Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_004116864.1 RHSP_RS11850 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000359745.1:WP_004116864.1 Length = 402 Score = 566 bits (1458), Expect = e-166 Identities = 281/402 (69%), Positives = 336/402 (83%), Gaps = 4/402 (0%) Query: 1 MSSANTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQ 60 MSSAN E S+V+S+G +IR+NIREYGMLIALV IM+ FQ+ T G+LFRP NLTN++LQ Sbjct: 1 MSSANPATESSHVVSIGDHIRNNIREYGMLIALVVIMLLFQYLTNGVLFRPQNLTNIVLQ 60 Query: 61 NSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGII 120 NSFIVIMALGMLLVIVAGHIDLSVGS+V FVGA+A +L VQ MN A +ICL++G + Sbjct: 61 NSFIVIMALGMLLVIVAGHIDLSVGSVVGFVGAVAGVLVVQMHMNLAAATVICLLMGAAV 120 Query: 121 GAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLG----GKNIGPFPTDFQVISTGFLPD 176 GA GY+IAYHRIPSFIVTL+GMLVFRGLT ++ G +IGPFP FQV++TGF+PD Sbjct: 121 GAWHGYFIAYHRIPSFIVTLSGMLVFRGLTYTIINTTGNGSSIGPFPPAFQVVATGFIPD 180 Query: 177 IGGIEGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFL 236 + G+ +TS+ LT+ I + +F L+WRRR VN KHGIDVEPF FF+ QNL+++ A +F+ Sbjct: 181 FVDMGGVRSTSIFLTIAIPIVMFLLSWRRRTVNEKHGIDVEPFSFFLGQNLVVAAATIFI 240 Query: 237 GYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFL 296 GYQ+S+YRGLPNVLI+ML LIALYSF T+RTTIGRR+YAMGGNEKATKLSGI+T RL+F Sbjct: 241 GYQISSYRGLPNVLILMLALIALYSFATQRTTIGRRIYAMGGNEKATKLSGIDTRRLTFY 300 Query: 297 TFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGA 356 TF+NMG+LA +AG+IIATRLNSAT K G G ELDVIAACFIGGASASGGVGK+TGAVIGA Sbjct: 301 TFINMGILASIAGIIIATRLNSATAKGGDGLELDVIAACFIGGASASGGVGKVTGAVIGA 360 Query: 357 FIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNKG 398 IMGV+N GMSI+G D Q+M+KG VLLAAVF DVYNKNKG Sbjct: 361 LIMGVLNQGMSILGYQTDSQKMIKGAVLLAAVFIDVYNKNKG 402 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: 712 Number of extensions: 37 Number of successful extensions: 2 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: 402 Length adjustment: 31 Effective length of query: 367 Effective length of database: 371 Effective search space: 136157 Effective search space used: 136157 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