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 BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 217 bits (552), Expect = 4e-61 Identities = 134/339 (39%), Positives = 190/339 (56%), Gaps = 24/339 (7%) Query: 2 TAPSSPAPLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSI 61 + P+ + R DL+ +K + L++L+ F + F + N + + +V+ Sbjct: 6 SGPNQALDRQVQQRRRDLI---QKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTS 62 Query: 62 YGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLA 121 + V T VI+ GGID++VGS+LA A +AAA +V A V P +A+L L+G A Sbjct: 63 IAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAGV---PIP--VAMLGGMLVGAA 117 Query: 122 GGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFL-- 179 G+V G VT + +P FI TLG M V RG L + P+SG DA+ G+G + + Sbjct: 118 CGWVNGICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISH 177 Query: 180 --------------PVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDF 225 P PVVI ++ AA + L T GR +YAVG NAEAARLSGVNV Sbjct: 178 IGADGFPDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQG 237 Query: 226 ITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGT 285 + Y + G LAG +G +L +RL +A+ G YEL IAS VIGG SL GG G + GT Sbjct: 238 VKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGT 297 Query: 286 VLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 +GA +IGVL NGL M V+S++QQ++IG++I+ V D Sbjct: 298 AIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWID 336 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: 264 Number of extensions: 19 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: 343 Length adjustment: 28 Effective length of query: 304 Effective length of database: 315 Effective search space: 95760 Effective search space used: 95760 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