Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_077278049.1 B1C78_RS05010 PLP-dependent lyase/thiolase
Query= CharProtDB::CH_107419 (405 letters) >NCBI__GCF_002000365.1:WP_077278049.1 Length = 474 Score = 77.8 bits (190), Expect = 6e-19 Identities = 102/356 (28%), Positives = 156/356 (43%), Gaps = 40/356 (11%) Query: 33 YDYSSIKIDMEKLKTECPSVWKYAKLLPVEREPVTIQEGGTPLYKCD-------RLAEKI 85 Y+ + D E++ + + + A V+RE G TPL + RLA Sbjct: 29 YETGVLAFDYERMLAD--TGYDIAAAQAVQRETAV---GDTPLVELHNITALVRRLASPG 83 Query: 86 GIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGMNTVACASTGNTSAALAIYGAKAGIP 145 +++VK E NP+GSFKDR ++ V +A G VA A++GN AA+A AKAG+ Sbjct: 84 KGARIFVKDEAANPSGSFKDRRASLSVHEARRRGYPGVAAATSGNYGAAVASQAAKAGLR 143 Query: 146 VVVLLPA---GKVALGKVAQAL----MHGAKVLSIRGNFDDALALVRTLCSQEKIYLLNS 198 +V+ A VA ++ + +GA+V IR + L V + +E Y S Sbjct: 144 CIVVQEAFDSRGVAQPEIEEKTRACEAYGAEV--IRLSVGPELFYVFLMVLRETGYFNAS 201 Query: 199 I-NPYRLEGQKTIGFEIADQLDFKV---PDRIVLPVGNAGNITAIYKGFREFKILGITDS 254 + PY + G +T+G E+A Q + PD ++ GN+T +G R+ G TD+ Sbjct: 202 LYTPYSVLGIETLGHELAVQTKERTGRFPDVVIATHAGGGNVTGTARGLRK---AGATDT 258 Query: 255 LPKMTGIQAEG---SCPIVKAIKSGAPAITPEENPETVATAIRIGNPVNATKALSAIRES 311 + G + KS T P T R P NA + L + Sbjct: 259 QVIAASVDLAGLHMASDHDFNRKSFTTGHTGFSMPFT-TWPDRADVPRNAARPLRYL--- 314 Query: 312 GGTAESVTDEEILAAQKDLARLEGIGVEPAS----AASVAGLRKLVDMGVIGRDET 363 +VT E+ A + LA LEG+ PA AA+ A R+L + V+ ET Sbjct: 315 -DRFVTVTQGEVFYATQVLAELEGLERGPAGNTSLAAAFAIARELDEAQVVVVQET 369 Lambda K H 0.317 0.135 0.389 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: 387 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 405 Length of database: 474 Length adjustment: 32 Effective length of query: 373 Effective length of database: 442 Effective search space: 164866 Effective search space used: 164866 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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