Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_011813928.1 HHAL_RS05760 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000015585.1:WP_011813928.1 Length = 283 Score = 130 bits (327), Expect = 3e-35 Identities = 90/247 (36%), Positives = 127/247 (51%), Gaps = 9/247 (3%) Query: 14 VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAK-AFAAGADIKEMAE 72 +A IT+NRP+ NA Q + E+ QAL D +IG ++LTG AF +G D + + Sbjct: 33 IAKITINRPEVRNAFRPQTVLEMQQALADARFDQEIGVVILTGYGDLAFCSGGDQRVRGD 92 Query: 73 LTYPQI----YLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNARFG 128 Y +L+ D I + KP+IA VAGYA+GGG L L+CD+ AA+NARFG Sbjct: 93 SGYQDEQGTHHLNVLDLQRD-IRSCPKPVIAMVAGYAIGGGHVLHLICDLTVAAENARFG 151 Query: 129 QPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAESLLEE 188 Q +G G G + VG+ KA ++ RQ DA EA+ LV V P E L +E Sbjct: 152 QTGPRVGSFDGGFGASYMASVVGQKKAREIWFLCRQYDAQEAQAMDLVNTVVPLEELEQE 211 Query: 189 TLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIR-FERRVFHAVFATADQKEGMAAFS 247 T+ + I E S A +K + N + GI+ + T + +EG A+ Sbjct: 212 TIAWCQRILEHSPIALRALKSAFNAGVDG--QAGIQELAGNATMLFYMTEEGQEGRNAYL 269 Query: 248 EKRKPEF 254 EKRKP+F Sbjct: 270 EKRKPDF 276 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: 133 Number of extensions: 9 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: 283 Length adjustment: 25 Effective length of query: 232 Effective length of database: 258 Effective search space: 59856 Effective search space used: 59856 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