Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_066601421.1 V473_RS05770 2,3-dehydroadipyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_001046645.1:WP_066601421.1 Length = 260 Score = 182 bits (463), Expect = 5e-51 Identities = 104/250 (41%), Positives = 147/250 (58%) Query: 6 LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGA 65 L+ + + L+ LNRP+ NAL L+ + AL DP I +V+TG+ + FAAGA Sbjct: 9 LVEPLAAHILLLRLNRPEKRNALATDLLGRIADALDAAAGDPAIRAVVITGADRFFAAGA 68 Query: 66 DIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNA 125 DI E+A D A RI KPLIAAV G++LG G EL + CD++ A ++A Sbjct: 69 DIAELASRDTGGALADPRPAIWTRIRGFAKPLIAAVEGWSLGAGNELVMCCDLVVAGESA 128 Query: 126 RFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAESL 185 +FGQPE NLG++PG GGT L R VG+++AM M L G + AAEA +AGL+A++ Sbjct: 129 KFGQPETNLGIIPGAGGTAILPRLVGRSRAMRMVLLGDPLSAAEALQAGLIAQMVEDGQA 188 Query: 186 LEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMAA 245 L + A IA ++ A K V FET + + ER+ F A+F TAD++EG +A Sbjct: 189 LSVATELATRIAARAPLAMQQGKAMVRATFETHQSAHLLLERQAFSALFGTADKREGTSA 248 Query: 246 FSEKRKPEFT 255 F EKR P+++ Sbjct: 249 FFEKRDPQWS 258 Lambda K H 0.321 0.135 0.375 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: 160 Number of extensions: 4 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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