Alignments for a candidate for puuB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for puuB in Shewanella oneidensis MR-1

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 200452 SO1274 conserved hypothetical protein (NCBI ptt file)

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



>FitnessBrowser__MR1:200452
          Length = 428

 Score =  661 bits (1706), Expect = 0.0
 Identities = 321/427 (75%), Positives = 362/427 (84%), Gaps = 1/427 (0%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           M+  P+  SYYAASAN    R  LQ+ +E DVCVIGAGYTGLS+AL LLE GF V VL+A
Sbjct: 1   MSAIPHTGSYYAASANDKVERARLQESIEADVCVIGAGYTGLSAALHLLELGFSVVVLDA 60

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
           A++G+GASGRNGGQIVNSYSRDID IE++VG +QA+L G MAFEGGRIIRER+AKY I C
Sbjct: 61  ARIGWGASGRNGGQIVNSYSRDIDTIEKTVGKEQAKLFGKMAFEGGRIIRERIAKYNISC 120

Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMS 179
           DLKDGGVFAA+  KQMGHL  QK+LWE  GH  QLELLD + IR VV  E YVGGMLD S
Sbjct: 121 DLKDGGVFAAMNEKQMGHLRHQKQLWESHGHMGQLELLDGKGIRSVVNTERYVGGMLDKS 180

Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAY 239
           GGHIHPLNLALGEA AVESLGG I+E S  +R++ G +PVVHT  G V+AKF++VAGNAY
Sbjct: 181 GGHIHPLNLALGEARAVESLGGKIFEDSAVLRVDEGDNPVVHTATGSVKAKFVVVAGNAY 240

Query: 240 LGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIF 299
           LG L+PEL AKSMPCGTQVI TEPL ++LA SLLPQDYCVEDCNYLLDY+RL+GDKR+I+
Sbjct: 241 LGKLMPELQAKSMPCGTQVITTEPLDEDLAASLLPQDYCVEDCNYLLDYFRLSGDKRMIY 300

Query: 300 GGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIY 359
           GGGVVYGARDPA+IE++I P MLK FPQLK VK+DYAWTGNFLLTLSRLPQVGR+G NIY
Sbjct: 301 GGGVVYGARDPADIESLIIPNMLKTFPQLKGVKVDYAWTGNFLLTLSRLPQVGRIGKNIY 360

Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419
           YSQGCSGHGVTYTHLAGK++AE L GQA RFDAFA LPHYPFPGG  LR PF+A+GAWYY
Sbjct: 361 YSQGCSGHGVTYTHLAGKLIAEMLNGQATRFDAFAALPHYPFPGGHALRVPFSALGAWYY 420

Query: 420 GLRDKLG 426
            LRDKLG
Sbjct: 421 SLRDKLG 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: 713
Number of extensions: 26
Number of successful extensions: 2
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: 428
Length adjustment: 32
Effective length of query: 395
Effective length of database: 396
Effective search space:   156420
Effective search space used:   156420
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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