Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate HSERO_RS19510 HSERO_RS19510 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__HerbieS:HSERO_RS19510 Length = 508 Score = 451 bits (1159), Expect = e-131 Identities = 243/502 (48%), Positives = 331/502 (65%), Gaps = 8/502 (1%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL + VYDVA E+PLELA LS R+ Y KRED Q VFSFKLRGAYN M++L+ Sbjct: 5 YLKKILTARVYDVAQETPLELANTLSQRIDNRIYFKREDMQSVFSFKLRGAYNKMAHLTP 64 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216 +L +GVI ASAGNHAQGVAL+ RL C A IVMPTTTPQ+KIDAV+A GG+VVL+G +F Sbjct: 65 AQLKRGVICASAGNHAQGVALSAARLGCRAVIVMPTTTPQVKIDAVKARGGEVVLFGDSF 124 Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGGLIA 275 +A HAL L +K L ++ PFDDP VI GQGT+G EI RQ D IHA+F+ +GGGGLIA Sbjct: 125 TDAYEHALTLEKKQKLTFVHPFDDPYVIAGQGTVGMEILRQHPDPIHAIFVAIGGGGLIA 184 Query: 276 GVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAK 335 GVA++ K + P+ KIIGV+ + +M SL G RV L +V F+DG AV LVGE TF Sbjct: 185 GVASYVKAVRPDIKIIGVQTTDSDAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFRI 244 Query: 336 CQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYK-----IKNEN 390 +EL+D +++V D + AIKD++ + R+I+E +GA+A+AGA AY E K IK E+ Sbjct: 245 AKELVDEVIIVDTDAVCTAIKDIFQDTRSIVEPAGALAVAGAKAYVERAKASKKPIKGES 304 Query: 391 IVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTY 450 ++ IA GANM+F +L V E+A G +EA+ A + E++GSF+ F VG N TE Y Sbjct: 305 LITIACGANMNFDRLRFVAEMADAGEAREAVFAVTIPEERGSFRRFCETVGPRNVTEFNY 364 Query: 451 RFTSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANI 510 R S+ K A + + V + K+ + + + L+L+H+EL H++HLVGG +++ Sbjct: 365 RI-SDAKAAHVFVGIQVSAADEAGKIARNFEKAGFGVLDLTHDELAKVHIRHLVGGKSDL 423 Query: 511 S-DEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEF 569 + DE+ F PE+ L FL + +P WNI+L YRNQG +L+G QVP+ EM EF Sbjct: 424 TGDELLYRFEFPERPGALMKFLSSMNPGWNISLFHYRNQGGDVGRILIGLQVPKKEMKEF 483 Query: 570 KNQADKLGYPYELDNYNEAFNL 591 + +LGY + ++ N + L Sbjct: 484 RAFLAQLGYRHWDESKNPLYKL 505 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: 659 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: 508 Length adjustment: 36 Effective length of query: 559 Effective length of database: 472 Effective search space: 263848 Effective search space used: 263848 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