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 BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 192 bits (488), Expect = 1e-53 Identities = 117/306 (38%), Positives = 175/306 (57%), Gaps = 22/306 (7%) Query: 32 LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91 L+LL+ F A+ F+ N L IL ++ G++A+ TFVI+ GGID++VG+L+ F ++ Sbjct: 38 LILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAV 97 Query: 92 AAAYVVTAVVGDGPATWLIALLVSTLI----GLAGGYVQGKAVTWLHVPAFIVTLGGMTV 147 +T W + + L G G V G + +P FI TLG M + Sbjct: 98 ICGVFLTY--------WHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMML 149 Query: 148 WRGATLLLNDGGPISGFNDAYRWWGS------GEIL-FLPVP--VVIFALVAAAGHVALR 198 +G +L+++ PI F D ++ G++L LPVP V+I +A + L Sbjct: 150 LKGLSLVVSADKPIY-FTDTENFYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLN 208 Query: 199 YTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGT 258 T GR +A+G N EA RLSGVNVD ++Y + GA+ G++G L+++RL SA+ G Sbjct: 209 RTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQ 268 Query: 259 GYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIV 318 GYEL IA+VVIGG SL+GG+G + GT++GA ++ VL+NGL ++ V Q VV GLII+ Sbjct: 269 GYELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIII 328 Query: 319 AAVAFD 324 AV D Sbjct: 329 LAVYGD 334 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: 236 Number of extensions: 19 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