Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate GFF3271 HP15_3213 threonine dehydratase biosynthetic
Query= SwissProt::P25306 (595 letters) >lcl|FitnessBrowser__Marino:GFF3271 HP15_3213 threonine dehydratase biosynthetic Length = 511 Score = 422 bits (1086), Expect = e-122 Identities = 227/503 (45%), Positives = 321/503 (63%), Gaps = 4/503 (0%) Query: 96 QYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLS 155 +Y+ IL + VYDVAIE+PL A LS R G N +KRED Q VFSFK+RGAYN ++ LS Sbjct: 4 RYIKKILDARVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLS 63 Query: 156 REELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKT 215 E+ KGVI ASAGNHAQGVALA + L A IVMP TTP+IK+ +VR G VVL G Sbjct: 64 EEQKAKGVICASAGNHAQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDA 123 Query: 216 FDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQL-KDIHAVFIPVGGGGLI 274 FDEA HA EL K G YIPP+DDP VI GQGT+ EI Q K IHA+FI VGGGGLI Sbjct: 124 FDEAAAHAQELIAKHGYTYIPPYDDPDVIAGQGTVAMEIMWQFSKPIHAIFICVGGGGLI 183 Query: 275 AGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFA 334 AG+A + K + P K+IGVEP + + ++ G RV L V FADGVAV +G+Y + Sbjct: 184 AGMAAYIKYLRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFADGVAVKQIGKYPWE 243 Query: 335 KCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAI 394 C++ +D ++ V+ D I AAIKDV+++ R+I E +GA+ +AG Y E K++ EN++A Sbjct: 244 ICKDHVDEVITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIAT 303 Query: 395 ASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTS 454 SGANM+F +L ++E +G +EA+LA + E+ G+FKTF+ + + TE YR+ + Sbjct: 304 LSGANMNFDRLRYISERTEVGEKREAILAVTIPEKPGAFKTFINALHKRSITEFNYRY-A 362 Query: 455 ERKNALILYRVNVDKES-DLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSA-NISD 512 + NA I + + E +++D++ S + ++L+ ++L H++H+VGG A I++ Sbjct: 363 DATNATIFVGIQIAAGGHGREDLVQDLRESGYSVVDLTDSDLAKQHIRHMVGGHAPTITN 422 Query: 513 EIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQ 572 E +F PE+ L FL + RWNI++ YRN G + +L+G QV E+ +F+ Sbjct: 423 EKVFQFEFPERPGALLKFLMSLGTRWNISMFHYRNHGAAYSRVLLGAQVDDHEVQDFEKM 482 Query: 573 ADKLGYPYELDNYNEAFNLVVSE 595 DK+G+ YE NEA+ L + + Sbjct: 483 LDKVGFRYENMTDNEAYQLFLGQ 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: 712 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: 511 Length adjustment: 36 Effective length of query: 559 Effective length of database: 475 Effective search space: 265525 Effective search space used: 265525 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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