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 Pf6N2E2_163 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_163 Length = 325 Score = 181 bits (459), Expect = 2e-50 Identities = 109/295 (36%), Positives = 167/295 (56%), Gaps = 5/295 (1%) Query: 32 LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91 LL +VA+F A + FL+ + +++ ++AVGMTF+++IGGID++VGS+LA + Sbjct: 27 LLAMVALFSALSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGIDLSVGSVLA---L 83 Query: 92 AAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGA 151 AA+ V AV+G G + W ALL + LAG V W +P+FIV+LG + + RG Sbjct: 84 AASTVSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITVAW-RIPSFIVSLGVLEMARGL 142 Query: 152 TLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGG 211 + G + D++ W + + +I LV L T +GR + +G Sbjct: 143 AYQMT-GSRTAYIGDSFAWLSNPIAFGISPSFIIALLVIFIAQAVLTRTVFGRYLIGIGT 201 Query: 212 NAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIG 271 N EA RL+G+N V++++G LAG++ +RL +A+ AG+G EL+VIA+VVIG Sbjct: 202 NEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIG 261 Query: 272 GASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326 G SL GG G V T G L+I VL+ GL + T ++++ G +IV AV D Y Sbjct: 262 GTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316 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: 247 Number of extensions: 17 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: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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