Aligments for a candidate for puuB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for puuB in Pseudomonas putida KT2440

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PP_2448 PP_2448 gamma-glutamylputrescine oxidase

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



>FitnessBrowser__Putida:PP_2448
          Length = 427

 Score =  814 bits (2103), Expect = 0.0
 Identities = 392/427 (91%), Positives = 417/427 (97%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           MANTPYP+SYYAASANPVPPRPALQ +VETDVC+IGAGYTGLSSALFLLENGFKV+++EA
Sbjct: 1   MANTPYPQSYYAASANPVPPRPALQGEVETDVCIIGAGYTGLSSALFLLENGFKVSIVEA 60

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
           AKVGFGASGRNGGQIVNSYSRDIDVIER+VGP+QAQLLG+MAFEGGRIIRERVAKY IQC
Sbjct: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERTVGPKQAQLLGHMAFEGGRIIRERVAKYNIQC 120

Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
           DLKDGGVFAALT+KQMGHLESQKRLWERFGH QLEL+DQ+RIREVVAC+ Y+GGMLDMSG
Sbjct: 121 DLKDGGVFAALTSKQMGHLESQKRLWERFGHNQLELMDQKRIREVVACDSYIGGMLDMSG 180

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GHIHPLNLALGEAAAVESLGG+IYEQ+PAVRIERGA+PVVHTPQGKVRAKFIIVAGNAYL
Sbjct: 181 GHIHPLNLALGEAAAVESLGGIIYEQTPAVRIERGANPVVHTPQGKVRAKFIIVAGNAYL 240

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
           GNLVPELAAKSMPCGTQVI TEPLG+ELA +LLPQDYCVEDCNYLLDYYRLT DKRLIFG
Sbjct: 241 GNLVPELAAKSMPCGTQVITTEPLGEELARTLLPQDYCVEDCNYLLDYYRLTSDKRLIFG 300

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
           GGVVYGARDPANIEAIIRPKMLKAFPQLK+VKIDYAWTGNFLLTLSRLPQVGR+GDNIYY
Sbjct: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKNVKIDYAWTGNFLLTLSRLPQVGRIGDNIYY 360

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420
           SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFA LPHYPFPGGQ+LR PF+A+GAWYY 
Sbjct: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFAGLPHYPFPGGQMLRVPFSAIGAWYYS 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: 850
Number of extensions: 18
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources