GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Burkholderia phytofirmans PsJN

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS13555 BPHYT_RS13555 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__BFirm:BPHYT_RS13555
          Length = 375

 Score =  311 bits (798), Expect = 1e-89
 Identities = 167/377 (44%), Positives = 235/377 (62%), Gaps = 3/377 (0%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           M+F  +E++R+L +++   +   Y F +R + A+   G+S  +W +FAE G++G  F E 
Sbjct: 1   MNFQHTEDRRMLADTLNRFVSEQYAFSTRDRIAQSDQGYSGELWSRFAELGIIGALFDEA 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
           DGGFG G  +  +V E+LG  LV+EP+L T+++G   + R+G+ AQKA  L  +IDGS+ 
Sbjct: 61  DGGFGGGGFDIAVVFESLGRGLVVEPFLDTLIVGRA-IARSGNEAQKAV-LGELIDGSRI 118

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
            A A  E +S ++L  VS  A++SG  W ++G K VV +GE A   +V+ART G      
Sbjct: 119 VALAHGEPDSHYELSRVSARAERSGSTWQLNGAKAVVQHGEHASLFLVSARTGGDDDSDA 178

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           G+ +FLVP DA G++ +GY   DG  AA++T   V +  DA +G P+     +E  +   
Sbjct: 179 GITLFLVPRDAAGVSVRGYRKIDGGRAAEVTLDNVTLSDDALLGTPDAGFATLEYAIGCG 238

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
             ALC+EAVG MD +   T+EY++TRKQFGVPIGSFQ LQHR AD+ +  EQARS A+  
Sbjct: 239 VFALCSEAVGAMDVAKDYTLEYLRTRKQFGVPIGSFQALQHRMADLLLEIEQARS-AVIN 297

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
             AA   + K R  A++AAK  IG+ G  V ++ IQLHGGIGMT E  + HY KRL MI+
Sbjct: 298 AAAALGAERKVRERAVSAAKYSIGRIGALVAEECIQLHGGIGMTWELPLAHYAKRLVMID 357

Query: 361 QTFGDTDHHLARVSAGG 377
              GD DHHL R  A G
Sbjct: 358 HQLGDEDHHLERFVALG 374


Lambda     K      H
   0.318    0.135    0.388 

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: 426
Number of extensions: 19
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: 380
Length of database: 375
Length adjustment: 30
Effective length of query: 350
Effective length of database: 345
Effective search space:   120750
Effective search space used:   120750
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 (21.7 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