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

GapMind for catabolism of small carbon sources

Aligments 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.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources