Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
Query= BRENDA::Q9YEJ7 (270 letters) >FitnessBrowser__SB2B:6936711 Length = 659 Score = 101 bits (252), Expect = 4e-26 Identities = 76/223 (34%), Positives = 112/223 (50%), Gaps = 10/223 (4%) Query: 17 RETVVEVEG--VRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSP 74 +ETV EV+ + IG G +A ++ E +K AG L R P Sbjct: 425 KETVSEVQAGALLIGNGHSGALAMLSLPDTLEGFEPFLKQLKAAGFAGLVLDNLSERPDP 484 Query: 75 YSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLRE 134 + L +A ++ GL V +E +++ I + M N PLL Sbjct: 485 -------AKALDACTKAAEKFGLITAAAVNREDELEHAISRVELILIRGKQMFNQPLLER 537 Query: 135 VGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVA 194 +G+ PV+L+R ++ELLAAA+ IL EGN Q++L E G+ +F+ ST TLD+A + Sbjct: 538 LGKLHLPVVLERNTMADIDELLAAADTILAEGNQQLMLCESGVSSFKSSTLATLDLAGLV 597 Query: 195 VLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEV 237 LK +HLPV+V+PS+ A P AKA GADGL++EV Sbjct: 598 ELKARSHLPVLVNPSY-AVTPEACPRQAKAVKRLGADGLLLEV 639 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: 269 Number of extensions: 6 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: 659 Length adjustment: 32 Effective length of query: 238 Effective length of database: 627 Effective search space: 149226 Effective search space used: 149226 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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