GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Burkholderia phytofirmans PsJN

Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate BPHYT_RS21415 BPHYT_RS21415 3-oxoadipate CoA-transferase subunit A

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



>FitnessBrowser__BFirm:BPHYT_RS21415
          Length = 235

 Score =  213 bits (542), Expect = 3e-60
 Identities = 106/220 (48%), Positives = 149/220 (67%), Gaps = 3/220 (1%)

Query: 1   MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60
           +NKI+ S   A+   V DG T+ +GGFG  G+P +LI AL + G ++LT ++NNAG    
Sbjct: 2   INKIFESLQSAVAD-VNDGATVMIGGFGTAGMPSELIDALIEQGARELTIVNNNAGNGDI 60

Query: 61  GLGLLLETRQISKMVSSYVGENKE--FERQYLAGELALEFTPQGTLAEKLRAGGAGIPAF 118
           GL  LL+ +++ K++ S+  ++    F+  Y AGEL LE  PQG LAE++RA GAGI  F
Sbjct: 61  GLAALLKAKRVRKIICSFPRQSDSYVFDALYRAGELELELVPQGNLAERIRAAGAGIGGF 120

Query: 119 YTKTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPL 178
           +T TGYGT +AEGKETR  +G  YV+E  L AD AL+KA++ D+ GNL +RKTARNF P+
Sbjct: 121 FTPTGYGTKLAEGKETRLIDGRHYVLEAPLHADFALIKAYRGDRWGNLTYRKTARNFGPI 180

Query: 179 AAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNP 218
            A A +  +V+V ++V  GELDP+ I  PGI+V R++  P
Sbjct: 181 MATAAKTAIVQVSQVVPLGELDPENIVTPGIFVQRVIEVP 220


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: 157
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: 235
Length adjustment: 23
Effective length of query: 208
Effective length of database: 212
Effective search space:    44096
Effective search space used:    44096
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