GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Burkholderia phytofirmans PsJN

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate BPHYT_RS30200 BPHYT_RS30200 FAD-dependent oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS30200 BPHYT_RS30200 FAD-dependent
           oxidoreductase
          Length = 424

 Score =  199 bits (507), Expect = 1e-55
 Identities = 133/400 (33%), Positives = 207/400 (51%), Gaps = 11/400 (2%)

Query: 29  DVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQLVNSYSRDIDVIEKSY 88
           DV V+GGG+TGLS+A  L + G  V VL+A RIG GASGRNGGQ+    ++D   +    
Sbjct: 27  DVVVIGGGFTGLSAAQALGKRGAAVTVLDAGRIGGGASGRNGGQVNTGVAQDFVALVAQL 86

Query: 89  GMDTARMLGSMMFEGGEIIRERIKRYQIDCDY-RPGGLFVAMNDKQLATLEEQKENWERY 147
           G++ A        +  + +   I+   IDC+Y   G L +A     LA LE+  E   R 
Sbjct: 87  GVERASACYRAFSDAVDTVERLIREENIDCNYIATGKLKLASKPHHLAHLEKTAEAIRRE 146

Query: 148 GNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEADAIRLNGGRVYELSAV 207
            +  +EL+D + IR E+ SD + G LL   GG +H     +G A+A    G ++YE +AV
Sbjct: 147 VDTDIELIDRSRIRSEIQSDSFHGGLLQRHGGQMHMGKFTVGLAEAAVRRGAKLYENAAV 206

Query: 208 TQIQHTTPAV-VRTAKGQVTAKYVIVA-GNAYLGDKVEPELAKRSMPCGTQVITTERLSE 265
           T I        + TA+G+V AK V++A G +  G        +R  P G+ ++ TE LS 
Sbjct: 207 TAIAKDGNGYRITTARGEVRAKQVLIATGPSRHGP--FGWYRRRLAPVGSFIVVTEPLSP 264

Query: 266 DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGARD-PDDVE--RLVVPKLLK 322
           +L   + P          + +Y+R+T D+RLL+GG   + A + P D +  R++   L  
Sbjct: 265 ELLAQVFPNRRAYTTTRLMHNYFRVTPDSRLLFGGRARFTASERPSDAKSGRILQEGLAA 324

Query: 323 TFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQGYSGHGVTCTHLAGRLIAELL 382
            FP L   +IDY W G   ++  R+P  G+ D  IY+  GYSGHG   +   G+++A+++
Sbjct: 325 MFPTLASARIDYCWGGLVDMSADRLPHAGQHD-GIYFSMGYSGHGTQMSTHMGQVMADVM 383

Query: 383 RGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSLRD 422
            G  ++     +   +P   G T +  F  +   YY ++D
Sbjct: 384 DGHEDKNPWRES--EWPAIPGHTGKPWFLPLVGTYYRIKD 421


Lambda     K      H
   0.320    0.138    0.411 

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: 503
Number of extensions: 32
Number of successful extensions: 6
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: 426
Length of database: 424
Length adjustment: 32
Effective length of query: 394
Effective length of database: 392
Effective search space:   154448
Effective search space used:   154448
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