Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 3608677 Dshi_2070 Glyoxalase/bleomycin resistance protein/dioxygenase (RefSeq)
Query= BRENDA::P0A0T3 (138 letters) >FitnessBrowser__Dino:3608677 Length = 131 Score = 76.6 bits (187), Expect = 1e-19 Identities = 51/128 (39%), Positives = 72/128 (56%), Gaps = 7/128 (5%) Query: 2 RLLHTMLRVGNLEKSLDFYQNVLGMKLLRRKDYPEGRFTLAFVGYGDETDSTVLELTHN- 60 + +H+M+RV + +S+DFY+ G+ + R D+ + FTL ++ DET LELT N Sbjct: 3 KAIHSMIRVLDEARSVDFYKRAFGLDVADRLDFSD--FTLVYLS-NDETGFE-LELTVNK 58 Query: 61 WDTERYDLGNAYGHIAVEVDDAYEACERVKRQGGNVVREAGPMKHGTTV--IAFVEDPDG 118 TE YDLGN YGH AV VDD R + +G N + G V FV DPDG Sbjct: 59 GQTEPYDLGNGYGHFAVSVDDLDAEHARFEAEGLNPRKLVEFAPDGKLVGRFFFVADPDG 118 Query: 119 YKIEFIQK 126 Y+IE +++ Sbjct: 119 YQIEVLER 126 Lambda K H 0.318 0.137 0.405 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: 69 Number of extensions: 3 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: 138 Length of database: 131 Length adjustment: 15 Effective length of query: 123 Effective length of database: 116 Effective search space: 14268 Effective search space used: 14268 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 42 (20.8 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