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 SM_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 211 bits (536), Expect = 3e-59 Identities = 123/302 (40%), Positives = 180/302 (59%), Gaps = 5/302 (1%) Query: 30 LFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFA 89 L L++L VF N RF+T N +NIL +V++ I A GMT+VIL+G ID++VGS++A A Sbjct: 23 LSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTWVILLGEIDLSVGSIIAVA 82 Query: 90 SIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWR 149 + A +G PA L L L+G+ G + K L +P+FIVT+ M ++R Sbjct: 83 GMVGAQCFAFGMGFAPAIAL-TLAAGALMGMLNGVLTAK----LLLPSFIVTVATMGIYR 137 Query: 150 GATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAV 209 G L +G P N+ + G+ L LP+ + + A++ + L T +GR+ Y Sbjct: 138 GMVSLPTNGAPAMIENETWTAIGTESFLGLPIIIWVVAVLFVINQIVLSKTSFGRRAYLT 197 Query: 210 GGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVV 269 GGN EAA SG+ VD + ++ I G +A +SG LLS+RL SA+ AG YEL IA+ V Sbjct: 198 GGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQTNAGMSYELDAIAAAV 257 Query: 270 IGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYART 329 +GG SL GG G + GT++GAL+IGV++NG+ ML V + Q +V GL+I+ AV D A+ Sbjct: 258 LGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKGLVILVAVWLDVRAKQ 317 Query: 330 HK 331 K Sbjct: 318 AK 319 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: 260 Number of extensions: 15 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: 320 Length adjustment: 28 Effective length of query: 304 Effective length of database: 292 Effective search space: 88768 Effective search space used: 88768 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: 48 (23.1 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