Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 192 bits (488), Expect = 1e-53 Identities = 105/303 (34%), Positives = 177/303 (58%), Gaps = 9/303 (2%) Query: 43 LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102 + ++ L FS +P F+ ++N +++L+ A G+ A A T +II+ ID+SVG M+ F +V Sbjct: 33 IAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGPMVAFVSV 92 Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162 +L + +PL + + GAL G ++G++ VP F+ATLG+ L+G+ L + Sbjct: 93 CLAFLL-QFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLWSALRGMGLFM 151 Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTF 222 + P+ ++ E D L G L +P + LI+ ++ I KT FGR F Sbjct: 152 TNALPVPIDENE-----VLDWLGGQF---LGVPVSALIMIVLFALFVFISRKTAFGRSVF 203 Query: 223 ALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAA 282 A+G N A +L G+ V ++ ++T SG + + G+++A+RL S G E D IAA Sbjct: 204 AVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVIAA 263 Query: 283 VVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILR 342 VV+GGT+LSGG G++ GT++G +++++ NGL ++ + +Q VV GVII++AV +IL Sbjct: 264 VVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANILL 323 Query: 343 RRR 345 +R Sbjct: 324 TQR 326 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: 228 Number of extensions: 8 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: 332 Length adjustment: 28 Effective length of query: 319 Effective length of database: 304 Effective search space: 96976 Effective search space used: 96976 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