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_RS07245 BWI76_RS07245 ABC transporter
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Koxy:BWI76_RS07245 Length = 343 Score = 211 bits (537), Expect = 2e-59 Identities = 133/333 (39%), Positives = 198/333 (59%), Gaps = 29/333 (8%) Query: 12 TDKPRFDLLAFAR-KHR----TILFLLLLV-------AVFGAANERFLTARNALN-ILSE 58 T+KP F F + +HR T +F+++LV A + ++ FL N L I+ + Sbjct: 12 TEKPSF----FGQLRHRLPKDTGIFIVMLVIALTFEIAGWYVRDQSFLLNTNRLILIVLQ 67 Query: 59 VSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPA-------TWLIA 111 V+I GIIAVG+T VI+ GID++ GS++A A++ AA + P +I Sbjct: 68 VAIIGIIAVGVTQVIITTGIDLSSGSVIALAAVVAASLAQTSDSLSPMFPSLVNMPAIIP 127 Query: 112 LLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWW 171 + +GL G G VT +P FI TLG M RG G PIS +D++ Sbjct: 128 IGAGIGVGLLCGLTNGFLVTRTGIPPFIATLGMMVSARGLAQYYTQGNPISFLSDSFTAI 187 Query: 172 GSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVY 231 G G + PV+IF +VAA H+AL++TRYG+ VYA+GGN +A++SG+NV+ VY Sbjct: 188 GQGAM-----PVIIFFVVAAVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLVIVY 242 Query: 232 AIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALL 291 AI GAL+GL+G +L+AR+ S ++ G YEL IA+ VIGG+SL GG G + GT++GA++ Sbjct: 243 AIAGALSGLAGVVLAARVSSGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIGAMI 302 Query: 292 IGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 +G++ +G + V +YVQ ++ G+IIVAAV D Sbjct: 303 LGLIKSGFTFVGVDAYVQDIIKGIIIVAAVTID 335 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: 270 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: 343 Length adjustment: 28 Effective length of query: 304 Effective length of database: 315 Effective search space: 95760 Effective search space used: 95760 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