Align L-threonine dehydratase catabolic TdcB; L-serine dehydratase; Threonine deaminase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate WP_057509300.1 ABB28_RS14485 threonine dehydratase
Query= SwissProt::P11954 (329 letters) >NCBI__GCF_001431535.1:WP_057509300.1 Length = 366 Score = 211 bits (537), Expect = 2e-59 Identities = 123/310 (39%), Positives = 180/310 (58%), Gaps = 17/310 (5%) Query: 9 VAIEDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSS 68 V + D+L A+ RL + T + + F +LK EN+QRTGS+K+RGA N L + Sbjct: 16 VTVADVLAAQARLRRFLPPTPLHHAERFGT------WLKLENLQRTGSYKVRGALNALLA 69 Query: 69 LTEAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHG 128 E + ++ SAGNHAQGV+ + LG+ VMP GAP +K+A + A V HG Sbjct: 70 GRERGDLRPIICASAGNHAQGVAWAAHRLGVQAITVMPHGAPANKIAGVAHWGATVRQHG 129 Query: 129 DNFNDTIAKVSEIVETEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGL 188 ++++D A E+ + F+ +DD VIAGQGT+G+E+ DV VIVPIGGGGL Sbjct: 130 ESYDDAWAFAVELAQRHDYRFLSAFDDADVIAGQGTVGIELAPHSPDV--VIVPIGGGGL 187 Query: 189 IAGIAIAIKSINPTIKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTY 248 +G+A+A+KS ++++G Q E V MA + +G+I +LADG V PG LT Sbjct: 188 ASGVALALKS--QGVRIVGAQVEGVDSMARA-ISGDIRPIAPVPSLADGVRVKIPGFLTR 244 Query: 249 EIVRELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQNRKTVS 308 + L+DD+V+V E E+R +++ L +I EGAGALA AA + R+ + Sbjct: 245 RLCASLLDDVVIVREAELRETLVRLALEENLIAEGAGALALAA------GRRVAGRRKFA 298 Query: 309 IISGGNIDLS 318 ++SGGNID S Sbjct: 299 VVSGGNIDAS 308 Lambda K H 0.317 0.136 0.382 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: 247 Number of extensions: 7 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: 329 Length of database: 366 Length adjustment: 29 Effective length of query: 300 Effective length of database: 337 Effective search space: 101100 Effective search space used: 101100 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 24 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