GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Burkholderia phytofirmans PsJN

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate BPHYT_RS23120 BPHYT_RS23120 FAD-dependent oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_21495
         (427 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS23120 BPHYT_RS23120 FAD-dependent
           oxidoreductase
          Length = 423

 Score =  326 bits (836), Expect = 7e-94
 Identities = 175/414 (42%), Positives = 250/414 (60%), Gaps = 4/414 (0%)

Query: 9   SYYAASA-NPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGA 67
           SYY ASA  P+   PAL   +E DVCVIGAG++GLS AL     G  V VL+A + G+GA
Sbjct: 5   SYYEASAARPLADDPALDGTLEADVCVIGAGFSGLSVALECRARGLSVVVLDAHRPGWGA 64

Query: 68  SGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGV 127
           SGRNGGQ +  +++D +++ER +G   A+    M+ EG  ++RER+  Y I+CD   G +
Sbjct: 65  SGRNGGQTLVGFAKD-EIMERQLGLDGARAAWAMSVEGVSLVRERIEHYGIECDFTSGYL 123

Query: 128 FAALTAKQMGHLES-QKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPL 186
             A   K++  L S  +   +R+G+T+L  LD   +R  VA + Y+ G+ D   GH+HPL
Sbjct: 124 TVATKPKRVPDLRSWMESASQRWGYTKLSWLDTDEVRSRVASKRYLAGVYDPFSGHLHPL 183

Query: 187 NLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPE 246
              LG A A    G  ++  SP + + RGA PVV T +G+VR +F+   GNA +G+++P 
Sbjct: 184 KYCLGLADAARREGAQLFAHSPVIEVVRGARPVVRTARGEVRCRFVAACGNATIGDVLPA 243

Query: 247 -LAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVY 305
            +AA+  P  + ++ATEPLG E A +L+     + D N+ LDY+RL+ D R++FGG    
Sbjct: 244 AVAARIAPIASYIVATEPLGKERADALIKGREAICDNNFFLDYFRLSADHRVLFGGRASS 303

Query: 306 GARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCS 365
               P  +   IR +M+  FPQL DVKIDYAW G   +T +R P  G +  N +Y QG S
Sbjct: 304 TGASPVQLGEEIRQRMIGVFPQLGDVKIDYAWGGFVDVTRNRAPDFGSIDPNYFYVQGFS 363

Query: 366 GHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419
           GHGV  T +AG+V+A+A+ G+ + FD FA L H  FPGG  LR P   +G  Y+
Sbjct: 364 GHGVALTGIAGRVVAQAMAGETKAFDLFARLRHARFPGGPALRGPALELGMMYH 417


Lambda     K      H
   0.320    0.139    0.421 

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: 481
Number of extensions: 15
Number of successful extensions: 4
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: 427
Length of database: 423
Length adjustment: 32
Effective length of query: 395
Effective length of database: 391
Effective search space:   154445
Effective search space used:   154445
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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