Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate WP_008345541.1 BA79_RS09595 VOC family protein
Query= BRENDA::P0A0T3 (138 letters) >NCBI__GCF_000691145.1:WP_008345541.1 Length = 127 Score = 62.8 bits (151), Expect = 2e-15 Identities = 39/126 (30%), Positives = 65/126 (51%), Gaps = 2/126 (1%) Query: 1 MRLLHTMLRVGNLEKSLDFYQNVLGMKLLRRKDYPEGRFTLAFVGYGDETDSTVLELTHN 60 +RL HT + V N+++S+DFY+ V+GMKL R + G LAF+G+ DE + T +EL Sbjct: 4 LRLDHTGIMVTNIDQSIDFYEKVVGMKLKDRITHTNGVIELAFLGFKDEAE-TEIELIQG 62 Query: 61 WDTERYDLGNAYGHIAVEVDDAYEACERVKRQGGNVVREAGPMKHGTTVIAFVEDPDGYK 120 + ++ G + H+A D+ + R+++ ++ E F PD Sbjct: 63 YSSDLPSEGKVH-HLAFTTDNIHAEFNRIQKLQIELIDEEITTLPNGYCYFFFRGPDQEW 121 Query: 121 IEFIQK 126 IEF Q+ Sbjct: 122 IEFFQR 127 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: 64 Number of extensions: 3 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: 138 Length of database: 127 Length adjustment: 15 Effective length of query: 123 Effective length of database: 112 Effective search space: 13776 Effective search space used: 13776 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: 41 (20.4 bits)
This GapMind analysis is from Sep 24 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