Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_012410317.1 NPUN_RS20040 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000020025.1:WP_012410317.1 Length = 277 Score = 118 bits (296), Expect = 1e-31 Identities = 92/266 (34%), Positives = 123/266 (46%), Gaps = 18/266 (6%) Query: 2 TFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAK-- 59 T+E +L + +A IT+NRP NA + + EL A D IG ++ TG Sbjct: 10 TYEDILYQKTDGIAKITINRPHKRNAFRPETVFELYDAFCNAREDTTIGVVLFTGYGPHT 69 Query: 60 ----AFAAGADIKEMAELTYPQIYLDDF------FADADR-IATRRKPLIAAVAGYALGG 108 AF +G D Y +DD D R I + K +IA VAGYA+GG Sbjct: 70 DGKYAFCSGGDQSVRGHAGY----VDDTGIPRLNVLDLQRLIRSMPKVVIALVAGYAIGG 125 Query: 109 GCELALLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAA 168 G L L+CD+ AADNA FGQ +G G G L R VG+ KA ++ RQ DA Sbjct: 126 GHVLHLICDLTIAADNAIFGQTGPKVGSFDGGFGASYLARIVGQKKAREIWFLCRQYDAQ 185 Query: 169 EAERAGLVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERR 228 +A GL+ V P E L E ++ A+ I EKS A +K + N + A Sbjct: 186 QALEMGLINFVVPVEQLEAEGIQWAQEILEKSPIAIRCLKSAFNADCDGQ-AGLQELAGN 244 Query: 229 VFHAVFATADQKEGMAAFSEKRKPEF 254 + T + EG AF EKR P+F Sbjct: 245 ATLLYYMTEEGSEGKQAFLEKRPPDF 270 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: 132 Number of extensions: 6 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: 257 Length of database: 277 Length adjustment: 25 Effective length of query: 232 Effective length of database: 252 Effective search space: 58464 Effective search space used: 58464 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