Align Probable lactoylglutathione lyase; EC 4.4.1.5; Aldoketomutase; Glyoxalase I; Glx I; Ketone-aldehyde mutase; Methylglyoxalase; S-D-lactoylglutathione methylglyoxal lyase (uncharacterized)
to candidate GFF2088 PGA1_c21210 putative lactoylglutathione lyase
Query= curated2:Q9KT93 (138 letters) >FitnessBrowser__Phaeo:GFF2088 Length = 142 Score = 89.0 bits (219), Expect = 3e-23 Identities = 51/130 (39%), Positives = 79/130 (60%), Gaps = 9/130 (6%) Query: 5 RILHTMLRVGDLDKSIEFYTQVMGMSLLRKNENTEYKYTLAFLGYGDESQGAVIELTYNW 64 + LHTM+RV DL+KS+ FY ++G+ ++ ++ + +++L F+ + + IELTYNW Sbjct: 4 KYLHTMVRVKDLEKSMAFYA-LLGLKETKRYDSEKGRFSLIFMA-AEGQEDTPIELTYNW 61 Query: 65 GVADYEKGNA--YGHIAIGVDDIYATCDTIKAAGGIVTREPGPVKGGTTHIAFVKDPDGY 122 D ++ +GH+A GVDDIYATC + G + R P + G H+AFV+ PD Sbjct: 62 DGDDALPSDSRHFGHLAYGVDDIYATCQHLMDNGVTINRPP---RDG--HMAFVRSPDNI 116 Query: 123 MIELIQNKQA 132 IEL+QN A Sbjct: 117 SIELLQNGDA 126 Lambda K H 0.317 0.138 0.408 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: 87 Number of extensions: 8 Number of successful extensions: 4 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: 142 Length adjustment: 15 Effective length of query: 123 Effective length of database: 127 Effective search space: 15621 Effective search space used: 15621 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 (21.6 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