Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_058930538.1 AU252_RS09735 pyridoxal-5'-phosphate-dependent protein subunit beta
Query= curated2:Q58860 (405 letters) >NCBI__GCF_001484605.1:WP_058930538.1 Length = 377 Score = 164 bits (414), Expect = 5e-45 Identities = 112/328 (34%), Positives = 169/328 (51%), Gaps = 11/328 (3%) Query: 53 WRYLEYLPVKDESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTV 112 WRY LPV + + V+L EG TP+ N +G E+ VK E NPT SFKDRG +V Sbjct: 53 WRYRAALPVDIQDR-VTLGEGCTPMLTTN-----IGGIEVKVKPEWFNPTASFKDRGSSV 106 Query: 113 GVTRANELGVEVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKV 172 V+ G+ + S+GN +S+AAY+A +G +L P A K+ Q+ F+ A++ Sbjct: 107 MVSILRSHGITSILEDSSGNGGSSVAAYAAAAGMHAKILAPASTSA-NKILQSRFHNAEI 165 Query: 173 IQVKGNFDD-ALDMVKQLAKEKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVP 231 V G D+ A + ++Q E+ Y ++ +P+ L+G K IA+EI + L ++ P+ +IVP Sbjct: 166 ELVPGTRDETAAEALRQ--SEQFFYASHNWHPYFLQGVKLIAYEIWEDLGFEAPENIIVP 223 Query: 232 VGNAGNISAIWKGFKEFEITGIIDELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETI 291 G + GF E G I LP++ Q + P+ A A D + TI Sbjct: 224 AGAGSLVLGCSIGFGELLRAGQIARLPRILVAQPEHCSPLARAHAISALDAVERDWKPTI 283 Query: 292 ATAIRIGNPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGL 351 A I PV P+ L A+ +SGG + V + I A + LA + G++ EP SA + A + Sbjct: 284 AEGTSIARPVRGPEVLAAVRASGGTFQTVAEGHIAPAVRELASR-GLYAEPTSAVAAAAV 342 Query: 352 KKLLEEGIIDRDERIVCITTGHGLKDPD 379 +G + DER V + TG LK D Sbjct: 343 PGFAAQGFLAPDERTVMVLTGSALKAAD 370 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: 312 Number of extensions: 21 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: 405 Length of database: 377 Length adjustment: 31 Effective length of query: 374 Effective length of database: 346 Effective search space: 129404 Effective search space used: 129404 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