Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_050656189.1 C1M55_RS20280 crotonase/enoyl-CoA hydratase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_002893965.1:WP_050656189.1 Length = 253 Score = 155 bits (391), Expect = 1e-42 Identities = 85/260 (32%), Positives = 143/260 (55%), Gaps = 13/260 (5%) Query: 4 ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCA 63 + + T++ G IT+NRP+ NA+N+ + L AV + ++D ++ + ++TG G FCA Sbjct: 3 DEVLTERRGRTLIITINRPEARNAINSAVSHALAAAVEELDADDDLSLAVLTGAGGNFCA 62 Query: 64 GADITQF----NQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACD 119 G D+ F N L P F++ KP I+ + G+AL GG EL LA D Sbjct: 63 GMDLKAFVAGENVLVPGRGLGFTEGPPR---------KPIISAVEGFALAGGTELVLATD 113 Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179 + +A+ EA+ G+PE+ G+ G GG RL + I +ALE+ +TGD ++A +YG VN Sbjct: 114 LVVASSEAKFGIPEVKRGLVAGGGGLLRLPKRIPYQKALELALTGDSFTAEEAYRYGFVN 173 Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 + + +LA++I + P+++A+ KE++ + A + VF++E Sbjct: 174 TLTEPGKALEGALELADRITRNGPLAVAVTKEIIVKAGGWSDDEAFAKQLQVMAPVFASE 233 Query: 240 DKKEGVSAFLEKREPTFKGK 259 D +EG +AF EKR P ++G+ Sbjct: 234 DAREGATAFAEKRAPVWEGR 253 Lambda K H 0.315 0.135 0.382 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: 146 Number of extensions: 5 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: 253 Length adjustment: 24 Effective length of query: 235 Effective length of database: 229 Effective search space: 53815 Effective search space used: 53815 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: 42 (22.0 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