Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate Echvi_3354 Echvi_3354 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Cola:Echvi_3354 Length = 416 Score = 247 bits (631), Expect = 6e-70 Identities = 144/405 (35%), Positives = 231/405 (57%), Gaps = 8/405 (1%) Query: 95 FQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNL 154 FQ +++ + + +V +PL+ E+LS+ G Y+KRED Q V S+K+RGAY+ +S+L Sbjct: 6 FQGIIEA-SEALQEVLHPTPLQFNEQLSEEYGCRVYLKREDLQAVRSYKIRGAYHKISSL 64 Query: 155 SREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVL 211 S EE +GV+ ASAGNHAQGVA A ++L I +P+TT KI+ ++ G + +VL Sbjct: 65 SEEEKSRGVVCASAGNHAQGVAFACKKLGIKGTIFIPSTTSAQKINRMKLFGKEMVEIVL 124 Query: 212 YGKTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-DIHAVFIPVGG 270 G T+D+A A E E+ G ++ PFDDP VI+GQGTI EI + + +F+P+GG Sbjct: 125 SGDTYDDAYQTAAEYCEERGAVFVHPFDDPKVIEGQGTIAKEILDDAEFPVDYLFLPIGG 184 Query: 271 GGLIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGE 330 GG+ AGV+T+F+Q +P TK+IG EP GA SM S+ L +D F DG AV VG Sbjct: 185 GGMAAGVSTYFEQSSPETKLIGTEPKGAPSMLTSIQNLKNTVLDEIDGFVDGAAVKKVGN 244 Query: 331 YTFAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNEN 390 TF C++ +D M+LV I I ++Y+ ++E +GA+ +A + Y + K+K +N Sbjct: 245 ITFEICRKSLDEMLLVPEGRICTTILNLYNNEGIVVEPAGAMTLAALSLY-DKEKLKGKN 303 Query: 391 IVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTY 450 +V + SG N D + ++ E + L G + ++ G+ K FV + + + Sbjct: 304 VVCVVSGGNNDIMRTAEIKERSLLYEGLKHYFMVQFPQRPGALKDFVSKILGPDDDIAYF 363 Query: 451 RFT--SERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHN 493 +FT + R+N + + + +L + + +K + L+ N Sbjct: 364 QFTKKNNRENGPAVVGIELKDPQNLPGIFDRLKENRFKYNYLNEN 408 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: 560 Number of extensions: 28 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: 416 Length adjustment: 34 Effective length of query: 561 Effective length of database: 382 Effective search space: 214302 Effective search space used: 214302 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 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