Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012503218.1 CPAR_RS10115 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000020505.1:WP_012503218.1 Length = 286 Score = 122 bits (307), Expect = 9e-33 Identities = 81/247 (32%), Positives = 132/247 (53%), Gaps = 21/247 (8%) Query: 122 IVGPCAVESYEQVAEVAAAA----KKQGIKILRGGAFKP--RTSPYDFQGLGV-EGLQIL 174 + GPC +E+ + VA +++GI ++ G+++ R+S + G+G E L+IL Sbjct: 20 VAGPCLIENRQMAVAVATELDRIRQEEGISVIFKGSYRKANRSSASSYTGIGDREALEIL 79 Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234 + D FD+ V++++ + +E A Y+DV+QI A + EL+ AA + + +K+G Sbjct: 80 CEIRDVFDMPVLTDVHETSDVELAASYVDVLQIPAFLSRQTELIVAAASTGLAINIKKGQ 139 Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDV 294 + AAE S GN +I+L ERG T +D +PI+ ++ PV D Sbjct: 140 FMAPEDMALAAEKAASTGNRKIMLTERG--TTFGYHNLVVDYRGLPIM-ADSGWPVIFDA 196 Query: 295 THST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEF 343 THS G R L+P A+AA+A G DG+ EVHP+PS A+SD+A Q+ + +F Sbjct: 197 THSVQLPSASSGVSGGDRRFLMPLARAAVAAGVDGLFFEVHPEPSNAMSDAATQVPLDQF 256 Query: 344 EKWLNEL 350 + EL Sbjct: 257 HAMVREL 263 Lambda K H 0.316 0.134 0.369 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: 209 Number of extensions: 10 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: 358 Length of database: 286 Length adjustment: 28 Effective length of query: 330 Effective length of database: 258 Effective search space: 85140 Effective search space used: 85140 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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