GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Escherichia coli BW25113

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate 16330 b2222 acetyl-CoA:acetoacetyl-CoA transferase, beta subunit (NCBI)

Query= BRENDA::P0A102
         (213 letters)



>FitnessBrowser__Keio:16330
          Length = 216

 Score =  152 bits (385), Expect = 3e-42
 Identities = 83/193 (43%), Positives = 117/193 (60%), Gaps = 5/193 (2%)

Query: 8   SRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGDK-EVFLHSENGLLGMGPSPAPGEED 66
           ++  +A+RVA ++++G  VNLGIG PT+VANYL +   + L SENG LG+GP        
Sbjct: 3   AKQRIARRVAQELRDGDIVNLGIGLPTMVANYLPEGIHITLQSENGFLGLGPVTTA---H 59

Query: 67  DDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGS 126
            DL+NAG Q   +L G A F  A SF+++RGGH+D  VLG  QV  + +LANW    +  
Sbjct: 60  PDLVNAGGQPCGVLPGAAMFDSAMSFALIRGGHIDACVLGGLQVDEEANLANWVVPGK-M 118

Query: 127 IPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVTP 186
           +P +GGAMDL TG+R+V + M+H  K G +K++  CT PLT    V  + T+LAV     
Sbjct: 119 VPGMGGAMDLVTGSRKVIIAMEHCAKDGSAKILRRCTMPLTAQHAVHMLVTELAVFRFID 178

Query: 187 EGLKVVEICADID 199
             + + EI    D
Sbjct: 179 GKMWLTEIADGCD 191


Lambda     K      H
   0.318    0.137    0.399 

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: 153
Number of extensions: 7
Number of successful extensions: 4
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: 213
Length of database: 216
Length adjustment: 22
Effective length of query: 191
Effective length of database: 194
Effective search space:    37054
Effective search space used:    37054
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: 45 (21.9 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