Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_001519075.1:WP_156424864.1 Length = 277 Score = 162 bits (410), Expect = 7e-45 Identities = 101/262 (38%), Positives = 152/262 (58%), Gaps = 12/262 (4%) Query: 4 KNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVA 63 ++I +E+ G V ITL RP LNA+NA +E++ A N A DD + ++TG G+ F A Sbjct: 22 EHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQGRGFCA 81 Query: 64 GADIAEMKDLTAVEG-RKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRI 122 G+D+ + A EG R + G + + +KP+IAA+NG ALGGG E++L+CD+ I Sbjct: 82 GSDLKAV----AAEGFRSYPAHGYAGLIERFDCDKPIIAAVNGLALGGGFEVALACDLII 137 Query: 123 ASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVV 182 A+ A+FG PE +G GG RLAR IG+ A +I + + ++A E R+G V +VV Sbjct: 138 AAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERLGFVTEVV 197 Query: 183 EPDKLLEEA-KALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAE----VFGECFA 237 PD LE A + V+AI++ AP+++R K A+ +GL + A A+ F A Sbjct: 198 -PDTDLESAVERWVEAILLGAPLSIRASKQAVMRGLD-EAGVAAAMAAQPGYPAFAAWSA 255 Query: 238 TEDRVEGMTAFVEKRDKAFKNK 259 + D EG TAF EKR ++ + Sbjct: 256 SADLREGTTAFAEKRPPVWQGR 277 Lambda K H 0.318 0.136 0.376 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: 172 Number of extensions: 7 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: 259 Length of database: 277 Length adjustment: 25 Effective length of query: 234 Effective length of database: 252 Effective search space: 58968 Effective search space used: 58968 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: 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