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 PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 164 bits (414), Expect = 4e-45 Identities = 96/298 (32%), Positives = 163/298 (54%), Gaps = 8/298 (2%) Query: 30 LFLLLLVAVFGAAN---ERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLL 86 + LL V +F A + FL+ N + +S GI A M + + G D++VGS+ Sbjct: 26 VMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSV- 84 Query: 87 AFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMT 146 IA A VV AVV + + + + ++GL G + G + L V A I TL M Sbjct: 85 ----IACAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQ 140 Query: 147 VWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQV 206 + RG + +G + +++ +G+G++ +PVP++I + L YT YGR Sbjct: 141 IVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNT 200 Query: 207 YAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIA 266 A+GGN EAA L+GVNVD ++A+ G + L+G +L++R+ S + + G G+EL VI+ Sbjct: 201 MAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVIS 260 Query: 267 SVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 + V+GG SL+GG G + + G L++ ++ N + + ++ ++ Q V+ G I++ AV D Sbjct: 261 ACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVID 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: 234 Number of extensions: 14 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: 323 Length adjustment: 28 Effective length of query: 304 Effective length of database: 295 Effective search space: 89680 Effective search space used: 89680 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