Align Triosephosphate isomerase; TIM; TPI; EC 5.3.1.1; Triose-phosphate isomerase (uncharacterized)
to candidate WP_089214033.1 CHB69_RS00475 thiazole synthase
Query= curated2:Q9YBR1 (223 letters) >NCBI__GCF_900188185.1:WP_089214033.1 Length = 256 Score = 45.1 bits (105), Expect = 1e-09 Identities = 41/134 (30%), Positives = 64/134 (47%), Gaps = 20/134 (14%) Query: 93 EHKVTYRHLQAVVSKARSLGLE----VLACADTPEEAAAAALLRPSMVALEPPEL-IGTG 147 E K Y +++ ++ +L E ++ C D P AA L VA+ P IG+G Sbjct: 105 EAKTLYPNMRETLTATETLAKEGFLPMVYCVDDP--IAAKQLEDAGAVAIMPLGAPIGSG 162 Query: 148 IPV-SQAKPEVITRGVEAVARVAPGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKA 206 + + ++ +I G V VL AG+ DA A+ELG GVL+ +A+ +A Sbjct: 163 LGIQNRVTIRLIVEGAS--------VPVLVDAGVGTASDAAVAMELGCDGVLMNTAIAEA 214 Query: 207 KDPHGKMLELAEAM 220 KDP + +A AM Sbjct: 215 KDP----VRMARAM 224 Lambda K H 0.316 0.130 0.359 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: 108 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: 223 Length of database: 256 Length adjustment: 23 Effective length of query: 200 Effective length of database: 233 Effective search space: 46600 Effective search space used: 46600 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: 46 (22.3 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