Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SMc02031 SMc02031 permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 151 bits (382), Expect = 2e-41 Identities = 117/379 (30%), Positives = 187/379 (49%), Gaps = 61/379 (16%) Query: 20 IRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGH 79 +++ + + G LIALV +M + F T L NL+N+ Q++F+ I+A+G VI+ G Sbjct: 23 LKAVVFQAGPLIALVLLMAYLAFATSNFLTLD-NLSNVARQSAFVAILAVGQTFVILTGG 81 Query: 80 IDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVT 139 IDLSV +I A +I A+L Q LV+ GI + +P + Sbjct: 82 IDLSVAAIAALSASITAVLLTQ-----------PLVLFGI---------DFGFVPPPVAI 121 Query: 140 LAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALF 199 L G+L+ G+ L G I F +PD G T Sbjct: 122 LIGILI--GMAAGALNGWLISKFK----------IPDFIATLGTMT-------------- 155 Query: 200 YLAWRRRVVNVKHGIDVEPF--GFFIVQNLL-ISGAILFLGYQLSTYRGLPNVLIVMLVL 256 A+R + V G+ V F G + ++L+ + G LF G+P ++ L+ Sbjct: 156 --AFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLF---------GVPVSALIALLC 204 Query: 257 IALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRL 316 A +V R T +GR +YA+GGN A SGI+ R +T+ G+LA +AG+I+ RL Sbjct: 205 AAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRL 264 Query: 317 NSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQ 376 NSA G EL IA+ IGG + GG G + G++IGA I+GV+ NG++++ + +Q Sbjct: 265 NSANALMADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQ 324 Query: 377 QMVKGLVLLAAVFFDVYNK 395 ++ +G+V++ V FD + + Sbjct: 325 RIAQGVVIVVVVIFDQWRR 343 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: 454 Number of extensions: 33 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: 398 Length of database: 349 Length adjustment: 30 Effective length of query: 368 Effective length of database: 319 Effective search space: 117392 Effective search space used: 117392 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: 50 (23.9 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