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_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 218 bits (555), Expect = 2e-61 Identities = 128/306 (41%), Positives = 186/306 (60%), Gaps = 9/306 (2%) Query: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 +LF L + + G F +A N +NIL +V+I ++A GMTFVIL GID++VGS+LA Sbjct: 38 LLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAV 97 Query: 89 ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148 +++ V +G P W I + + + GL G V G V L++ AF+VTLG MT + Sbjct: 98 SAVLGMQVS---LGAAPG-WAIPMFIFS--GLVMGMVNGAMVALLNINAFVVTLGTMTAF 151 Query: 149 RGATLLLNDGGPISGFND--AYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQV 206 RGA LL DG + ND ++ W G+G+ L +P + + V V LR T G + Sbjct: 152 RGAAYLLADGTTVLN-NDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHI 210 Query: 207 YAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIA 266 YA+GGN +AARL+G+ V + VY+I G +GL+G + ++RL A G+GYEL IA Sbjct: 211 YAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIA 270 Query: 267 SVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326 +VV+GG SL GG G + GTV+GAL+IGV++NGL +L ++S+ Q V G +IV AV D + Sbjct: 271 AVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKW 330 Query: 327 ARTHKA 332 + A Sbjct: 331 RQKDAA 336 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: 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: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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