Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Pf6N2E2_1562 Threonine dehydratase (EC 4.3.1.19)
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1562 Length = 318 Score = 177 bits (449), Expect = 5e-49 Identities = 106/297 (35%), Positives = 162/297 (54%), Gaps = 4/297 (1%) Query: 25 VYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQ-KAHGVI 83 +YE T L+ RL + VK E+ P +FK+RG + L E +A G++ Sbjct: 16 LYEVMPATAQYAWPLLAERLGCTVWVKHENHTPTGAFKVRGGLTFVRWLKREHPEAKGIV 75 Query: 84 TASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAI 143 TA+ GNH Q +A +++ LG+KALIV+P + K +A+RGFGGEV+ +G +FDEA+ +A+ Sbjct: 76 TATRGNHGQSLALAASALGLKALIVVPQGNSVEKNNAMRGFGGEVVEYGRDFDEAREEAV 135 Query: 144 ELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAGVAVLIKQL 203 L+Q G VPPF HP ++ G T LEL LD V+VP+G G V L Sbjct: 136 RLAQSHGLYLVPPF-HPELVKGVATYGLELFNAVPDLDTVYVPIGCGSGICAVIAARDAL 194 Query: 204 MPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDII 263 + +V+ V + ++ K + +AG + FA+G+AV+R E F + I+ Sbjct: 195 GLKTQVVGVVSTEALAAKLSFEAGRLCETASANTFADGLAVRRPVPEAFAIYGAGAARIV 254 Query: 264 TVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVN 320 V I AM+ + D +AE +GA ALA + + +RG+R+A ILSG N++ Sbjct: 255 AVSDAEIAGAMRAYYTDTHNLAEGAGAAALAALMQ--ERETMRGKRVAVILSGGNID 309 Lambda K H 0.321 0.138 0.403 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: 399 Number of extensions: 16 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: 514 Length of database: 318 Length adjustment: 31 Effective length of query: 483 Effective length of database: 287 Effective search space: 138621 Effective search space used: 138621 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: 50 (23.9 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