Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_029934590.1 N746_RS0105335 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000711195.1:WP_029934590.1 Length = 278 Score = 104 bits (260), Expect = 2e-27 Identities = 77/259 (29%), Positives = 128/259 (49%), Gaps = 25/259 (9%) Query: 95 FTIIAGPCSVEGREMLMETAHFLSEL----GVKVLRGGAYKP--RTSPYSFQGLG-EKGL 147 F +IAGPC +E ++ ++TA L EL G+ + +Y R+S SF+GLG ++GL Sbjct: 14 FFLIAGPCVIESEQLAIDTAGQLKELTDSLGIPFIFKSSYDKANRSSTASFRGLGIDEGL 73 Query: 148 EYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLK 207 L++ D+ G+ V+T+ + L +VA D++Q A + + PV +K Sbjct: 74 RILQKVKDEIGVPVLTDVHEDTPLSEVASVVDVMQTPAFLVRQTNFIQNVCRQGIPVNIK 133 Query: 208 RGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTL--DISAVPIIRKESHLP 265 +G + GN +I++C+RG NTL D+ + +R ++ P Sbjct: 134 KGQFQAPWDMDQVVAKAREVGNEQIMVCDRGT----SFGYNTLVSDMRGLASMR-QTGCP 188 Query: 266 ILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSL 314 ++ D +HS GG+R+ V L+RAAIA G G+ +E HP+P A SDG Sbjct: 189 VVFDATHSVQQPGGQGSTSGGQREFVPVLARAAIAAGVSGVFMETHPDPVNAKSDGPNMW 248 Query: 315 DFELFKELVQEMKKLADAL 333 K +++ +K L D + Sbjct: 249 PLHNLKPVLEVLKALDDTV 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: 204 Number of extensions: 10 Number of successful extensions: 2 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: 278 Length adjustment: 27 Effective length of query: 311 Effective length of database: 251 Effective search space: 78061 Effective search space used: 78061 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 10 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