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 18114 b4086 D-allose transporter subunit (NCBI)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Keio:18114 Length = 326 Score = 215 bits (547), Expect = 1e-60 Identities = 121/315 (38%), Positives = 188/315 (59%), Gaps = 5/315 (1%) Query: 11 ATDKPRFDLLAFARKHRTILFLLLLVAVFGAAN-ERFLTARNALNILSEVSIYGIIAVGM 69 A++K F+ F K+ T L ++VA+FG+ + E FLT N I + S+ +I +G Sbjct: 11 ASEKKPFNFALFWDKYGTFFILAIIVAIFGSLSPEYFLTTNNITQIFVQSSVTVLIGMGE 70 Query: 70 TFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKA 129 F IL+ GID++VG++LA + + A ++ A G +L A++ L+G A G + G Sbjct: 71 FFAILVAGIDLSVGAILALSGMVTAKLMLA----GVDPFLAAMIGGVLVGGALGAINGCL 126 Query: 130 VTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALV 189 V W + FI+TLG ++RG TL+++D + GF+ + + + ++ +PVPV+ +V Sbjct: 127 VNWTGLHPFIITLGTNAIFRGITLVISDANSVYGFSFDFVNFFAASVIGIPVPVIFSLIV 186 Query: 190 AAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARL 249 A R GR +YA+GGN +A SG++V F V+ I G AGL+G + +ARL Sbjct: 187 ALILWFLTTRMRLGRNIYALGGNKNSAFYSGIDVKFHILVVFIISGVCAGLAGVVSTARL 246 Query: 250 GSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQ 309 G+AE +AG G+E IAS +IGG S GG G + V+G L+IG ++NGL +L V +Y Q Sbjct: 247 GAAEPLAGMGFETYAIASAIIGGTSFFGGKGRIFSVVIGGLIIGTINNGLNILQVQTYYQ 306 Query: 310 QVVIGLIIVAAVAFD 324 VV+G +I+AAVA D Sbjct: 307 LVVMGGLIIAAVALD 321 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: 284 Number of extensions: 15 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: 326 Length adjustment: 28 Effective length of query: 304 Effective length of database: 298 Effective search space: 90592 Effective search space used: 90592 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