Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate RR42_RS34275 RR42_RS34275 virulence protein
Query= BRENDA::Q8ZM36 (144 letters) >FitnessBrowser__Cup4G11:RR42_RS34275 Length = 135 Score = 103 bits (257), Expect = 1e-27 Identities = 55/132 (41%), Positives = 76/132 (57%), Gaps = 5/132 (3%) Query: 17 IQMIIDRIDHLVLTVSDISTTIRFYEEVLGFSAVTFKQN---RKALIFGAQKINLHQQEM 73 + ++IDR DH+VL V D+ T+ +YE VLG F+ R ++ FG QKINL + Sbjct: 1 MSIVIDRFDHIVLNVKDVETSAAWYESVLGMRREDFESRTGKRVSVRFGQQKINLRPIDT 60 Query: 74 EFEP--KASRPTPGSADLCFITSTPINDVVSEILQAGISIVEGPVERTGATGEIMSIYIR 131 + PT GS DLCFIT + V++ + + I GP RTGA G + S+Y R Sbjct: 61 DTVAWFTGVHPTTGSDDLCFITHNTLESVIAHWIAHHVPIEAGPAARTGALGPMTSVYCR 120 Query: 132 DPDGNLIEISQY 143 DPDGNLIE++ Y Sbjct: 121 DPDGNLIEVAAY 132 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: 61 Number of extensions: 4 Number of successful extensions: 2 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: 135 Length adjustment: 15 Effective length of query: 129 Effective length of database: 120 Effective search space: 15480 Effective search space used: 15480 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