Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 5207772 Shew_0293 threonine dehydratase (RefSeq)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__PV4:5207772 Length = 516 Score = 389 bits (1000), Expect = e-112 Identities = 215/498 (43%), Positives = 306/498 (61%), Gaps = 6/498 (1%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL S VYDVA +PL KLS RLG ++KRED Q V SFKLRGAYN ++ LS+ Sbjct: 16 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAELSQ 75 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216 EE +GV+ ASAGNHAQGVA++ A IVMP TTP IK+DAVR LGG VVLYG++F Sbjct: 76 EECQRGVVCASAGNHAQGVAMSASARGVSAVIVMPQTTPDIKVDAVRRLGGTVVLYGQSF 135 Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIAG 276 D A HA +L+ +G Y+ PFDD VI GQGT+ E+ +Q +D+ VF+PVGGGGLIAG Sbjct: 136 DMANEHAQQLARDEGRIYVAPFDDEAVIAGQGTVAQEMLQQQRDLEVVFVPVGGGGLIAG 195 Query: 277 VATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKC 336 +A ++K + P KIIGVEP +A + +L RV LS V FADGVAV +G F Sbjct: 196 IAAYYKAVMPQVKIIGVEPEDSACLKAALEADERVVLSQVGLFADGVAVKQIGAEPFRLA 255 Query: 337 QELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIAS 396 +E +D +V V +D I AA+KD++++ R I E +GA+++AG Y + K + + AI S Sbjct: 256 REYVDQVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYIG-DEGKGQKVAAILS 314 Query: 397 GANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTSER 456 GAN++F L V+E LG KEA+LA + E G F F L+ TE YRF+S R Sbjct: 315 GANVNFHSLRYVSERCELGEQKEAILAVKVPEHPGIFLRFCELLEKRAMTEFNYRFSS-R 373 Query: 457 KNALILYRVNVDK-ESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG--SANISDE 513 + A++ + + +++L++++ ++ +LSH+E H++++VGG + + Sbjct: 374 EKAVVFAGIRLSHGQAELDEIVARLEGDGFEVQDLSHDETAKLHVRYMVGGLPPEPLQER 433 Query: 514 IFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQA 573 +F F PE L FL +WNI+L YRN G +L GF+VP+++ F+ Sbjct: 434 LF-SFEFPEHPGALFKFLTTLRSKWNISLFHYRNHGAAYGRVLAGFEVPESDSVAFQQFL 492 Query: 574 DKLGYPYELDNYNEAFNL 591 +LG+ Y+ + + A+ L Sbjct: 493 TELGFVYQEETQSPAYKL 510 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: 662 Number of extensions: 22 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: 516 Length adjustment: 36 Effective length of query: 559 Effective length of database: 480 Effective search space: 268320 Effective search space used: 268320 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