Align Triosephosphate isomerase; TIM; TPI; EC 5.3.1.1; Triose-phosphate isomerase (uncharacterized)
to candidate WP_011385082.1 AMB_RS13590 thiazole synthase
Query= curated2:Q9YBR1 (223 letters) >NCBI__GCF_000009985.1:WP_011385082.1 Length = 324 Score = 44.7 bits (104), Expect = 2e-09 Identities = 42/128 (32%), Positives = 62/128 (48%), Gaps = 18/128 (14%) Query: 98 YRHLQAVVSKARSL---GLEVLA-CADTPEEAAAAALLRPSMVALEP-PELIGTGIPVSQ 152 Y ++ + A +L G EV+ C+D P +A L VA+ P LIG+G+ + Sbjct: 178 YPNMPETLKAAEALIKDGFEVMVYCSDDPIQAKM--LEDMGCVAIMPLGSLIGSGLGI-- 233 Query: 153 AKPEVITRGVEAVARVAPGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKAKDPHGK 212 P I + + V VL AG+ DA A+ELG GVL+ +A+ AKDP Sbjct: 234 LNPTTIR-----IIKDTVKVPVLVDAGVGTASDAALAMELGCDGVLMNTAIAHAKDP--- 285 Query: 213 MLELAEAM 220 + +A AM Sbjct: 286 -IRMARAM 292 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: 135 Number of extensions: 10 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: 324 Length adjustment: 25 Effective length of query: 198 Effective length of database: 299 Effective search space: 59202 Effective search space used: 59202 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: 47 (22.7 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