GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcrA in Escherichia coli BW25113

Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate 18358 b4334 putative enzyme (VIMSS)

Query= BRENDA::Q8VUG0
         (301 letters)



>FitnessBrowser__Keio:18358
          Length = 255

 Score =  160 bits (404), Expect = 4e-44
 Identities = 94/251 (37%), Positives = 139/251 (55%), Gaps = 8/251 (3%)

Query: 41  GIDVGSVSSQAVLVCDGELYGYNSMRTGNNSPDSAKNALQGIMDKIGMKLEDINYVVGTG 100
           GID GS +++ +L+ DG +    + R    +P     A+    + +   LE   ++  TG
Sbjct: 6   GIDSGSTATKGILLADGVI----TRRFLVPTPFRPATAITEAWETLREGLETTPFLTLTG 61

Query: 101 YGRVNVPFAHKAITEIACHARGANYMGGNKVRTILDMGGQDCKAIHCDDKGKVTNFLMND 160
           YGR  V FA K +TEI+CH  GA ++     R ++D+GGQD K I  DD G + +FLMND
Sbjct: 62  YGRQLVDFADKQVTEISCHGLGARFLAP-ATRAVIDIGGQDSKVIQLDDDGNLCDFLMND 120

Query: 161 KCAAGTGRGMEVISDLMQIPIAELGPRSFDVETEPEAVSSICVVFAKSEALGLLKAGYTK 220
           KCAAGTGR +EVIS  +   + +L   S      P A++S+C VFA+SEA+ L  AG   
Sbjct: 121 KCAAGTGRFLEVISRTLGTSVEQLD--SITENVTPHAITSMCTVFAESEAISLRSAGVAP 178

Query: 221 NMVIAAYCQAMAERVVSLLERIGVEEGFFITGGIAKNPGVVKRIERLLGIKQLETKIDSQ 280
             ++A    AMA R  + + R+  E     TGG++      + +E  L +  + T  D+Q
Sbjct: 179 EAILAGVINAMARRSANFIARLSCEAPILFTGGVSHCQKFARMLESHLRM-PVNTHPDAQ 237

Query: 281 IAGALGAALFG 291
            AGA+GAA+ G
Sbjct: 238 FAGAIGAAVIG 248


Lambda     K      H
   0.318    0.134    0.395 

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: 195
Number of extensions: 18
Number of successful extensions: 5
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: 301
Length of database: 255
Length adjustment: 25
Effective length of query: 276
Effective length of database: 230
Effective search space:    63480
Effective search space used:    63480
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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