Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate GFF2295 HP15_2243 phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::P39912 (358 letters) >FitnessBrowser__Marino:GFF2295 Length = 375 Score = 152 bits (384), Expect = 1e-41 Identities = 98/260 (37%), Positives = 143/260 (55%), Gaps = 20/260 (7%) Query: 111 GEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGLGVEG 170 G + G CAV+ E V + A ++ G R GA+KPRT+PY FQG G Sbjct: 95 GVEFSQSNLNIFAGLCAVDVPEHVDMMMQALEEHGEVCTRMGAYKPRTNPYSFQGHGKGC 154 Query: 171 LQILKRVADEFDLAVIS-EIVTPAHIEEALDYID--------VIQIGARNMQNFELLKAA 221 L + A + + VI+ EI +HIEE + ++ ++Q+G RN QNFELLKA Sbjct: 155 LPWVFEKAGKHGIKVIAMEITHESHIEEIDNCLEKLGRPTGVMLQVGTRNTQNFELLKAI 214 Query: 222 GAVKK-PVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYE-TATRNTLDISAV 279 G PVLLKRG T++E +NAAEY+ S+GN +I C RG++T RN +D + V Sbjct: 215 GRQSTYPVLLKRGFGITLNESLNAAEYLASEGNANVIFCLRGMKTEAGQPHRNMVDFAHV 274 Query: 280 PILKQETHLPVFVDVTHSTGRR--------DLLLPTAKAALAIGADGVMAEVHPDPSVAL 331 P +K+ T +PV VD +HS G R D++ TA+ +A GA+ V+ + HP P AL Sbjct: 275 PAVKRLTRMPVCVDPSHSVGSREQSPDGILDVMHATAQGVVA-GANMVLVDFHPKPERAL 333 Query: 332 SDSAQQMAIPEFEKWLNELK 351 D Q + + E +L +++ Sbjct: 334 VDGPQALLMNELPAYLEDIR 353 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: 290 Number of extensions: 15 Number of successful extensions: 5 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: 375 Length adjustment: 30 Effective length of query: 328 Effective length of database: 345 Effective search space: 113160 Effective search space used: 113160 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 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