Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate GFF2094 PS417_10680 enoyl-CoA hydratase
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__WCS417:GFF2094 Length = 263 Score = 138 bits (347), Expect = 1e-37 Identities = 87/263 (33%), Positives = 137/263 (52%), Gaps = 14/263 (5%) Query: 6 IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65 ++ + + +A + +NR NAL+ TL + + N DPAV ++++TG+G +SF AG Sbjct: 7 VLTQVQAGVAWITLNRGPQRNALDIPTLKHLHALLDTFNTDPAVRVVVLTGNG-RSFCAG 65 Query: 66 ADIAFMQNLSAMEAREFGAL--------GQKVFRLIEAMEKPVIAAVNGFALGGGCELAM 117 AD+A +A EAR GAL + + ++KP IAA+NG A+G G +L + Sbjct: 66 ADLA---EWAAAEAR--GALETYGWTDTAHALMTRLHTLDKPTIAAINGTAVGAGMDLTL 120 Query: 118 CCDFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIG 177 CCD R+AA +A+F + +P G + LPRL+G AK+LL+ ++ +AD A G Sbjct: 121 CCDLRVAAQSARFKAGYTSMAYSPDAGASWHLPRLIGSEQAKRLLFLDELWSADRALAAG 180 Query: 178 LVNKVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCF 237 LV +VV + L +A R+ + A +K +G + + + E A LC Sbjct: 181 LVGEVVTDDHLHAHTNALATRLANGPTFAFAQTKTLIRDGAERSLPAQLQAELAAGLLCG 240 Query: 238 ATQDQKEGMTAFLEKRKANFISK 260 + D E + A LEKR F K Sbjct: 241 RSADGTEALRASLEKRLPIFSGK 263 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: 123 Number of extensions: 4 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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 17 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