Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate GFF2586 Psest_2636 tryptophan synthase, beta subunit
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__psRCH2:GFF2586 Length = 402 Score = 54.7 bits (130), Expect = 5e-12 Identities = 67/228 (29%), Positives = 95/228 (41%), Gaps = 31/228 (13%) Query: 29 LSEVTGG-EIYLKMENLQKTGSFKIRGAYNKIAHLSEEERKRGVVAASAGNHAQGVALAA 87 LSE GG +IYLK E+L TG+ KI + +K+ + AG H +A A Sbjct: 73 LSEQLGGAQIYLKREDLNHTGAHKINHCLGEALLAKFMGKKKVIAETGAGQHGVALATAC 132 Query: 88 QIFGIPATIVMPRY---APLSKITKTRNLGAQVILE-------GNIFDEAYEAALR---- 133 + GIP I M + +TK + LG ++I D A+E L+ Sbjct: 133 ALVGIPCEIHMGQVDIEKEHPNVTKMKILGCKLIAVTRGAATLKEAVDSAFEEYLKDPHN 192 Query: 134 -IQEKTGAVFVHPFNDPHVIAG-QGTIGLEIMED-------LPDVEVVVVPVGGGGLISG 184 I V HPF P ++ Q IG E E LPD VV VGGG G Sbjct: 193 YIYAIGSVVGPHPF--PKMVRDFQSIIGTEAREQFLAKHGRLPD--HVVACVGGGSNAMG 248 Query: 185 VSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIA 232 + A + V+++G+ E + R A +GKP+ G+A Sbjct: 249 MFTAFLE-DAAVELVGI--EPAGESLDKPGRHSATLSKGKPSELHGMA 293 Lambda K H 0.317 0.136 0.367 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: 272 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: 401 Length of database: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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