Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_086509903.1 BZY95_RS10660 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_002151265.1:WP_086509903.1 Length = 264 Score = 189 bits (481), Expect = 4e-53 Identities = 102/257 (39%), Positives = 157/257 (61%), Gaps = 2/257 (0%) Query: 4 ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCA 63 ET+ + G + I NRP +LNA+ EL A+++AE DPE+R +I+TG+G+AFC Sbjct: 7 ETLIVDRRGAVMEIRFNRPHRLNAVVEAFYSELLAALAEAERDPEVRCVILTGEGRAFCV 66 Query: 64 GADITQFN--QLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121 GAD+ + Q T + ++ + G ++ + I KP IA +NGYALG G E+A+ACD Sbjct: 67 GADMKEHGSAQRTLFQRRRYLQLGNDVCEAILRHPKPVIAAVNGYALGAGAEMAVACDFI 126 Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181 + AEEAQ+G PE ++G G G ++ L +++G A +++ TG RI G++A + GL Sbjct: 127 VMAEEAQIGFPETSIGTCVGGGVSKLLPQLVGLNMARQLLYTGRRIDGREAARVGLATSS 186 Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDK 241 + E + LAE +A+++P+S+A++K +VN+G D+ L S L E +T D Sbjct: 187 HAADAMPAEAQALAESLARQAPVSIAMLKRLVNQGSDTGLDSQLQQELDAVFTCSTTADW 246 Query: 242 KEGVSAFLEKREPTFKG 258 +EGV AF EKR P FKG Sbjct: 247 QEGVDAFAEKRTPQFKG 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: 135 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: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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