Align 2-oxopent-4-enoate hydratase subunit (EC 4.2.1.80) (characterized)
to candidate GFF4097 HP15_4037 hydratase/decarboxylase
Query= metacyc::MONOMER-3403 (222 letters) >FitnessBrowser__Marino:GFF4097 Length = 264 Score = 161 bits (408), Expect = 1e-44 Identities = 93/224 (41%), Positives = 128/224 (57%), Gaps = 5/224 (2%) Query: 1 MDKTLINE----LGDELYQAMVQRETVTPLTSRGFDISVEDAYHISLRMLERRLAAGERV 56 M KTL E L + + A +Q +T +T+ D++ EDAY + + R+ A G ++ Sbjct: 1 MSKTLNQEQVLALAEHVENAELQAHDITKVTNDFPDMTFEDAYDVQWEIRRRKEARGNKI 60 Query: 57 IGKKIGVTSKAVQNMLGVHQPDFGYLTDAMVYNSGEAMPISEKLIQPRAEGEIAFILKKD 116 +G K+G+TS A +GV P +G+L D G + E LI P+ E EIAF+ K Sbjct: 61 VGMKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVNTKE-LIHPKIEAEIAFVTKAP 119 Query: 117 LMGPGVTNADVLAATECVIPCFEVVDSRIQDWKIKIQDTVADNASCGLFVLGDQAVSPRQ 176 L GPG VLAAT+ VIP EV+DSR +++K + VADNAS F+ G Q Sbjct: 120 LKGPGCHIGQVLAATDFVIPAVEVIDSRYENFKFDLVSVVADNASSTRFITGGQMADVAD 179 Query: 177 VDLVTCGMLVEKNGQLLSTGAGAAALGSPVNCVAWLANTLGHFG 220 VDL T G++VEKNG+++ GAGAA LG P + VA LAN L G Sbjct: 180 VDLKTLGVVVEKNGEVVDVGAGAAVLGHPASSVAMLANLLAERG 223 Lambda K H 0.319 0.136 0.395 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: 117 Number of extensions: 2 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: 222 Length of database: 264 Length adjustment: 23 Effective length of query: 199 Effective length of database: 241 Effective search space: 47959 Effective search space used: 47959 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 (21.8 bits) S2: 46 (22.3 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