GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Dinoroseobacter shibae DFL-12

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 3608835 Dshi_2227 FAD dependent oxidoreductase (RefSeq)

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



>FitnessBrowser__Dino:3608835
          Length = 434

 Score =  304 bits (779), Expect = 3e-87
 Identities = 170/424 (40%), Positives = 242/424 (57%), Gaps = 4/424 (0%)

Query: 6   YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65
           YP SYYA++    P  PA Q  + TDVC++G GYTGLS+AL L E G+ V VLEA +VGF
Sbjct: 13  YPPSYYASTVPARPALPAAQGPIHTDVCIVGGGYTGLSAALHLAERGYDVVVLEAQRVGF 72

Query: 66  GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           GASGRNGGQ+ +    D+  +E   G + A     +A E  +++ E VA+  + CDL+ G
Sbjct: 73  GASGRNGGQVASGPRLDLSTLEARYGRETAHAQWALAREARKLVDELVAR-GLDCDLRAG 131

Query: 126 GVFAALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184
            ++A   A  + G+      +    G+  +  LD+ RI  +V    Y GG+LD    H++
Sbjct: 132 VIYATDRAGDVAGYHAEAAHVQAAVGYDGVTPLDRDRIAALVGSAVYAGGVLDAGAAHLN 191

Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRI-ERGASPVVHTPQGKVRAKFIIVAGNAYLGNL 243
           PL L LG A   +  G  I+E S    + + G   VV T    + A+ +I+AGN Y+G L
Sbjct: 192 PLKLVLGLADLAQVAGAQIFEGSQVRSVADAGPHVVVTTDAATIAAEQVILAGNGYIGGL 251

Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303
               AA  MP  + ++ATEPLG + A ++LP+ + V D  ++++Y+R   D RL+FGGG 
Sbjct: 252 DSATAAHVMPINSYMVATEPLGPD-ADAILPEGHAVADNKFVVNYFRRAPDGRLLFGGGE 310

Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQG 363
            Y  R   +I   +R  + + FPQL+ + IDYAW G   +T SRLP   ++   ++ + G
Sbjct: 311 SYRYRFTPDIAGKVRGPLERIFPQLRGIGIDYAWGGTLAITRSRLPFARKVSPRVFSAGG 370

Query: 364 CSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423
            SGHGV  + L GK +AEA  G+ ERF+  A LPH PFPGG  LR P         GLRD
Sbjct: 371 YSGHGVALSLLFGKAMAEAAAGEPERFNQLAALPHAPFPGGAALRAPLLLGAMSLAGLRD 430

Query: 424 KLGF 427
           +L F
Sbjct: 431 RLPF 434


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: 557
Number of extensions: 28
Number of successful extensions: 5
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: 434
Length adjustment: 32
Effective length of query: 395
Effective length of database: 402
Effective search space:   158790
Effective search space used:   158790
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