Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 262 bits (670), Expect = 8e-75 Identities = 150/336 (44%), Positives = 211/336 (62%), Gaps = 20/336 (5%) Query: 4 KTITAPVTAAPR--NRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSIN 61 K PV + R L + L G+ LVF + ++ S + M + + ++ Q SI Sbjct: 8 KPAAVPVKSRRRFPTELSIFLVLIGIGLVFEMFGWIVRDQS-FLMNSQRLVLMILQVSII 66 Query: 62 GILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAA------------VSAG 109 G+LA+G+T VI+T GIDLS GS+LA + + +A +A A V G Sbjct: 67 GLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIVG 126 Query: 110 MFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGK 169 + G + G +NG ++A IPPF+ATLGM+ ARG+ +G P++ L D+Y A+G G Sbjct: 127 LGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG- 185 Query: 170 IGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSG 229 +P+IIF VVA+IF + LRYT YG+Y YA+GGN ++ARTSGI V++ + VY ++G Sbjct: 186 ----AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAG 241 Query: 230 LLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVI 289 LLAGLAGVV SAR + G+SYELDAIAA VIGGTSL+GG G I GT+ GAL++GV+ Sbjct: 242 LLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVM 301 Query: 290 NNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKKR 325 +G +GV +Y Q + KGLIIV AV+ID +R K++ Sbjct: 302 ASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 Lambda K H 0.326 0.141 0.412 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: 291 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: 325 Length of database: 340 Length adjustment: 28 Effective length of query: 297 Effective length of database: 312 Effective search space: 92664 Effective search space used: 92664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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