GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfB in Cupriavidus basilensis 4G11

Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate RR42_RS35920 RR42_RS35920 3-oxoadipate CoA-transferase

Query= uniprot:P23673
         (221 letters)



>FitnessBrowser__Cup4G11:RR42_RS35920
          Length = 215

 Score =  177 bits (449), Expect = 1e-49
 Identities = 89/209 (42%), Positives = 138/209 (66%), Gaps = 4/209 (1%)

Query: 5   KNLAKEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKIN 64
           + L ++ +A RVA+++ +G +VNLG+GLPT+V +++P + +I   SENG++GMG +P   
Sbjct: 2   QRLTRDQMAARVAKDIPDGAVVNLGIGLPTLVGNHLPADREILLHSENGLLGMGKAPPAG 61

Query: 65  EADKDVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWI--V 122
           E D D++NAG    T+ P G++F  + SF+++RGGH+D  VLGA QV  KG++ANW    
Sbjct: 62  EEDGDLINAGKQPVTIKPGGSYFHHADSFAMMRGGHLDFCVLGAFQVSVKGDLANWHTGA 121

Query: 123 PGKMLSGMGGAMDLVNGAKKVIIAMRH-TNKGQPKILKKCTLPLTAKSQANLIVTELGVI 181
           PG  +  +GGAMDL  GAK+V + M H T +G+ KI+ +CT PLT  +    I T+L  I
Sbjct: 122 PG-AIPAVGGAMDLAIGAKEVFVMMEHQTKQGESKIVAECTYPLTGMTCVTRIYTDLATI 180

Query: 182 EVINDGLLLTEINKNTTIDEIRSLTAADL 210
           +V  DGL+  ++ +  + DE++ LT   L
Sbjct: 181 DVTPDGLVARDLVEGLSFDELQRLTGVPL 209


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: 167
Number of extensions: 4
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: 215
Length adjustment: 22
Effective length of query: 199
Effective length of database: 193
Effective search space:    38407
Effective search space used:    38407
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: 45 (21.9 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