Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__Keio:15432 Length = 280 Score = 142 bits (359), Expect = 7e-39 Identities = 87/274 (31%), Positives = 151/274 (55%), Gaps = 10/274 (3%) Query: 37 VSRIVIWC----VIVMVLLPMWFVVIASFNPSNSYISF--SLFPSNASLANYKALFQGG- 89 +SRI +C +++ L P + +++ SF + IS +L P +L +Y +F Sbjct: 8 LSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFNPMI 67 Query: 90 -QFWTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQMFPNILAIA 148 F + RNSLVV VV ++ F+ + A+A S+LRF GR + + MF IL + Sbjct: 68 FPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGILLVV 127 Query: 149 AFYTALAKLNMIDMLGSYILVMLG-TSAFNIWLLKGYMDSVPKELDEAAVIDGATTWQRF 207 + + L + D + I+ M+ T +++LK Y D++P E++EAA++DG Q Sbjct: 128 PLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQII 187 Query: 208 IHVTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISGQFAKNWGE 267 +T+PL+ ++ +F + +++Y+FA L S N+TL VG+ L S WG Sbjct: 188 FRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTP-DYIWGR 246 Query: 268 FAAAALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301 AA+L++A+P+ I++A+++R++ GL AG VKG Sbjct: 247 MMAASLVTALPVVIMYALSERFIKSGLTAGGVKG 280 Lambda K H 0.328 0.136 0.417 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: 209 Number of extensions: 13 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: 301 Length of database: 280 Length adjustment: 26 Effective length of query: 275 Effective length of database: 254 Effective search space: 69850 Effective search space used: 69850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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