Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 17824 b3772 threonine dehydratase (NCBI)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Keio:17824 Length = 514 Score = 385 bits (988), Expect = e-111 Identities = 216/514 (42%), Positives = 315/514 (61%), Gaps = 7/514 (1%) Query: 84 NKPTGGDSDELFQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFK 143 ++P G + E +YL +L +PVY+ A +PL+ EKLS RL +KRED+Q V SFK Sbjct: 4 SQPLSG-APEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFK 62 Query: 144 LRGAYNMMSNLSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVR 203 LRGAY MM+ L+ E+ GVITASAGNHAQGVA + RL A IVMPT T IK+DAVR Sbjct: 63 LRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVR 122 Query: 204 ALGGDVVLYGKTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHA 263 GG+V+L+G FDEA+ A+ELS++ G ++PPFD P VI GQGT+ E+ +Q + Sbjct: 123 GFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDR 182 Query: 264 VFIPVGGGGLIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGV 323 VF+PVGGGGL AGVA KQ+ P K+I VE +A + +L GH V L V FA+GV Sbjct: 183 VFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGV 242 Query: 324 AVALVGEYTFAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEF 383 AV +G+ TF CQE +D ++ V +D I AA+KD++++ R + E SGA+A+AG Y Sbjct: 243 AVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIAL 302 Query: 384 YKIKNENIVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSL 443 + I+ E + I SGAN++F L V+E LG +EALLA + E++GSF F L+G Sbjct: 303 HNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGR 362 Query: 444 NFTELTYRFTSERKNALILYRVNVDKE-SDLEKMIEDMKSSNMTTLNLSHNELVVDHLKH 502 + TE YRF ++ KNA I V + + + +++++ + + ++LS +E+ H+++ Sbjct: 363 SVTEFNYRF-ADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRY 421 Query: 503 LVGG--SANISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQ 560 +VGG S + + ++ F PE L FL+ WNI+L YR+ G +L F+ Sbjct: 422 MVGGRPSHPLQERLY-SFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE 480 Query: 561 VPQAEMDEFKNQADKLGYPYELDNYNEAFNLVVS 594 + E D F+ + ++LGY + N AF ++ Sbjct: 481 LGDHEPD-FETRLNELGYDCHDETNNPAFRFFLA 513 Lambda K H 0.317 0.135 0.382 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: 674 Number of extensions: 30 Number of successful extensions: 3 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: 595 Length of database: 514 Length adjustment: 36 Effective length of query: 559 Effective length of database: 478 Effective search space: 267202 Effective search space used: 267202 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 (21.7 bits) S2: 53 (25.0 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