Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_089299754.1 CHB84_RS02110 threonine ammonia-lyase
Query= BRENDA::P9WG59 (360 letters) >NCBI__GCF_900188115.1:WP_089299754.1 Length = 401 Score = 82.8 bits (203), Expect = 1e-20 Identities = 84/280 (30%), Positives = 125/280 (44%), Gaps = 23/280 (8%) Query: 39 TPLIAATNLSKQTGCTIHLKVEGLNPTGSFKDRGMTMAVTDALAHGQRA--VLCASTGNT 96 TP+ A +L++ G +HLK E L TGSFK RG + + L+ QRA V+ AS GN Sbjct: 23 TPMEHAMDLARLHGGDVHLKCENLQRTGSFKIRGAYTRIHN-LSEEQRAHGVVAASAGNH 81 Query: 97 SASAAAYAARAGITCAVLIPQGKIAMGKLAQAVMHGAKIIQIDGNFDDCLELARKMAADF 156 + A A+ G V +P+ + + KLA +GA + G ++ L A + + Sbjct: 82 AQGVALAASLLGTRSTVFMPE-RAPLPKLAATRDYGADVHLHGGQLEETLREATEFSERT 140 Query: 157 PTISLVNSVNPVRIEGQKTAAFEIVDVLGTAPDVHALPVGNAGNITAYWKGYTEYHQLGL 216 + + +P I GQ T E VL PDV + V G G L Sbjct: 141 GAVFIHPFDHPDIIAGQGTVGLE---VLEQVPDVATVLVATGGG------GLVSGIGAAL 191 Query: 217 IDKLP--RMLGTQAAGAA----PLVLGEPVS--HPETIATAIRIGSPASWTSAVEAQQQS 268 ++ P R++ QAA AA L G+PVS T+A I +G+P + Sbjct: 192 RERKPDARVVAVQAANAAAFPPSLRAGQPVSLASTNTVADGIAVGTPG--PLGLSHVDSL 249 Query: 269 KGRFLAASDEEILAAYHLVARVEGVFVEPASAASIAGLLK 308 + S+E + A L + VEPA AA++A LL+ Sbjct: 250 VDEVVTVSEESLSRAVLLCLERRKLVVEPAGAAAVAALLE 289 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: 308 Number of extensions: 16 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: 401 Length adjustment: 30 Effective length of query: 330 Effective length of database: 371 Effective search space: 122430 Effective search space used: 122430 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 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