Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_066603969.1 V473_RS11265 threonine/serine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_001046645.1:WP_066603969.1 Length = 330 Score = 196 bits (497), Expect = 1e-54 Identities = 115/301 (38%), Positives = 162/301 (53%), Gaps = 5/301 (1%) Query: 20 RTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNH 79 RT L+ +H +++LG + K E Q TG+FK RGA N + + A GV+ S+GNH Sbjct: 25 RTPLLENHALNDRLGRRVLIKFEGAQHTGSFKFRGAYNRLARLDAQQRAAGVVAWSSGNH 84 Query: 80 AQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERG 139 AQGVA +A LL +P+T+ MP P K+ R GAE+V R+ + A RG Sbjct: 85 AQGVAAAAQLLALPATIVMPSDAPAIKLANNRALGAEIVTYDRHSESREEIATALAHSRG 144 Query: 140 ALFVHPFDDPLVMAGQGTIGLEVLQELPD----VANILVPIGGGGLIAGIATAIRETHPH 195 A V FDDP V+AGQGT GLE+L + + + ILV GGGGL AGIATA++ P Sbjct: 145 ATLVPSFDDPFVIAGQGTAGLEILDQAAEAGAIIGQILVCCGGGGLTAGIATAVKARAPE 204 Query: 196 VRIIGVETAAAPSAHYSLQKGKIVQV-PVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLV 254 + + VE A SL G + P ++ D + PG TFPI + L+ ++V Sbjct: 205 IALYAVEPAGFDDTARSLASGVRENIAPDARSICDALMAPSPGAMTFPINQALLSGGLVV 264 Query: 255 EEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNIDVKTISVV 314 ++++ A+ KL+VE GAV LAA+LN +V VLSG N+D + + Sbjct: 265 SDDQVRDAMRFAFSTLKLVVEPGGAVALAAVLNGLAPPCGDASVVVLSGSNVDPAAYAAI 324 Query: 315 V 315 V Sbjct: 325 V 325 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: 266 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: 402 Length of database: 330 Length adjustment: 29 Effective length of query: 373 Effective length of database: 301 Effective search space: 112273 Effective search space used: 112273 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