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 BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 229 bits (585), Expect = 6e-65 Identities = 128/311 (41%), Positives = 192/311 (61%), Gaps = 5/311 (1%) Query: 14 KPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVI 73 K FD + + ++ LL+L+ + F N LNI +S+ I+A GMTFVI Sbjct: 13 KAPFDFAKWWDRVGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVI 72 Query: 74 LIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWL 133 L GID++VGS++A + + + VV A+ G PA +A+L +G G + G +L Sbjct: 73 LTSGIDLSVGSIVAVSGVVS--VVAAMAGI-PAP--LAILAGVGVGALCGLLNGVLTAYL 127 Query: 134 HVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAG 193 + FIVTLG MT RG + +G PI + ++R G+G ++ +P+PV+I +V Sbjct: 128 ALAPFIVTLGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLA 187 Query: 194 HVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAE 253 L TR+GR +YAVGGNA+AARL+GV V + +VY I G AGL+G + +AR+ SA+ Sbjct: 188 WFILERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQ 247 Query: 254 AVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVI 313 AGTGYEL IA+VV+GG SL GG G + GT++G++++GVLS GL++L V + Q ++ Sbjct: 248 PTAGTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIK 307 Query: 314 GLIIVAAVAFD 324 G++I+ AVA D Sbjct: 308 GIVIILAVAID 318 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: 265 Number of extensions: 19 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: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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 Apr 09 2024. 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