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 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 168 bits (426), Expect = 1e-46 Identities = 100/297 (33%), Positives = 167/297 (56%), Gaps = 9/297 (3%) Query: 30 LFLLLLVAVFGA---ANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLL 86 L LL+ + +F A A+ FL A N + + +IA M +I+ G ID++V S++ Sbjct: 26 LLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSVASII 85 Query: 87 AFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMT 146 A AS A V VG P LI L V GL G G VT + +P+ +VT+G M+ Sbjct: 86 ALASTAMGAAVQMGVGT-PGLVLIGLGV----GLLCGAFNGVLVTRMGLPSIVVTIGTMS 140 Query: 147 VWRGATLLLNDGGPISGFNDAYRWWGSGEILF-LPVPVVIFALVAAAGHVALRYTRYGRQ 205 ++RG + ++ G+ +++ W+G G + + + +V+FA++A + L T +GR Sbjct: 141 LFRGISYIVLGDQAFRGYPESFSWFGQGYVWWVISFELVLFAIIAVIYAMLLHKTNFGRA 200 Query: 206 VYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVI 265 VYA+G NA A SG+ V + ++ + G ++G++ L+ARLGS G+EL V+ Sbjct: 201 VYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWELEVV 260 Query: 266 ASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVA 322 VV+GG S+ GGSG + G V+ A ++G+++ GL +L+V V +VIG +++ +A Sbjct: 261 TMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIA 317 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: 262 Number of extensions: 16 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: 328 Length adjustment: 28 Effective length of query: 304 Effective length of database: 300 Effective search space: 91200 Effective search space used: 91200 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