 168 bits (426), Expect = 2e-46 Identities = 112/285 (39%), Positives = 152/285 (53%), Gaps = 12/285 (4%) Query: 30 SEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNHAQGVAFSADL 89 +E GIP+ FK E LQ GAFKIRGA + +T+ E KGV+ S+GNHAQGVA++A Sbjct: 31 AEIRGIPVMFKAECLQPIGAFKIRGAWHRLTAIDPEQREKGVVAFSSGNHAQGVAWAAKR 90 Query: 90 LGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERGALFVHPFDDP 149 LG+P+ + MP P K +T GAEVV R ++ A RGA V PFDDP Sbjct: 91 LGIPAVIVMPADAPAAKRDSTLALGAEVVAYDRMKEDRVKIAAHLAHARGATLVPPFDDP 150 Query: 150 LVMAGQGTIGLEVLQE-----LPDVANILVPIGGGGLIAGIATAIRETHPHVRIIGVETA 204 ++ GQG++ +EVL + LPD I+VP GGGGL +G+ A+ E + VE Sbjct: 151 WIIEGQGSMAIEVLTQAAEMRLPDPGRIVVPCGGGGLASGVTLALPEAQTTI----VEPE 206 Query: 205 AAPSAHYSLQKGKIVQVPVT--VTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEEIALA 262 SL G I + + T D + +P TF ++ V V E E+ A Sbjct: 207 GWDDMCRSLANGWIESIGESPPPTACDALQTFQPAQLTFDVLSRRGATGVAVSEAEVRAA 266 Query: 263 IVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNID 307 + +L+VE GAV LAALL +V D + T+ +LSGGN D Sbjct: 267 QRWAARKLRLVVEPGGAVALAALLAGKV-DPTPDTLVILSGGNAD 310 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: 264 Number of extensions: 12 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: 402 Length of database: 322 Length adjustment: 29 Effective length of query: 373 Effective length of database: 293 Effective search space: 109289 Effective search space used: 109289 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 Aug 03 2021. The underlying query database was built on Aug 03 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