Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate Ga0059261_1586 Ga0059261_1586 Threonine synthase
Query= curated2:Q58860 (405 letters) >FitnessBrowser__Korea:Ga0059261_1586 Length = 475 Score = 222 bits (566), Expect = 2e-62 Identities = 127/376 (33%), Positives = 202/376 (53%), Gaps = 3/376 (0%) Query: 5 CIKCGKTYDVDEIIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDE 64 C G+ YD D + G L + YD + I+ VS L R +WRY E LPV+ Sbjct: 82 CSMTGERYDADTLHGLSRTGRPLLVRYDLDAIRAAVSPADLALRPADLWRYRELLPVRRT 141 Query: 65 SKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEV 124 IVSL E TP+ N + G L VK+E PTGSFK RG+ + ++ A ELGV Sbjct: 142 ENIVSLGEIATPIVPLNKVAAGAGASTLLVKDESRLPTGSFKARGLVMAISMAKELGVTT 201 Query: 125 VGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALD 184 + + GN A+ AAY+A++G + ++ P+ + + + GA+V +V G DD Sbjct: 202 IAMPTNGNAGAAAAAYAAQAGIEAVIFCPDDTPEI-NVREIAAQGARVYRVNGLIDDCGK 260 Query: 185 MVKQLAKEKLIYLLNSI-NPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWK 243 +V + + L+++ P+R+EG+KT+ E+ +QL W++PD + P G + +WK Sbjct: 261 LVGAGKEANGWFDLSTLKEPYRIEGKKTMGLELAEQLGWELPDVIFYPTGGGTGLIGMWK 320 Query: 244 GFKEFEITGII-DELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVN 302 F+E E G I + P+M +QA+G P+V A++ + +++ T+A IR+ V Sbjct: 321 AFEELEALGWIGSKRPRMVAVQAEGCAPMVRAWQGGERHATRWEDAHTLAAGIRVPQAVG 380 Query: 303 APKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDR 362 LDA+ +S G+A AV+D I+EA AR +G+ + P +++A +K L +G+I Sbjct: 381 DFLILDAVRASNGFAMAVSDSAILEAVDDAARLDGLLLCPEGGATLAAWRKALVDGLIAP 440 Query: 363 DERIVCITTGHGLKDP 378 D+R V GLK P Sbjct: 441 DDRAVLFNCATGLKYP 456 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: 461 Number of extensions: 22 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: 475 Length adjustment: 32 Effective length of query: 373 Effective length of database: 443 Effective search space: 165239 Effective search space used: 165239 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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