Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate SM_b20432 SM_b20432 threonine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Smeli:SM_b20432 Length = 334 Score = 202 bits (515), Expect = 7e-57 Identities = 117/317 (36%), Positives = 180/317 (56%), Gaps = 4/317 (1%) Query: 3 ITYDLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGA 62 ++ LPV IDDI A +R++GR+ T + S SE C + LK E+ Q TGSFK+RGA Sbjct: 1 MSVSLPVTIDDIEVAARRISGRVLTTPLAMSGSLSELCGVPVGLKLEHHQTTGSFKLRGA 60 Query: 63 FNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSA 122 N + SL+ ++ GV+A S GNH + ++ + G + M P +KV+ A Sbjct: 61 TNAVLSLSAGDRALGVIAASTGNHGRALAHAAKAEGSVATICMSHLVPVNKVSEIRRLGA 120 Query: 123 EVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVP 182 V + G++ ++ +V +V G + +PP+D ++AGQGT+GLE++ + DV V+VP Sbjct: 121 NVRIVGNSQDEAQEEVERLVAENGLVMVPPFDHRAIVAGQGTLGLEVVAQMPDVAMVLVP 180 Query: 183 IGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLAD--GCDV 240 + GGGL AG+A A+K+ P RVIG+ E M ASF +G +LAD G + Sbjct: 181 VSGGGLAAGVAAAVKARRPATRVIGLTMERGAAMKASFAAGGPALVDEQPSLADSLGGGI 240 Query: 241 SRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQY 300 +T+ + REL+DDI+L++E EI M + + EGAGA+ +ALL+GK+ Sbjct: 241 GLDNRVTFRMCRELLDDIILLTEAEIAAGMRHAYAEEREIVEGAGAVGISALLAGKIKDI 300 Query: 301 IQNRKTVSIISGGNIDL 317 + IISG N+D+ Sbjct: 301 --DGPIAVIISGRNVDM 315 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: 244 Number of extensions: 12 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: 329 Length of database: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 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 17 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