Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_086510351.1 BZY95_RS13015 threonine/serine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_002151265.1:WP_086510351.1 Length = 315 Score = 220 bits (560), Expect = 5e-62 Identities = 129/313 (41%), Positives = 183/313 (58%), Gaps = 2/313 (0%) Query: 1 MLPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMT 60 MLP IQEA R+ + T L+ H SEK G I+ K E QRTG+FK RG LN++ Sbjct: 1 MLPLERIQEAQRRIADSLPPTPLLLDHVLSEKFGRRIWLKGELFQRTGSFKPRGGLNWLR 60 Query: 61 SQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLT 120 S E LA G+ SAGNHA G+A++A VP T+ MPE+ P KV +R GAEV+L Sbjct: 61 SAGEEELAGGLGAVSAGNHALGLAWAAGQADVPVTIVMPENASPFKVEGSRKLGAEVILH 120 Query: 121 GRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGG 180 G + +EA+ + ERG VHP+DD +MAGQGT+GLE+L++ P+ IL P+GGGG Sbjct: 121 G-DINEAWELMHRLVAERGLTLVHPYDDERIMAGQGTVGLEILEQAPEATAILCPVGGGG 179 Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNT 240 LIAGI +A P + +IGVE + A S + G ++ T A + G +T Sbjct: 180 LIAGIGSAAAALRPGLALIGVEPSGAASMAAAWSAGAPERLERVATCAKSLGAAIVGEHT 239 Query: 241 FPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVT-DLSGKTVC 299 +P+ R+ +++ V+++ I A+ LL + KL+ E AV +AALL VT G V Sbjct: 240 YPVCRETTQKLLQVDDDAIGRAMRHLLYQAKLMAEPGAAVGVAALLEDLVTLPPEGDVVV 299 Query: 300 VLSGGNIDVKTIS 312 V++GGN+ + +S Sbjct: 300 VITGGNMSPEELS 312 Lambda K H 0.319 0.137 0.383 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: 281 Number of extensions: 13 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: 402 Length of database: 315 Length adjustment: 29 Effective length of query: 373 Effective length of database: 286 Effective search space: 106678 Effective search space used: 106678 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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