Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate Ac3H11_745 Threonine synthase (EC 4.2.3.1)
Query= BRENDA::P83823 (351 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_745 Length = 307 Score = 103 bits (256), Expect = 8e-27 Identities = 97/317 (30%), Positives = 150/317 (47%), Gaps = 26/317 (8%) Query: 22 ISLLEGSTPLIPLKGPEEARKKGIR-LYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAV 80 +SL EG+TP + L P A++ GIR L AK+EGLNPTGS KDR AV++A+ A V Sbjct: 1 VSLGEGNTPCLGL--PRLAQRLGIRQLSAKHEGLNPTGSHKDRMSAQAVARALAVDAHKV 58 Query: 81 ACASTGNTAASAAAYAARAGILAIVV----LPAGYV-ALGKVAQSLVHGARIVQVEGNFD 135 AS+GN A SAAAY A AG+ V +PA + AL ++ GAR V + D Sbjct: 59 VLASSGNAAVSAAAYCAAAGLPCEVATYRDMPAPFARALDRL------GARRVAFDQGPD 112 Query: 136 DALRLTQKLTEAFPVALVNSVNP------HRLEGQKTLAFEVVDELGDAPHYHALPVGNA 189 + +++ E AL N P +EG + +A E V E G P + +P Sbjct: 113 RWAHVRRQVEEEGAFALTNFSVPAVGSPAFGVEGYRAVALECVAE-GCVPDHVIVPTARG 171 Query: 190 GNITAHWMGYKAYHALGKAKRLPRMLGFQA-AGAAPLVLGRPVERPETLATA--IRIGNP 246 + + + A G R+PR+ + A + ++ G P + +TA G+ Sbjct: 172 DLLWGMYSALRDLLAAGLIARMPRLWAVEPFARLSQVLAGAPAQADFGGSTAQFSIAGST 231 Query: 247 ASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRL 306 + Q + + GG + V D + L +G++ E + A + +L + G + Sbjct: 232 VTLQQQIAVQRSGGGAV-VVGDADAARGVAELG-AQGLWVELCAGACVGAAAQLCQHGHI 289 Query: 307 EPESTVVLTLTGHGLKD 323 P+ V+L LT G +D Sbjct: 290 APQDHVLLLLTAKGDRD 306 Lambda K H 0.317 0.134 0.385 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: 213 Number of extensions: 10 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: 351 Length of database: 307 Length adjustment: 28 Effective length of query: 323 Effective length of database: 279 Effective search space: 90117 Effective search space used: 90117 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 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