Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_015819030.1 TERTU_RS12585 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000023025.1:WP_015819030.1 Length = 283 Score = 90.9 bits (224), Expect = 4e-23 Identities = 69/239 (28%), Positives = 115/239 (48%), Gaps = 25/239 (10%) Query: 129 ESYEQVAEVAAAAKKQGIKILRGGAFKP--RTSPYDFQGLGVE-GLQILKRVADEFDLAV 185 E Y QV + K GI + +F R+S + ++G G+E GL+I + V EF + V Sbjct: 39 EKYVQVTQ------KLGIPYVFKASFDKANRSSIHSYRGPGMEKGLRIFEAVKKEFGIPV 92 Query: 186 ISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISEFINAA 245 I+++ P + +DVIQ+ A + +L++A + +K+ + + N Sbjct: 93 ITDVHEPQQAAPVAEVVDVIQLPAFLARQTDLVEAMAKTDAVINVKKPQFLSPGQMRNIV 152 Query: 246 EYIMSQGNDQIILCERG-IRTYETATRNTLDISAVPILKQETH-LPVFVDVTH------- 296 E GN+ +ILCERG Y+ +D+ +K+ ++ LPV DVTH Sbjct: 153 EKFAEGGNENVILCERGACMGYDNL---VVDMLGFRTMKEVSNGLPVIFDVTHALQCRDP 209 Query: 297 ----STGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNELK 351 S GRR A+A LA+G G+ E HP+P+ A D + + + E +L ++K Sbjct: 210 LGAASGGRRQQTAELARAGLAVGLAGLFIEAHPNPNEAKCDGPSALPLDKLEPFLGQMK 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: 230 Number of extensions: 11 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: 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 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