Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011159503.1 TX73_RS20245 threonine/serine dehydratase
Query= BRENDA::P9WG59 (360 letters) >NCBI__GCF_000195775.1:WP_011159503.1 Length = 331 Score = 87.0 bits (214), Expect = 6e-22 Identities = 89/305 (29%), Positives = 131/305 (42%), Gaps = 27/305 (8%) Query: 39 TPLIAATNLSKQTGCTIHLKVEGLNPTGSFKDRGMTMAVTDALAHGQRA-VLCASTGNTS 97 TPL+++ L TG + LK E L TGSFK RG + +RA V+ S+GN + Sbjct: 31 TPLLSSPALDAATGARVFLKPEVLQRTGSFKFRGAYNKLASLSPELRRAGVVGFSSGNHA 90 Query: 98 ASAAAYAARAGITCAVLIPQGKIAMGKLAQAVMHGAKIIQIDGNFDDCLELARKMAADFP 157 AA A G+ +++P A K + GA+++ D + +D +AR +A Sbjct: 91 QGVAAAAQLLGVHATIVMPSDAPA-SKRERTAGFGAEVVLYDRDREDREAIARDIAERSG 149 Query: 158 TISLVNSVNPVRIEGQKTAAFEIVD---VLGTAPDVHALPVGNAGNITAYWKGYTEYHQL 214 + +P+ I GQ T EI + LG APD+ P G I L Sbjct: 150 ATLVRPFDDPMVIAGQGTVGREIAEDLAALGLAPDLVVAPASGGGLIAG--------TAL 201 Query: 215 GLIDKLPRMLGTQAA------GAAPLVLGEPVSHP---ETIATAIRIGSPASWTSAVEAQ 265 + + P+ L A A LV G S+P TI A+ + P T A+ Sbjct: 202 AVKARFPQALAMSAEPEGFDDHARSLVAGRRESNPAGGRTICDALMMSIPGEVTFAINRV 261 Query: 266 QQSKGRFLAASDEEILAAYHLVARVEGVFVEPASAASIAGLLKAIDDGWVARGSTVVCTV 325 + G +AASD E+ A R + VEP A ++A LL D RG TV + Sbjct: 262 LLAGG--VAASDAEVGTAVGFAFRELKLVVEPGGAVALAALLAGKLD---VRGKTVAIVL 316 Query: 326 TGNGL 330 +G + Sbjct: 317 SGGNV 321 Lambda K H 0.317 0.132 0.392 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: 254 Number of extensions: 12 Number of successful extensions: 2 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: 360 Length of database: 331 Length adjustment: 29 Effective length of query: 331 Effective length of database: 302 Effective search space: 99962 Effective search space used: 99962 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 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