Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate AZOBR_RS32335 AZOBR_RS32335 PTS fructose transporter subunit IIBC
Query= TCDB::D2RXA4 (150 letters) >FitnessBrowser__azobra:AZOBR_RS32335 Length = 580 Score = 107 bits (266), Expect = 4e-28 Identities = 58/130 (44%), Positives = 77/130 (59%) Query: 2 KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61 K VA+TSCPTGIAH+ MAAE ++Q A GH + VE QG++G + L+ I EAD V+I Sbjct: 113 KIVAITSCPTGIAHTFMAAEGIQQAAQALGHAVRVETQGSVGARDTLTEQEIREADVVLI 172 Query: 62 AADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADASAS 121 AADT V+ RF GK V + K A+ND L+ERA+A A + A A A+ + Sbjct: 173 AADTQVDLARFAGKRVFKSGTKPAINDGRALVERALAEAQPHGTAPALADGVAAGKAAKA 232 Query: 122 DAEAADSGAP 131 + AA P Sbjct: 233 EHAAAQRSGP 242 Score = 51.2 bits (121), Expect = 3e-11 Identities = 28/86 (32%), Positives = 44/86 (51%) Query: 18 MAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVIIAADTSVNQDRFEGKPV 77 +AAE L + A GH I VEV+ ++G N L + A A VI+ + ++RF G Sbjct: 19 LAAEALRKAAAALGHTIQVEVRSSLGVRNTLPTGAAQGAQGVILVGSGDLGEERFAGLKR 78 Query: 78 VTAPVKDAVNDVEDLLERAIAAADGE 103 A + + D +LE+A+A A + Sbjct: 79 SAAALDAVLRDARAVLEQALATAPAQ 104 Lambda K H 0.307 0.122 0.323 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: 139 Number of extensions: 7 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: 2 Length of query: 150 Length of database: 580 Length adjustment: 26 Effective length of query: 124 Effective length of database: 554 Effective search space: 68696 Effective search space used: 68696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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