Align mannitol-specific PTS enzyme IIA component CmtB (EC 2.7.1.197) (characterized)
to candidate 17013 b2934 predicted mannitol-specific enzyme IIA component of PTS (NCBI)
Query= ecocyc::CMTB-MONOMER (147 letters) >FitnessBrowser__Keio:17013 Length = 147 Score = 290 bits (743), Expect = 5e-84 Identities = 147/147 (100%), Positives = 147/147 (100%) Query: 1 MRLSDYFPESSISVIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYYILA 60 MRLSDYFPESSISVIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYYILA Sbjct: 1 MRLSDYFPESSISVIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYYILA 60 Query: 61 PGVAMPHARPECGALKTGMSLTLLEQGVYFPGNDEPIKLLIGLSAADADSHIGAIQALSE 120 PGVAMPHARPECGALKTGMSLTLLEQGVYFPGNDEPIKLLIGLSAADADSHIGAIQALSE Sbjct: 61 PGVAMPHARPECGALKTGMSLTLLEQGVYFPGNDEPIKLLIGLSAADADSHIGAIQALSE 120 Query: 121 LLCEEEILEQLLTASSEKQLADIISRG 147 LLCEEEILEQLLTASSEKQLADIISRG Sbjct: 121 LLCEEEILEQLLTASSEKQLADIISRG 147 Lambda K H 0.315 0.133 0.375 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: 160 Number of extensions: 1 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: 147 Length of database: 147 Length adjustment: 16 Effective length of query: 131 Effective length of database: 131 Effective search space: 17161 Effective search space used: 17161 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: 42 (20.8 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