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 H281DRAFT_01120 H281DRAFT_01120 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_01120 Length = 333 Score = 226 bits (575), Expect = 8e-64 Identities = 134/306 (43%), Positives = 191/306 (62%), Gaps = 5/306 (1%) Query: 19 LLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGI 78 LL R + + +L+ VF A+ FL+ N LNI + ++ IIA+GMTFVI+ I Sbjct: 29 LLQGDRPYALYIAFAVLLVVFSFASPWFLSIDNFLNIGRQTALVSIIAIGMTFVIIARQI 88 Query: 79 DVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAF 138 D++VGS LA + ++AA + A +GD WLI + G G + G T L++P+F Sbjct: 89 DLSVGSSLALSGMSAALAM-AYIGDH---WLIGAVAGIGTGALVGVINGLVTTRLNIPSF 144 Query: 139 IVTLGGMTVWRGATLLLNDGGPISGFNDAY-RWWGSGEILFLPVPVVIFALVAAAGHVAL 197 +VTLG ++ RG LL+ P+ ND++ +G G+I +PVP++ L AG + L Sbjct: 145 LVTLGSLSAARGLALLVTTTKPVIITNDSFIAIFGEGDIAGVPVPIIWTVLAVIAGILLL 204 Query: 198 RYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAG 257 Y+ +GRQVYA GGN AAR SG+++ +TT + + G LAGL+ +LSAR +A Sbjct: 205 HYSVFGRQVYAAGGNPTAARYSGIDIRRVTTLAFILTGVLAGLAALVLSARSHAARPDVV 264 Query: 258 TGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLII 317 G EL VIASV +GG SL GG G V GT+LG+L+IG L+NGLV+L V+S +Q V+ G+II Sbjct: 265 QGLELDVIASVTLGGCSLFGGRGFVLGTLLGSLIIGTLNNGLVLLGVSSSLQLVIKGIII 324 Query: 318 VAAVAF 323 VAAVAF Sbjct: 325 VAAVAF 330 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: 272 Number of extensions: 18 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: 332 Length of database: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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