Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 219 bits (558), Expect = 8e-62 Identities = 131/303 (43%), Positives = 183/303 (60%), Gaps = 9/303 (2%) Query: 23 ARKHRTILF----LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGI 78 A K T+ + LL++ V A++ FL+ N N+L +VSI IIAVGMT VIL GGI Sbjct: 30 ALKRSTLFYPFIGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGI 89 Query: 79 DVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAF 138 D++VGS++A A AA ++ A + + AL + +GL G G V + +P Sbjct: 90 DLSVGSVMALAGTLAAGLMVAGMNA-----VAALAIGIAVGLGFGAANGFFVAFAGMPPI 144 Query: 139 IVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALR 198 IVTL M + RG L+ G PI G D ++GSG+IL + PVVI A++ V L Sbjct: 145 IVTLATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLE 204 Query: 199 YTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGT 258 +GR VYA+GGN +A RLSGV V + VY I G + + +L+ARL S + AG Sbjct: 205 RMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGV 264 Query: 259 GYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIV 318 G+EL IA+VV+GG S++GG G + GT++GALL+GVL+NGL M+ V YVQ V+ G II+ Sbjct: 265 GFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIIL 324 Query: 319 AAV 321 A+ Sbjct: 325 LAI 327 Lambda K H 0.325 0.140 0.413 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: 282 Number of extensions: 12 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: 332 Length of database: 335 Length adjustment: 28 Effective length of query: 304 Effective length of database: 307 Effective search space: 93328 Effective search space used: 93328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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