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 RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 194 bits (492), Expect = 3e-54 Identities = 126/317 (39%), Positives = 179/317 (56%), Gaps = 18/317 (5%) Query: 19 LLAFARKHRTILFLL-LLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGG 77 L A AR LF L LL + A++ FLT N LN+L + S+ ++A G+T VIL GG Sbjct: 10 LSADARSFAYRLFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGG 69 Query: 78 IDVAVGSLLAFASIAAAYVVTAV------VGDGPATWLIALLVSTLIGLAGGYVQGKAVT 131 +D++VG+ +A ++ AA V+ A VG G T LIGLA G + V Sbjct: 70 LDLSVGANVAMSACVAATVMKATGSTMLGVGAGLGT-------GALIGLANGLL----VA 118 Query: 132 WLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAA 191 L +P FI T G + V G T G I GF A+R GSG + +P+PV + + Sbjct: 119 MLRIPPFIATYGMLWVLHGVTYWFMAGETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLV 178 Query: 192 AGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGS 251 AG + T YG+++YA+G N AARLSGV V VY + GA+AG++ + ARL S Sbjct: 179 AGTAMSQKTTYGQEIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNS 238 Query: 252 AEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQV 311 AE G L IA+V+IGG SL GG G V GT++GA+++ ++ NG+ +L V++ Q + Sbjct: 239 AEGDIGEALTLPAIAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPL 298 Query: 312 VIGLIIVAAVAFDHYAR 328 V G+I+V AV D +R Sbjct: 299 VTGVIVVLAVFLDTLSR 315 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: 260 Number of extensions: 19 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: 322 Length adjustment: 28 Effective length of query: 304 Effective length of database: 294 Effective search space: 89376 Effective search space used: 89376 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: 48 (23.1 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