GapMind for catabolism of small carbon sources

 

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

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_058859371.1 AS188_RS14080 3-oxoacid CoA-transferase subunit A

Query= uniprot:P33752
         (218 letters)



>NCBI__GCF_001482365.1:WP_058859371.1
          Length = 230

 Score =  155 bits (391), Expect = 8e-43
 Identities = 80/202 (39%), Positives = 124/202 (61%), Gaps = 2/202 (0%)

Query: 16  KDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIA 75
           +DG T+MIGGF   G P +LID L++    +LT+++N+    + G+ KLI   +V+++I 
Sbjct: 16  EDGATVMIGGFGVAGQPVELIDALIDHGATDLTVVNNNAGNGDVGLAKLIQLGRVRRIIC 75

Query: 76  SYIGSNPDT--GKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKK 133
           S+   +      +K    E+E+E+ PQG L ERIRA G+G+G   T TG GT + +GK+ 
Sbjct: 76  SFPRQSDSWHFDEKYRAGEIELEVVPQGNLAERIRAAGAGIGAFFTPTGYGTPLAEGKEV 135

Query: 134 ISINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLV 193
             I+G  Y+LE P+ AD +L K  + D AGN  Y+ T +NF P MA AA T IV+   +V
Sbjct: 136 REIDGRHYVLEHPIRADYSLTKAHVADRAGNLVYRKTARNFGPIMAAAATTSIVQVAEIV 195

Query: 194 SCEKLEKEKAMTPGVLINYIVK 215
              +L+ E  +TPG+ ++ +V+
Sbjct: 196 ERGELDPEVVVTPGIYVDTVVR 217


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: 106
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: 230
Length adjustment: 22
Effective length of query: 196
Effective length of database: 208
Effective search space:    40768
Effective search space used:    40768
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