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 N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 138 bits (348), Expect = 2e-37 Identities = 100/306 (32%), Positives = 159/306 (51%), Gaps = 17/306 (5%) Query: 29 ILFLLLLVAVFGAANERFLTAR--------NALNILSEVSIYGIIAVGMTFVILIGGIDV 80 +L L+LL+A G N FL + N ++I + ++++GMT VI + G+D+ Sbjct: 34 LLTLILLLAGNGLFNPGFLALQWRDGHLYGNLIDIAHRAAPLALVSLGMTLVIALRGLDI 93 Query: 81 AVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPA--- 137 +VG++LA A+ AA+ + V DG L+ L ++ LA G + G WL V A Sbjct: 94 SVGAVLAIAATVAAWTIGHVSNDG----LLPLWLAIAAALAAGALCGLWNGWLVVGAGMQ 149 Query: 138 -FIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVA 196 + TL M RG ++ G ++ + Y + G+G +L LP + + A V A +A Sbjct: 150 PIVATLILMVAGRGIAQSISGGQILTLYYAPYSFLGNGFVLGLPFSLFVVAAVFALLQLA 209 Query: 197 LRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEA-V 255 LR T G V A+G N +AA ++GV IT Y G A L+G L+S+ + SA+A Sbjct: 210 LRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSNVNSADANN 269 Query: 256 AGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGL 315 AG EL I +V +GG+ L GG + G++LGAL+I L+ + + V V V + Sbjct: 270 AGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPPQVNLAVKAV 329 Query: 316 IIVAAV 321 ++ A + Sbjct: 330 LVFAVM 335 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: 282 Number of extensions: 13 Number of successful extensions: 1 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: 358 Length adjustment: 29 Effective length of query: 303 Effective length of database: 329 Effective search space: 99687 Effective search space used: 99687 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