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_110806514.1 C8J30_RS14100 ABC transporter permease
Query= TCDB::B8H230 (332 letters) >NCBI__GCF_003217355.1:WP_110806514.1 Length = 339 Score = 195 bits (495), Expect = 2e-54 Identities = 121/314 (38%), Positives = 182/314 (57%), Gaps = 23/314 (7%) Query: 29 ILFLLLLVAVFGAA------NERFLTARNALNILS-EVSIYGIIAVGMTFVILIGGIDVA 81 ILF+L+ +A+ + FL + + L I+ +VS+ GII+VG+T VI+ GGID++ Sbjct: 24 ILFVLVGIALVFEILGWIFQGQSFLMSIDRLKIMILQVSVIGIISVGVTQVIIAGGIDLS 83 Query: 82 VGSL--------LAFASIAA-AYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTW 132 GS+ ++FA ++ A V + D PA ++ + + + G G + G + + Sbjct: 84 SGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPA--IVPIALGLMAGALVGLINGALIAY 141 Query: 133 LHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAA 192 +P FI TLG M RG G PIS D + + G G + PV IF VAA Sbjct: 142 AKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGMM-----PVAIFLAVAAI 196 Query: 193 GHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSA 252 HVA++YTRYG+ YA+G N +AAR+SG+NV+ VY + LA L+G +++AR +A Sbjct: 197 FHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAATLAALAGMVVAARGQTA 256 Query: 253 EAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVV 312 +A G YEL IA VIGG SLTGG G + GT++G ++ GV+ +G L + +Y Q+++ Sbjct: 257 QAGMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVIISGFTFLRLDAYYQEMI 316 Query: 313 IGLIIVAAVAFDHY 326 G+IIVAAV D Y Sbjct: 317 KGVIIVAAVVADVY 330 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: 291 Number of extensions: 13 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: 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 24 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