Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_089323102.1 CHB58_RS05475 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_900188395.1:WP_089323102.1 Length = 262 Score = 120 bits (302), Expect = 3e-32 Identities = 88/259 (33%), Positives = 131/259 (50%), Gaps = 22/259 (8%) Query: 97 IIAGPCSVEGREMLMETAHFLSELGVK------VLRGGAYKP-RTSPYSFQGLG-EKGLE 148 +IAGPC +E R+++ E A + L + + + K R+S +SF+G G EKGLE Sbjct: 3 VIAGPCVIENRDVVFEVAEVILRLQERFKEHKFIFKASFDKANRSSIHSFRGPGLEKGLE 62 Query: 149 YLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKR 208 L E K+ + V+T+ + D IQI A + LL A KPV +K+ Sbjct: 63 ILAEVKSKFSLPVLTDIHESWQAEPAGKVVDFIQIPAFLCRQTDLLIAAAKTGKPVNVKK 122 Query: 209 GFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILV 268 G + E + SG ++I+L ERG T +D ++PI+ K +P++ Sbjct: 123 GQFMAPWDMGNVVEKLKESGASEIMLTERG--TTFGYNNLVVDFRSIPIM-KSFGVPVIF 179 Query: 269 DPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFE 317 D +HS GG R+ V LSRAA+AVG G+ E HP PEKALSDG + + Sbjct: 180 DATHSVQKPGGLGKASGGDREFVPYLSRAAVAVGVDGLFFETHPFPEKALSDGPNMIPLK 239 Query: 318 LFKELVQEMKKLADALGVK 336 F +L++E+ +L D L K Sbjct: 240 QFPDLIEELLQLEDFLNGK 258 Lambda K H 0.318 0.138 0.388 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: 198 Number of extensions: 8 Number of successful extensions: 3 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: 338 Length of database: 262 Length adjustment: 26 Effective length of query: 312 Effective length of database: 236 Effective search space: 73632 Effective search space used: 73632 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: 48 (23.1 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