Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate PP_3191 PP_3191 putative threonine ammonia-lyase / dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Putida:PP_3191 Length = 350 Score = 212 bits (540), Expect = 1e-59 Identities = 125/304 (41%), Positives = 184/304 (60%), Gaps = 4/304 (1%) Query: 5 EDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSE 64 ++I++A L+ V T L +S LS +TG E+ LK E+LQ TGSFK RGA NK+ L Sbjct: 38 QNIQDAHAALRPAVSITPLLHSPRLSALTGCEVLLKCEHLQHTGSFKFRGASNKMRLLPA 97 Query: 65 EERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVI-LEGNI 123 E RK+GV+AAS+GNH Q +ALA ++ G+P + A K R LGA+V+ L + Sbjct: 98 EARKQGVIAASSGNHGQALALAGKMAGVPVKVYTTTGASAYKTEAMRALGAEVVCLPTDP 157 Query: 124 FDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLIS 183 EAA R + G FV P+ND VIAGQGTIG+E++E PD++ V V VGGGG+IS Sbjct: 158 LSAELEAA-RQAKAQGVPFVSPYNDLQVIAGQGTIGMELLEQAPDLDAVFVAVGGGGMIS 216 Query: 184 GVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIA-VKKPGDLTFE 242 G+ A++ + P ++IG N P++ SL+ G ++ TL+DG A +PG +TF Sbjct: 217 GIGAALRVLKPGTEIIGCWPANDPTLQQSLKAGEIIELDACETLSDGTAGGVEPGSITFP 276 Query: 243 LVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIVIS 301 L + + + V V+E+EI A+ + + + EGA AV VA + + +GK+VA+++ Sbjct: 277 LCQALLTDTVLVSEDEIRCAMRDIASSERWIIEGAAAVAVAGMQRLAERYQGKRVAVILC 336 Query: 302 GGNI 305 G NI Sbjct: 337 GRNI 340 Lambda K H 0.317 0.136 0.367 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: 260 Number of extensions: 7 Number of successful extensions: 4 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: 401 Length of database: 350 Length adjustment: 30 Effective length of query: 371 Effective length of database: 320 Effective search space: 118720 Effective search space used: 118720 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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