Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_011384972.1 AMB_RS13040 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000009985.1:WP_011384972.1 Length = 255 Score = 158 bits (400), Expect = 9e-44 Identities = 95/258 (36%), Positives = 147/258 (56%), Gaps = 10/258 (3%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 M F + T + G +F +TL P +NAL+ L+++L A+ E+D IRV+ + + KA Sbjct: 1 MSFSVLNTARRGAVFVVTLASPP-VNALSRALIKDLHAAMDMVEADKTIRVLHLRSEQKA 59 Query: 61 FCAGADITQFNQ------LTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLEL 114 FCAGAD+ + + L A+ F + + ++ +IE L+ T+A + G A+GGGLEL Sbjct: 60 FCAGADLAEMRENLANPDLVDAQI-AFVRDLQNVLKRIETLALATVAEVGGAAMGGGLEL 118 Query: 115 ALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEK 174 ALACD R+AA EA+L LPE+NLG+ PG GGTQRLTR+ G A +++ + + G+ AE Sbjct: 119 ALACDFRMAANEAKLALPEVNLGLIPGAGGTQRLTRLCGPAIAKRLILGAEILDGQSAEA 178 Query: 175 YGLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALE-SVGWG 233 G+V+ P A L + LA+++A ++A K + LD P G E + Sbjct: 179 MGIVHWSAPRAELADKAATLADRLATLPRAAVAASKSCIEASLD-PSRDGYEEELTATRN 237 Query: 234 VVFSTEDKKEGVSAFLEK 251 ++ + + V AFL K Sbjct: 238 LLLHEPETRHRVEAFLSK 255 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: 125 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: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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