GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfB in Kocuria flava HO-9041

Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_058859370.1 AS188_RS14075 3-oxoacid CoA-transferase subunit B

Query= uniprot:P23673
         (221 letters)



>NCBI__GCF_001482365.1:WP_058859370.1
          Length = 230

 Score =  147 bits (372), Expect = 1e-40
 Identities = 81/206 (39%), Positives = 122/206 (59%), Gaps = 3/206 (1%)

Query: 7   LAKEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEA 66
           L  E +A+ VA ++  G  VNLG+G PT+VA+++     +T  +ENG++GMG     +E 
Sbjct: 21  LGPEELARVVAADIPAGSYVNLGIGQPTLVANHLTAEHDVTLHTENGMLGMGREAHGDEV 80

Query: 67  DKDVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIV-PGK 125
           D D++NAG       P  ++F  + SF+++RGGH+D  VLGA QVD +GN+ANW     +
Sbjct: 81  DPDLINAGKIPVVETPGCSYFHHADSFAMMRGGHLDCCVLGAFQVDVEGNLANWHTGKPE 140

Query: 126 MLSGMGGAMDLVNGAKKVIIAMR-HTNKGQPKILKKCTLPLTAKSQANLIVTELGVIEVI 184
            +  +GGAMDL  GAK+  + M   T KGQ K+++KCT+PLT     + + T+  V  V 
Sbjct: 141 AIPAVGGAMDLATGAKQTFVMMTLLTKKGQSKLVEKCTMPLTGVGCVSRVYTDRAVFLVD 200

Query: 185 NDGLLLTEINKNTTIDEIRSLTAADL 210
            DGL + E    T  +E++ L    L
Sbjct: 201 EDGLSVRE-TFGTDFEELQELVGLPL 225


Lambda     K      H
   0.316    0.136    0.376 

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: 129
Number of extensions: 6
Number of successful extensions: 3
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: 221
Length of database: 230
Length adjustment: 22
Effective length of query: 199
Effective length of database: 208
Effective search space:    41392
Effective search space used:    41392
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 (21.6 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