Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_013840102.1 DESRU_RS00075 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000215085.1:WP_013840102.1 Length = 402 Score = 273 bits (699), Expect = 5e-78 Identities = 143/377 (37%), Positives = 225/377 (59%), Gaps = 3/377 (0%) Query: 5 CIKCGKTYDVDEIIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDE 64 C KC K Y+ +E+ CECG L + YD IK+ +E L+ RE +WRY E LP+KD+ Sbjct: 9 CSKCNKQYNSEEVHQLCECGAPLIVKYDLARIKENFRKEDLKDREPSLWRYWELLPLKDK 68 Query: 65 SKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEV 124 +VSL EG TP+ + E+G+ LY+K+EG P+G+FK RG TVGV+RA ELG++ Sbjct: 69 KNLVSLGEGMTPIIKMEVAGPEIGLNNLYLKDEGIIPSGTFKSRGATVGVSRAKELGIKT 128 Query: 125 VGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALD 184 + + GN AS + Y AR+G K ++++P+ + + + GA + V G DA Sbjct: 129 LAMPTNGNAGASWSTYGARAGIKSVIVMPQDAPEITR-NECAITGADLYLVDGLISDAGK 187 Query: 185 MVKQLAKEKLIYLLNSI-NPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWK 243 +V + ++ + ++++ P+R+EG+KT+ EI +Q NW+VPD ++ P G I I+K Sbjct: 188 IVARAVQKYGWFDVSTLKEPYRIEGKKTMGLEIAEQFNWEVPDVILYPTGGGVGIIGIYK 247 Query: 244 GFKEFEITGIIDE-LPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVN 302 +E + G I E +P++ +QA+G PIV+A+ ++ + + N T A I + + Sbjct: 248 ALRELQTIGWIGEKMPRLVAVQAEGCAPIVKAWEEKKTESEFWNNASTCAFGITVPKALG 307 Query: 303 APKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDR 362 LDAIY + G A A+ D +++EAQ +LA KEG FV P AS + +KL E+G I Sbjct: 308 DFLVLDAIYKTNGCAVAIADNDLLEAQAVLAAKEGTFVCPEGASLYSAARKLREQGWIKE 367 Query: 363 DERIVCITTGHGLKDPD 379 +E++V + TG GLK P+ Sbjct: 368 NEKVVLLNTGTGLKYPE 384 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: 486 Number of extensions: 30 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: 402 Length adjustment: 31 Effective length of query: 374 Effective length of database: 371 Effective search space: 138754 Effective search space used: 138754 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