Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_011912719.1 PST_RS07885 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000013785.1:WP_011912719.1 Length = 281 Score = 88.2 bits (217), Expect = 2e-22 Identities = 72/241 (29%), Positives = 113/241 (46%), Gaps = 23/241 (9%) Query: 127 AVESYEQVAEVAAAAKKQGIKILRGGAFKP--RTSPYDFQGLGVE-GLQILKRVADEFDL 183 A E Y +V E K GI + +F R+S F+G G+E G++I ++V F + Sbjct: 37 ACEEYVRVTE------KLGIPYVFKASFDKANRSSITSFRGPGLEEGMKIFEKVKKTFGV 90 Query: 184 AVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISEFIN 243 VI+++ P + D D+IQ+ A + +L+ A + +K+ E + Sbjct: 91 PVITDVHEPWQAQPVADVCDIIQLPAFLSRQTDLVVAMAKTGAVINIKKAQFLAPQEMKH 150 Query: 244 AAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHST----- 298 + GNDQ+ILCERG + +D+ I+KQ + PVF DVTH+ Sbjct: 151 ILKKCEEAGNDQLILCERG--SSFGYNNLVVDMLGFGIMKQFEY-PVFFDVTHALQMPGG 207 Query: 299 ------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNELKP 352 GRR + AKA L+ G G+ E HPDP A D + + + E +L +LK Sbjct: 208 RADSAGGRRAQVTDLAKAGLSQGLAGLFLEAHPDPDNAKCDGPCALRLNKLEAFLTQLKQ 267 Query: 353 M 353 + Sbjct: 268 L 268 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: 221 Number of extensions: 9 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: 281 Length adjustment: 27 Effective length of query: 331 Effective length of database: 254 Effective search space: 84074 Effective search space used: 84074 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