Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_015886807.1 NGR_RS03340 hydroxyectoine utilization dehydratase EutB
Query= BRENDA::P9WG59 (360 letters) >NCBI__GCF_000018545.1:WP_015886807.1 Length = 321 Score = 74.3 bits (181), Expect = 4e-18 Identities = 80/277 (28%), Positives = 120/277 (43%), Gaps = 17/277 (6%) Query: 39 TPLIAATNLSKQTGCTIHLKVEGLNPTGSFKDRGMTMAVTD-ALAHGQRAVLCASTGNTS 97 TPL +T+LS++TG + LK+E TGSFK RG T AV + R V+ ASTGN Sbjct: 21 TPLTISTSLSERTGAQVSLKLEHRQSTGSFKLRGATNAVLQLSQVERDRGVIAASTGN-H 79 Query: 98 ASAAAYAARAGITCAVLIPQGKIAMGKLAQAVMHGAKIIQIDGNFDDCLELARKMAADFP 157 A +YAARA +CA + + K+A+ GA + + + DD + A+ Sbjct: 80 GRALSYAARAVGSCATICMSRLVPENKVAEIRRLGATVRIVGSSQDDAQAEVERQVAEEG 139 Query: 158 TISLVNSVNPVRIEGQKTAAFEIVDVLGTAPDVHALPV-----GNAGNITAYWKGYTEYH 212 + +P I GQ T EIV+ + P+V + V G A + A K Sbjct: 140 LSMIPPFDHPHVITGQGTVGLEIVEEM---PEVATVLVPLSGGGLAAGVAAAVKTIRPQA 196 Query: 213 QLGLIDKLPRMLGTQAAGAAPLVLGEPVSHPE--TIATAIRIGSPASWTSAVEAQQQSKG 270 ++ + + AA A + G PV E ++A ++ G + T + Sbjct: 197 KV-----IGVTMDRGAAMKASIDAGHPVQVKEYRSLADSLGGGIGVNNTWTFPMCKTLLD 251 Query: 271 RFLAASDEEILAAYHLVARVEGVFVEPASAASIAGLL 307 + ++ EI A E VE A A IA LL Sbjct: 252 DIVLVNEGEIAAGVRHAYEQEREIVEGAGAVGIAALL 288 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: 240 Number of extensions: 11 Number of successful extensions: 1 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: 321 Length adjustment: 28 Effective length of query: 332 Effective length of database: 293 Effective search space: 97276 Effective search space used: 97276 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 Jul 25 2024. The underlying query database was built on Jul 25 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