GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfA in Cloacibacillus porcorum CL-84

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_066742194.1 BED41_RS01550 CoA transferase subunit A

Query= uniprot:P33752
         (218 letters)



>NCBI__GCF_001701045.1:WP_066742194.1
          Length = 229

 Score =  200 bits (508), Expect = 2e-56
 Identities = 101/199 (50%), Positives = 136/199 (68%)

Query: 16  KDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIA 75
           K G ++M+GGF   G P  L D L +     LT+ISNDT Y   G GKL++  + KK+IA
Sbjct: 20  KSGDSVMVGGFNYGGIPYTLTDALYDQGTDQLTLISNDTIYEFCGQGKLVAGGRCKKVIA 79

Query: 76  SYIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKKIS 135
           S++G N  TG+     ++E+EL PQGT VE+IRAGG+GLGG LT TG+GT++E+GK+ I 
Sbjct: 80  SHVGLNKTTGRLFHEGKMELELFPQGTYVEKIRAGGAGLGGFLTPTGVGTVVEEGKEVIE 139

Query: 136 INGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLVSC 195
           ING +Y+LELPLTADVAL++    D  GN  Y GT KNFNP MA AAK VI E + +V+ 
Sbjct: 140 INGKKYILELPLTADVALVRAFRADRMGNLTYTGTNKNFNPTMATAAKIVIAEVDEVVNV 199

Query: 196 EKLEKEKAMTPGVLINYIV 214
            +L  +  +T GVL++ +V
Sbjct: 200 GELNPDNIVTQGVLVDMLV 218


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: 174
Number of extensions: 8
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: 229
Length adjustment: 22
Effective length of query: 196
Effective length of database: 207
Effective search space:    40572
Effective search space used:    40572
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