Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase
Query= reanno::psRCH2:GFF2389 (257 letters) >FitnessBrowser__SynE:Synpcc7942_0597 Length = 279 Score = 122 bits (307), Expect = 6e-33 Identities = 94/255 (36%), Positives = 121/255 (47%), Gaps = 16/255 (6%) Query: 12 ERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAK------AFAAGA 65 E +A IT+NRP NA + + EL A D IG I+LTG+ AF AG Sbjct: 22 EGIAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPHTDGRYAFCAGG 81 Query: 66 DIKEMAELTY------PQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMI 119 D Y P++ + D I T K +IA VAGYA+GGG L +LCD+ Sbjct: 82 DQSVRGAGGYIDEEGLPRLNVLDL---QRLIRTIPKVVIALVAGYAIGGGHVLHILCDLT 138 Query: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179 AADNA FGQ +G G G L R VG+ KA ++ RQ A EA + GLV V Sbjct: 139 IAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEALQMGLVNTV 198 Query: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQ 239 P E L E ++ A I EKS A +K + N + +A H + T + Sbjct: 199 VPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELD-GMAGIQELAGHATHLYYLTEEG 257 Query: 240 KEGMAAFSEKRKPEF 254 EG AF EKR P+F Sbjct: 258 SEGKQAFLEKRSPDF 272 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: 123 Number of extensions: 7 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: 279 Length adjustment: 25 Effective length of query: 232 Effective length of database: 254 Effective search space: 58928 Effective search space used: 58928 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 17 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