Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_086509359.1 BZY95_RS07325 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_002151265.1:WP_086509359.1 Length = 285 Score = 97.4 bits (241), Expect = 4e-25 Identities = 80/269 (29%), Positives = 124/269 (46%), Gaps = 24/269 (8%) Query: 83 IDLGDVKIGNGYFTIIAGPCSV-EGREMLMETAHFLSELGVKVLRGGAYKP------RTS 135 I + GN ++ G +V E RE+ +E A E+ ++ +K R+S Sbjct: 10 ISFAGLTAGNSLPLMLLGGMNVLESRELALEVAETYVEVTGRLGMPYVFKASFDKANRSS 69 Query: 136 PYSFQGLG-EKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLL 194 +SF+G G EKGLE L E ++G+ V+T+ VAE ADIIQ+ A A+ L+ Sbjct: 70 IHSFRGPGLEKGLEILAEIKQRFGVPVITDVHEPWQAEPVAEVADIIQLPAFLARQTDLV 129 Query: 195 SKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISA 254 + +K+ E +GN +++LCERG N L + Sbjct: 130 VAMAKTGAVINIKKPQFLAPHEMRHIIRKCEEAGNDRVLLCERG----SSFGYNNLIVDM 185 Query: 255 VPI-IRKESHLPILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPE 302 + K++ P+ D +HS GGRR V L+RA IAVG G+ +E HP+ Sbjct: 186 LGFGDMKQTGCPVFFDVTHSLQRPGGRADSAGGRRQQVAELARAGIAVGLAGLFLEAHPD 245 Query: 303 PEKALSDGKQSLDFELFKELVQEMKKLAD 331 P+ AL DG +L + + + + K L D Sbjct: 246 PDSALCDGPCALPLDQLEPFLTQAKALDD 274 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: 207 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: 285 Length adjustment: 27 Effective length of query: 311 Effective length of database: 258 Effective search space: 80238 Effective search space used: 80238 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