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) >FitnessBrowser__Marino:GFF3271 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:
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