Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_041099452.1 SUTH_RS11730 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000828635.1:WP_041099452.1 Length = 276 Score = 119 bits (298), Expect = 9e-32 Identities = 86/258 (33%), Positives = 138/258 (53%), Gaps = 26/258 (10%) Query: 97 IIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKP------RTSPYSFQGLG-EKGLEY 149 +IAGPC +E REM ++TA L ++ K+ YK R+S SF+GLG E+GL+ Sbjct: 16 LIAGPCVIESREMALDTAGQLRDICRKLGLNFIYKSSYDKANRSSGKSFRGLGMEQGLDI 75 Query: 150 LREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRG 209 L + + G+ V+T+ E ++ VA D++Q A + + + KPV +K+G Sbjct: 76 LADVKKQIGVPVLTDVHAEHEVAAVASVVDVLQTPAFLCRQTDFIQACAASGKPVNIKKG 135 Query: 210 -FM--NTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPI 266 FM +++ +L A+ AN+G I++CERG N + I +E+ P+ Sbjct: 136 QFMAPGDMKQVVLKAKE-ANAGADSIMVCERGASF---GYNNLVSDMRSLAIMRETGCPV 191 Query: 267 LVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLD 315 + D +HS GG+R+ V L+RAA+AVG G+ +E HP+P KALSDG + Sbjct: 192 VFDATHSVQLPGGQGDRSGGQREFVPVLARAAVAVGVSGLFMETHPDPAKALSDGPNAWP 251 Query: 316 FELFKELVQEMKKLADAL 333 L++++ +L DAL Sbjct: 252 LPQMATLLEQLVEL-DAL 268 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: 207 Number of extensions: 10 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: 276 Length adjustment: 27 Effective length of query: 311 Effective length of database: 249 Effective search space: 77439 Effective search space used: 77439 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