Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_027177586.1 G496_RS0100765 fructose-bisphosphate aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000429985.1:WP_027177586.1 Length = 265 Score = 316 bits (810), Expect = 3e-91 Identities = 150/259 (57%), Positives = 199/259 (76%) Query: 10 LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69 +GK +RLERIFNR + KTVIVPMDHGVS GPI GL+D+R+ V D+ +GGANAVL+ KG+V Sbjct: 3 MGKSIRLERIFNRNTGKTVIVPMDHGVSVGPIDGLVDMREAVGDMVKGGANAVLMQKGLV 62 Query: 70 RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWE 129 R GHR G DVGLI+HLS T++SP P KV+V TVE+AIRMGADAVS+HVN+G + + Sbjct: 63 RCGHRMEGGDVGLIVHLSASTSLSPFPNAKVLVATVEDAIRMGADAVSVHVNLGDETESR 122 Query: 130 AYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTG 189 +DLG +A WGMP++AM+Y RG ++NE PE+VAH AR+G ELGAD+VK YTG Sbjct: 123 MLKDLGEVASCAAGWGMPVLAMVYGRGPKVENEFAPEVVAHCARVGEELGADVVKVPYTG 182 Query: 190 DIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGI 249 D +SFR VV C PVV+AGGPK ++ +F+QM+ D++EAG AG++VGRN+FQH + V + Sbjct: 183 DQESFRRVVDSCCVPVVIAGGPKLDSTRDFIQMVSDSVEAGGAGLSVGRNVFQHKNRVNL 242 Query: 250 TRAVCKIVHENADVEEALK 268 + + K+VHE+ V+ AL+ Sbjct: 243 VKVLSKVVHEDESVDSALE 261 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: 280 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: 265 Length adjustment: 25 Effective length of query: 248 Effective length of database: 240 Effective search space: 59520 Effective search space used: 59520 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