Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 7023121 Shewana3_0359 threonine dehydratase (RefSeq)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__ANA3:7023121 Length = 547 Score = 383 bits (983), Expect = e-110 Identities = 215/505 (42%), Positives = 306/505 (60%), Gaps = 9/505 (1%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL S VYDVA +PL KLS RLG ++KRED Q V SFKLRGAYN ++ LS+ Sbjct: 35 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAQLSQ 94 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216 E +GV+ ASAGNHAQGVA++ A IVMP TTP IK+DAVR LGG+VVL+G+ F Sbjct: 95 AECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTPDIKVDAVRRLGGNVVLHGQAF 154 Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIAG 276 D+A A+E+++ +G YI PFDD VI GQGTI E+ +Q +D+ VF+PVGGGGLIAG Sbjct: 155 DQANGFAMEMAKLEGRVYIAPFDDEAVIAGQGTIAQEMLQQQRDLEVVFVPVGGGGLIAG 214 Query: 277 VATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKC 336 +A ++K + P KI+GVEP AA + ++ G V L+ V FADGVAV +G F Sbjct: 215 IAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLAQVGLFADGVAVKRIGTEPFRLA 274 Query: 337 QELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKI----KNENIV 392 + +D +V V +D I AA+KD++++ R I E +GA+++AG Y K E + Sbjct: 275 KWFVDEVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYVSTNAAGESGKGEKVA 334 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452 AI SGAN++F L V+E LG KEA+LA + E+ GSF F L+ TE YRF Sbjct: 335 AILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPGSFLRFCELLEKRVMTEFNYRF 394 Query: 453 TSERKNALILYRVNVDK-ESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG--SAN 509 +S R A++ + + K +LE++I ++ + +LS +E H++++VGG Sbjct: 395 SS-RDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLSGDETAKLHVRYMVGGHPPEP 453 Query: 510 ISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEF 569 + + +F F PE L FL +WNI+L YRN G +L GF+VP+ + F Sbjct: 454 LEERLF-SFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAFGRVLAGFEVPEGDALPF 512 Query: 570 KNQADKLGYPYELDNYNEAFNLVVS 594 + +LG+ Y+ + + A+ L ++ Sbjct: 513 QQFLTELGFVYQEETQSPAYQLFLN 537 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: 673 Number of extensions: 21 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: 547 Length adjustment: 36 Effective length of query: 559 Effective length of database: 511 Effective search space: 285649 Effective search space used: 285649 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