Align 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / chorismate mutase (EC 2.5.1.54; EC 5.4.99.5) (characterized)
to candidate WP_007474517.1 CMTB2_RS05095 3-deoxy-8-phosphooctulonate synthase
Query= reanno::Cola:Echvi_0120 (367 letters) >NCBI__GCF_000170735.1:WP_007474517.1 Length = 264 Score = 75.9 bits (185), Expect = 1e-18 Identities = 79/268 (29%), Positives = 119/268 (44%), Gaps = 40/268 (14%) Query: 18 VIIAGPCSAETPEQVEKVCLEMKEQN-IIPSMFRAGIWKP-RTRPGSFEGIGED-GLKWM 74 ++IAGPC E+ EQ+ K+ +K N F+A K RT S+ G G D GL+ + Sbjct: 2 ILIAGPCVIESKEQIFKIAEYLKPYNEKYDFYFKASFDKANRTSLDSYRGPGIDKGLEIL 61 Query: 75 EIVRHHLNIPITTEVGNTAHVELALKHKVDVLWIGARTTVNPFAVQE---IAEALKGTDI 131 V+ + T++ T V+ A + VDVL I A F ++ + EA K I Sbjct: 62 NEVKEKFGYKLLTDIHETWQVKKAAE-VVDVLQIPA------FLCRQTDLLVEAAKTNKI 114 Query: 132 PVMVKNPMNPDLQLWIGALERLHAVGINKLA----------AIHRGFSDAYDKRFRNKPN 181 + K + L+ L G N+++ RG + Y + + Sbjct: 115 VNIKKGQFMNPADMKYSVLKVLKTRGCNEVSYENSKKYGVWLTERGTTFGYGNLVVDMRS 174 Query: 182 WSMPIHLKREWKGMEVINDPSHIV-----------GKRDGILEISQRAINFGLDGLMIET 230 + + RE+ VI D +H V GKR+ + +S+ A G+DG ET Sbjct: 175 ----LVIMREF--APVIFDATHSVQMPGGAGGKSSGKREFVPYLSKAAAAVGVDGFFFET 228 Query: 231 HHDPDNAWSDAKQQVTPAQLKDILSKID 258 H++PDNA SD +TP LKDIL ID Sbjct: 229 HYNPDNALSDGPNMITPEMLKDILKDID 256 Lambda K H 0.318 0.135 0.409 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: 231 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 264 Length adjustment: 27 Effective length of query: 340 Effective length of database: 237 Effective search space: 80580 Effective search space used: 80580 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