Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF2295 HP15_2243 phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::Q9WYH8 (338 letters) >FitnessBrowser__Marino:GFF2295 Length = 375 Score = 174 bits (442), Expect = 2e-48 Identities = 115/342 (33%), Positives = 186/342 (54%), Gaps = 30/342 (8%) Query: 1 MIVVLKPGST--EEDIRKVVKLAESY---NLKCHISKG--QERTVIGIIGDDRYVVADKF 53 M+ +L P + E+ R+ + E+ +++ H +G Q T I ++GD + + ++ Sbjct: 1 MLAILHPNTALDSEEYRQTMHYLENLPNVSVRVHEVQGATQRLTEIYLLGDTKPLNKEEI 60 Query: 54 ESLDCVESVVRVLKPYKLVSREFHPED---TVIDLGDVKIGNGYFTIIAGPCSVEGREML 110 E+L VE +R+ Y+++ R H +D + V+ I AG C+V+ E + Sbjct: 61 EALPAVERAIRISDDYRILGR--HRDDRRQSGFTYNGVEFSQSNLNIFAGLCAVDVPEHV 118 Query: 111 METAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVT-EALGED 169 L E G R GAYKPRT+PYSFQG G+ L ++ E A K+G+ V+ E E Sbjct: 119 DMMMQALEEHGEVCTRMGAYKPRTNPYSFQGHGKGCLPWVFEKAGKHGIKVIAMEITHES 178 Query: 170 DLPKVAEYAD--------IIQIGARNAQNFRLLSKAGSYNK-PVLLKRGFMNTIEEFLLS 220 + ++ + ++Q+G RN QNF LL G + PVLLKRGF T+ E L + Sbjct: 179 HIEEIDNCLEKLGRPTGVMLQVGTRNTQNFELLKAIGRQSTYPVLLKRGFGITLNESLNA 238 Query: 221 AEYIANSGNTKIILCERGIRT-FEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDL 279 AEY+A+ GN +I C RG++T + RN +D + VP +++ + +P+ VDPSHS G R+ Sbjct: 239 AEYLASEGNANVIFCLRGMKTEAGQPHRNMVDFAHVPAVKRLTRMPVCVDPSHSVGSREQ 298 Query: 280 -------VIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSL 314 V+ + + GA+ ++V+ HP+PE+AL DG Q+L Sbjct: 299 SPDGILDVMHATAQGVVAGANMVLVDFHPKPERALVDGPQAL 340 Lambda K H 0.318 0.138 0.388 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: 20 Number of successful extensions: 6 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: 338 Length of database: 375 Length adjustment: 29 Effective length of query: 309 Effective length of database: 346 Effective search space: 106914 Effective search space used: 106914 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: 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