Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 203422 SO4344 threonine dehydratase (NCBI ptt file)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__MR1:203422 Length = 545 Score = 382 bits (982), Expect = e-110 Identities = 216/517 (41%), Positives = 311/517 (60%), Gaps = 10/517 (1%) Query: 86 PTGGDSDELFQ-YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKL 144 P + +L Q YL IL S VYDVA +PL KLS RLG ++KRED Q V SFKL Sbjct: 21 PASVEKSQLAQHYLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKL 80 Query: 145 RGAYNMMSNLSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRA 204 RGAYN ++ LS+ E +GV+ ASAGNHAQGVA++ A IVMP TTP IK+DAVR Sbjct: 81 RGAYNRIAQLSQAECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTPDIKVDAVRR 140 Query: 205 LGGDVVLYGKTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAV 264 LGG+VVL+G+ FD+A A+ +++++G YI PFDD VI GQGTI E+ +Q +D+ + Sbjct: 141 LGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEMLQQQRDLEVI 200 Query: 265 FIPVGGGGLIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVA 324 F+PVGGGGLIAG+A ++K + P KI+GVEP AA + ++ G V LS V FADGVA Sbjct: 201 FVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQVGLFADGVA 260 Query: 325 VALVGEYTFAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFY 384 V +G F + +D +V V +D I AA+KD++++ R I E +GA+++AG Y Sbjct: 261 VKRIGTEPFRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYVSTN 320 Query: 385 KI----KNENIVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLV 440 + E + AI SGAN++F L V+E LG KEA+LA + E+ GSF F L+ Sbjct: 321 ATGESGRGEKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPGSFLRFCELL 380 Query: 441 GSLNFTELTYRFTSERKNALILYRVNVDK-ESDLEKMIEDMKSSNMTTLNLSHNELVVDH 499 TE YRF+S R A++ + + K +LE++I ++ + +LS +E H Sbjct: 381 EKRVMTEFNYRFSS-RDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLSGDETAKLH 439 Query: 500 LKHLVGG--SANISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLM 557 ++++VGG + + +F F PE L FL +WNI+L YRN G +L Sbjct: 440 VRYMVGGHPPEPLEERLF-SFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAFGRVLA 498 Query: 558 GFQVPQAEMDEFKNQADKLGYPYELDNYNEAFNLVVS 594 GF+VP ++ F+ +LG+ Y+ + + A+ L ++ Sbjct: 499 GFEVPASDALPFQQFLTELGFVYQEETQSPAYQLFLN 535 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: 666 Number of extensions: 20 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: 595 Length of database: 545 Length adjustment: 36 Effective length of query: 559 Effective length of database: 509 Effective search space: 284531 Effective search space used: 284531 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