Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_017600514.1 D471_RS0121385 hypothetical protein
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000341125.1:WP_017600514.1 Length = 273 Score = 218 bits (556), Expect = 9e-62 Identities = 103/250 (41%), Positives = 160/250 (64%) Query: 9 NLGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGI 68 + G+ +R +R+F + ++ ++VP+DH V+NGPI G + V +A +AV++HKG Sbjct: 6 SFGRRLRTQRLFRHDEQRLLVVPLDHSVTNGPITGGNKLNILVGQLATNNVDAVVVHKGS 65 Query: 69 VRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDW 128 +RH + L++HLS T + +P K +V++VEEA+R GADAVS+HVN+GS E+ Sbjct: 66 LRHIDPEWFTRTSLVVHLSASTMHAVDPDGKYLVSSVEEALRQGADAVSVHVNLGSLEEH 125 Query: 129 EAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYT 188 D+ +A+ C+ W +PL+AM+YPRG + + ++ E+VAHA L A+LGAD+VKT Y Sbjct: 126 RQIADMAAVADACDRWNVPLLAMVYPRGPKVADPQNTEMVAHAVSLAADLGADLVKTEYV 185 Query: 189 GDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVG 248 G + ++ P PV+V GGP++ D L+ ++D M GAAGVA+GRNIFQ + Sbjct: 186 GSVPDMLELTSNAPIPVIVVGGPRSRDDGRVLRYVEDVMAGGAAGVAMGRNIFQAPNPGE 245 Query: 249 ITRAVCKIVH 258 + AV + VH Sbjct: 246 MAAAVAERVH 255 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: 239 Number of extensions: 9 Number of successful extensions: 1 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: 273 Length adjustment: 25 Effective length of query: 248 Effective length of database: 248 Effective search space: 61504 Effective search space used: 61504 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