Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 5208561 Shew_1072 chorismate mutase (RefSeq)
Query= BRENDA::Q9YEJ7 (270 letters) >FitnessBrowser__PV4:5208561 Length = 654 Score = 100 bits (250), Expect = 6e-26 Identities = 78/244 (31%), Positives = 118/244 (48%), Gaps = 9/244 (3%) Query: 13 SEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRT 72 +E + T V ++IG G IA + + + A +KEAG + Sbjct: 419 AEHPQVTSVICRQLQIGNGQFGAIAQLALSQESDHYGQLAKQIKEAGFQAVT-------V 471 Query: 73 SPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLL 132 S + + L +RRA ++ L + + + S +ADML I + M N LL Sbjct: 472 SELNTNPMANRQLSEMRRALNQFDLACIVAIEHESELTLASDHADMLLISGKQMHNRDLL 531 Query: 133 REVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAA 192 +VG PV+L+R +++E L AAE IL GN Q+VL E GIRTF R TLD++ Sbjct: 532 EQVGALHMPVILERNTMASLDEWLGAAEVILAAGNQQLVLSEAGIRTFNEQQRPTLDLSG 591 Query: 193 VAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEV-HPNPEEALSDAKQQ 251 + LKE +HLPV+++ + + L + A A A ADGL++ V P + SD + Sbjct: 592 LISLKERSHLPVLLNTRYACQQEELA-SQAGAAKALKADGLVLGVSDPQQLKGHSDILAR 650 Query: 252 LTPG 255 L G Sbjct: 651 LYRG 654 Lambda K H 0.318 0.136 0.392 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: 285 Number of extensions: 5 Number of successful extensions: 1 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: 270 Length of database: 654 Length adjustment: 31 Effective length of query: 239 Effective length of database: 623 Effective search space: 148897 Effective search space used: 148897 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 (21.7 bits) S2: 50 (23.9 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