Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_013518970.1 ALIDE2_RS11590 threonine/serine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_000204645.1:WP_013518970.1 Length = 328 Score = 221 bits (562), Expect = 3e-62 Identities = 123/305 (40%), Positives = 174/305 (57%) Query: 4 YTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQP 63 Y + EA RL+ T ++ S LG ++FKCENLQR GAFK RGA N + Sbjct: 11 YEDVAEAAHRLKGMAHHTPVLRSSTADALLGAELFFKCENLQRMGAFKFRGAFNALVQFS 70 Query: 64 REALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRN 123 A+GV+ S+GNHAQ +A SA LL +P+ + MPE P K+ ATR YGAEVV R Sbjct: 71 DAQRARGVLAFSSGNHAQAIALSARLLQMPAVIVMPEDAPAAKIAATRGYGAEVVTYDRF 130 Query: 124 FDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIA 183 ++ A + + ERG + PFD V+AGQGT+ E+ +E+P + + VP+GGGGL++ Sbjct: 131 TEDREAISQRLASERGMTLIPPFDHAHVIAGQGTVAKELFEEVPHLDYLFVPLGGGGLLS 190 Query: 184 GIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPI 243 G A + P R+IGVE A A SL+ GKIV++ T+ADG + G TFPI Sbjct: 191 GSLLAAQRLAPQCRVIGVEPEAGNDAQQSLRAGKIVRIGTPRTIADGAQSQALGSLTFPI 250 Query: 244 IRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSG 303 I V ++V + ++ A+ ER K++VE GA+ LA + V + V+SG Sbjct: 251 IHAGVSDIVTATDAQLIEAMHFFAERMKIVVEPTGALGLAGARHGGVALRGRRVGVVISG 310 Query: 304 GNIDV 308 GN+D+ Sbjct: 311 GNVDM 315 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: 306 Number of extensions: 11 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: 402 Length of database: 328 Length adjustment: 29 Effective length of query: 373 Effective length of database: 299 Effective search space: 111527 Effective search space used: 111527 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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