Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_011384227.1 AMB_RS09220 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000009985.1:WP_011384227.1 Length = 283 Score = 92.4 bits (228), Expect = 1e-23 Identities = 78/241 (32%), Positives = 115/241 (47%), Gaps = 25/241 (10%) Query: 122 IVGPCAVESYEQVAEVAAAAK----KQGIKILRGGAFKP--RTSPYDFQGLGVE-GLQIL 174 I GPC +ES + E A A K + GI ++ +F RTS +G+G++ L I Sbjct: 25 IAGPCQMESRDHAMECAEALKIMAAEAGIALIYKSSFDKANRTSLAGQRGVGLDKALPIF 84 Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234 + + L V++++ T A DV+QI A + +LL AAG + +K+G Sbjct: 85 AEIKAKLGLPVLTDVHTEEQCVIAAKVADVLQIPAFLCRQTDLLVAAGRTGAVINVKKGQ 144 Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL--DISAVPILKQETHLPVFV 292 + N A I S GN +++L ERG + NTL D+ +PI+ + T PV + Sbjct: 145 FLAPWDMANVAAKIESTGNSRVLLTERG----ASFGYNTLVTDMRGLPIMAR-TGWPVIM 199 Query: 293 DVTH-----------STGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIP 341 D TH S G R A+AA+AIG GV E HPDP A SD +A+ Sbjct: 200 DATHAVQAPGGQGNSSGGDRRFAPVLARAAVAIGVAGVFVECHPDPDHAPSDGPNMIAMK 259 Query: 342 E 342 + Sbjct: 260 D 260 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: 196 Number of extensions: 13 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: 283 Length adjustment: 27 Effective length of query: 331 Effective length of database: 256 Effective search space: 84736 Effective search space used: 84736 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 09 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