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_RS25385 BPHYT_RS25385 acyl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS25385
          Length = 384

 Score =  276 bits (705), Expect = 9e-79
 Identities = 155/375 (41%), Positives = 213/375 (56%), Gaps = 4/375 (1%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           M+F LS EQ+LL++SV   +   Y F++R  + K +   S   W  FA+ G L     E 
Sbjct: 1   MNFTLSAEQQLLQDSVRRFVDRDYSFETRMAFVKARSTCSATHWQTFADNGWLAAALPES 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
            GGF     +T+++   LG  LV+EPYL   V+    L    + AQ+   LP + DGS+ 
Sbjct: 61  CGGFDGSLTDTVLIASELGRGLVIEPYLGCAVLAAQTLLAGATPAQREQWLPALADGSRK 120

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
           FA A  E  SR     V T+A  + DG+ + G K +VL G  AD+ IV+AR +    D  
Sbjct: 121 FALAYSEAQSRGFPEFVETSATPTPDGYSLAGSKTLVLGGADADSFIVSARAQ----DAE 176

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           G+ + LVP DA G+ R+  P  DG  AA++T  GV+V  +A +G P   L  +   +  A
Sbjct: 177 GITLMLVPGDAPGLARRVLPLHDGSFAAELTLDGVRVTREAVLGVPGPGLTALRHALSHA 236

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
             AL AE VG M++S+  T EY++ RKQFGVPIGSFQ LQHR ADM    E ARSM    
Sbjct: 237 TAALGAELVGAMEKSIELTAEYLRVRKQFGVPIGSFQALQHRLADMAAEMELARSMLHAL 296

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
             + E D    R  A++ AK  IG++ +FV  Q+IQLHGGIGMT E ++GHY+KR  + +
Sbjct: 297 LGSLENDAPPARLRAVSQAKSVIGRAARFVCGQAIQLHGGIGMTEEYQVGHYYKRAVVAD 356

Query: 361 QTFGDTDHHLARVSA 375
             FG +D H A  +A
Sbjct: 357 ALFGSSDQHDAACAA 371


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: 362
Number of extensions: 20
Number of successful extensions: 2
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: 384
Length adjustment: 30
Effective length of query: 350
Effective length of database: 354
Effective search space:   123900
Effective search space used:   123900
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