Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate PP_4430 PP_4430 putative threonine dehydratase
Query= curated2:P53607 (507 letters) >FitnessBrowser__Putida:PP_4430 Length = 330 Score = 191 bits (485), Expect = 3e-53 Identities = 115/303 (37%), Positives = 177/303 (58%), Gaps = 9/303 (2%) Query: 14 RVYDVAFETELEPARNLSARLRNPVYLKREDNQPVFSFKLRGAYNKMAHIPADALARGVI 73 R+ + ET +E + +LS ++ PVYLK E +Q SFKLRGA N +A + + A GV+ Sbjct: 15 RIKHLVRETRMELSPSLSDFMKVPVYLKLECHQATGSFKLRGATNAIAGLTSQQRALGVV 74 Query: 74 TASAGNHAQGVAFSAARMGVKAVIVVPVTTPQVKVDAVRAHGGPGVEVIQAGESYSDAYA 133 TAS GNH + ++++AA GV+A + + P KV A+RA G V+V+ G S DA Sbjct: 75 TASTGNHGRALSYAAAAAGVRATVCLSRLVPSNKVAAIRALGA-AVQVV--GNSQDDAQF 131 Query: 134 HALKVQEERGLTFVHPFDDPYVIAGQGTIAMEILRQHQGPIHAIFVPIGGGGLAAGVAAY 193 A ++ +E GLTF+ PFD VIAGQ T+ +EI Q + + +P+ GGGL +GV+ Sbjct: 132 EAARLAQEEGLTFIPPFDHQDVIAGQATLGLEIAEQLPS-VSQVLIPLSGGGLFSGVSLA 190 Query: 194 VKAVRPEIKVIGVQAEDSCAMAQSLQAGKRVELAEVGLFAD--GTAVKLVGEETFRLCKE 251 +KA+ P++K GV AMAQSL+AGK V + EV AD G + L + TF L + Sbjct: 191 LKALLPQVKTHGVSMRLGAAMAQSLEAGKPVNVEEVATLADSLGGGIGLRNQYTFELTRR 250 Query: 252 YLDGVVTVDTDALCAAIKDVFQDTRSVLEPSGALAVAGAKLYAEREGIENQTLVAVTSGA 311 ++D V+ ++ D++ A+ + + R V+E +GA+ +A R+ +V V SG Sbjct: 251 FIDRVILLNEDSIADAMLHAYLEERLVIEGAGAVGIAA---LLTRQVEAQGPIVIVVSGG 307 Query: 312 NMN 314 N++ Sbjct: 308 NVD 310 Lambda K H 0.320 0.135 0.388 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: 313 Number of extensions: 13 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: 507 Length of database: 330 Length adjustment: 31 Effective length of query: 476 Effective length of database: 299 Effective search space: 142324 Effective search space used: 142324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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