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:A3DE71 (289 letters) >FitnessBrowser__Keio:15432 Length = 280 Score = 149 bits (377), Expect = 5e-41 Identities = 80/270 (29%), Positives = 150/270 (55%), Gaps = 11/270 (4%) Query: 25 LAILVVLTLGPIVFMVLTSLMD-HNAIARGKWIAPTRFS--NYVEVFQKL--PFGIYFRN 79 LA+ +++TL P M++TS AI+ + P +++ +YV++F + PF YFRN Sbjct: 17 LALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFNPMIFPFVDYFRN 76 Query: 80 SLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKI 139 SL+V + VVA+ + L Y+L++ +F G + G++ ++PL+ Sbjct: 77 SLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGILLVVPLF------ 130 Query: 140 KQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRV 199 K T + + ++ L+I +P ++++++ +F +IP E+EEAA +DG N+ R+ Sbjct: 131 KIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFRI 190 Query: 200 MLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARYDLLMAA 259 +PLA+ G+++ +Y F+ AW++ +FA + L T+P G+ + + +MAA Sbjct: 191 TVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTPDYIWGRMMAA 250 Query: 260 GTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + +PV+IM+ ++ SG+TAG VKG Sbjct: 251 SLVTALPVVIMYALSERFIKSGLTAGGVKG 280 Lambda K H 0.332 0.145 0.434 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: 234 Number of extensions: 15 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: 289 Length of database: 280 Length adjustment: 26 Effective length of query: 263 Effective length of database: 254 Effective search space: 66802 Effective search space used: 66802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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