GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Pseudomonas putida KT2440

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PP_3146 PP_3146 putative Oxidoreductase

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



>FitnessBrowser__Putida:PP_3146
          Length = 431

 Score =  378 bits (970), Expect = e-109
 Identities = 193/428 (45%), Positives = 269/428 (62%), Gaps = 4/428 (0%)

Query: 3   NTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAK 62
           NT +  SYYAA+A    P P+L  ++  DVCVIG G TG+++AL L E G  V +LEA +
Sbjct: 4   NTQHTASYYAATARDAAPYPSLDSELTADVCVIGGGLTGVNTALELAERGLSVVLLEARR 63

Query: 63  VGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDL 122
           +G+GASGRNGGQ++     D+    R VG    + L     +   ++ ER+A+Y I CDL
Sbjct: 64  IGWGASGRNGGQLIRGIGHDVSGFARHVGQDGVRYLKQAGIDSVELVAERIARYGIACDL 123

Query: 123 KDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMSGG 181
           + G    A TA Q    + ++      G+  +  L+   ++ E+VA ++Y GG++DM  G
Sbjct: 124 RWGFCELANTAAQFAAFKEEQDDLAALGYRHETRLVSAGQLNEIVASDQYAGGLVDMGSG 183

Query: 182 HIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLG 241
           H+HPL+L  GEA A  SLG  I+EQSP +RIE G    +HT +GKVRA  +++  NA+L 
Sbjct: 184 HLHPLDLVQGEARAAHSLGVRIFEQSPVLRIEHGPRLTLHTARGKVRASSLVLGCNAHLD 243

Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301
            L P L+ K +P G+ V+ATEPL + LA SL+PQ+  + D    LDYYRLT D+RL+FGG
Sbjct: 244 ELEPRLSGKVLPAGSYVVATEPLPEALASSLIPQNMALCDQKVGLDYYRLTADRRLLFGG 303

Query: 302 GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIY 359
              Y  R P +I A +RPK+LK FPQL +V+IDY W G   +T +R PQVGRL    N+Y
Sbjct: 304 ACHYSGRHPKDIAAYMRPKVLKVFPQLANVRIDYQWGGMIGITANRFPQVGRLNQHPNVY 363

Query: 360 YSQGCSGHGVTYTHLAGKVLAEALR-GQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418
           Y+QG SGHG+  TH   K+LAE++  G +   D F+ +PH  FPGG+ LR+P  A+G  +
Sbjct: 364 YAQGYSGHGLNVTHWTAKLLAESIALGHSHGLDVFSAVPHLTFPGGKALRSPLLALGMLW 423

Query: 419 YGLRDKLG 426
           Y LR+ LG
Sbjct: 424 YRLREALG 431


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: 612
Number of extensions: 25
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: 431
Length adjustment: 32
Effective length of query: 395
Effective length of database: 399
Effective search space:   157605
Effective search space used:   157605
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