Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate Echvi_1189 Echvi_1189 Threonine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Cola:Echvi_1189 Length = 319 Score = 172 bits (437), Expect = 8e-48 Identities = 106/320 (33%), Positives = 167/320 (52%), Gaps = 4/320 (1%) Query: 1 MHITYDLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIR 60 M TY +P ID I +A QR+ I+ T + ++ +++ K EN Q+ G+FK R Sbjct: 1 MQQTYRIPQLID-IKQAYQRIMAYIHHTPILTCEAINKMADCQLYFKCENFQKVGAFKAR 59 Query: 61 GAFNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDY 120 GA N + L K+ GV S+GNHA ++ + G +VMP A K AA Y Sbjct: 60 GATNAILKLPPGLKKNGVATHSSGNHAAALARAAKETGTKAYIVMPSTAAAIKKAAVRTY 119 Query: 121 SAEVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVI 180 E++ N + ++VE G FIPPYD VI GQ T LE+ ++ D +I Sbjct: 120 GGEIIECEPNLKARETTLEKVVEETGAAFIPPYDYMDVIEGQATCALEMWDEGIPFDAII 179 Query: 181 VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDV 240 P+GGGGL+AG A+ ++ V G + + S + +I T+ADG + Sbjct: 180 TPVGGGGLLAGTALTTHYLSRKTPVYGAEPKGADDAYRSLKANKIIPMENPNTIADGL-L 238 Query: 241 SRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQY 300 + G + I+ + V DI+ VS+D+I +M + +R K+V E + A+ AA+L+ K Sbjct: 239 TSLGKRNFTIISKNVADILTVSDDQIIAAMRLVFERMKLVIEPSSAVPLAAILANK--PL 296 Query: 301 IQNRKTVSIISGGNIDLSRV 320 QN++ +ISGGN+D+S++ Sbjct: 297 FQNKRVGIVISGGNVDVSKL 316 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: 211 Number of extensions: 8 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: 319 Length adjustment: 28 Effective length of query: 301 Effective length of database: 291 Effective search space: 87591 Effective search space used: 87591 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: 48 (23.1 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