Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate Ac3H11_506 biphenyl-2,3-diol 1,2-dioxygenase III-related protein
Query= BRENDA::Q8ZM36 (144 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_506 Length = 128 Score = 127 bits (319), Expect = 6e-35 Identities = 60/126 (47%), Positives = 83/126 (65%) Query: 19 MIIDRIDHLVLTVSDISTTIRFYEEVLGFSAVTFKQNRKALIFGAQKINLHQQEMEFEPK 78 +++D +DHLVLTV+ I TI FYE VLG +A FK R AL FG QKINLH+ +P Sbjct: 3 LVLDSLDHLVLTVASIKNTIAFYERVLGMAAREFKPQRYALHFGTQKINLHEVGTVVDPN 62 Query: 79 ASRPTPGSADLCFITSTPINDVVSEILQAGISIVEGPVERTGATGEIMSIYIRDPDGNLI 138 GS DLCF+T TP+ +V++ + G+++V+GPV TGA + S+YI +PD NLI Sbjct: 63 VRHAKAGSGDLCFLTRTPLEEVIAHLQAEGVAVVQGPVGATGARHRLRSVYIYNPDDNLI 122 Query: 139 EISQYV 144 EI+ + Sbjct: 123 EIANEI 128 Lambda K H 0.321 0.137 0.383 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: 58 Number of extensions: 2 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: 144 Length of database: 128 Length adjustment: 15 Effective length of query: 129 Effective length of database: 113 Effective search space: 14577 Effective search space used: 14577 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: 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