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 Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 186 bits (471), Expect = 1e-51 Identities = 113/302 (37%), Positives = 171/302 (56%), Gaps = 8/302 (2%) Query: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 ++ L+LL N F T N +N+L+ + GIIAVGM FVI+ GGID++VGS+ A Sbjct: 44 VIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAAL 103 Query: 89 ASIAAAYVVTA---VVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGM 145 + + + A V+G A ++ +L++ ++G G V G +T + FIVTLG + Sbjct: 104 IAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTL 163 Query: 146 TVWRGATLLLNDGGPIS---GFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRY 202 ++R ++GG I+ +D Y +L +P+PV IF LVA G V L T Y Sbjct: 164 GIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVILNRTAY 223 Query: 203 GRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYEL 262 GR V A+G N + A+ + V+V I Y ++G G++ L RLGSA G +EL Sbjct: 224 GRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLWEL 283 Query: 263 RVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTS-YVQQVVIGLIIVAAV 321 IA+V++GG L GG+G + GTV+GA+L+ V+SN L + + S Y+ V G +I+ AV Sbjct: 284 EAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVII-AV 342 Query: 322 AF 323 AF Sbjct: 343 AF 344 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: 296 Number of extensions: 25 Number of successful extensions: 4 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: 350 Length adjustment: 28 Effective length of query: 304 Effective length of database: 322 Effective search space: 97888 Effective search space used: 97888 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