Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_072908596.1 BUB13_RS10295 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_900142125.1:WP_072908596.1 Length = 336 Score = 284 bits (727), Expect = 2e-81 Identities = 143/309 (46%), Positives = 208/309 (67%), Gaps = 8/309 (2%) Query: 31 VKEIGKAKEAQGVNRFDPVRERTMLNNIIENNDGPFENSTIQHIFKEIFKAGLELQEEDH 90 + E+ KA EA G+ + +P+ + N G ++STI+ + +G+ Sbjct: 14 IDEVIKAVEAMGL-KAEPIPGSLRTAIGVLGNQGYVDDSTIRTL------SGVRETIHVS 66 Query: 91 SKALLVSRKKKPEDTIVDIKGEKIGDGQQR-FIVGPCAVESYEQVAEVAAAAKKQGIKIL 149 +VSR PE T+V++ G + GD ++ I GPC++E+ EQ+ A K G ++L Sbjct: 67 KPYKMVSRDFHPESTVVNVGGVRFGDSEKPVMIAGPCSIETEEQMMAAAEQVKSGGAQML 126 Query: 150 RGGAFKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGA 209 RGGAFKPRT PY FQGLG+EGL+ L+R + L V++E++ +E ++ D++QIGA Sbjct: 127 RGGAFKPRTGPYSFQGLGIEGLKYLQRAGKAYGLPVVTEVMRIGQLEAVCEHADMVQIGA 186 Query: 210 RNMQNFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETA 269 RNMQNF+LLK G + PVLLKRG++ATI EF+ AAEYI+++GNDQ++LCERGIRT+E Sbjct: 187 RNMQNFDLLKEVGKTRHPVLLKRGMSATIEEFLAAAEYILAEGNDQVVLCERGIRTFEKT 246 Query: 270 TRNTLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSV 329 TRNTLD+S VP++K+ +HLP+ VD +H+TG+R+L+ KAAL +GA G+M EVHPDP+ Sbjct: 247 TRNTLDLSVVPLIKEMSHLPIIVDPSHATGKRNLVTSMGKAALVVGAHGLMVEVHPDPAR 306 Query: 330 ALSDSAQQM 338 AL D AQ + Sbjct: 307 ALCDGAQSL 315 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: 327 Number of extensions: 12 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: 336 Length adjustment: 29 Effective length of query: 329 Effective length of database: 307 Effective search space: 101003 Effective search space used: 101003 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: 49 (23.5 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