GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Methylocapsa aurea KYG

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_036261633.1 DL86_RS11555 3-oxoacid CoA-transferase subunit A

Query= CharProtDB::CH_021928
         (231 letters)



>NCBI__GCF_000746085.1:WP_036261633.1
          Length = 217

 Score =  177 bits (449), Expect = 1e-49
 Identities = 92/210 (43%), Positives = 134/210 (63%), Gaps = 2/210 (0%)

Query: 8   SIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGLAALLM 67
           S A A   I DG+++M GGF   G P+ +ID L+A GAR LTII N+     +G+  L+ 
Sbjct: 6   SAADAAALIPDGASVMFGGFMGVGSPNRIIDALVARGARGLTIIGNDTAFPGVGVGKLID 65

Query: 68  AGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFFSPTGYG 127
           AG V +   S      + V  +   AG+I ++++PQG LAERI A G+G+G   +PTG G
Sbjct: 66  AGCVAEARVS--HIGTNPVTQKKMIAGEISVDLIPQGTLAERIRAGGNGLGGILTPTGVG 123

Query: 128 TLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMAMAAKT 187
           T++ +GK   E+DGR ++LE+P+ ADFAL++AH+ D   NLTYR  A NF P+MA AA  
Sbjct: 124 TVVEKGKRVIEVDGRDFLLELPIRADFALLRAHESDYNCNLTYRLTATNFNPLMAFAAVC 183

Query: 188 AIAQVDQVVELGELDPEHIITPGIFVQRVV 217
            IA+ D++V +G + P+ + TPGI V  ++
Sbjct: 184 VIAEPDEIVPVGVIPPDAVRTPGILVHHLI 213


Lambda     K      H
   0.318    0.135    0.381 

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: 138
Number of extensions: 5
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: 231
Length of database: 217
Length adjustment: 22
Effective length of query: 209
Effective length of database: 195
Effective search space:    40755
Effective search space used:    40755
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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