GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Pseudomonas fluorescens FW300-N1B4

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate Pf1N1B4_6047 Nucleoside-diphosphate-sugar epimerases

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6047
          Length = 427

 Score =  830 bits (2145), Expect = 0.0
 Identities = 407/427 (95%), Positives = 417/427 (97%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           MANTPYPESYYAASAN  PPRPALQDDVETDVCVIGAGYTGLSSALFLLENGF+VTVLEA
Sbjct: 1   MANTPYPESYYAASANVAPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFRVTVLEA 60

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
           AKVGFGASGRNGGQIVNSYSRDIDVIERSVGP+QAQLLG MAFEGGRIIRERVAKY IQC
Sbjct: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPKQAQLLGQMAFEGGRIIRERVAKYNIQC 120

Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
           DLKDGGVFAA+TAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVAC++YVGGMLDMSG
Sbjct: 121 DLKDGGVFAAITAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACDQYVGGMLDMSG 180

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GHIHPLNL LGEAAAVESLGG IYEQSPAVRIERG +PVV+TPQGKVRAKFIIVAGNAY+
Sbjct: 181 GHIHPLNLVLGEAAAVESLGGTIYEQSPAVRIERGTNPVVYTPQGKVRAKFIIVAGNAYI 240

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
           GNLVPELAAKSMPCGTQVIATEPLGDELA  LLPQDYCVEDCNYLLDYYRL+ DKRLIFG
Sbjct: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAKRLLPQDYCVEDCNYLLDYYRLSADKRLIFG 300

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
           GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY
Sbjct: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420
           SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAA+GAWYYG
Sbjct: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAALGAWYYG 420

Query: 421 LRDKLGF 427
           LRDKLGF
Sbjct: 421 LRDKLGF 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: 872
Number of extensions: 23
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 (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