GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Burkholderia phytofirmans PsJN

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__BFirm:BPHYT_RS28040
          Length = 377

 Score =  172 bits (435), Expect = 2e-47
 Identities = 116/373 (31%), Positives = 181/373 (48%), Gaps = 7/373 (1%)

Query: 56  TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLS 114
           T E++ IR   R+   +++AP   ++  +A+ P  +  ++G +G  G  +   +G     
Sbjct: 6   TDEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWGGSYTD 65

Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174
             A A+A  EIA   A+C+T + VH+S+G   I   G+EAQK++YL  LA    +  + L
Sbjct: 66  YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLATGRRIGAFCL 125

Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA---RNTTTNQINGFI 231
           TEP  GS+A+ L T A   +G W +NG K+++ N + ADL I+FA    +     +  FI
Sbjct: 126 TEPQAGSEANNLRTRAVLRDGKWILNGSKQFVTNGSRADLAIVFAVTDPDRGKRGLTAFI 185

Query: 232 VKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL--PGVNSFQDTSKVLAVSRV 289
           V  D PG    K  +K+G+R      I L +  VP+ + L  PG    +     L   R+
Sbjct: 186 VPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPG-EGLRIALSNLEGGRI 244

Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK 349
            +A Q +GI+   +D    Y  ER QFG  L   Q     L  M   + A  L+     +
Sbjct: 245 GIAAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNAARLLVHHAAR 304

Query: 350 LYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEG 409
           L   G+    +AS  K + S  A E  S   ++ GG G L D+ V + + D      YEG
Sbjct: 305 LRTAGKPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYRDARITQIYEG 364

Query: 410 TYDINTLVTGREV 422
           T ++  ++  R V
Sbjct: 365 TSEVQRMLIARHV 377


Lambda     K      H
   0.319    0.133    0.399 

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: 310
Number of extensions: 12
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: 436
Length of database: 377
Length adjustment: 31
Effective length of query: 405
Effective length of database: 346
Effective search space:   140130
Effective search space used:   140130
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 (21.7 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:

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