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 HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 204 bits (520), Expect = 2e-57 Identities = 125/334 (37%), Positives = 188/334 (56%), Gaps = 21/334 (6%) Query: 8 APLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAV 67 A L R LLAFA LLL++ F A+ F+ N ++IL ++ G++A+ Sbjct: 26 ARLFNPAARQKLLAFAS-------LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAI 78 Query: 68 GMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQG 127 T+VI+ GID++VG+++ F ++ A V+T P + + + G G++ G Sbjct: 79 ACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLP----LGIAAAIFFGALSGWISG 134 Query: 128 KAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGE-------ILFLP 180 + L VP FI TLG M + +G +L+++ PI FND + + I LP Sbjct: 135 MVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIY-FNDTEGFSAIAQDSLIGDLIPSLP 193 Query: 181 VP--VVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALA 238 +P V+I LVA + L T +GR +A+G N EA RLSGV VDF +VY GA+ Sbjct: 194 IPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAIC 253 Query: 239 GLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNG 298 G++G ++++RL SA+ G GYEL IA+VVIGG SL+GG+G + GT++GA ++ VL NG Sbjct: 254 GIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNG 313 Query: 299 LVMLHVTSYVQQVVIGLIIVAAVAFDHYARTHKA 332 L ++ V Q VV G+II+ AV D R +A Sbjct: 314 LRIMSVAQEWQTVVTGVIIILAVYLDILRRRRRA 347 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: 241 Number of extensions: 18 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: 347 Length adjustment: 28 Effective length of query: 304 Effective length of database: 319 Effective search space: 96976 Effective search space used: 96976 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