Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate SM_b20706 SM_b20706 amino acid uptake ABC transporter substrate-binding protein precursor
Query= uniprot:Q92PA9 (260 letters) >FitnessBrowser__Smeli:SM_b20706 Length = 258 Score = 256 bits (654), Expect = 3e-73 Identities = 128/246 (52%), Positives = 170/246 (69%), Gaps = 6/246 (2%) Query: 19 MAGVAMAEG----EKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALCEEMKAECTFVTQ 74 +AG A++ EK+ IGTEGAYPPFN ++S G + GFD++I ALCE MK EC V Q Sbjct: 10 LAGTALSSSAVAAEKLKIGTEGAYPPFNFVDSSGKIGGFDVEIGLALCERMKVECEVVAQ 69 Query: 75 DWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDSPITEATAAAL 134 DWDGIIP L+AKK+D I+ASM ITEERK+QV FTN YY PK + I+ + AL Sbjct: 70 DWDGIIPGLLAKKYDMIIASMFITEERKKQVAFTNPYYLAAMTHAAPKGAGISAFSNEAL 129 Query: 135 SGKALGAQGSTTHSNYAEAHMKESEVKLYPTADEYKLDLANGRIDAAIDDVVVLSEWL-K 193 GK +GAQ TT ++Y A ++E+KLYPT DE LD+ NGR+D + D++ L +W+ K Sbjct: 130 QGKVIGAQSGTTQADYIAAVYPDAEIKLYPTQDEANLDMVNGRLDLQVGDMLPLLDWVTK 189 Query: 194 TEDG-ACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRANGKYKQINEKY 252 +DG CC+L+G D G+G GIA+R+ D+ +REKLNKA++ IRA+G YK+IN+KY Sbjct: 190 NDDGKGCCELVGEPITDKKFVGDGVGIAVRQEDNEMREKLNKALDEIRADGTYKKINDKY 249 Query: 253 FPFDVY 258 F DVY Sbjct: 250 FTIDVY 255 Lambda K H 0.315 0.132 0.377 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: 239 Number of extensions: 8 Number of successful extensions: 2 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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