Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_051305489.1 G494_RS0107330 inner-membrane translocator
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000429965.1:WP_051305489.1 Length = 383 Score = 259 bits (661), Expect = 1e-73 Identities = 158/386 (40%), Positives = 232/386 (60%), Gaps = 24/386 (6%) Query: 19 YIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAG 78 ++ ++E G L+ALVA+ + F F P NLTNL Q + I I+++GM +VI+ Sbjct: 13 HVAGFLKENGTLVALVALALIFSLMDEAF-FTPRNLTNLARQTTIIGIISVGMTMVIIIN 71 Query: 79 HIDLSVGSIVAFVGAIAAILTVQWGMNPFLAA-LICLVIGGIIGAAQGYWIAYHRIPSFI 137 IDLSVGSIV + AI L +Q GMN +LA L L G +IG G+WIA++ IP FI Sbjct: 72 GIDLSVGSIVG-LSAIVVTLLMQQGMNVWLAIPLTLLTTGTLIGLWNGFWIAHYNIPPFI 130 Query: 138 VTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVA 197 +TL M + RGL L + G ++ ++ P +GG S IL +++T++ Sbjct: 131 ITLGMMTIARGLALTLSNGSSVP--------VTDPIFPQLGGSYIPPAVSGIL-IILTLS 181 Query: 198 LFYLAWRRRV-VNVKHGIDVEPFGFFIVQNLLISGAILFLG-----YQLSTYRGLPNVLI 251 LF A R V K+G V+ +Q L+ S I +G Y +TYRG+P + Sbjct: 182 LFIFALFREVGQRRKYGAVVK------LQPLIASTLITVVGLGLSFYVFTTYRGIPYPVA 235 Query: 252 VMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMI 311 V ++ + F+ T GRR+YA+GGNE+A +LSGI R+ + + + LA L+G++ Sbjct: 236 VFSIIAFIGIFMLNNTIFGRRIYAIGGNEEAARLSGIRIYRVKLIVYSIITTLAALSGVL 295 Query: 312 IATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGL 371 +A+RLN A+P G FELD I+A IGG S SGGVG I+G VIGAFI+G++NNGMS++G+ Sbjct: 296 LASRLNGASPNLGNMFELDAISAVIIGGTSFSGGVGTISGTVIGAFIIGILNNGMSLLGV 355 Query: 372 GIDFQQMVKGLVLLAAVFFDVYNKNK 397 +Q ++KGL+++ AV+FDV NK K Sbjct: 356 PTFYQLIIKGLIIILAVWFDVLNKKK 381 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: 521 Number of extensions: 41 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: 383 Length adjustment: 31 Effective length of query: 367 Effective length of database: 352 Effective search space: 129184 Effective search space used: 129184 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 24 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