Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 169 bits (428), Expect = 1e-46 Identities = 117/373 (31%), Positives = 182/373 (48%), Gaps = 67/373 (17%) Query: 19 YIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAG 78 + ++ + E LIAL+ ++ + F NL N++ Q S IMA+GM LVI+ Sbjct: 12 FTKAWLMEQKSLIALLVLIAIVSTLSPNF-FTINNLFNILQQTSVNAIMAVGMTLVILTS 70 Query: 79 HIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIV 138 IDLSVGS++A GA+AA + V +N +A L +G IGA Sbjct: 71 GIDLSVGSLLALTGAVAASI-VGIEVNALVAVAAALALGAAIGAV--------------- 114 Query: 139 TLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVAL 198 TG + G ++ T +++ +L V + Sbjct: 115 --------------------------------TGVIVAKGRVQAFIATLVMMLLLRGVTM 142 Query: 199 FYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIA 258 Y VN + + FG+F + L G+P + +M ++ Sbjct: 143 VYT--NGSPVNTGFTENADLFGWFGIGRPL----------------GVPTPVWIMGIVFL 184 Query: 259 LYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNS 318 ++ T +GR +YA+GGNE AT+LSGIN ++ + + G+LA LAG+I RL+S Sbjct: 185 AAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSS 244 Query: 319 ATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQM 378 A P AG G+ELD IAA +GG S +GG G+I G +IGA I+G +NNG++++G+ +Q + Sbjct: 245 AQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMI 304 Query: 379 VKGLVLLAAVFFD 391 VK +V+L AV D Sbjct: 305 VKAVVILLAVLVD 317 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: 428 Number of extensions: 24 Number of successful extensions: 4 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: 321 Length adjustment: 29 Effective length of query: 369 Effective length of database: 292 Effective search space: 107748 Effective search space used: 107748 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