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 GFF2333 PS417_11895 ABC transporter
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__WCS417:GFF2333 Length = 340 Score = 209 bits (532), Expect = 8e-59 Identities = 119/294 (40%), Positives = 176/294 (59%), Gaps = 16/294 (5%) Query: 47 LTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYV---------V 97 + ++ + ++ +VSI G++A+G+T VI+ GID++ GS+LA +++ AA + V Sbjct: 51 MNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAV 110 Query: 98 TAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLND 157 + D P W I + + +GL G + G + +P FI TLG M RG + Sbjct: 111 FPSLTDLPV-W-IPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTE 168 Query: 158 GGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAAR 217 G P+S +D+Y G G + PV+IF +VA H+ALRYT+YG+ YA+GGN +AAR Sbjct: 169 GQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAAR 223 Query: 218 LSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTG 277 SG+NV VY+I G LAGL+G + SAR + +A G YEL IA+ VIGG SL G Sbjct: 224 TSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAG 283 Query: 278 GSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYARTHK 331 G G + GTV+GAL++GV+++G + V +Y+Q ++ GLIIV AV D Y K Sbjct: 284 GVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 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: 277 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 304 Effective length of database: 312 Effective search space: 94848 Effective search space used: 94848 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