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 Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 235 bits (599), Expect = 1e-66 Identities = 127/306 (41%), Positives = 195/306 (63%), Gaps = 6/306 (1%) Query: 25 KHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGS 84 K ++++ L++L V ++RFLT N N++ +VS+ I+VGMT VIL GID++VGS Sbjct: 6 KFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGS 65 Query: 85 LLAFA-SIAAAYVVTAVVGDGPATW-----LIALLVSTLIGLAGGYVQGKAVTWLHVPAF 138 +LA ++ A+ + + +G L A+++ +G G+ G +T VP F Sbjct: 66 ILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPF 125 Query: 139 IVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALR 198 + TL +T+ RG T+L G PI+G + + + G+G L +P+PV I A++ A + + Sbjct: 126 VATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTK 185 Query: 199 YTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGT 258 T++GR VYA+GGN AARLSG+N+ + +VYAI G LA + G ++++RL SA+ AG Sbjct: 186 KTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGI 245 Query: 259 GYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIV 318 YEL IA+VVIGG SL+GG G + G VLG ++IGVL+NGLV+L+V+ + QQVV G +I+ Sbjct: 246 SYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVIL 305 Query: 319 AAVAFD 324 AV D Sbjct: 306 LAVVID 311 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: 262 Number of extensions: 12 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: 318 Length adjustment: 28 Effective length of query: 304 Effective length of database: 290 Effective search space: 88160 Effective search space used: 88160 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: 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