GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Escherichia coli BW25113

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Keio:17272
          Length = 241

 Score =  119 bits (299), Expect = 4e-32
 Identities = 74/224 (33%), Positives = 114/224 (50%), Gaps = 3/224 (1%)

Query: 21  YGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPT 80
           Y   R +  V + VN GEIV L+G NGAGK+T    + G      G+++ +  DI+ +P 
Sbjct: 13  YKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIIDDDDISLLPL 72

Query: 81  HEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFPRLKERHAQ- 139
           H  AR  I   P+   IF R++V +NL     + +     +  ++   L       H + 
Sbjct: 73  HARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRANELMEEFHIEHLRD 132

Query: 140 -RGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVF 198
             G +LSGGE++ + I RAL A PK +LLDEP  G+ P+ V  I   I  L ++ GL V 
Sbjct: 133 SMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKRIIEHLRDS-GLGVL 191

Query: 199 LVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           + + N    L +  RAY++  G +   G+  E+L +  V+  YL
Sbjct: 192 ITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYL 235


Lambda     K      H
   0.320    0.137    0.387 

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: 142
Number of extensions: 5
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: 247
Length of database: 241
Length adjustment: 24
Effective length of query: 223
Effective length of database: 217
Effective search space:    48391
Effective search space used:    48391
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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