Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 152 bits (383), Expect = 2e-41 Identities = 99/316 (31%), Positives = 158/316 (50%), Gaps = 3/316 (0%) Query: 24 PASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLA 83 P + K LA R+ + L LL+ + + FLT N +++L + ++ + Sbjct: 9 PLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVG 68 Query: 84 ESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFI 143 + ++L G D+++ S + A A +V G W A LL ++G G++ Sbjct: 69 MTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDG-PATWLIA--LLVSTLIGLAGGYV 125 Query: 144 NGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWL 203 G V L + AFIVTL + V RG + GG + ++ + +L LP+ V + Sbjct: 126 QGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVI 185 Query: 204 AAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIV 263 A A LRY R GR +YA+GGN EAAR +G+ V+ IT V+ + LA + G ++ Sbjct: 186 FALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLL 245 Query: 264 TGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVP 323 + +G+ A G G V A+ VIGG SL GG G + G + G LL+GV+ N L + V Sbjct: 246 SARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVT 305 Query: 324 SFWIQAIYGAIILGSL 339 S+ Q + G II+ ++ Sbjct: 306 SYVQQVVIGLIIVAAV 321 Lambda K H 0.326 0.140 0.397 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: 314 Number of extensions: 15 Number of successful extensions: 1 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: 351 Length of database: 332 Length adjustment: 29 Effective length of query: 322 Effective length of database: 303 Effective search space: 97566 Effective search space used: 97566 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 (21.6 bits) S2: 49 (23.5 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