Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 158 bits (399), Expect = 2e-43 Identities = 113/384 (29%), Positives = 183/384 (47%), Gaps = 71/384 (18%) Query: 12 NVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGM 71 N + + +R+ + G+ ++LV + + F F+ + VN N++ Q + + I A GM Sbjct: 4 NTAAKAALVRALKQYGGIFLSLVMLCIVFSFFNPRFM-TVVNFMNILQQVAVVAIAAFGM 62 Query: 72 LLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYH 131 VI+ G IDLSVGSI + + G++GA Q + Sbjct: 63 TWVILLGEIDLSVGSI--------------------------IAVAGMVGA-QCFAFGMG 95 Query: 132 RIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILT 191 P+ +TLA + +G + G+ T ++L Sbjct: 96 FAPAIALTLAAGAL-------------------------------MGMLNGVLTAKLLLP 124 Query: 192 VLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLI 251 I +R V +G +++N + ++ GLP ++ Sbjct: 125 SFIVTVATMGIYRGMVSLPTNGAPA------MIENET------WTAIGTESFLGLPIIIW 172 Query: 252 VMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMI 311 V+ VL + V +T+ GRR Y GGN +A SGI +RL L F+ GV+A ++G++ Sbjct: 173 VVAVLFVINQIVLSKTSFGRRAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVL 232 Query: 312 IATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGL 371 +++RL SA AG+ +ELD IAA +GG S +GGVG + G +IGA I+GVMNNGM+++ + Sbjct: 233 LSSRLFSAQTNAGMSYELDAIAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSV 292 Query: 372 GIDFQQMVKGLVLLAAVFFDVYNK 395 +Q +VKGLV+L AV+ DV K Sbjct: 293 PYFYQLIVKGLVILVAVWLDVRAK 316 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: 468 Number of extensions: 32 Number of successful extensions: 3 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: 320 Length adjustment: 29 Effective length of query: 369 Effective length of database: 291 Effective search space: 107379 Effective search space used: 107379 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