Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_052296991.1 PYRFU_RS04105 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000223395.1:WP_052296991.1 Length = 340 Score = 201 bits (512), Expect = 2e-56 Identities = 111/279 (39%), Positives = 169/279 (60%), Gaps = 9/279 (3%) Query: 83 LELQEEDHSKALLVSRKKKPEDTIVDIKGEKIGDGQQRFIV--GPCAVESYEQVAEVAAA 140 +EL SK L SR+ D++ I ++G + FIV GPC +ES EQV E +A Sbjct: 53 VELVSNVGSKLQLSSREWLGGDSVARIGNVEVG---RDFIVIAGPCGIESREQVEEAVSA 109 Query: 141 AKKQGIKILRGGAFKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALD 200 G ++RGGA+KPRTSPY FQG+G+E + L A L I+E++ P + + Sbjct: 110 VWSAGAHVVRGGAWKPRTSPYSFQGIGLEAAKWLAEAAHSKGLPAITEVMDPRDARQVFN 169 Query: 201 YIDVIQIGARNMQNFELLKAAGAV----KKPVLLKRGLAATISEFINAAEYIMSQGNDQI 256 +D + +GAR+MQ LL+ G + K VL+KRG T+ E++ A+EY+M +G + Sbjct: 170 IVDGVWVGARSMQVTPLLRELGRLCRETGKAVLIKRGFGNTLEEWLLASEYVMLEGCSNV 229 Query: 257 ILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGA 316 L ERG R + + +R +LD++ +P+ + +THLP+ VD +H G+R+L+ P A AA A GA Sbjct: 230 ALIERGSRCWASVSRFSLDVAIIPVARGKTHLPIIVDPSHPAGKRELVEPLALAATAAGA 289 Query: 317 DGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNELKPMVK 355 G+M EVHP P ALSD QQ+ EF++ + +LK +++ Sbjct: 290 QGLMIEVHPWPEKALSDKQQQLTPGEFKRLMEKLKLLLE 328 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: 282 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: 340 Length adjustment: 29 Effective length of query: 329 Effective length of database: 311 Effective search space: 102319 Effective search space used: 102319 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