Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate AZOBR_RS09775 AZOBR_RS09775 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__azobra:AZOBR_RS09775 Length = 263 Score = 156 bits (394), Expect = 5e-43 Identities = 94/244 (38%), Positives = 138/244 (56%), Gaps = 4/244 (1%) Query: 12 GNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQF 70 G + +TLNRP KLNA++ L + + E D +R II+TG G +AF AGADI +F Sbjct: 20 GGIATLTLNRPAKLNAISTALAAAMLDTLDALEVDAAVRAIIVTGAGERAFSAGADIAEF 79 Query: 71 NQLT---PAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEA 127 P A + + G+ + +IE+ KP IA +NG GGG E+ A + +A+E A Sbjct: 80 TPAVRRGPEAAVRAFRPGQTLCARIESFPKPIIAAVNGICYGGGCEILEASHLAVASERA 139 Query: 128 QLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANL 187 EI LG+ P +GGTQRL R G+ RALE ++TGD P A GLVN+VVP L Sbjct: 140 SFSKAEIRLGMMPTFGGTQRLPRNAGRKRALEWLLTGDTFPPAMALAVGLVNQVVPHDAL 199 Query: 188 EQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSA 247 +LA +I + SP +++ I V RGL+ + GLA+E+ + + D ++G+ A Sbjct: 200 LPAAFELAGRIVRHSPAAVSGILGAVTRGLNMTIGEGLAVETERFARLAPGADLRDGLEA 259 Query: 248 FLEK 251 +L + Sbjct: 260 WLAR 263 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: 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: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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 17 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