GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfA in Acidovorax sp. GW101-3H11

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate Ac3H11_132 Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5)

Query= uniprot:P33752
         (218 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_132
          Length = 235

 Score =  172 bits (435), Expect = 6e-48
 Identities = 84/206 (40%), Positives = 126/206 (61%)

Query: 9   ENLRSFFKDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNN 68
           E L+    DG  + +GGF  CG P  LID L +   KNLT+ISN+      G+GKL+   
Sbjct: 10  EALKGVVADGQLMAVGGFGLCGIPEALIDALRDSGAKNLTVISNNAGVDGFGLGKLLETR 69

Query: 69  QVKKLIASYIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIE 128
           Q+KK+I+SY+G N +  ++    ELE+E +PQGTL E++RAGG+G+    TKTG+GT++ 
Sbjct: 70  QIKKMISSYVGENKEFERQYLAGELELEFTPQGTLAEKLRAGGAGIPAFFTKTGVGTIVA 129

Query: 129 KGKKKISINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVE 188
            GK+    +G  Y++E  L  +V+L+K  + D++GN  +  T +NFNP  A A K  IVE
Sbjct: 130 DGKELREFDGETYVMERSLVPEVSLVKADVADKSGNLRFNLTARNFNPAAATAGKVCIVE 189

Query: 189 AENLVSCEKLEKEKAMTPGVLINYIV 214
            E +V   +L  +    PG+ ++ IV
Sbjct: 190 VEKIVEVGELAPDDIHLPGIYVHRIV 215


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: 162
Number of extensions: 11
Number of successful extensions: 1
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