GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Escherichia coli BW25113

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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