Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_008803957.1 KVAR_RS07040 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000025465.1:WP_008803957.1 Length = 285 Score = 129 bits (325), Expect = 5e-35 Identities = 94/252 (37%), Positives = 130/252 (51%), Gaps = 16/252 (6%) Query: 14 VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSA-KAFAAGADIKEMAE 72 +A IT+NRPQ NA + E+ QAL D IG IVLTG KAF AG D K + Sbjct: 34 IAKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGEKAFCAGGDQKVRGD 93 Query: 73 LTYPQIYLDDF------FADADR-IATRRKPLIAAVAGYALGGGCELALLCDMIFAADNA 125 Y DD D R I T KP++A VAGY++GGG L ++CD+ AADNA Sbjct: 94 YGG---YQDDSGVHHLNVLDFQRQIRTCPKPVVAMVAGYSIGGGHVLHMMCDLTIAADNA 150 Query: 126 RFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAESL 185 FGQ +G G G + R VG+ KA ++ RQ DA +A GLV V P L Sbjct: 151 IFGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPLAEL 210 Query: 186 LEETLKAARVIAEKSLPATMMIKESVNRAF--ETTLAEGIRFERRVFHAVFATADQKEGM 243 +ET++ R + + S A +K ++N + L E +F + T + +EG Sbjct: 211 EKETVRWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNATMLF---YMTEEGQEGR 267 Query: 244 AAFSEKRKPEFT 255 AF++KR+P+F+ Sbjct: 268 NAFNQKRQPDFS 279 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: 153 Number of extensions: 10 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: 285 Length adjustment: 25 Effective length of query: 232 Effective length of database: 260 Effective search space: 60320 Effective search space used: 60320 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