Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_015949963.1 G491_RS0128335 fructose-bisphosphate aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000429905.1:WP_015949963.1 Length = 268 Score = 315 bits (806), Expect = 9e-91 Identities = 150/267 (56%), Positives = 202/267 (75%), Gaps = 1/267 (0%) Query: 7 IKNLGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHK 66 + N+GK +R+ER+ +R + + V+VPMDHGV+ GPI GL+DI + VN +AEGGANAV+ H Sbjct: 1 MSNIGKEIRMERLMDRNTGRMVVVPMDHGVTVGPIFGLVDIAQAVNTIAEGGANAVIGHI 60 Query: 67 GIVRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDE 126 G+ R GHR GKD+GLI+HLS T +SP P KKV+V TVE A+RMGAD VS+HVN+G D+ Sbjct: 61 GLPRWGHRKGGKDIGLILHLSASTMVSPRPNKKVLVNTVENALRMGADGVSVHVNLGDDD 120 Query: 127 DWEAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTS 186 + + LG +A C YWGMPL+AMMYPRG++I+NE DPE+V AAR+GAELGAD VK S Sbjct: 121 EPAMLQALGEVAVECNYWGMPLLAMMYPRGRNIENETDPEMVRLAARVGAELGADFVKVS 180 Query: 187 YTGDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDV 246 YTGD +SF VV+GCPAP+++AGG K + +E F+ I++AM+AGA G++VGRN+FQ D Sbjct: 181 YTGDPESFARVVEGCPAPILIAGGSKLSAEEMFV-TIENAMKAGAKGLSVGRNVFQSKDP 239 Query: 247 VGITRAVCKIVHENADVEEALKEIRKK 273 V + C IVH+ +EA ++ R+K Sbjct: 240 VAFLQYACSIVHDGMTAQEAAEKYREK 266 Lambda K H 0.318 0.138 0.401 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: 275 Number of extensions: 10 Number of successful extensions: 2 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: 273 Length of database: 268 Length adjustment: 25 Effective length of query: 248 Effective length of database: 243 Effective search space: 60264 Effective search space used: 60264 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: 47 (22.7 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