Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011384227.1 AMB_RS09220 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000009985.1:WP_011384227.1 Length = 283 Score = 105 bits (262), Expect = 1e-27 Identities = 83/262 (31%), Positives = 133/262 (50%), Gaps = 22/262 (8%) Query: 87 DVKIGNGY-FTIIAGPCSVEGREMLMETAHFL----SELGVKVLRGGAYKP--RTSPYSF 139 DV +GN +IAGPC +E R+ ME A L +E G+ ++ ++ RTS Sbjct: 13 DVILGNDLPLVLIAGPCQMESRDHAMECAEALKIMAAEAGIALIYKSSFDKANRTSLAGQ 72 Query: 140 QGLG-EKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAG 198 +G+G +K L E K G+ V+T+ E+ A+ AD++QI A + LL AG Sbjct: 73 RGVGLDKALPIFAEIKAKLGLPVLTDVHTEEQCVIAAKVADVLQIPAFLCRQTDLLVAAG 132 Query: 199 SYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPII 258 + +K+G + A I ++GN++++L ERG +F T T D+ +PI+ Sbjct: 133 RTGAVINVKKGQFLAPWDMANVAAKIESTGNSRVLLTERGA-SFGYNTLVT-DMRGLPIM 190 Query: 259 RKESHLPILVDPSH-----------SGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKAL 307 + P+++D +H SGG R L+RAA+A+G G+ VE HP+P+ A Sbjct: 191 ARTGW-PVIMDATHAVQAPGGQGNSSGGDRRFAPVLARAAVAIGVAGVFVECHPDPDHAP 249 Query: 308 SDGKQSLDFELFKELVQEMKKL 329 SDG + + LV+ + KL Sbjct: 250 SDGPNMIAMKDMPALVEVLMKL 271 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: 187 Number of extensions: 11 Number of successful extensions: 4 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: 283 Length adjustment: 27 Effective length of query: 311 Effective length of database: 256 Effective search space: 79616 Effective search space used: 79616 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 09 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