GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natG in Escherichia coli BW25113

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)

Query= TCDB::Q8YPM8
         (308 letters)



>lcl|FitnessBrowser__Keio:1936976 b3269 predicted amino-acid
           transporter subunit (NCBI)
          Length = 393

 Score =  159 bits (402), Expect = 1e-43
 Identities = 101/226 (44%), Positives = 131/226 (57%), Gaps = 22/226 (9%)

Query: 91  FVGIILTTIVGIL--AGIARLSDNWLVRNISL-----VYVEIFRNTPLLLQLLFWYFAVF 143
           F+  IL  ++ I+   G+ R +  + ++   L     +   +    PLL Q LF   A+ 
Sbjct: 182 FIAFILAVVMAIVLSVGLFRFNKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGA-ALH 240

Query: 144 LGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSV 203
             +P        GG + +             PE +AL L L  YT AFIAEI+R GIQ+V
Sbjct: 241 WDVPALRGFNFRGGMVLI-------------PELAALTLALSVYTSAFIAEIIRAGIQAV 287

Query: 204 SKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPD-IYF 262
             GQ EA RSLGL   + +R VI PQALRVIIPPLTSQYLN+ KNSSLA AIGYPD +  
Sbjct: 288 PYGQHEAARSLGLPNPVTLRQVIIPQALRVIIPPLTSQYLNIVKNSSLAAAIGYPDMVSL 347

Query: 263 VASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQIKER 308
            A T  NQTG+A+E + + M  YL +SLTISL+MN +NR + I ER
Sbjct: 348 FAGTVLNQTGQAIETIAMTMSVYLIISLTISLLMNIYNRRIAIVER 393



 Score =  126 bits (316), Expect = 9e-34
 Identities = 67/166 (40%), Positives = 94/166 (56%)

Query: 20  QLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLAL 79
           Q++A+     +V  L  N   NL   GI  GF FL + A F I + LI Y+  DTY    
Sbjct: 25  QILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDTYGRVF 84

Query: 80  WVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWY 139
            VGL+N+L ++ + I+  +++G   G+ARLSDNWL+R +S +Y+EIFRN P LLQ+ FWY
Sbjct: 85  IVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQIFFWY 144

Query: 140 FAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLI 185
           FAV   LP     +S      LS  GL +P       F A +L ++
Sbjct: 145 FAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVV 190


Lambda     K      H
   0.328    0.143    0.430 

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: 338
Number of extensions: 16
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: 308
Length of database: 393
Length adjustment: 29
Effective length of query: 279
Effective length of database: 364
Effective search space:   101556
Effective search space used:   101556
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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