Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_102106165.1 C0029_RS05670 enoyl-CoA hydratase
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_002869505.1:WP_102106165.1 Length = 264 Score = 142 bits (359), Expect = 5e-39 Identities = 82/227 (36%), Positives = 133/227 (58%), Gaps = 3/227 (1%) Query: 6 IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65 +I+ + E +A+L +NRP + NAL+ L + A++ +++DP V +++TG G K+F G Sbjct: 13 LIVSQGEGVALLELNRPDSFNALSVSLLDALVAALSTLSEDPTVSAIVLTGRG-KAFSVG 71 Query: 66 ADIAFMQNLSA-MEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIA 124 D+ + + + ME+ E G G V R +KP+I AVNGFA+ GG E+A+ CDF A Sbjct: 72 VDLKELASGNGLMESGELGP-GGSVMRAFNGCQKPIIGAVNGFAVTGGFEIALACDFLYA 130 Query: 125 ASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQ 184 A +A+F +G+ PG+G +Q+LPRLVG A+++ +T + A +A GLVN+V Sbjct: 131 AESARFADTHARVGLIPGWGLSQKLPRLVGINRAREISFTGNYFGAADAEAWGLVNRVCS 190 Query: 185 PEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEAD 231 +LL E A +I + A+ KA NEG + + A+ +E + Sbjct: 191 DNDLLAEALDTAHQIATALPEALFAIKAMMNEGWEDTLGHALVMEGE 237 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: 164 Number of extensions: 9 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: 260 Length of database: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 Sep 24 2021. 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