Align Inositol ABC transporter, periplasmic inositol-binding protein IbpA, 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 18116 b4088 D-allose transporter subunit (NCBI)
Query= TCDB::B8H228 (326 letters) >FitnessBrowser__Keio:18116 Length = 311 Score = 122 bits (305), Expect = 1e-32 Identities = 99/299 (33%), Positives = 140/299 (46%), Gaps = 25/299 (8%) Query: 13 GLAAGLGLGTAALGLMTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQV 72 G GL L T+A A AE V LS PF+V M++ +EDEA LGV V + Sbjct: 10 GTLVGLMLSTSAF----------AAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDI 59 Query: 73 L--DAQNNSSKQISDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVDRNI-- 128 ++ + Q+ + + + K + AP S L ++G+ ++++D I Sbjct: 60 FASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDM 119 Query: 129 -----AGGKTAVPHVGADNVAGGRAMADWVVKTYPA-GARVVVITNDPGSSSSIERVKGV 182 AGG V DNVA G A +++ A G V +I G++S R G Sbjct: 120 DNLKKAGGNVEA-FVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGA 178 Query: 183 HDGLAAGGPAFKIVTEQTANSKRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAV 242 + K+V Q A+ R +AL V N+L R+ I C ND MAMG +AV Sbjct: 179 TEAFKKASQ-IKLVASQPADWDRIKALDVATNVL--QRNPNIKAIYCANDTMAMGVAQAV 235 Query: 243 RAAGLDSAKVKVIGFDAIPEALARIKAGEMVATVEQNPGLQIRTALRQAVDKIKSGAAL 301 AG + KV V+G D IPEA ++AG+M ATV QNP T L+ VD KSG + Sbjct: 236 ANAG-KTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVI 293 Lambda K H 0.315 0.130 0.353 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: 219 Number of extensions: 18 Number of successful extensions: 4 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: 326 Length of database: 311 Length adjustment: 27 Effective length of query: 299 Effective length of database: 284 Effective search space: 84916 Effective search space used: 84916 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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