Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_028320307.1 H567_RS0103335 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000422285.1:WP_028320307.1 Length = 361 Score = 135 bits (339), Expect = 2e-36 Identities = 91/305 (29%), Positives = 157/305 (51%), Gaps = 9/305 (2%) Query: 73 GGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEVVGCASTGN 132 G T L R N+E+E G++++Y+K EG NPTG+ KDR A E++ A+ GN Sbjct: 56 GDTNLSRARNIEREYGLRQIYLKFEGGNPTGTQKDRIAFAQAMDALRRRFEIITTATCGN 115 Query: 133 TSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALDMVKQLAKE 192 + A ++ G CIV +PEG G++ + + +GA++++V G+++ A+ ++ A+ Sbjct: 116 YGVATALAASVVGVGCIVYIPEG-YHTGRVKEMVDHGAEIVRVPGDYEAAVMASRRFAEG 174 Query: 193 KLIYLLN---SINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWKGFKEFE 249 IY N + + ++ IA+EI D+L P V VPV N ++ I++GF Sbjct: 175 DDIYDANPGGANSGLQMRAYGEIAYEIYDELR-DAPAAVAVPVSNGTTLAGIYRGFLSLY 233 Query: 250 ITGIIDELPKMTGIQADGAKPIVEAFRKR---AKDIIPYKNPETIATAIRIG-NPVNAPK 305 G +P+M + G PIV+A+ K +D+ P + ET I + ++ + Sbjct: 234 RRGKTSRMPRMVAGSSFGKNPIVKAYMKNTPGCEDLAPARIRETAVNEPLINWHAIDGDE 293 Query: 306 ALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDRDER 365 AL A+ +GG+A +D + LL R+EG+ V PAS + L ++ + D Sbjct: 294 ALLAVRKTGGWAGYASDRGMTSCSGLLRRREGLNVLPASTVGLIVLLDRHQKTKLPGDRY 353 Query: 366 IVCIT 370 +V +T Sbjct: 354 VVILT 358 Lambda K H 0.317 0.137 0.395 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: 391 Number of extensions: 23 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: 405 Length of database: 361 Length adjustment: 30 Effective length of query: 375 Effective length of database: 331 Effective search space: 124125 Effective search space used: 124125 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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