Alignments for a candidate for prpE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Escherichia coli BW25113

Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate 15820 b1701 short chain acyl-CoA synthetase, anaerobic (RefSeq)

Query= SwissProt::M4IS88
         (568 letters)



>FitnessBrowser__Keio:15820
          Length = 548

 Score =  132 bits (333), Expect = 3e-35
 Identities = 106/356 (29%), Positives = 158/356 (44%), Gaps = 22/356 (6%)

Query: 203 YTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCNGWCYTWGMAAFC 262
           +TSGT   PKGV+L+H        +      +    +++   P+ H  G+ +        
Sbjct: 195 FTSGTEGLPKGVMLTHNNILASERAYCARLNLTWQDVFMMPAPLGHATGFLHGVTAPFLI 254

Query: 263 GTNICLRQV-TAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHLVHVMTAGA 321
           G    L  + T     + + +   T    A   +  ++N   E+    L  L   +  G 
Sbjct: 255 GARSVLLDIFTPDACLALLEQQRCTCMLGATPFVYDLLNVL-EKQPADLSALRFFLCGGT 313

Query: 322 APPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNARQGVRYIA 381
             P  V     ++G K+   YG +E+   + +    P          +R     G     
Sbjct: 314 TIPKKVARECQQRGIKLLSVYGSTESSPHAVVNLDDP---------LSRFMHTDGYAAAG 364

Query: 382 LEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESF-ADGWFHSGDLAV 440
           +E   V D +   P   +G    E   RG  V  GY   P+    +   +GW++SGDL  
Sbjct: 365 VEIKVVDDARKTLPPGCEG----EEASRGPNVFMGYFDEPELTARALDEEGWYYSGDLCR 420

Query: 441 KHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWGESPCAFV 500
               GYI+I  R KDII+ GGENISS EVE+ L  HP + +  VVA  DER GE  CA+V
Sbjct: 421 MDEAGYIKITGRKKDIIVRGGENISSREVEDILLQHPKIHDACVVAMSDERLGERSCAYV 480

Query: 501 TLK-PNIDKSNEQVLAEDIIKFCKSKMPAYWVPKS-VVFGPLPKTATGKIQKHVLR 554
            LK P+   S E+V+A     F + ++  Y  P+  VV   LP+T +GKIQK +LR
Sbjct: 481 VLKAPHHSLSLEEVVA----FFSRKRVAKYKYPEHIVVIEKLPRTTSGKIQKFLLR 532


Lambda     K      H
   0.318    0.134    0.415 

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: 713
Number of extensions: 30
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: 568
Length of database: 548
Length adjustment: 36
Effective length of query: 532
Effective length of database: 512
Effective search space:   272384
Effective search space used:   272384
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis