GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcrA in Klebsiella michiganensis M5al

Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate BWI76_RS03740 BWI76_RS03740 hypothetical protein

Query= BRENDA::Q8VUG0
         (301 letters)



>FitnessBrowser__Koxy:BWI76_RS03740
          Length = 255

 Score =  171 bits (432), Expect = 2e-47
 Identities = 97/254 (38%), Positives = 147/254 (57%), Gaps = 8/254 (3%)

Query: 38  ITCGIDVGSVSSQAVLVCDGELYGYNSMRTGNNSPDSAKNALQGIMDKIGMKLEDINYVV 97
           +T GID GS +++ +L+ DG +      R    +P    +A+    + +   L +  ++ 
Sbjct: 3   VTVGIDSGSTATKGILLADGVI----QRRFLCPTPFRPADAIVEAWETLRAGLSERPFLT 58

Query: 98  GTGYGRVNVPFAHKAITEIACHARGANYMGGNKVRTILDMGGQDCKAIHCDDKGKVTNFL 157
            TGYGR  V FA K +TEI+CH  GA  +   + RT++D+GGQD K I  DD G +T+FL
Sbjct: 59  LTGYGRQLVDFADKQVTEISCHGLGARLLAP-QTRTVIDIGGQDSKVIQLDDAGNLTDFL 117

Query: 158 MNDKCAAGTGRGMEVISDLMQIPIAELGPRSFDVETEPEAVSSICVVFAKSEALGLLKAG 217
           MNDKCAAGTGR +EVIS  +   + +L   S     EP A++S+C VFA+SE + L  AG
Sbjct: 118 MNDKCAAGTGRFLEVISRTLGASVDQLD--SITEGVEPHAITSMCTVFAESEVISLRSAG 175

Query: 218 YTKNMVIAAYCQAMAERVVSLLERIGVEEGFFITGGIAKNPGVVKRIERLLGIKQLETKI 277
                ++A    AMA R  + + R+  +     TGG+++     +R+E  +G+  ++T  
Sbjct: 176 VPPEAILAGVINAMARRSANFIGRLSAQGPLLFTGGVSRCAAFARRLEEHVGM-AVQTHP 234

Query: 278 DSQIAGALGAALFG 291
           D+Q AGA+GAAL G
Sbjct: 235 DAQFAGAIGAALIG 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: 187
Number of extensions: 12
Number of successful extensions: 6
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.

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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