Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_012991580.1 THAL_RS02685 fructose-bisphosphate aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000025605.1:WP_012991580.1 Length = 266 Score = 328 bits (842), Expect = 6e-95 Identities = 158/263 (60%), Positives = 208/263 (79%), Gaps = 1/263 (0%) Query: 9 NLGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGI 68 ++GK VRLERI NRE+ KT+IVPMDHGVS+GPI+G++DIR V DVAEGGA+AV+LHKG+ Sbjct: 2 SIGKQVRLERIMNRETGKTIIVPMDHGVSSGPIEGIVDIRSAVADVAEGGADAVVLHKGM 61 Query: 69 VRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDW 128 VR GHRG G+D+GLI+HLS T +P KV+V TVEEAI++GAD VS+HVN+G+D + Sbjct: 62 VRAGHRGRGRDIGLIVHLSASTDWAPTKNDKVLVCTVEEAIKLGADGVSVHVNIGADLER 121 Query: 129 EAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYT 188 E RDLG +A+ CE WGMPL+AM+Y RGK + N+ DP++VAH ARLGAELGADIVK YT Sbjct: 122 EMLRDLGYVAKVCEEWGMPLLAMVYGRGKDM-NQYDPQVVAHCARLGAELGADIVKVPYT 180 Query: 189 GDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVG 248 GD ++F V+GCP PVV+AGGPK T+EE L+M+ A++AGA G+++GRN+FQ D V Sbjct: 181 GDPETFCKAVEGCPVPVVIAGGPKMKTEEEVLRMVYGALQAGAKGLSIGRNVFQAKDRVR 240 Query: 249 ITRAVCKIVHENADVEEALKEIR 271 + RA+ +VH+ V+EAL ++ Sbjct: 241 MVRALYHLVHKGGTVDEALSILK 263 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: 315 Number of extensions: 15 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: 266 Length adjustment: 25 Effective length of query: 248 Effective length of database: 241 Effective search space: 59768 Effective search space used: 59768 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