Align Triosephosphate isomerase; TIM; TPI; EC 5.3.1.1; Triose-phosphate isomerase (uncharacterized)
to candidate WP_028585932.1 G494_RS0119970 triosephosphate isomerase
Query= curated2:Q03SL6 (252 letters) >NCBI__GCF_000429965.1:WP_028585932.1 Length = 246 Score = 90.9 bits (224), Expect = 2e-23 Identities = 70/245 (28%), Positives = 103/245 (42%), Gaps = 26/245 (10%) Query: 5 LIAGNWKMNKSVTEARQFIDAVQGQLPQADVIETAVAAPAL-FLQTMLDANAEGTLRVAA 63 L+ NWK N + A Q+ D G +E +A PAL L+ + + +AA Sbjct: 22 LVLANWKANFAPQRAYQWCDTFAGSYRPLPGVEVVIAVPALCMLEVAARLGSLPGVALAA 81 Query: 64 ETCYYEDEGAYTGETSPRALHEMGIPYTIVGHSERRRYFNETDDVINRKVQAVFRNGMTP 123 + +G+YTG T L + Y+++GH ERR YF+ET + R+V + P Sbjct: 82 QGVSSYPQGSYTGATPAAWLRGLA-RYSLLGHRERRHYFHETVQDVARQVAESLAEEVQP 140 Query: 124 ILCCDETMGRRTAGEKIHWVVNQVSAALKGVSAEDAAKIVVAYEPSWAIGSGTSASSDQA 183 I+C D+ R A ED KI AY P A + Sbjct: 141 IVCVDQETARSQAAI---------------FDTEDLLKIHWAYTPQ-------DAEQLER 178 Query: 184 EEGCYLIRQTLADIYSDDLANGVRVLYGGSVKPDNIAGLMAKSNVDGVLAGGSSLDETSF 243 I +T+A + +LYGG V P N A L + + + G+L G LD +F Sbjct: 179 SHSARAIEETVASL--GRAVGNQPMLYGGGVGPQNGAQLASLAGISGLLVGRECLDAQAF 236 Query: 244 IQLAN 248 +QL N Sbjct: 237 VQLLN 241 Lambda K H 0.316 0.131 0.379 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: 169 Number of extensions: 12 Number of successful extensions: 3 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: 252 Length of database: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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