Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate GFF5275 PS417_27010 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__WCS417:GFF5275 Length = 504 Score = 423 bits (1088), Expect = e-123 Identities = 230/501 (45%), Positives = 320/501 (63%), Gaps = 4/501 (0%) Query: 94 LFQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSN 153 L QY+ IL S VYDVA+E+PL+ A +LS+RLG ++KRED Q VFSFK+RGAYN ++ Sbjct: 2 LEQYVKKILTSRVYDVAVETPLQTARQLSERLGNQVWLKREDLQPVFSFKIRGAYNKLTQ 61 Query: 154 LSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYG 213 L+ EE +GV+TASAGNHAQG+ALA + L A IVMP TTP+IK++ VR+ GG VVL+G Sbjct: 62 LTAEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHG 121 Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-DIHAVFIPVGGGG 272 +F EA ++L+L ++ G YI P+DDP I GQGT+ EI RQ + A+F+PVGGGG Sbjct: 122 DSFPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGPLDAIFVPVGGGG 181 Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332 LIAG+A + K + P+ KIIGVEP + + +L G RV L V FADGVAVA +G++T Sbjct: 182 LIAGIAAYVKYLRPDIKIIGVEPDDSNCLQAALAAGERVVLPTVGIFADGVAVAQIGQHT 241 Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392 F C++ +D ++ V+ D I AAIKD+YD+ R+I E +GA+ +AG Y E + + +V Sbjct: 242 FDICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVETRGVTGQTLV 301 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452 AI SGAN++F +L V E A LG G+EA++A + E+ GSFK F VG TE YRF Sbjct: 302 AIDSGANVNFDRLRHVAERAELGEGREAIIAVTIPERPGSFKAFCEAVGKRQITEFNYRF 361 Query: 453 TSERKNALILYRVNVDKESD-LEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG-SANI 510 S A I V E+D +I + L+L+ NEL H++H+VGG +A++ Sbjct: 362 HS-GSEAHIFVGVQTHPENDPRSALIASLTRQGFPVLDLTENELAKLHIRHMVGGHAAHV 420 Query: 511 SDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFK 570 S+E+ F PE+ L FL+ RWNI++ YRN G + ++ G QVP E Sbjct: 421 SNEVVFRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPADERHLVP 480 Query: 571 NQADKLGYPYELDNYNEAFNL 591 + +GYPY ++ N A+ L Sbjct: 481 AALEAIGYPYWDESDNPAYTL 501 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: 714 Number of extensions: 30 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: 504 Length adjustment: 36 Effective length of query: 559 Effective length of database: 468 Effective search space: 261612 Effective search space used: 261612 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