Align Triosephosphate isomerase; TIM; TPI; EC 5.3.1.1; Triose-phosphate isomerase (uncharacterized)
to candidate HSERO_RS02130 HSERO_RS02130 thiazole synthase
Query= curated2:Q9YBR1 (223 letters) >FitnessBrowser__HerbieS:HSERO_RS02130 Length = 269 Score = 40.8 bits (94), Expect = 3e-08 Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 20/134 (14%) Query: 93 EHKVTYRHLQAVVSKARSL---GLEVLA-CADTPEEAAAAALLRPSMVALEPP--ELIGT 146 + K + ++ + A +L G +V+ C+D P +A +L VA P LIG+ Sbjct: 117 DEKTLFPNMPETLKAAETLVKDGFDVMVYCSDDPIQAR---MLEDLGVAAVMPLASLIGS 173 Query: 147 GIPVSQAKPEVITRGVEAVARVAPGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKA 206 G+ + P ++ +E V VL AG+ DA A+ELG GVL+ +A+ A Sbjct: 174 GMGI--LNPWNLSLIIEQAR-----VPVLVDAGVGTASDAAIAMELGCDGVLMNTAIACA 226 Query: 207 KDPHGKMLELAEAM 220 +DP + +A AM Sbjct: 227 RDP----IRMARAM 236 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: 112 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: 269 Length adjustment: 24 Effective length of query: 199 Effective length of database: 245 Effective search space: 48755 Effective search space used: 48755 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 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