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_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_04148 Length = 335 Score = 222 bits (565), Expect = 1e-62 Identities = 141/325 (43%), Positives = 192/325 (59%), Gaps = 13/325 (4%) Query: 5 SSP--APLATDKP----RFDLLAFARKHRTILFLLLLVA--VFGAANERFLTARNALNIL 56 SSP + +++D P RF A R F+ LLV V A++ FL+ N N+L Sbjct: 8 SSPKTSTVSSDTPGAPVRFTWAALKRSTLFYPFIGLLVVCIVMVFASDSFLSGANIENVL 67 Query: 57 SEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVST 116 +VSI IIAVGMT VIL GGID++VGS++A A AA ++ A + L AL V Sbjct: 68 RQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNA-----LAALAVGV 122 Query: 117 LIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEI 176 +GL G G V + +P IVTL M + RG L+ G PI G D ++GSG+I Sbjct: 123 AVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKI 182 Query: 177 LFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGA 236 L + PVVI A++ V L +GR VYA+GGN +A RLSGV V + VY I G Sbjct: 183 LGIQAPVVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGL 242 Query: 237 LAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLS 296 + + +L+ARL S + AG G+EL IA+VV+GG S++GG G + GT++GALL+GVL+ Sbjct: 243 TSSFAAIVLTARLMSGQPNAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLN 302 Query: 297 NGLVMLHVTSYVQQVVIGLIIVAAV 321 NGL M+ V YVQ V+ G II+ A+ Sbjct: 303 NGLNMVGVNPYVQNVIKGGIILLAI 327 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: 279 Number of extensions: 12 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: 335 Length adjustment: 28 Effective length of query: 304 Effective length of database: 307 Effective search space: 93328 Effective search space used: 93328 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