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 BWI76_RS02155 BWI76_RS02155 D-allose transporter subunit
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Koxy:BWI76_RS02155 Length = 326 Score = 213 bits (541), Expect = 7e-60 Identities = 122/313 (38%), Positives = 185/313 (59%), Gaps = 5/313 (1%) Query: 13 DKPRFDLLAFARKHRTILFLLLLVAVFGA-ANERFLTARNALNILSEVSIYGIIAVGMTF 71 +K F+ F K+ T L ++VA+FG ++E FLT N I + S+ +I +G F Sbjct: 13 EKKPFNFALFWDKYGTFFILAIIVAIFGTLSSEYFLTTNNITQIFVQSSVTVLIGMGEFF 72 Query: 72 VILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVT 131 IL+ GID++VG++LA + + A ++ A G +L AL+ L+G A G + G V Sbjct: 73 AILVAGIDLSVGAILALSGMVTAKLMLA----GVDPFLAALIGGVLVGGALGAINGCLVN 128 Query: 132 WLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAA 191 W + FI+TLG ++RG TL+++D + GF+ + + + L +PVPV+ +VA Sbjct: 129 WTGLHPFIITLGTNAIFRGITLVISDANSVYGFSFDFVNFFAATPLGIPVPVIFSLIVAV 188 Query: 192 AGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGS 251 R GR +YA+GGN +A SG++V F V+ I G AGL+G + +ARLG+ Sbjct: 189 ILWFLTTRMRVGRNIYALGGNKNSAFYSGIDVKFHMLLVFIISGVCAGLAGVVSTARLGA 248 Query: 252 AEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQV 311 AE +AG G+E IAS +IGG S GG G + V+G L+IG ++NGL +L V +Y Q V Sbjct: 249 AEPLAGMGFETYAIASAIIGGTSFFGGKGRIFSVVIGGLIIGTINNGLNILQVQTYYQLV 308 Query: 312 VIGLIIVAAVAFD 324 V+G +I+AAVA D Sbjct: 309 VMGGLIIAAVALD 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: 280 Number of extensions: 13 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: 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