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 BWI76_RS07235 BWI76_RS07235 hypothetical protein
Query= TCDB::B8H228 (326 letters) >FitnessBrowser__Koxy:BWI76_RS07235 Length = 307 Score = 127 bits (318), Expect = 5e-34 Identities = 89/283 (31%), Positives = 140/283 (49%), Gaps = 7/283 (2%) Query: 37 EAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQVLDAQNNSSKQISDLQAAAVQGAKV 96 + V VS F +R ++ E K GVK QV DA+ + S+Q+ +Q QG Sbjct: 24 DISVGVSMALFDDNFLTILRTAMQKEMQKDGVKAQVEDAKGDVSQQLQQVQNFIGQGVDA 83 Query: 97 VIVAPTDSKALAGAADDLVEQGVAVISVDRNIAGGKT-AVPHVGADNVAGGRAMADWVVK 155 +IV P D+ A+ D + G+ +I V+R T + +VG+D+V GR + + K Sbjct: 84 IIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQLTDKMAYVGSDSVLAGRLQMEALAK 143 Query: 156 TYPAGARVVVITNDPGSSSSIERVKGVHDGLAAGGPAFKIVTEQTANSKRDQALTVTQNI 215 V ++ D + S+ +R KGV + + A P KIV +QTA R+ A+ V N Sbjct: 144 AMNGKGNVAILLGDLANESTRDRTKGVEE-VVAKYPDIKIVQKQTAKFTRNDAVDVVSNW 202 Query: 216 LTSMRDTPPDVILCLNDDMAMGALEAVRAAGLDSAKVKVIGFDAIPEALARIKAGEMVAT 275 +TS D I ND+MA+GAL+A+ G + + + G D P+AL +K G+M+AT Sbjct: 203 MTSGEDI--QAIASNNDEMAIGALQAL---GKNPNHILIAGVDGTPDALQMLKNGKMIAT 257 Query: 276 VEQNPGLQIRTALRQAVDKIKSGAALKSVSLKPVLITSGNLTE 318 + Q+ Q A+ A+ K + + LIT N+ E Sbjct: 258 IFQDAKGQGEGAVDAAIKLANGEKVEKVIDVPYQLITKDNMAE 300 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: 214 Number of extensions: 13 Number of successful extensions: 5 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: 307 Length adjustment: 27 Effective length of query: 299 Effective length of database: 280 Effective search space: 83720 Effective search space used: 83720 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