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 WP_200808618.1 B9O00_RS21325 ABC transporter permease
Query= TCDB::B8H230 (332 letters) >NCBI__GCF_900177295.1:WP_200808618.1 Length = 341 Score = 186 bits (471), Expect = 9e-52 Identities = 119/332 (35%), Positives = 168/332 (50%), Gaps = 11/332 (3%) Query: 1 MTAPSSPAPLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVS 60 M P P A + F R L++ V VF ++ FLT RN N+ + Sbjct: 1 MAMLEQPTPGAAAPSLWLKRLFVRLGVLPFLLIVAVIVFTLMSDNFLTGRNLANVARQSV 60 Query: 61 IYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVG---DGPATWL-IALLVST 116 I+++G F +L GG D++VG++LA S+ A + A G D P + I L Sbjct: 61 YLTIVSLGQMFALLTGGFDLSVGTILALTSVVGALAMAAAFGAMPDAPGLAIAIGCLAGI 120 Query: 117 LIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISG----FNDAYRWWG 172 L G A G G V +V FI+TLG ++ G L L G P+ G F D + G Sbjct: 121 LAGTAIGLFNGVGVAIFNVSPFIMTLGMASIGFGIALFLTGGVPVYGMPQEFGDVF---G 177 Query: 173 SGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYA 232 G + VPV + AL+ ++ + +T GR YAVGGN +AARLSG+ + + Y Sbjct: 178 FGAWFGIDVPVYVAALLIVVVYLLVNWTPLGRYFYAVGGNIKAARLSGIGTRTVLFATYV 237 Query: 233 IIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLI 292 I L L G LL+ARL + EA G L IA+ VI G SL GG G V VLGAL I Sbjct: 238 ICALLTALGGMLLTARLDTGEANIGASMPLESIAACVIAGVSLRGGVGRVENVVLGALFI 297 Query: 293 GVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 ++ NG+ + + SY+Q VV+G++++ AV D Sbjct: 298 NLVQNGMNLARIESYLQTVVLGVLLILAVVAD 329 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: 256 Number of extensions: 15 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 Apr 09 2024. 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