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 Pf1N1B4_4386 Inositol transport system sugar-binding protein
Query= TCDB::B8H228 (326 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386 Length = 308 Score = 121 bits (303), Expect = 3e-32 Identities = 85/279 (30%), Positives = 141/279 (50%), Gaps = 5/279 (1%) Query: 36 AEAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQVLDAQNNSSKQISDLQAAAVQGAK 95 A + VS + F +R LED A K V++Q DAQ + +Q++ +Q Q Sbjct: 21 ASYRIGVSIARVDDNFMTYVRSGLEDAARKENVQIQFEDAQGDVVRQLNQVQGFLGQKVD 80 Query: 96 VVIVAPTDSKALAGAADDLVEQGVAVISVDRNIAGG--KTAVPHVGADNVAGGRAMADWV 153 VIV P D+ A A VE + ++ V+R+ V V +++V G+ ++ Sbjct: 81 AVIVLPVDTAATANMTRAAVEAKIPLVYVNRHPDERVLPKGVVTVASNDVEAGQLQMRYL 140 Query: 154 VKTYPAGARVVVITNDPGSSSSIERVKGVHDGLAAGGPAFKIVTEQTANSKRDQALTVTQ 213 + + +I D +S+ +R +GV+ L P KIV +Q+A +R++ + +T Sbjct: 141 AEKMAGKGNIAIIKGDLAQNSTQDRTEGVNQVLK-DYPGIKIVEQQSAEWQRNKGMDLTS 199 Query: 214 NILTSMRDTPPDVILCLNDDMAMGALEAVRAAGLDSAKVKVIGFDAIPEALARIKAGEMV 273 N L + D D I+ ND+MA+GA A++ AG ++ ++G D +P+ LA IK G +V Sbjct: 200 NWLLAGADF--DAIVANNDEMAIGAAMALQQAGKAKGEIAIVGIDGLPDGLAAIKRGMLV 257 Query: 274 ATVEQNPGLQIRTALRQAVDKIKSGAALKSVSLKPVLIT 312 A+V Q+P Q +AL+ A+ IK V + LIT Sbjct: 258 ASVFQDPKAQATSALQAAIKMIKGEPVETDVWVPFQLIT 296 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: 205 Number of extensions: 13 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: 326 Length of database: 308 Length adjustment: 27 Effective length of query: 299 Effective length of database: 281 Effective search space: 84019 Effective search space used: 84019 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