Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_011425014.1 RHE_RS08795 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_000092045.1:WP_011425014.1 Length = 259 Score = 155 bits (391), Expect = 1e-42 Identities = 96/261 (36%), Positives = 146/261 (55%), Gaps = 10/261 (3%) Query: 1 MAYENIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDK 60 MA + ++ + +A+L I+RP+ +NAL+ D L + DA AV +P + + ++TG G K Sbjct: 1 MASGTVRVDVDRHVAILTISRPEKLNALDLDMLKALADAADAVEANPDLRVAVLTGEG-K 59 Query: 61 SFVAGADI-AFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCC 119 F AG DI A+ L + + G ++F + + P+IAA+NG ALGGG ELA Sbjct: 60 GFSAGGDIKAWGGMLPQVFGHAWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAGVA 119 Query: 120 DFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLV 179 D R+A + K G PE GLG+ PG+ GTQRL R G +++ ++ A+EA +G+V Sbjct: 120 DIRVAEEHIKIGLPETGLGMVPGWSGTQRLVRRFGAQAVRRMALGGEIFTAEEARLLGIV 179 Query: 180 NKVVQPEELLPEVKKIAGRILSKGQLAVRLSK---AAANEGMQTDIDRAMSIEADAFGLC 236 + VV + ++ AGRI ++G AV ++K A+AN D ++EA L Sbjct: 180 DAVVPTGNSVAAARQYAGRIAARGPAAVEIAKLMIASAN-----GEDNGTAVEALGSILA 234 Query: 237 FATQDQKEGMTAFLEKRKANF 257 T D KEG+ +F EKR A F Sbjct: 235 AKTGDLKEGVASFSEKRPATF 255 Lambda K H 0.319 0.136 0.378 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: 188 Number of extensions: 15 Number of successful extensions: 3 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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