Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate WP_092348548.1 BLU87_RS11570 threonine ammonia-lyase, biosynthetic
Query= SwissProt::P25306 (595 letters) >NCBI__GCF_900107645.1:WP_092348548.1 Length = 502 Score = 376 bits (966), Expect = e-108 Identities = 211/494 (42%), Positives = 294/494 (59%), Gaps = 4/494 (0%) Query: 101 ILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELD 160 IL S VY+ AIE+PLE A LS L ++KRED Q VFSFKLRGAYN ++ LS E + Sbjct: 8 ILTSKVYEAAIETPLEEAVNLSTELKNRVFLKREDLQPVFSFKLRGAYNKIAQLSEAEKN 67 Query: 161 KGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTFDEAQ 220 KGVI ASAGNHAQGVA + Q+L A IVMP TTPQIKIDAV+A G +VL+G + EA Sbjct: 68 KGVIAASAGNHAQGVAFSAQKLGLKALIVMPATTPQIKIDAVKAFGAKIVLHGDNYSEAA 127 Query: 221 THALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-DIHAVFIPVGGGGLIAGVAT 279 + + G+ YI PFDD VI GQGT+ E+ RQ + AVF+PVGGGGLI+G+ Sbjct: 128 ERCKAILAETGMTYIHPFDDKLVIAGQGTVADELLRQSSGKLDAVFVPVGGGGLISGIGA 187 Query: 280 FFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQEL 339 + K ++P K+IGVEP + +M SL RV L +V FADGVAV VG+ TF C++ Sbjct: 188 YLKALSPQVKVIGVEPNDSDAMYQSLQANKRVILPSVGIFADGVAVQQVGKLTFDLCRQH 247 Query: 340 IDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGAN 399 +D ++ V D + +AIK +Y R+I+E +GA+ +AG Y + YK+ + +V I SGAN Sbjct: 248 VDEIIRVNTDELCSAIKTIYQATRSIVEPAGALGMAGLKQYIQKYKVTGQTLVTINSGAN 307 Query: 400 MDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFV-GLVGSLNFTELTYRFTSERKN 458 M+F +L V+E G G E+L A + E+ G+ + F ++ N TE YR S+R Sbjct: 308 MNFERLRYVSERTQAGEGSESLFAVTIPEEPGALRYFCQHILNKTNITEFNYRL-SDRTQ 366 Query: 459 ALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG-SANISDEIFGE 517 A + V++ + + T++LS+NEL HL++++GG SA + E Sbjct: 367 AQLFIGVSIGNGDIRNNFANRLNKAGYKTIDLSNNELAKTHLRYMIGGRSAEATRERLFR 426 Query: 518 FIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQADKLG 577 F PE+ L FL WNI+L YR+QG +L+G ++P + K+ D LG Sbjct: 427 FWFPERPGALIRFLADMGEDWNISLFHYRSQGGEFGRVLIGLEIPDKNEKKLKSFLDNLG 486 Query: 578 YPYELDNYNEAFNL 591 Y Y + + A+ L Sbjct: 487 YHYIEETDDSAYKL 500 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: 26 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: 502 Length adjustment: 36 Effective length of query: 559 Effective length of database: 466 Effective search space: 260494 Effective search space used: 260494 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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