Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate CA265_RS08910 CA265_RS08910 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >FitnessBrowser__Pedo557:CA265_RS08910 Length = 270 Score = 102 bits (255), Expect = 9e-27 Identities = 78/247 (31%), Positives = 126/247 (51%), Gaps = 21/247 (8%) Query: 122 IVGPCAVESYE---QVAE-VAAAAKKQGIKILRGGAFKP--RTSPYDFQGLGVE-GLQIL 174 + GPCA+E + ++AE + K I + G+++ R+ F G+G E L+IL Sbjct: 19 MAGPCAIEGEDIAMRIAEKIITITDKLQIPYIFKGSYRKANRSKGSSFTGIGDEKALRIL 78 Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234 +R+ EF + +++I A Y+DV+QI A + +LL AA K V +K+G Sbjct: 79 ERIGREFGVPTVTDIHESGEAAMAAAYVDVLQIPAFLCRQTDLLIAAAETGKVVNVKKGQ 138 Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDV 294 + A E + GN+++IL +RG T+ +D +P + Q +PV +D Sbjct: 139 FLSAGSMKFAVEKVKEAGNNKVILTDRG-NTFGYQDL-IVDYRGLPEM-QSFGVPVVMDC 195 Query: 295 THST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEF 343 THS G+ +L+ AKAA+A+GADG+ E HPDP+ A SD A + + Sbjct: 196 THSLQQPNQSSGVTGGKPELISTIAKAAIAVGADGLFIETHPDPANAKSDGANMLHLDLL 255 Query: 344 EKWLNEL 350 E+ L +L Sbjct: 256 EETLTKL 262 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: 203 Number of extensions: 13 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: 270 Length adjustment: 27 Effective length of query: 331 Effective length of database: 243 Effective search space: 80433 Effective search space used: 80433 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 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