Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate GFF1177 HP15_1154 glyoxalase/bleomycin resistance protein/dioxygenase
Query= BRENDA::P0A0T3 (138 letters) >FitnessBrowser__Marino:GFF1177 Length = 140 Score = 93.2 bits (230), Expect = 1e-24 Identities = 51/126 (40%), Positives = 73/126 (57%), Gaps = 11/126 (8%) Query: 7 MLRVGNLEKSLDFYQNVLGMKLLRRKDYPEGRFTLAFVGYGD------ETDSTVLELTHN 60 M+RV NL+++L F+ ++LGM + RK +GRFTL F+ D E + ++ELT+N Sbjct: 1 MIRVSNLDETLHFFCDLLGMVEISRKSSDKGRFTLVFLAAPDDEARAREDRAPMIELTYN 60 Query: 61 WDTERYDLGNAYGHIAVEVDDAYEACERVKRQGGNVVREAGPMKHGTTVIAFVEDPDGYK 120 WD E Y G +GH+A VDD Y CE +K G + R P + G +AF+ PD Sbjct: 61 WDPEEYTGGRNFGHLAYRVDDIYALCEHLKANGVTINR---PPRDGH--MAFIRTPDNIS 115 Query: 121 IEFIQK 126 IE +QK Sbjct: 116 IELLQK 121 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: 70 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: 140 Length adjustment: 15 Effective length of query: 123 Effective length of database: 125 Effective search space: 15375 Effective search space used: 15375 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