Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 167 bits (424), Expect = 3e-46 Identities = 118/345 (34%), Positives = 174/345 (50%), Gaps = 73/345 (21%) Query: 53 NLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAA-ILTVQWGMNP---FL 108 N N++ + S I+A+GM VI+ G ID++VGS++AF AA ++T G P + Sbjct: 51 NALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLI 110 Query: 109 AALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQV 168 A L+ +IG G QG + + +P+FIVTL GM V+RG TL Sbjct: 111 ALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLL---------------- 154 Query: 169 ISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLL 228 L D G I G N Y W Sbjct: 155 -----LNDGGPISGFNDA-------------YRWWG------------------------ 172 Query: 229 ISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGI 288 SG ILFL P +++ ++ A R T GR+VYA+GGN +A +LSG+ Sbjct: 173 -SGEILFL----------PVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGV 221 Query: 289 NTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGK 348 N + ++ + +G LAGL+G +++ RL SA AG G+EL VIA+ IGGAS +GG G Sbjct: 222 NVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGG 281 Query: 349 ITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVY 393 + G V+GA ++GV++NG+ ++ + QQ+V GL+++AAV FD Y Sbjct: 282 VGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326 Lambda K H 0.329 0.145 0.422 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: 476 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 332 Length adjustment: 29 Effective length of query: 369 Effective length of database: 303 Effective search space: 111807 Effective search space used: 111807 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 (21.8 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