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 SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 216 bits (550), Expect = 7e-61 Identities = 127/293 (43%), Positives = 179/293 (61%), Gaps = 17/293 (5%) Query: 44 ERFLTARNALNILS-EVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAV-- 100 + FL L I+ +VS+ GIIAVG+T VI+ GGID++ GS++ ++ +A V A Sbjct: 48 QSFLMNSQRLTIMILQVSVIGIIAVGVTQVIITGGIDLSSGSVVGMTAMISASVAQASTW 107 Query: 101 -------VGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATL 153 + D PA I L V IGL G++ G+ + +P FI TLG M RG + Sbjct: 108 PRALYPSLTDLPAIVPIGLGVG--IGLLAGFINGQLIARTKIPPFIATLGMMVSARGVSK 165 Query: 154 LLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNA 213 G P+SG + + + G+G PV++F +VA H+ALRYTRYG+ YA+G N Sbjct: 166 WYTKGQPVSGLTEQFNFIGTGIW-----PVIVFLVVALIFHIALRYTRYGKFTYAIGANV 220 Query: 214 EAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGA 273 +AAR+SG+NV+ VYAI G LAGL+G + +AR +A+A G YEL IA+ VIGG Sbjct: 221 QAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAARAQTAQAGMGVMYELDAIAATVIGGT 280 Query: 274 SLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326 SLTGG G V GTV+G +++GV+++G L V +Y Q++V G+IIVAAV D Y Sbjct: 281 SLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYYQEIVKGIIIVAAVVVDVY 333 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: 275 Number of extensions: 14 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: 341 Length adjustment: 28 Effective length of query: 304 Effective length of database: 313 Effective search space: 95152 Effective search space used: 95152 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