Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_002117405.1:WP_085772004.1 Length = 728 Score = 94.0 bits (232), Expect = 8e-24 Identities = 62/189 (32%), Positives = 93/189 (49%), Gaps = 22/189 (11%) Query: 12 VLLLTLNRPA-ARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAE 70 V LLT + P + N + ++ +L +E A D +I CVI F+ GADL+ M + Sbjct: 15 VALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGKNAFSGGADLS-MLQ 73 Query: 71 KDLAAT----------------LNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELAL 112 K AA R QL+ RL+ KP A++G LG ELAL Sbjct: 74 KSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVCLGGAFELAL 133 Query: 113 LCD--VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQ 170 C V+ + + GLPE+ +G+ PGAGGTQR+ R + A + + GE ++ + A+ Sbjct: 134 ACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGEQLSGKAAKA 193 Query: 171 AGLVSDVFP 179 AGL ++ P Sbjct: 194 AGLAQELAP 202 Lambda K H 0.318 0.130 0.356 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: 307 Number of extensions: 11 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: 255 Length of database: 728 Length adjustment: 32 Effective length of query: 223 Effective length of database: 696 Effective search space: 155208 Effective search space used: 155208 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 (21.8 bits) S2: 51 (24.3 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