Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate 3609317 Dshi_2702 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Dino:3609317 Length = 330 Score = 163 bits (412), Expect = 6e-45 Identities = 106/309 (34%), Positives = 156/309 (50%), Gaps = 7/309 (2%) Query: 12 DDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTD 71 D I A+ RL G + +T + + + +K E +Q TGSFK RG + +S+L Sbjct: 8 DRIKAAEARLDGHVRRTPILSAPALDALAGRRVLVKAECLQHTGSFKARGGWAAVSALPA 67 Query: 72 AEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNF 131 A + +GV+ACS+GNHAQGV+ + A G +VMP AP KV T AEVV + Sbjct: 68 AVRARGVIACSSGNHAQGVARAAAAHGTRALIVMPGDAPAPKVENTRALGAEVVFYDRAR 127 Query: 132 NDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDL----YDVDNVIVPIGGGG 187 D + + E +G I PYDD +VIAGQ T GLEI V+V GGGG Sbjct: 128 EDRDGLTATLAERDGLTLIKPYDDTEVIAGQATTGLEIAAQAAAEGVHAAEVLVCCGGGG 187 Query: 188 LIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSG-EITTHRTTGTLADGCDVSRPGNL 246 L AGIA+A+ P +RV V+ + MA S +G + G++ D PG + Sbjct: 188 LSAGIALALAETAPRMRVRPVEPDGFDDMARSLAAGTRLANSARDGSICDAILTPMPGEI 247 Query: 247 TYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKT 306 T+ ++ ++V+E E+ +M Q K+V E GA+A AA L + Sbjct: 248 TFPVLASRAGPGLVVTEGEVLRTMKLAFQHLKLVLEPGGAVALAAALF--RPDALSGDAV 305 Query: 307 VSIISGGNI 315 +++ +GGN+ Sbjct: 306 IAVATGGNV 314 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: 223 Number of extensions: 5 Number of successful extensions: 1 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: 330 Length adjustment: 28 Effective length of query: 301 Effective length of database: 302 Effective search space: 90902 Effective search space used: 90902 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