GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxA in Acidovorax sp. GW101-3H11

Align Benzoyl-CoA oxygenase component A; Benzoyl-CoA 2,3-dioxygenase subunit A; Benzoyl-CoA dioxygenase reductase component; EC 1.14.13.208 (characterized)
to candidate Ac3H11_3083 Benzoyl-CoA oxygenase component A

Query= SwissProt::Q9AIX6
         (414 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3083
          Length = 422

 Score =  508 bits (1308), Expect = e-148
 Identities = 245/419 (58%), Positives = 299/419 (71%), Gaps = 9/419 (2%)

Query: 5   AEHANLARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPCPTGA 64
           A  A + +QHLIDPEICIRCNTCE  CPV AITHD  NYVV+ + CNGC+ACISPCPTG+
Sbjct: 4   AVEAAVIKQHLIDPEICIRCNTCEATCPVGAITHDDNNYVVRADVCNGCMACISPCPTGS 63

Query: 65  IDSWRNVDKATPHSLADQYSWDYLPDTTELDQF--EATVMGAAELP-----AEVQQITEV 117
           ID+WR +  A  +++ +Q +W+ LP     D    E     A  +P     A V+  T+ 
Sbjct: 64  IDNWRTMPLARAYTIEEQLTWEELPPELPPDALAAEGVAPSADAVPPTTPAAPVEPGTQA 123

Query: 118 ATAGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPF 177
             + Q G  + PWSA+HPY NL+ P +P  ATV GN+  T     ++ HH+VLDFG+ PF
Sbjct: 124 FRSAQYGATVPPWSAAHPYTNLFPPKSPTEATVVGNFNCTEAGFENETHHVVLDFGSMPF 183

Query: 178 PVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTR 237
           PVLEGQSIGIIPPG D  GK H  R YS+ASPR+GERP YNNL+LTVKRV  DH+GN  R
Sbjct: 184 PVLEGQSIGIIPPGTDALGKEHHARQYSIASPRNGERPGYNNLALTVKRVTTDHDGNAVR 243

Query: 238 GVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTE--RRRRR 295
           G+ASN+VCDLK GDKVQV GP+GS++LMPNHP S I+MICTGTGSAPMRAMTE  RR R 
Sbjct: 244 GIASNFVCDLKVGDKVQVVGPFGSSFLMPNHPRSHIVMICTGTGSAPMRAMTEWRRRLRS 303

Query: 296 MDRKEGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERA 355
             + EGG+L+LFFGAR  +ELPYFGPLQ LPK+FIDIN AFSR  G+PKRYVQD +RERA
Sbjct: 304 SGKFEGGKLMLFFGARTQQELPYFGPLQNLPKDFIDINLAFSRTAGQPKRYVQDLMRERA 363

Query: 356 DKVFQMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414
             +  +L+D + + Y+CGLK ME GV+ A RDI    G DWD +   L  + R H+ETY
Sbjct: 364 ADLAALLRDGSGHFYVCGLKSMEEGVVMALRDIASEAGLDWDTVGAALQREGRLHLETY 422


Lambda     K      H
   0.319    0.136    0.425 

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: 624
Number of extensions: 20
Number of successful extensions: 5
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: 414
Length of database: 422
Length adjustment: 32
Effective length of query: 382
Effective length of database: 390
Effective search space:   148980
Effective search space used:   148980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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