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 WP_011841961.1 RSPH17029_RS14660 ABC transporter permease
Query= TCDB::B8H230 (332 letters) >NCBI__GCF_000015985.1:WP_011841961.1 Length = 330 Score = 198 bits (504), Expect = 1e-55 Identities = 118/315 (37%), Positives = 179/315 (56%), Gaps = 11/315 (3%) Query: 14 KPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVI 73 +PRF L +L L +L+A+ N FL+ N N+L+ + GIIAVGMTFVI Sbjct: 8 RPRFHLHVLG----PLLALFVLIALGAWLNPNFLSYGNVTNVLARSAFIGIIAVGMTFVI 63 Query: 74 LIGGIDVAVGSLLAFAS---IAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAV 130 GGID++VGS+ AF + I + + +G+G + + +LV+ GL G++ G + Sbjct: 64 TSGGIDLSVGSMAAFIAGLMILSMNALLPHMGEGVSVIFVGVLVAAGAGLLAGWLNGFLI 123 Query: 131 TWLHVPAFIVTLGGMTVWRGATLLLNDGGPIS---GFNDAYRWWGSGEILFLPVPVVIFA 187 + + FIVTLG M ++R L DGG +S G YR G IL + P+++FA Sbjct: 124 AKVGIEPFIVTLGTMGIYRSLVTWLADGGTLSLDFGLRGLYRPVYYGGILGVAWPIIVFA 183 Query: 188 LVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSA 247 +VA G + +R T +GR V A+G N + AR S V V + + YA++G L G++ + Sbjct: 184 IVAILGEIVMRQTAFGRHVAAIGANEQVARYSAVKVPRVRIATYALLGLLVGIATIMYVP 243 Query: 248 RLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTS- 306 RLGSA G +EL IA+V+IGG L GG G V GTV+G L++ ++ N L + + S Sbjct: 244 RLGSASGSTGVLWELEAIAAVIIGGTVLKGGYGRVWGTVVGVLILSLIDNILNLASIVSP 303 Query: 307 YVQQVVIGLIIVAAV 321 Y+ + G+I++ AV Sbjct: 304 YLNGTIQGVIVILAV 318 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: 294 Number of extensions: 21 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: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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 Apr 10 2024. 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