Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= TCDB::D2RXA4 (150 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 89.4 bits (220), Expect = 9e-23 Identities = 50/114 (43%), Positives = 69/114 (60%), Gaps = 2/114 (1%) Query: 2 KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61 K VAVT+CPTG+AH+ MAAE L+Q A +G+++ VE +G++G N L +D IA AD V++ Sbjct: 119 KLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLL 178 Query: 62 AADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAI--AAADGETSTADSAQSE 113 AAD V+ RF GK V A+ E L+RA+ A + A SA E Sbjct: 179 AADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVLSGNAVATSASGE 232 Score = 50.8 bits (120), Expect = 3e-11 Identities = 35/112 (31%), Positives = 52/112 (46%), Gaps = 1/112 (0%) Query: 1 MKFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVI 60 M + VT+CP G+ S + + LE A G VEV + L+ IA AD V+ Sbjct: 1 MNLLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVV 60 Query: 61 IAADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQS 112 + ++ RF GK V + +A+ D E L R+ A E AD A++ Sbjct: 61 VVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFL-RSAADTASELQQADEAEA 111 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: 132 Number of extensions: 4 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: 579 Length adjustment: 26 Effective length of query: 124 Effective length of database: 553 Effective search space: 68572 Effective search space used: 68572 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