GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Escherichia coli BW25113

Align Fructose import permease protein FruG (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__Keio:17810
          Length = 321

 Score =  169 bits (427), Expect = 1e-46
 Identities = 103/328 (31%), Positives = 180/328 (54%), Gaps = 12/328 (3%)

Query: 1   MTTATANKVKAPKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHA 60
           MTT T +  +   K + ++++      +++  +++I +   L   +  +  + ++    +
Sbjct: 1   MTTQTVSGRRYFTKAWLMEQK------SLIALLVLIAIVSTLSPNFFTINNLFNILQQTS 54

Query: 61  YLIILAVAMTLPILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLL 120
              I+AV MTL ILT GIDLSVG+++A+T  V   +    V A + +   L +GA  G +
Sbjct: 55  VNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAV 114

Query: 121 AGTLIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISN 180
            G ++ +  +Q FIATL  M L RG+  + +  S   P    F+  +++        I  
Sbjct: 115 TGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGS---PVNTGFTENADLFGWFG---IGR 168

Query: 181 DLSFNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSA 240
            L     V I  +V +  +  LHHTR GR IYA+GG+ ++  L G+ V + + I+Y    
Sbjct: 169 PLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCG 228

Query: 241 TLAALASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSIL 300
            LA+LA I+  A + SA+ T G G+ELDA+A+VV+GGT + GG G ++G+++G+L+   L
Sbjct: 229 LLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFL 288

Query: 301 DPLTSDFGVPAEWTTIVIGLMILVFVVL 328
           +   +  GV + +  IV  ++IL+ V++
Sbjct: 289 NNGLNLLGVSSYYQMIVKAVVILLAVLV 316


Lambda     K      H
   0.327    0.142    0.400 

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: 264
Number of extensions: 13
Number of successful extensions: 3
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: 340
Length of database: 321
Length adjustment: 28
Effective length of query: 312
Effective length of database: 293
Effective search space:    91416
Effective search space used:    91416
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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