GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Pseudomonas stutzeri RCH2

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF1925 Psest_1966 Glycine/D-amino acid oxidases (deaminating)

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



>lcl|FitnessBrowser__psRCH2:GFF1925 Psest_1966 Glycine/D-amino acid
           oxidases (deaminating)
          Length = 427

 Score =  704 bits (1817), Expect = 0.0
 Identities = 341/427 (79%), Positives = 375/427 (87%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           M N  YP SYYAA+AN    R  LQD+ + DVCVIGAGYTGLS+ALFLLE G+ V VLEA
Sbjct: 1   MPNKGYPASYYAATANSATARSELQDNKQVDVCVIGAGYTGLSTALFLLEKGYSVAVLEA 60

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
           AKVGFGASGRNGGQIVNSYSRD+D IER+     A+L+G MAFEGGRIIRERVA+Y IQC
Sbjct: 61  AKVGFGASGRNGGQIVNSYSRDLDSIERTASAAAAKLIGEMAFEGGRIIRERVARYDIQC 120

Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
           DLKDGGVFAA   KQM HLE+QK LWER+G+  LELLD R IR+VVAC+ YVGGMLD  G
Sbjct: 121 DLKDGGVFAAFNQKQMLHLETQKALWERYGYQHLELLDDRGIRQVVACDRYVGGMLDKHG 180

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GHIHPLNLALGEAAAVESLGG I+E SPA+RIERG +P+VHTP+G VRAKF+++AGNAYL
Sbjct: 181 GHIHPLNLALGEAAAVESLGGTIHEHSPAIRIERGETPLVHTPKGTVRAKFVVIAGNAYL 240

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
           GNLVPELAAKSMPCGTQVIATEPL +ELAHSLLPQDYCVEDCNYLLDYYRL  DKRLI+G
Sbjct: 241 GNLVPELAAKSMPCGTQVIATEPLSEELAHSLLPQDYCVEDCNYLLDYYRLAADKRLIYG 300

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
           GGVVYGARDPA+IE+IIRPKMLK FPQL+ VKIDYAWTGNFLLTLSRLPQVGRLG NIYY
Sbjct: 301 GGVVYGARDPADIESIIRPKMLKTFPQLEKVKIDYAWTGNFLLTLSRLPQVGRLGGNIYY 360

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420
           SQGCSGHGVTYTH+AGKV+AEAL GQAERFDAFA LPHYPFPGGQ L+ P +A+GA YY 
Sbjct: 361 SQGCSGHGVTYTHVAGKVIAEALSGQAERFDAFASLPHYPFPGGQRLQVPLSALGAMYYN 420

Query: 421 LRDKLGF 427
           LRD+LGF
Sbjct: 421 LRDRLGF 427


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: 766
Number of extensions: 27
Number of successful extensions: 1
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: 427
Length adjustment: 32
Effective length of query: 395
Effective length of database: 395
Effective search space:   156025
Effective search space used:   156025
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, 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