Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS05105 RR42_RS05105 2-keto-4-pentenoate hydratase
Query= BRENDA::Q1XGK3 (264 letters) >FitnessBrowser__Cup4G11:RR42_RS05105 Length = 263 Score = 161 bits (407), Expect = 1e-44 Identities = 91/222 (40%), Positives = 127/222 (57%) Query: 42 AYDVQWEIRRRKEARGNKIVGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCS 101 AY VQ +R A G ++VG K+GLTS A Q+GV P +G L +V +G +D Sbjct: 33 AYQVQEINTQRWLAAGRRLVGRKIGLTSRAVQQQLGVGEPDFGMLFADMAVAEGEEIDLR 92 Query: 102 KLIHPKIEAEISVVTKAPLHGPGCHLGDVIAAIDYVIPTVEVIDSRYENFKFDLISVVAD 161 +++ P+IEAEI++V PL + D+I A Y +P E++ SR N+ L +AD Sbjct: 93 RVLQPRIEAEIALVLAHPLAHERHTIADLIRATAYALPAAEIVGSRVANWDIRLNDTIAD 152 Query: 162 NASSTRFITGGRMASLEEVDLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAE 221 NASS F G R L ++DL G+ ME+ GE V LGAGAA LG+PL + LA+ + Sbjct: 153 NASSGLFALGSRPVKLADLDLIGCGMAMERRGEQVSLGAGAACLGNPLHAALWLADTMVR 212 Query: 222 RGEHIPAGTFIMTGGITAAVPVAPGDNITVRYQGLGSVSARF 263 G + AG +MTG + VPVA GD + +GLG +S RF Sbjct: 213 VGRPLQAGDIVMTGALGPMVPVAAGDVFDLEIEGLGRLSTRF 254 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: 180 Number of extensions: 5 Number of successful extensions: 1 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: 264 Length of database: 263 Length adjustment: 25 Effective length of query: 239 Effective length of database: 238 Effective search space: 56882 Effective search space used: 56882 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: 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