GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Pseudomonas stutzeri RCH2

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3726 Psest_3795 Glycine/D-amino acid oxidases (deaminating)

Query= SwissProt::P37906
         (426 letters)



>FitnessBrowser__psRCH2:GFF3726
          Length = 444

 Score =  362 bits (928), Expect = e-104
 Identities = 191/426 (44%), Positives = 266/426 (62%), Gaps = 5/426 (1%)

Query: 2   TEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRI 61
           ++H  SYYAAS N+   F+ L      DVC+VGGG++GL++A+ LAE G  V++LEA RI
Sbjct: 19  SDHAPSYYAASVNRELSFEPLQGEQRADVCIVGGGFSGLNTAIELAERGLSVILLEAHRI 78

Query: 62  GFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYR 121
           G+GASGRNGGQL+     D++      G +    L  M FE  +I+R+RI+RY IDCD  
Sbjct: 79  GWGASGRNGGQLIRGVGHDVEQFTNILGEEGVDELKRMGFEAVDIVRQRIERYAIDCDLT 138

Query: 122 PGGLFVAMNDKQLATLEEQKENWERYGNKQ-LELLDANAIRREVASDRYTGALLDHSGGH 180
            G   +A   + L   +E+  +  R G    L+ +    +   V S RY G LLD   GH
Sbjct: 139 WGYCDLATKPRHLKGFDEEYSDLLRLGYPHPLQRVSRPNLATVVGSQRYLGGLLDMGSGH 198

Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240
           +HPLNLA+GEA A +  G R++E SAV +I++     + TA+G V A  +++A NAYL +
Sbjct: 199 LHPLNLALGEAAAAQSLGVRLFEQSAVERIEYGPQVALHTAQGVVHADNLVLACNAYL-N 257

Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300
            ++P+LA + +P G+ +I TERL E L R L+P+N  V D    LDY+RL+AD RLL+GG
Sbjct: 258 GLQPKLAGKVLPAGSYIIATERLPEPLQRELLPQNMAVCDQRVALDYFRLSADGRLLFGG 317

Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRL--DTNIY 358
              Y  RDP D+   + PK+L+ FPQL G+ IDY+W G   +  +R+PQ GRL    N++
Sbjct: 318 ACHYSGRDPKDIAAYMQPKMLEVFPQLIGIGIDYQWGGMIGIGANRLPQIGRLPEQPNVF 377

Query: 359 YMQGYSGHGVTCTHLAGRLIAE-LLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAY 417
           Y Q YSGHG+  THLAG L+AE +   ++  FD FA +PH  FPGGR LR P  A+G  +
Sbjct: 378 YAQAYSGHGLNATHLAGHLLAEAIATQESHGFDLFAQVPHPTFPGGRALRSPLLALGMLW 437

Query: 418 YSLRDR 423
           Y L+DR
Sbjct: 438 YRLKDR 443


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: 556
Number of extensions: 29
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: 444
Length adjustment: 32
Effective length of query: 394
Effective length of database: 412
Effective search space:   162328
Effective search space used:   162328
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