GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_24770
          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 (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