GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Shewanella loihica PV-4

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 5209059 Shew_1537 FAD dependent oxidoreductase (RefSeq)

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



>FitnessBrowser__PV4:5209059
          Length = 429

 Score =  297 bits (760), Expect = 5e-85
 Identities = 159/419 (37%), Positives = 243/419 (57%), Gaps = 4/419 (0%)

Query: 9   SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68
           SYY A+       P+L+ +++ DV +IGAG+TG+++AL L E G KV V+EA KVG+GA+
Sbjct: 8   SYYNATIKQETYYPSLEGELDVDVVIIGAGFTGVATALELAERGVKVAVVEANKVGWGAT 67

Query: 69  GRNGGQIVNSYSRD---IDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           GRNGGQ+  S S D   +  +   +G    + + N+ + G  II++RV KYQI CDLK G
Sbjct: 68  GRNGGQVTGSLSGDNAMVKQLRNCIGHDAEEFVWNLRWRGHEIIKKRVEKYQIDCDLKFG 127

Query: 126 GVFAALTAKQMGHLESQKRLWERFGH-TQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184
            +  A     M  +++      R G   +L LL +  I + +    Y GG+L+    H+H
Sbjct: 128 HLHTAYKPAHMAEMQTTYEEGLRRGMGDELTLLSKADIPDYLDTPLYHGGLLNRRNMHLH 187

Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244
            +NL +GEA A E+ G +I+E S  + I       V T +G++ A   ++AGNAY     
Sbjct: 188 SVNLCIGEARAAEAYGALIFEGSQVLDISDDKRVTVTTDKGRITANCAVLAGNAYHRLAR 247

Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304
            +L     P      AT  L  +LA  L P D  V D  ++LDYYR+T D RL+FGGG  
Sbjct: 248 HKLRGMLFPASLGNCATVRLDPQLAKQLNPHDLAVYDSRFVLDYYRMTADNRLMFGGGTN 307

Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364
           Y  RD  N+ A +RP + + FP+LK V+I++ WTG   + ++R+PQ+G++ ++++Y QG 
Sbjct: 308 YSGRDSKNVAAELRPAIERTFPRLKGVEIEFDWTGMAGIVVNRIPQLGKVSEHLFYCQGY 367

Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423
           SGHGV  +H+ G+++++A++GQ E FD FA +     P G  L     A+G  YY + +
Sbjct: 368 SGHGVATSHIMGEIMSQAVQGQLEEFDLFAQMKQIRLPVGDWLGNQGMALGMLYYRMME 426


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: 555
Number of extensions: 28
Number of successful extensions: 3
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: 429
Length adjustment: 32
Effective length of query: 395
Effective length of database: 397
Effective search space:   156815
Effective search space used:   156815
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