Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_057509300.1 ABB28_RS14485 threonine dehydratase
Query= reanno::Korea:Ga0059261_3694 (420 letters) >NCBI__GCF_001431535.1:WP_057509300.1 Length = 366 Score = 215 bits (548), Expect = 2e-60 Identities = 136/341 (39%), Positives = 190/341 (55%), Gaps = 15/341 (4%) Query: 6 PMATQAATAAQPLPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFT 65 P A +A T VT+ADV AA AR+ + TP H++ +LK ENLQ T Sbjct: 2 PAADRAGTEPDVGDVTVADVLAAQARLRRFLPPTPLHHAERFG------TWLKLENLQRT 55 Query: 66 AAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKV 125 +YK RGALN LL + + +I ASAGNHAQG+A+ +RLG+ VMP P K+ Sbjct: 56 GSYKVRGALNALLAGRERGDLRPIICASAGNHAQGVAWAAHRLGVQAITVMPHGAPANKI 115 Query: 126 MQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAP 185 GAT+ GE++D+A+A A +L + Y F+ FDD +IAGQGTV +E+ +P Sbjct: 116 AGVAHWGATVRQHGESYDDAWAFAVELAQRHDYRFLSAFDDADVIAGQGTVGIELAPHSP 175 Query: 186 AIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGG-DTLA 244 D +IVPIGGGGL SG K+ + + +VG Q E SM +G PI +LA Sbjct: 176 --DVVIVPIGGGGLASGVALALKS--QGVRIVGAQVEGVDSMARAISGDIRPIAPVPSLA 231 Query: 245 EGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQ 304 +G+ VK PG LT ++ +L+D++++V E L E + L E + EGAGA LAA Sbjct: 232 DGVRVKIPGFLTRRLCASLLDDVVIVREAELRETLVRLALEENLIAEGAGALALAA---- 287 Query: 305 PERFRGKTVGVILTGGNIDTRLLANVLLRDLARSGRLARLR 345 R G+ +++GGNID +LA +L R+ R R R Sbjct: 288 GRRVAGRRKFAVVSGGNIDASVLAGLLTDVRPRAPRKPRRR 328 Lambda K H 0.319 0.135 0.374 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: 343 Number of extensions: 19 Number of successful extensions: 6 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: 420 Length of database: 366 Length adjustment: 31 Effective length of query: 389 Effective length of database: 335 Effective search space: 130315 Effective search space used: 130315 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 (21.7 bits) S2: 50 (23.9 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