Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 186 bits (471), Expect = 1e-51 Identities = 122/377 (32%), Positives = 187/377 (49%), Gaps = 55/377 (14%) Query: 21 RSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHI 80 R I+++ L +LV ++V F T F NL + LQ + I + + VI+ G I Sbjct: 21 RDLIQKFAALGSLVVLIVAFSL-TSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGI 79 Query: 81 DLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTL 140 DLSVGS++A G AA+L V+ G+ +A L +++G G G + +P FI TL Sbjct: 80 DLSVGSVLALAGVAAALL-VKAGVPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIATL 138 Query: 141 AGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFY 200 MLV RGL L + G + + F + G L I I Sbjct: 139 GMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISHI-------------------- 178 Query: 201 LAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALY 260 G D G+ + + G+P +++M+VL A Sbjct: 179 ------------GAD---------------------GFPDTVFPGIPYPVVIMVVLFAAV 205 Query: 261 SFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSAT 320 S + RT++GR +YA+G N +A +LSG+N + + T+V G+LAG G ++ +RL +A Sbjct: 206 SILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQ 265 Query: 321 PKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVK 380 P GV +ELD IA+ IGG S GGVG I+G IGAF++GV+ NG+++ G+ QQ++ Sbjct: 266 PNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIII 325 Query: 381 GLVLLAAVFFDVYNKNK 397 G+V+L V+ D K Sbjct: 326 GVVILGTVWIDQLRNRK 342 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: 453 Number of extensions: 33 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: 343 Length adjustment: 30 Effective length of query: 368 Effective length of database: 313 Effective search space: 115184 Effective search space used: 115184 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