GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfA in Paraburkholderia bryophila 376MFSha3.1

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate H281DRAFT_01597 H281DRAFT_01597 3-oxoadipate CoA-transferase alpha subunit

Query= uniprot:P33752
         (218 letters)



>FitnessBrowser__Burk376:H281DRAFT_01597
          Length = 235

 Score =  160 bits (405), Expect = 2e-44
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 11/218 (5%)

Query: 8   FENLRSFFKD---GMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKL 64
           FE+L+S   D   G T+MIGGF   G P++LID L+    + LTI++N+    + G+  L
Sbjct: 6   FESLQSAVADVHDGATVMIGGFGTAGMPSELIDALIEQGARELTIVNNNAGNGDIGLAAL 65

Query: 65  ISNNQVKKLIASYIGSNPDTGKKLFN-----NELEVELSPQGTLVERIRAGGSGLGGVLT 119
           +   +V+K+I S+      T   +F+      E+E+EL PQG L ERIRA G+G+GG  T
Sbjct: 66  LKAKRVRKIICSF---PRQTDSYVFDALYRAGEIELELVPQGNLAERIRAAGAGIGGFFT 122

Query: 120 KTGLGTLIEKGKKKISINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMA 179
            TG GT + +GK+   I+G  Y+LE PL AD ALIK    D  GN  Y+ T +NF P MA
Sbjct: 123 PTGYGTKLAEGKETRLIDGRHYVLESPLHADFALIKAYKGDRWGNLVYRKTARNFGPIMA 182

Query: 180 MAAKTVIVEAENLVSCEKLEKEKAMTPGVLINYIVKEP 217
            AAKT IV+   +V    L+ E  +TPG+ +  +++ P
Sbjct: 183 SAAKTAIVQVSEVVPLGALDPENIVTPGIFVQRVIEVP 220


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: 124
Number of extensions: 3
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 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