Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012475790.1 CPHAMN1_RS12050 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000020545.1:WP_012475790.1 Length = 294 Score = 121 bits (303), Expect = 3e-32 Identities = 82/251 (32%), Positives = 131/251 (52%), Gaps = 21/251 (8%) Query: 121 FIVGPCAVESYEQVAEVA----AAAKKQGIKILRGGAFKP--RTSPYDFQGLGVEG-LQI 173 FI GPC +E E +VA A + +GI + G+F+ R+S F G+G L+I Sbjct: 32 FIAGPCVIEGREMALDVASVLHAIRESEGIACIFKGSFRKANRSSAASFTGIGDSAALEI 91 Query: 174 LKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRG 233 L + FD+ V++++ +E Y+DV+QI A + +LL AAG V +K+G Sbjct: 92 LGEIRGRFDMPVLTDVHETQEVERVSPYVDVLQIPAFLSRQTDLLTAAGRSGLCVNIKKG 151 Query: 234 LAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVD 293 + AA+ + GN +I+L ERG T +D +P + + T PV D Sbjct: 152 QFMAPEDMAFAAQKVAETGNTRIMLTERG--TTFGYHNLVVDFRGIPEMSK-TGYPVVYD 208 Query: 294 VTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPE 342 THS G R+ LLP A+AA+A G G+ EVHP+P A+SD+A Q+++ E Sbjct: 209 ATHSLQLPSSAQGTSGGVREYLLPMARAAVAAGVHGLFFEVHPEPQHAMSDAATQVSLKE 268 Query: 343 FEKWLNELKPM 353 F + +++++ + Sbjct: 269 FPEIVHQMQKL 279 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: 216 Number of extensions: 13 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: 358 Length of database: 294 Length adjustment: 28 Effective length of query: 330 Effective length of database: 266 Effective search space: 87780 Effective search space used: 87780 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 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