GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Pseudomonas fluorescens FW300-N2E3

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AO353_24770 AO353_24770 FAD-dependent oxidoreductase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_24770 AO353_24770
           FAD-dependent oxidoreductase
          Length = 436

 Score =  355 bits (910), Expect = e-102
 Identities = 183/425 (43%), Positives = 259/425 (60%), Gaps = 4/425 (0%)

Query: 6   YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65
           +  SYY ASAN +   P L  D++ DVCVIG G+TG+++A+ L + G  V +LE  ++G+
Sbjct: 12  HARSYYNASANAMVQHPTLTSDLQADVCVIGGGFTGVNTAIELAQRGLSVILLEGRRIGW 71

Query: 66  GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           GASGRNGGQ++     D+    R VG +  + L     E   ++  R+ ++ I CDL+ G
Sbjct: 72  GASGRNGGQLIRGIGHDVSGFARYVGQEGVRYLERAGIESVEVVGNRIREHGIDCDLRWG 131

Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQL-ELLDQRRIREVVACEEYVGGMLDMSGGHIH 184
               A T  Q    + ++   +  G+     L+    +R+VV    Y GG++DM  GH+H
Sbjct: 132 FCELANTPAQFAAFQVEQETLDAQGYAHATRLVRPEDMRQVVNSGVYAGGLVDMGSGHLH 191

Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244
           PLNL LGEA   ESLG  I+EQSP + I  G++  V    G VRA  +++  NA+L +L 
Sbjct: 192 PLNLVLGEARVAESLGVRIFEQSPVLEIIHGSTVQVRCAGGTVRAGSLVLGCNAHLEDLE 251

Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304
           P L+ K +P G+ +IATEPL  + A  L+PQ+  + D    LDYYRL+ D+RL+FGG   
Sbjct: 252 PRLSGKVLPAGSYIIATEPLSAQAAAELIPQNLALCDQKVGLDYYRLSADRRLLFGGACH 311

Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYSQ 362
           Y  RDP +I A +RPKMLK FPQL DV+IDY W G   +T +R PQVGRL    N++Y+Q
Sbjct: 312 YSGRDPTDIAAYMRPKMLKVFPQLTDVRIDYQWGGRIGITANRFPQVGRLSQYPNVFYAQ 371

Query: 363 GCSGHGVTYTHLAGKVLAEALR-GQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGL 421
           G SGHG+  TH   ++LAEA+  G +   D F+ +PH  FPGG+ LRTP  A+G  ++ L
Sbjct: 372 GYSGHGLNVTHWTARLLAEAIHAGHSHGLDVFSAVPHMTFPGGRALRTPLLALGMLWHRL 431

Query: 422 RDKLG 426
           R+ LG
Sbjct: 432 REVLG 436


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: 622
Number of extensions: 28
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: 436
Length adjustment: 32
Effective length of query: 395
Effective length of database: 404
Effective search space:   159580
Effective search space used:   159580
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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