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 GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 150 bits (380), Expect = 3e-41 Identities = 105/316 (33%), Positives = 162/316 (51%), Gaps = 27/316 (8%) Query: 29 ILFLLLLVAVFGAA-NERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLA 87 ++ L+L V VFG +F + IL +V I GI+A + VIL GID++VG+++ Sbjct: 45 LIVLVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMV 104 Query: 88 FASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTV 147 +S+ T G P +A+ + G G++ G V + +P FIVTLG + Sbjct: 105 LSSVVMGQF-TFRYGLPPE---VAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQI 160 Query: 148 WRGATLLLNDGGPISG------------FNDAYRWWGSG---EILFLPVPVVIFALVAAA 192 + L + I F + + G+ ++F+ + VV+ A V Sbjct: 161 VLASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVFTYGVIFMVILVVLLAYV--- 217 Query: 193 GHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSA 252 LR+T +GR VYAVG + EAA LSGV V + SVY + G + +G+ + R+GS Sbjct: 218 ----LRHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSV 273 Query: 253 EAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVV 312 +G + I +VVIGG SL GG G + GT GAL++GV + GL +L + ++ Sbjct: 274 SPTSGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTYLL 333 Query: 313 IGLIIVAAVAFDHYAR 328 IGL+I+AAVA D + R Sbjct: 334 IGLLIIAAVAVDQWIR 349 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: 246 Number of extensions: 11 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: 353 Length adjustment: 29 Effective length of query: 303 Effective length of database: 324 Effective search space: 98172 Effective search space used: 98172 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 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