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 HSERO_RS22210 HSERO_RS22210 branched-chain amino acid ABC transporter permease
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__HerbieS:HSERO_RS22210 Length = 339 Score = 176 bits (447), Expect = 6e-49 Identities = 109/334 (32%), Positives = 176/334 (52%), Gaps = 11/334 (3%) Query: 1 MTAPSSPAPLA---TDKPRFDLLAFARKHRTILFLLLLV--AVFGAANERFLTARNALNI 55 M P+SP +K RF R +L +LL++ AV G F N + Sbjct: 4 MNEPASPPRSRYRIDEKARFQPRDLLRHWEALLAILLVLVCAVNGLLLPHFFDPYNLADS 63 Query: 56 LSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVS 115 S +IA+ M +I+ ID++V +++A AS+A A V L LLV+ Sbjct: 64 TFNFSEKAMIALPMALLIICREIDISVSAIIALASVAMGLANQAGVPP-----LGLLLVA 118 Query: 116 TLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGE 175 G A G + G VT L +P+ +VT+G M+++RG ++ + + + WG G Sbjct: 119 IATGTACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQYPEVLGDWGQGY 178 Query: 176 IL-FLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAII 234 LP P V++ L A V L TR+GR++YA+G N AAR SGV VD +++ + Sbjct: 179 FFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAARFSGVAVDRYRLALFVLT 238 Query: 235 GALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGV 294 GA+AGL+ F L+ R+GS G+EL +I V++GG S+ GG+G +GG +L L++G+ Sbjct: 239 GAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIAGGTGSIGGVMLSVLVMGM 298 Query: 295 LSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYAR 328 L+ GL + ++ + +V+G +++A +A R Sbjct: 299 LTYGLALANIPGIIMTIVVGALLLATIAIPRLLR 332 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: 250 Number of extensions: 12 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: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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