GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tyrP in Escherichia coli BW25113

Align Tyrosine permease (characterized)
to candidate 17769 b3709 tryptophan transporter of low affinity (NCBI)

Query= TCDB::P0AAD4
         (403 letters)



>lcl|FitnessBrowser__Keio:17769 b3709 tryptophan transporter of low
           affinity (NCBI)
          Length = 415

 Score =  217 bits (553), Expect = 4e-61
 Identities = 133/408 (32%), Positives = 211/408 (51%), Gaps = 6/408 (1%)

Query: 2   KNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHV 61
           K+     V ++AGT IG GM A+P+  AG  F     +LI  W  M ++ LLLLE   + 
Sbjct: 8   KHSAFWGVMVIAGTVIGGGMFALPVDLAGAWFFWGAFILIIAWFSMLHSGLLLLEANLNY 67

Query: 62  PADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSAT 121
           P  +   T+ K  +G     ++G ++ F++Y LT AYIS  G +++ +IS   G   +  
Sbjct: 68  PVGSSFNTITKDLIGNTWNIISGITVAFVLYILTYAYISANGAIISETISMNLGYHANPR 127

Query: 122 -AGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQ 180
             G+    FVA  +     +   + + FL    I F++V         + +         
Sbjct: 128 IVGICTAIFVASVLWLSSLAASRITSLFLGLKIISFVIVFGSFFFQVDYSILRDATSSTA 187

Query: 181 GLA-----LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVA 235
           G +       A+PV   SFGFHG++PS++        KL    + GS + LV Y+FW   
Sbjct: 188 GTSYFPYIFMALPVCLASFGFHGNIPSLIICYGKRKDKLIKSVVFGSLLALVIYLFWLYC 247

Query: 236 TLGSIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLF 295
           T+G+I   +F  ++++   ++ L+++         +E  + +F++LA+A+SF GV LGLF
Sbjct: 248 TMGNIPRESFKAIISSGGNVDSLVKSFLGTKQHGIIEFCLLVFSNLAVASSFFGVTLGLF 307

Query: 296 DYLADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLL 355
           DYLADLF+  N+ GGR +T  +TFLPP    L +P GF+  +G AG+   + A+IIP++L
Sbjct: 308 DYLADLFKIDNSHGGRFKTVLLTFLPPALLYLIFPNGFIYGIGGAGLCATIWAVIIPAVL 367

Query: 356 TWQSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403
             ++RK  P   + V GG     +V L GI VI   F     +LP+ G
Sbjct: 368 AIKARKKFPNQMFTVWGGNLIPAIVILFGITVILCWFGNVFNVLPKFG 415


Lambda     K      H
   0.329    0.143    0.432 

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: 436
Number of extensions: 21
Number of successful extensions: 1
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: 403
Length of database: 415
Length adjustment: 31
Effective length of query: 372
Effective length of database: 384
Effective search space:   142848
Effective search space used:   142848
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 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