GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxA in Crocosphaera subtropica ATCC 51142

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 WP_009547107.1 CCE_RS04725 phycobilisome linker polypeptide

Query= SwissProt::Q9AIX6
         (414 letters)



>NCBI__GCF_000017845.1:WP_009547107.1
          Length = 408

 Score =  191 bits (486), Expect = 3e-53
 Identities = 108/288 (37%), Positives = 158/288 (54%), Gaps = 10/288 (3%)

Query: 137 VNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPVLEGQSIGIIPPGVDEKG 196
           VN+Y P +P       NY L AE  S  + H+  D        LEGQSIGIIPPG D+ G
Sbjct: 121 VNIYKPKDPFIGKCIENYPLVAEGGSGIVQHLTFDLSGGDLHYLEGQSIGIIPPGTDDNG 180

Query: 197 KPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDH-EGNPT-RGVASNYVCDLKKGDKVQ 254
           KPH LR+YS+AS R G++     +SL V+++   H E N T  GV S ++C+L+ G  V 
Sbjct: 181 KPHKLRLYSIASTRHGDKGDDKTVSLCVRQLEYQHPETNETVYGVCSTHLCNLEVGADVA 240

Query: 255 VTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERR--RRRMDRKEGGELVLFFGARA 312
           +TGP G   L+P+   ++I+M+ TGTG AP RA   R    +  D K  G+  L FG   
Sbjct: 241 ITGPVGKEMLLPDDEDANIVMLATGTGIAPFRAFLWRMFFEKHEDYKFKGKSWLIFGVPY 300

Query: 313 PEELPYFGPLQKLPKEFID---INFAFSRVPGEP---KRYVQDAIRERADKVFQMLQDDN 366
              + Y   L+++   + D   + +A SR        + Y+Q  + E+A+K++ MLQD  
Sbjct: 301 TANILYKDKLEEIETNYPDNFELTYAISREQKNSEGGRMYIQHRVAEQAEKLWTMLQDPK 360

Query: 367 CYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414
            ++Y+CGLKGME+G+ E        +G +W     +L  + R+HVE Y
Sbjct: 361 THLYMCGLKGMESGIEEGLSPFAAKQGVEWSDFVKKLKKEHRWHVEVY 408


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: 438
Number of extensions: 23
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: 414
Length of database: 408
Length adjustment: 31
Effective length of query: 383
Effective length of database: 377
Effective search space:   144391
Effective search space used:   144391
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 Apr 09 2024. 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