Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate BPHYT_RS11065 BPHYT_RS11065 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__BFirm:BPHYT_RS11065 Length = 516 Score = 419 bits (1076), Expect = e-121 Identities = 225/503 (44%), Positives = 325/503 (64%), Gaps = 6/503 (1%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL L + VYDVA E+ LE A LS RL Y+KRED Q VFSFK+RGAYN M+++S Sbjct: 14 YLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISA 73 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYG 213 E L++GVITASAGNHAQGVAL+ R+ A IV+P TTPQ+K+DAVRA GG +VV +G Sbjct: 74 EALERGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQFG 133 Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGG 272 +++ +A HA++L ++ L ++ PFDDP VI GQGT+ EI Q + IHA+F+P+GGGG Sbjct: 134 ESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGG 193 Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332 L AGVA + K + P K+IGV+ + +M SL G RV L+ V F+DG AV LVGE T Sbjct: 194 LAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEET 253 Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392 F C E +D ++LV D + AAIKDV+ + R++LE +G++A+AGA Y E I+N+ ++ Sbjct: 254 FRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTLI 313 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452 AI SGANM+F ++ V E A +G +EA+ A + E++GSF+ F LVG+ + TE YR Sbjct: 314 AITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYRI 373 Query: 453 TSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS- 511 ++ +A I V + S+ ++ ++ T++L+ +EL H++++VGG + ++ Sbjct: 374 -ADANSAHIFVGVQIRNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLAH 432 Query: 512 DEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKN 571 DE F PE+ L FL + +P WNI+L YRNQG +S+L+G QVP +E + F Sbjct: 433 DERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFNK 492 Query: 572 QADKLGYPYELDNYNEAFNLVVS 594 LGYP + N + L ++ Sbjct: 493 FLATLGYPNWEETQNPVYRLFLA 515 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: 661 Number of extensions: 31 Number of successful extensions: 5 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