Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_041098452.1 SUTH_RS08215 enoyl-CoA hydratase-related protein
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_000828635.1:WP_041098452.1 Length = 261 Score = 149 bits (376), Expect = 6e-41 Identities = 98/245 (40%), Positives = 136/245 (55%), Gaps = 12/245 (4%) Query: 14 LAVLYINRPKAMNALNKDTLLEIK---DAVTAVNDDPAVELLIITGSGDKSFVAGADIAF 70 LA L IN+P N L+ + EI DA A ND V+LL+ITG+G+K+F AG ++A Sbjct: 19 LATLTINKPP-FNVLDIPMMEEINVALDACLAAND---VKLLLITGAGEKAFSAGVEVA- 73 Query: 71 MQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIAASNAKF 130 + + + + +FR + M P +AAVNG ALGGG ELA+ CD +AA+ AKF Sbjct: 74 --DHTPDKVDRMIEVFHGIFRRLNRMPMPTLAAVNGAALGGGMELAIACDMLVAAAGAKF 131 Query: 131 GQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQPEELLP 190 GQPE+ L + P LPRLV P A +LL + I+ADEA RIGLVN+V E Sbjct: 132 GQPEIKLAVFPPIAAV-LLPRLVPPARAMELLLGGNNIDADEALRIGLVNRVFAKESFAA 190 Query: 191 EVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAF-GLCFATQDQKEGMTAF 249 ++K L+ + A+ ++ A D A+ + + AT+D KEG+ AF Sbjct: 191 DLKAFVDPYLALSRAALLSTRKAIRAASDKPFDAALDAAEEIYLKELMATEDAKEGLAAF 250 Query: 250 LEKRK 254 LEKRK Sbjct: 251 LEKRK 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: 184 Number of extensions: 11 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 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