Align Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components
Query= TCDB::C0H3V2 (143 letters) >FitnessBrowser__Marino:GFF3781 Length = 978 Score = 98.2 bits (243), Expect = 3e-25 Identities = 50/141 (35%), Positives = 85/141 (60%) Query: 1 MQVLAKENIKLNQTVSSKEEAIKLAGQTLIDNGYVTEDYISKMFEREETSSTFMGNFIAI 60 M L +++L T S ++A++ A + L G + +Y++ M RE+ SST +GN IAI Sbjct: 36 MLTLTANDVRLGATASDWQDALQQAARDLERAGRTSPEYLAGMNAREQQSSTVLGNGIAI 95 Query: 61 PHGTEEAKSEVLHSGISIIQIPEGVEYGEGNTAKVVFGIAGKNNEHLDILSNIAIICSEE 120 PHGT E++ VL +G+ I+Q PEGV + +G V+ IA +++EHLDIL ++ + + Sbjct: 96 PHGTPESRDAVLETGVRILQFPEGVSWHDGARVHVLVAIAAQSDEHLDILRHLTRVLDKP 155 Query: 121 ENIERLISAKSEEDLIAIFNE 141 E+L A +L+A+ ++ Sbjct: 156 GLAEKLGHATDATELVALLSK 176 Lambda K H 0.310 0.130 0.342 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: 217 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 143 Length of database: 978 Length adjustment: 29 Effective length of query: 114 Effective length of database: 949 Effective search space: 108186 Effective search space used: 108186 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 49 (23.5 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