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 GFF3462 PS417_17725 ribose ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 227 bits (578), Expect = 4e-64 Identities = 130/290 (44%), Positives = 182/290 (62%), Gaps = 5/290 (1%) Query: 32 LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91 L+++ V A++ FLTA N NI +VSI IIAVGMT VIL GGID++VG ++A + Sbjct: 38 LVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVILTGGIDLSVGPVMALSGT 97 Query: 92 AAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGA 151 A ++ A + G +A+ LIG+A G G V +LH+P IVTL M + RG Sbjct: 98 LTAGLMVAGLPPG-----LAIGAGMLIGVAFGIGNGLFVAYLHMPPIIVTLATMGIARGL 152 Query: 152 TLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGG 211 L+ DG PISG D + ++G + + VP++I L +V L++TR GR +YA+GG Sbjct: 153 GLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYVLLQHTRIGRYIYAIGG 212 Query: 212 NAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIG 271 N EA RLSGV VY I G A ++G +L++RL S + AG +EL IA+VV+G Sbjct: 213 NEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAGVSFELDAIAAVVLG 272 Query: 272 GASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAV 321 GAS+ GG G + GT+LGA+L+GVL+NGL ML V+ YVQ V+ G II+ A+ Sbjct: 273 GASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKGGIILLAI 322 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: 274 Number of extensions: 11 Number of successful extensions: 2 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: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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