GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Cupriavidus basilensis 4G11

Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate RR42_RS10005 RR42_RS10005 3-oxoadipate CoA-transferase

Query= reanno::psRCH2:GFF1045
         (231 letters)



>FitnessBrowser__Cup4G11:RR42_RS10005
          Length = 217

 Score =  201 bits (510), Expect = 1e-56
 Identities = 106/217 (48%), Positives = 143/217 (65%), Gaps = 3/217 (1%)

Query: 1   MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60
           ++K+Y +A  A+   V DG TIA+GGFG  G+P++LI AL + G KDLT +SNNAG    
Sbjct: 2   IDKLYATAREAVAD-VADGATIAIGGFGGAGMPDELIDALIEQGAKDLTVVSNNAGNGDA 60

Query: 61  GLGLLLETRQISKMVSSYVGENKE--FERQYLAGELALEFTPQGTLAEKLRAGGAGIPAF 118
           GL  LL+ R++ +++ S+  +     FE  Y AGE+ LE  PQGTLAE+LRA G GI  F
Sbjct: 61  GLAALLKARRVRRLMCSFPRQRDAYVFEALYRAGEIELEVIPQGTLAERLRAAGCGIGGF 120

Query: 119 YTKTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPL 178
           YT TG+GTL+A GKE R+     YV+E  +  D+AL+ A  AD+ GNL++ KTARNF P+
Sbjct: 121 YTPTGHGTLLAAGKEARRIGARDYVLEYPIHVDVALINAAAADRWGNLVYNKTARNFAPV 180

Query: 179 AAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIV 215
            AMA    +  V  + E GELDP+ I  PGI+V R+V
Sbjct: 181 MAMAATTTIAAVTRVCELGELDPEAIVTPGIFVKRVV 217


Lambda     K      H
   0.316    0.135    0.391 

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: 160
Number of extensions: 9
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 (21.6 bits)
S2: 46 (22.3 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