Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate SMc01027 SMc01027 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::Q9WYH8 (338 letters) >FitnessBrowser__Smeli:SMc01027 Length = 280 Score = 101 bits (252), Expect = 2e-26 Identities = 79/251 (31%), Positives = 122/251 (48%), Gaps = 25/251 (9%) Query: 96 TIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKP------RTSPYSFQGLG-EKGLE 148 T+IAGPC +E RE A L EL + G YK RTS +G+G +K +E Sbjct: 26 TLIAGPCQMESREHAFMIAGELVELCRSLGLGLVYKSSFDKANRTSLSGKRGIGLDKAME 85 Query: 149 YLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKR 208 + ++G V+T+ E+ VAE DI+QI A ++ LL A + + +K+ Sbjct: 86 VFADLKREFGFPVLTDIHTEEQCAAVAETVDILQIPAFLSRQTDLLVAAAKTGRTINVKK 145 Query: 209 GFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTL--DISAVPIIRKESHLPI 266 G + SGN ++LCERG NTL D+ ++PI+ P+ Sbjct: 146 GQFLAPWDMKNVLAKFTESGNPNVLLCERGA----SFGYNTLVSDMRSLPIMAALG-APV 200 Query: 267 LVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLD 315 + D +HS GG+R+ V L+RAA+AVG G+ VE H +P+ A SDG + Sbjct: 201 VFDATHSVQQPGGQGGSTGGQREFVETLARAAVAVGVAGVFVETHEDPDNAPSDGPNMVP 260 Query: 316 FELFKELVQEM 326 + L++++ Sbjct: 261 LKDMPRLLEKL 271 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: 189 Number of extensions: 12 Number of successful extensions: 4 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: 280 Length adjustment: 27 Effective length of query: 311 Effective length of database: 253 Effective search space: 78683 Effective search space used: 78683 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: 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