Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate AZOBR_RS07520 AZOBR_RS07520 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::Q9WYH8 (338 letters) >FitnessBrowser__azobra:AZOBR_RS07520 Length = 275 Score = 113 bits (283), Expect = 5e-30 Identities = 89/267 (33%), Positives = 140/267 (52%), Gaps = 28/267 (10%) Query: 83 IDLGDVKIGNGY-FTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKP------RTS 135 + +G++ I N FT+IAGPC +E R+ +ETA L E+ + G YK RTS Sbjct: 7 VQIGNLTIANDRPFTLIAGPCQMESRDHALETAAALVEMTGALGIGLIYKSSFDKANRTS 66 Query: 136 PYSFQGLG-EKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLL 194 + +GLG +K L E +++G V+T+ D VAE D++QI A + LL Sbjct: 67 ISTARGLGMDKALPIFAEIKERFGCPVITDVHEADQCAAVAEVMDVLQIPAFLCRQTDLL 126 Query: 195 SKAGSYNKPVLLKRG-FMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTL--D 251 A + V +K+G F+ + ++A+ +A SGN K++LCERG NTL D Sbjct: 127 IAAAKTGRVVNVKKGQFLAPWDMKNVAAKLVA-SGNDKVLLCERGA----SFGYNTLVSD 181 Query: 252 ISAVPIIRKESHLPILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVH 300 + ++PI+ E+ P++ D +HS GG+R+ V L+RAAIAVG + +E H Sbjct: 182 MRSLPIMA-ETGFPVVFDATHSVQQPGGQGTTSGGQREFVPVLARAAIAVGVAAVFMETH 240 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMK 327 P+ A SDG + + L+ ++ Sbjct: 241 ENPDCAPSDGPNMVPLKEMPALLARLQ 267 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: 178 Number of extensions: 13 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: 275 Length adjustment: 27 Effective length of query: 311 Effective length of database: 248 Effective search space: 77128 Effective search space used: 77128 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