GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS23120
          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:

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