GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Synechococcus elongatus PCC 7942

Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate Synpcc7942_1335 Synpcc7942_1335 probable branched-chain amino acid aminotransferase

Query= CharProtDB::CH_012531
         (298 letters)



>FitnessBrowser__SynE:Synpcc7942_1335
          Length = 264

 Score =  116 bits (290), Expect = 6e-31
 Identities = 66/215 (30%), Positives = 118/215 (54%), Gaps = 7/215 (3%)

Query: 7   FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66
           + NG+++P ++  ++V D G+  GDG+FE + V+ G V    +H  RL  SA+ + + +P
Sbjct: 4   YCNGQWIPTEDLTIAVTDRGFSLGDGLFETLLVWQGKVRLAEQHWQRLTSSAQQLRIPLP 63

Query: 67  YSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQE 126
            + +   +++  T+  N+L  G +R+ ++RG G  GL      +P +V++    SL   +
Sbjct: 64  PNAN--IDLLQATVDHNELETGALRVTLTRGCGQRGLQSPEPLQPLLVIVP---SLSQPQ 118

Query: 127 YYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAEG 186
           +  + + ++T  T R  P+ +  + K+L+YL N+L R EA+     EAL+L     ++E 
Sbjct: 119 F--QPLRLITAQTVRRCPESILSRFKTLSYLENVLARQEAEQRQADEALLLTPSDRLSEA 176

Query: 187 SGDNVFIVKGNKLITPPSSAGALEGITRNAILEIG 221
           +  N+F    +   TPP S GAL GI R  +L  G
Sbjct: 177 AAANIFFRLNDDWWTPPLSDGALPGIVRQRLLATG 211


Lambda     K      H
   0.317    0.138    0.390 

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: 152
Number of extensions: 6
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: 298
Length of database: 264
Length adjustment: 26
Effective length of query: 272
Effective length of database: 238
Effective search space:    64736
Effective search space used:    64736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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