Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_092054776.1 BQ4888_RS05610 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_900111775.1:WP_092054776.1 Length = 336 Score = 278 bits (712), Expect = 1e-79 Identities = 152/327 (46%), Positives = 212/327 (64%), Gaps = 10/327 (3%) Query: 31 VKEIGKAKEAQGVNRFD-PVRERTMLNNIIENNDGPFENSTIQHIFKEIFKAGLELQEED 89 ++ + KA EA G+ P ERT + + N G ++STI+ + G+ Sbjct: 14 IRSVEKAVEAMGLQASPIPGSERTAIG--VLGNQGYVDDSTIREL------PGVVECIHV 65 Query: 90 HSKALLVSRKKKPEDTIVDIKGEKIGDGQQRFIV-GPCAVESYEQVAEVAAAAKKQGIKI 148 LVSR PE TIV++ KIG+G ++ GPC++ES Q+ A K G +I Sbjct: 66 SKPYKLVSRDFHPEPTIVEVGPVKIGNGLPPVVMAGPCSIESEAQMLASARVVKAAGAQI 125 Query: 149 LRGGAFKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIG 208 LRGGAFKPRT P+ FQGLGVEGL+ L+R DE L V++E++ +++ Y D++QIG Sbjct: 126 LRGGAFKPRTGPHSFQGLGVEGLKYLRRAGDEAGLPVVTEVMRIEQLDDVCRYADILQIG 185 Query: 209 ARNMQNFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYET 268 ARNMQNF+LLK G + PVLLKRG++AT+ EF+ AAEYI+++GN Q+ILCERGIRT+E Sbjct: 186 ARNMQNFDLLKEVGKRRHPVLLKRGMSATLEEFLAAAEYIVAEGNGQVILCERGIRTFEK 245 Query: 269 ATRNTLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPS 328 ATRNTLD+S VP++++ +HLP+ VD +H+TG R L+ +KAAL GA G+M EVHP+P Sbjct: 246 ATRNTLDLSIVPLIRKMSHLPIIVDPSHATGIRALVPVMSKAALVAGAHGLMVEVHPEPE 305 Query: 329 VALSDSAQQMAIPEFEKWLNELKPMVK 355 AL D AQ + F + EL ++K Sbjct: 306 KALCDGAQSLTGEGFATLMGELSGLLK 332 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: 325 Number of extensions: 18 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