Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 168 bits (426), Expect = 2e-46 Identities = 102/317 (32%), Positives = 175/317 (55%), Gaps = 10/317 (3%) Query: 32 AARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDL 91 A+R+ LL A LLL+ L S P F+ NL + T+ +LAI VI+T IDL Sbjct: 7 ASRETLLIAAILLLLALIAS-RFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDL 65 Query: 92 SVGTMMTFCAVMAGVV-LTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLG 150 SV + ++ +V + G+P+ + +A AI G L G +G+++ KL++PP + TLG Sbjct: 66 SVAANLALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLG 125 Query: 151 MMMLLKGLSLVISGTRPIYFND-TEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGAS 209 M + +G+ +IS + + ++ + F A + L+G LP+ + + IL ++ + Sbjct: 126 TMTIFRGIIFLISDGKWVNSHEMSPAFKAFPRAELLG-----LPVLSWIAILAVILF--T 178 Query: 210 IILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQP 269 I++ +T GR +A G N A +G+ V + +T SGA+ G+ G + SR + Sbjct: 179 IVMTRTTLGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYV 238 Query: 270 ALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTG 329 + G+ELD +AA VIGG S+ GG GT+ G ++GA + ++ N L ++ ++ WQ ++G Sbjct: 239 DIAGGFELDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISG 298 Query: 330 VIIILAVYLDILRRRRR 346 II+AV L+ R++ Sbjct: 299 GAIIIAVALNAQANRKK 315 Lambda K H 0.326 0.139 0.398 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: 255 Number of extensions: 10 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: 347 Length of database: 327 Length adjustment: 28 Effective length of query: 319 Effective length of database: 299 Effective search space: 95381 Effective search space used: 95381 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 (21.7 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