Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_086511176.1 BZY95_RS17490 enoyl-CoA hydratase-related protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_002151265.1:WP_086511176.1 Length = 257 Score = 215 bits (547), Expect = 8e-61 Identities = 110/257 (42%), Positives = 168/257 (65%), Gaps = 1/257 (0%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-K 59 M + IE + +T+NRP LNALN+ +L EL+ +++ E ++R ++ITG G K Sbjct: 1 MSEKLIEMVDNAGVVRLTINRPKALNALNSAVLTELEALLTELEKRSDLRALLITGAGEK 60 Query: 60 AFCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACD 119 AF AGADIT+ TP EA F+ + + ++E L P +A++NG+ LGGG ELALACD Sbjct: 61 AFVAGADITEMRTKTPEEARAFASQALRTIKRLETLPVPVVALVNGFCLGGGCELALACD 120 Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179 +A++ A G PE+ LG+ PG+GGTQRL R +G AL+++ TG +I ++A + GLVN Sbjct: 121 WAVASDNAIFGQPEVLLGVIPGFGGTQRLPRRVGPAMALDLVTTGRKIDAQEALRIGLVN 180 Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 RV+P A LE +L +++A P+++ K+ V+ G+D L S LALE+ + + F+ Sbjct: 181 RVMPQAELEAYAEELTKQLAGNGPLAVRSAKQAVHDGMDQDLDSALALETSLFALGFAGS 240 Query: 240 DKKEGVSAFLEKREPTF 256 ++KEG+SAF+EKR+P F Sbjct: 241 EQKEGMSAFVEKRKPNF 257 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: 152 Number of extensions: 6 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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 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