GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfA in Shewanella halifaxensis HAW-EB4

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_041416478.1 SHAL_RS15280 3-oxoacid CoA-transferase subunit A

Query= uniprot:P33752
         (218 letters)



>NCBI__GCF_000019185.1:WP_041416478.1
          Length = 235

 Score =  155 bits (392), Expect = 6e-43
 Identities = 90/206 (43%), Positives = 124/206 (60%), Gaps = 4/206 (1%)

Query: 17  DGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIAS 76
           DG T+MIGGF   G+P +LI  L++   KNLT+I+N+T   + G+  LI N QV K+I S
Sbjct: 17  DGATVMIGGFGESGSPIELIHALIDQGAKNLTVINNNTGSGHVGLAALIENGQVGKMICS 76

Query: 77  YIGS-NPDTGKKLFN-NELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKKI 134
           +  + N      L+   ++E+EL PQGTL ERIRAGG+G+    T T +GT +  GKK  
Sbjct: 77  FPRTANSTVFPDLYRAGKIELELVPQGTLAERIRAGGAGIPAFYTATSVGTPLADGKKHE 136

Query: 135 SINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLVS 194
             +G E++ EL L AD ALIK    D  GN  Y  T +NF P MAMAA   IV+ +  V 
Sbjct: 137 IFDGREHVQELGLKADFALIKSLQADRLGNLRYNKTARNFAPIMAMAANYTIVQTQEYVE 196

Query: 195 CEKLEKEKAMTPGVLINYI--VKEPA 218
              ++ E  +TPG+ ++ I  VK+PA
Sbjct: 197 AGAIDPEIVVTPGIFVDRIVTVKQPA 222


Lambda     K      H
   0.315    0.136    0.380 

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: 143
Number of extensions: 8
Number of successful extensions: 2
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: 218
Length of database: 235
Length adjustment: 22
Effective length of query: 196
Effective length of database: 213
Effective search space:    41748
Effective search space used:    41748
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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