Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate AZOBR_RS30960 AZOBR_RS30960 thiazole synthase
Query= BRENDA::B6YUE5 (226 letters) >FitnessBrowser__azobra:AZOBR_RS30960 Length = 250 Score = 49.7 bits (117), Expect = 5e-11 Identities = 42/134 (31%), Positives = 67/134 (50%), Gaps = 17/134 (12%) Query: 98 ENRMILADLEAAIRRAEEV---GLMTM-VCSNNPAVSAAVAALGPDYVAVEP-PELIGTG 152 + ++ D+E +R EE+ G + C+++P +A LG AV P IG+G Sbjct: 97 DRELLYPDVEELLRATEELVADGFTVLPYCNDDPVTCRKLADLGA--AAVMPLGAFIGSG 154 Query: 153 IPVSKAKPEVITDTVELVKRVNPEVKVLTGAGISTGEDVKKALELGSVGVLLASGVTKAK 212 + + +E + +P V V+ AGI T D A+ELG VLL + V+KA+ Sbjct: 155 LGIRNPH------AIETICARSP-VPVVLDAGIGTASDAALAMELGCAAVLLNTAVSKAR 207 Query: 213 DPEK---AIRDLVS 223 DP + A+RD V+ Sbjct: 208 DPVRMAAAMRDAVA 221 Lambda K H 0.314 0.132 0.362 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: 130 Number of extensions: 4 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: 226 Length of database: 250 Length adjustment: 23 Effective length of query: 203 Effective length of database: 227 Effective search space: 46081 Effective search space used: 46081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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