Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012407502.1 NPUN_RS03670 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000020025.1:WP_012407502.1 Length = 352 Score = 239 bits (611), Expect = 6e-68 Identities = 121/268 (45%), Positives = 174/268 (64%), Gaps = 4/268 (1%) Query: 87 EEDHSKALLVSRKKKPEDTIVDIKGEKIGDGQQRFIV---GPCAVESYEQVAEVAAAAKK 143 E+ + +A R + + +V+ + G+ + +V GPC+VE+ E + E A K Sbjct: 67 EQPYKRASRQYRHGEASEVVVNTPNGAVVFGEHQPLVVVAGPCSVENEEMIVETARRVKT 126 Query: 144 QGIKILRGGAFKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYID 203 G K LRGGA+KPRTSPY FQG G L +L R + L +I+E++ A +++ ++ D Sbjct: 127 AGAKFLRGGAYKPRTSPYAFQGHGESALDLLARAREVSGLGIITEVMDAADLDKIVEVAD 186 Query: 204 VIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGI 263 VIQ+GARNMQNF LLK GA KPVLLKRG+AATI +++ AAEY+++ GN +ILCERGI Sbjct: 187 VIQVGARNMQNFSLLKKVGAQPKPVLLKRGMAATIEDWLMAAEYVLASGNSNVILCERGI 246 Query: 264 RTYETA-TRNTLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAE 322 RT++ TRNTLD+S VP+L++ THLP+ +D +H G + + A AA+A G D +M E Sbjct: 247 RTFDRQYTRNTLDLSVVPVLRKLTHLPIMIDPSHGVGWSEFVPSMAMAAIAAGTDSLMIE 306 Query: 323 VHPDPSVALSDSAQQMAIPEFEKWLNEL 350 VHP+P+ ALSD Q + F+ + EL Sbjct: 307 VHPNPAKALSDGPQSLTPDRFDNLMQEL 334 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: 272 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: 352 Length adjustment: 29 Effective length of query: 329 Effective length of database: 323 Effective search space: 106267 Effective search space used: 106267 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