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 SMc02031 SMc02031 permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 235 bits (600), Expect = 1e-66 Identities = 132/311 (42%), Positives = 187/311 (60%), Gaps = 11/311 (3%) Query: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 ++ L+LL+A A FLT N N+ + + I+AVG TFVIL GGID++V ++ A Sbjct: 33 LIALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILTGGIDLSVAAIAAL 92 Query: 89 ASIAAAYVVTAV-----VGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLG 143 ++ A ++T + G +A+L+ LIG+A G + G ++ +P FI TLG Sbjct: 93 SASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFIATLG 152 Query: 144 GMTVWRGATLLLNDGGPISGFN------DAYRWWGSGEILFLPVPVVIFALVAAAGHVAL 197 MT +RGA LL+ DG P+ FN ++ W G G++ +PV +I L AAAG L Sbjct: 153 TMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVSALIALLCAAAGWYVL 212 Query: 198 RYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAG 257 RYT GR +YAVGGN AA SG+++ YAI G LA ++G +L RL SA A+ Sbjct: 213 RYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRLNSANALMA 272 Query: 258 TGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLII 317 G ELR IASVVIGG +L GG GGV G+++GA +IGVL NGL +L V+ + Q++ G++I Sbjct: 273 DGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQRIAQGVVI 332 Query: 318 VAAVAFDHYAR 328 V V FD + R Sbjct: 333 VVVVIFDQWRR 343 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: 315 Number of extensions: 26 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: 349 Length adjustment: 28 Effective length of query: 304 Effective length of database: 321 Effective search space: 97584 Effective search space used: 97584 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