Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate WP_051402369.1 N177_RS12980 threonine/serine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >NCBI__GCF_000496075.1:WP_051402369.1 Length = 340 Score = 222 bits (566), Expect = 9e-63 Identities = 134/326 (41%), Positives = 192/326 (58%), Gaps = 10/326 (3%) Query: 6 DLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNK 65 DLP + DD+ A +RL+G +T + RS ER + LK E +QRTGSFK RGA+N Sbjct: 18 DLP-SFDDVRRASERLSGEAVRTPLVRSAILDERAGRPVLLKAEVLQRTGSFKFRGAYNA 76 Query: 66 LSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVV 125 ++SL + KGVVACS+GNHAQGV+ + + G+ +VMP AP KVA T A VV Sbjct: 77 IASLDADARAKGVVACSSGNHAQGVAEAARLFGVRATIVMPADAPALKVARTKRSGAHVV 136 Query: 126 LHGDNFNDTIAKVS-EIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDL----YDVDNVI 180 + D N++ +++ IV G F+PPYDD +VI+GQGT+G+EI E D ++ Sbjct: 137 TY-DRVNESREEIALRIVAETGADFVPPYDDRRVISGQGTVGIEIAEQAEALGLDPARIL 195 Query: 181 VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRT-TGTLADGCD 239 VP GGGL AGIA+A +++ P RV V+ E A SF SGE + +G++ D Sbjct: 196 VPCSGGGLSAGIALAAEALMPWARVTTVEPEAFDDHARSFRSGEREGNTARSGSICDALL 255 Query: 240 VSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQ 299 RPG +T+ + R V + VS+DE+R +M + K+V E GA+ AA+L+G+LD+ Sbjct: 256 ADRPGEITFAVNRPRVPSGLAVSDDEVRTAMRFAFEELKLVVEPGGAVGLAAVLAGRLDE 315 Query: 300 YIQNRKTVSIISGGNIDLSRVSQITG 325 Q V ++SGGN S ++ G Sbjct: 316 GPQ--PVVVVLSGGNAGPSAYAEAIG 339 Lambda K H 0.318 0.136 0.386 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: 245 Number of extensions: 11 Number of successful extensions: 3 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: 329 Length of database: 340 Length adjustment: 28 Effective length of query: 301 Effective length of database: 312 Effective search space: 93912 Effective search space used: 93912 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 (21.7 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