Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_028990559.1 G579_RS0113295 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >NCBI__GCF_000423825.1:WP_028990559.1 Length = 377 Score = 170 bits (431), Expect = 4e-47 Identities = 110/275 (40%), Positives = 153/275 (55%), Gaps = 20/275 (7%) Query: 9 LALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAF 68 L +++R T E GVR G + V AG C+V++ E V A++E G R GA+ Sbjct: 79 LGRHKDDQRPTAFEYNGVRFGQDNLNVFAGLCAVDTPEHVELMMKALREHGQVCTRMGAY 138 Query: 69 KPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVT-EVLDPRHV--------ETVSRYADML 119 KPRT+PYSFQG G L + + G+ V+ E+ HV +T + ML Sbjct: 139 KPRTNPYSFQGHGKACLPYVFELAGKYGIRVIAMEITHEAHVDEIREALRQTGNPTGVML 198 Query: 120 QIGARNMQNFPLLREVGRSGK-PVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIR 178 QIG RN QNF LL+ VGR + PVLLKRGFG T+EE L AAEY+ EGN +V+ RG++ Sbjct: 199 QIGTRNTQNFELLKSVGRQREFPVLLKRGFGITLEESLNAAEYLASEGNTRVIFGLRGMK 258 Query: 179 T--FEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVP-------ALAKAGLAAG 229 T +P F +D A V V+K T +PV +DPSH G R P + G+ AG Sbjct: 259 TNMGDPHRNF-VDFAHVPVVKRLTRMPVCIDPSHSVGSRERAPDGILDVMHVTAQGVIAG 317 Query: 230 ADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGEL 264 A+ ++V+ HPNP++AL D Q L E + + ++ Sbjct: 318 ANMILVDFHPNPQKALVDGPQALLLEELPQFLEDV 352 Lambda K H 0.318 0.136 0.392 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: 213 Number of extensions: 9 Number of successful extensions: 5 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: 270 Length of database: 377 Length adjustment: 27 Effective length of query: 243 Effective length of database: 350 Effective search space: 85050 Effective search space used: 85050 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