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 H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 215 bits (547), Expect = 1e-60 Identities = 117/303 (38%), Positives = 182/303 (60%), Gaps = 21/303 (6%) Query: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 +L + LL++VF + FLT N + + S+ ++++GM VI+ GGID++VGS++ Sbjct: 34 LLLVGLLISVF---SPYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGGIDLSVGSVMGL 90 Query: 89 ASIAAA------YVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTL 142 +S+ A Y A +G G A +G+A G G +TW+ +P FI TL Sbjct: 91 SSLVTALVFQHGYNAPAAIGAGLA-----------VGIAVGAFNGFMITWIQLPPFIATL 139 Query: 143 GGMTVWRGATLLLNDGGPIS-GFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTR 201 G +++ RG ++ G P++ D++ + G G I F+P PVVI + A V +R TR Sbjct: 140 GTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVVMRQTR 199 Query: 202 YGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYE 261 +GR VYA GGN AARLSGV + +VY + G +A ++G + +R SAE +G G E Sbjct: 200 FGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPASGFGAE 259 Query: 262 LRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAV 321 L VIA+ IGGASL+GG+G V G ++GA L G+++NG+V+L++ +Y QQ + G +I+ AV Sbjct: 260 LDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCVILIAV 319 Query: 322 AFD 324 + D Sbjct: 320 SID 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: 285 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 332 Length of database: 331 Length adjustment: 28 Effective length of query: 304 Effective length of database: 303 Effective search space: 92112 Effective search space used: 92112 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