Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_111391465.1 CLV31_RS03385 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_003253485.1:WP_111391465.1 Length = 801 Score = 57.4 bits (137), Expect = 9e-13 Identities = 41/139 (29%), Positives = 69/139 (49%), Gaps = 12/139 (8%) Query: 25 LNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKDLTAVEGRKFSVL 84 +N++ A ++ I+ AI + + ++I G F AGA++A + ++F + Sbjct: 507 MNSMGAEVIEGINTAIG--MAEKSYKGLVIGNEGGNFSAGANLAML--FMFAGDQEFDEI 562 Query: 85 GNKIFRKLENL-------EKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQPEVGLG 137 N + + +N PV+ A + ALGGGCELSL D A ++ G EVG+G Sbjct: 563 -NLMIAQFQNTMMRARYSSVPVVVAPHNMALGGGCELSLHADHIQAHAELYMGLVEVGVG 621 Query: 138 ITPGFGGTQRLARAIGVGM 156 + P GGT+ + R G+ Sbjct: 622 LIPAGGGTKEMTRRFANGV 640 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: 412 Number of extensions: 21 Number of successful extensions: 1 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: 801 Length adjustment: 33 Effective length of query: 226 Effective length of database: 768 Effective search space: 173568 Effective search space used: 173568 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: 51 (24.3 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