Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_011460067.1 DHAF_RS16340 UxaA family hydrolase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000021925.1:WP_011460067.1 Length = 385 Score = 229 bits (584), Expect = 1e-64 Identities = 151/399 (37%), Positives = 212/399 (53%), Gaps = 33/399 (8%) Query: 10 LEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIGF 69 L G+ R DG GIRN + + CA VA I Q P A V + Sbjct: 3 LWGFRRPDGLFGIRNHLLILPTSVCATTVAANIAAQV---------PGA-----VAIANQ 48 Query: 70 PGCYPNG--YAEKM--LERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTI 125 GC G Y + + L + +PNVGAVL V LGCE + + + + SG+PV+ L I Sbjct: 49 HGCCQLGADYEQTLRTLIGIGRNPNVGAVLVVGLGCEGIPILHTAEEIAKSGKPVQSLII 108 Query: 126 QEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGR 185 QE GGT T GV L+ ++ LSEL +G CGGSD TSG+ ANPA G Sbjct: 109 QEHGGTLKTTALGVQVAAQMARTLSMLKREEAPLSELSLGVECGGSDFTSGLAANPAAGT 168 Query: 186 AFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV----AKAARYYSILGH 241 A D ++ AG T + ET E +G E + RA P + +++ V +A + + L Sbjct: 169 ASDLVVKAGGTAMLSETTEFIGAEHVLAKRAKSPEVAAKLLGIVKETELRARQLHVDLRD 228 Query: 242 GSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFG 301 G GN GG+++ EEKSLG K+G S I I+ G+ P GLY++D Sbjct: 229 GQPTPGNIAGGISSIEEKSLGCIYKAGHSTIQDILAYGEAPQGKGLYVMDT--------- 279 Query: 302 FPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAG 361 P + IG ++A G +I+FTTGRG+ GS I+PVIKV AN TY N++ ++D+D Sbjct: 280 -PGQDVESMIG-MLAGGIQIIVFTTGRGTPTGSPIAPVIKVTANADTYLNMADNIDLDLS 337 Query: 362 RILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEF 400 IL G T+++ GR +F++ + V+ G +KSE+LGHQEF Sbjct: 338 PILSGAETIEDSGRRIFKEIIEVANGKLTKSESLGHQEF 376 Lambda K H 0.318 0.137 0.408 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: 487 Number of extensions: 27 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: 431 Length of database: 385 Length adjustment: 31 Effective length of query: 400 Effective length of database: 354 Effective search space: 141600 Effective search space used: 141600 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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