Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b20632 SM_b20632 sugar uptake ABC transporter permease
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__Smeli:SM_b20632 Length = 287 Score = 113 bits (282), Expect = 6e-30 Identities = 66/206 (32%), Positives = 111/206 (53%), Gaps = 7/206 (3%) Query: 105 NSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPNYILLRK 164 NS I++I V++ V V V A Y F++ RFP ++ LF + I +++P Q L P +I+L + Sbjct: 82 NSLIVSIGTVVLTVAVSVLAGYGFSRYRFPFKNALFVLIIATLMIPFQSILTPLFIILAR 141 Query: 165 LDMIGSFLSVILPGGFSA--FGVVLLRQYMRGIPDECCEAAMIDGAGYLKTFTKIILPQC 222 + S + ++L F V ++R +P E EAA IDGA LK +++LP Sbjct: 142 FGLNNSLVGLMLVYVTLQLPFSVFMMRNAFDAVPKEIEEAARIDGARDLKLLVRVLLPLV 201 Query: 223 KSIIASLAILAFIDNWNMVEQPLIFLSDSAKYPLSVYLAYINEGDLGL----AFASGVLY 278 IA+++I AF++ WN L+ LS + Y L V + + G LG A +GV Sbjct: 202 MPGIATVSIFAFLNAWNEFFAALVLLSSNDNYTLPVLMTAVRAGRLGAINWGAVQAGVAV 261 Query: 279 M-IPTVLIYLYGEKYFVEGIQLTGIK 303 M +P + ++L ++Y++ G+ +K Sbjct: 262 MVVPCLFVFLLLQRYYMRGLMAGAVK 287 Lambda K H 0.331 0.147 0.425 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: 164 Number of extensions: 11 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: 303 Length of database: 287 Length adjustment: 26 Effective length of query: 277 Effective length of database: 261 Effective search space: 72297 Effective search space used: 72297 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: 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