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 Pf6N2E2_524 Inositol transport system permease protein
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 210 bits (535), Expect = 4e-59 Identities = 126/327 (38%), Positives = 187/327 (57%), Gaps = 26/327 (7%) Query: 24 RKHRTILFLLLLVAVFGAANERF----------LTARNALNILSEVSIYGIIAVGMTFVI 73 R+ T L + L++ G E F + ++ + ++ +VSI G++A+G+T VI Sbjct: 18 RRLPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVI 77 Query: 74 LIGGIDVAVGSLLAFASIAAAYV---------VTAVVGDGPATWLIALLVSTLIGLAGGY 124 + GID++ GS+LA +++ AA + V + D P W I ++ +GL G Sbjct: 78 ITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPV-W-IPVVAGLGVGLLAGA 135 Query: 125 VQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVV 184 + G + +P FI TLG M RG +G P+S +D+Y G G + PV+ Sbjct: 136 INGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVI 190 Query: 185 IFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFL 244 IF +VA H+ALRYT+YG+ YA+GGN +AAR SG+NV VY+I G LAGL+G + Sbjct: 191 IFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVV 250 Query: 245 LSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHV 304 SAR + +A G YEL IA+ VIGG SL GG G + GTV+GAL++GV+++G + V Sbjct: 251 ASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGV 310 Query: 305 TSYVQQVVIGLIIVAAVAFDHYARTHK 331 +Y+Q ++ GLIIV AV D Y K Sbjct: 311 DAYIQDIIKGLIIVVAVVIDQYRNKRK 337 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: 273 Number of extensions: 12 Number of successful extensions: 4 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: 340 Length adjustment: 28 Effective length of query: 304 Effective length of database: 312 Effective search space: 94848 Effective search space used: 94848 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