Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_057508536.1 ABB28_RS10275 serine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_001431535.1:WP_057508536.1 Length = 320 Score = 159 bits (403), Expect = 8e-44 Identities = 103/309 (33%), Positives = 154/309 (49%), Gaps = 1/309 (0%) Query: 3 PYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQ 62 P + EA R+ T ++ S G + FK E+LQR+GAFK RGA N + S Sbjct: 8 PAQAVLEAAARIAPHAAVTPVLRSQTLDALAGAQLAFKAEHLQRSGAFKFRGACNAVWSL 67 Query: 63 PREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGR 122 + GV+T S+GNH +A +A G+ V +P+ K+ +GA + Sbjct: 68 SADRAPAGVVTHSSGNHGAALALAARTRGIACHVVVPDGAVAAKLANIARHGATLWRCAP 127 Query: 123 NFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLI 182 A Q Q + GA VHP+ D V+AGQGT LE+LQ ++VP+GGGGL Sbjct: 128 TIAAREAVCAQVQADTGATLVHPYADAAVIAGQGTAVLELLQAEGPFDVVVVPVGGGGLA 187 Query: 183 AGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFP 242 AG A A+++ PH R++ E A A SLQ G+ V T+ DG+ G F Sbjct: 188 AGTALALQQVSPHTRLVLAEPAGAADTARSLQAGERRIDFVPDTVCDGLR-GTLGAPNFQ 246 Query: 243 IIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLS 302 +++ EV++V++ A+ L + K VE + A+ LAA+L + + VLS Sbjct: 247 LLQAAGAEVIVVDDAATVAAMRLLWQVLKQTVEPSSAIALAAVLAQPQRFAGLRVGLVLS 306 Query: 303 GGNIDVKTI 311 GGN+D+ + Sbjct: 307 GGNVDIDAL 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: 252 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: 402 Length of database: 320 Length adjustment: 29 Effective length of query: 373 Effective length of database: 291 Effective search space: 108543 Effective search space used: 108543 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 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