GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Burkholderia phytofirmans PsJN

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate BPHYT_RS13575 BPHYT_RS13575 FAD-dependent oxidoreductase

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



>FitnessBrowser__BFirm:BPHYT_RS13575
          Length = 430

 Score =  209 bits (533), Expect = 1e-58
 Identities = 140/418 (33%), Positives = 213/418 (50%), Gaps = 7/418 (1%)

Query: 5   PYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVG 64
           P P S +AA+A P    P L +    DV ++GAGYTGLS+AL L E G +V V++A + G
Sbjct: 9   PLPPSLWAATAEPAVVTPPLDNSTVVDVAIVGAGYTGLSTALHLAEQGLRVCVIDANEPG 68

Query: 65  FGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD-LK 123
           +GASGRNGGQ++     D D + R  GP+    L  MA      + + VA++ I+CD  +
Sbjct: 69  WGASGRNGGQVIPGLKYDPDELIRRYGPRDGNALVQMAGGAADTVFDLVARHGIRCDATR 128

Query: 124 DGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHI 183
            G +    + K +  L ++   WE  G   +ELLD+ ++ + +  + +VGG +D   G +
Sbjct: 129 AGWIQPTHSHKLLKTLYARAGQWEARG-APVELLDRAQVSKRLGTDAFVGGWVDRRAGSV 187

Query: 184 HPLNLALGEAAAVESLGGVIYEQSPAVRIERGASP-VVHTPQGKV-RAKFIIVAGNAYLG 241
            PL+ A G A A ++ G  I+  + A  IERGA+   + T  G V  +K +++A N Y  
Sbjct: 188 QPLSYARGLARAAQAAGAQIHGGTRAAGIERGANGWRIRTAHGPVIESKQVLLATNGYTD 247

Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301
            L P LA   +   + ++AT+PL D++  ++L       D   LL Y+R   D RL+ GG
Sbjct: 248 GLWPRLAQSVIAANSFIVATKPLADDVGATILAGGEVASDSRRLLLYFRKDADGRLLMGG 307

Query: 302 -GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
            G     R+ A+   + R   L  FPQL+  + ++ W G   +T + LP V      +  
Sbjct: 308 RGPFREPRNAADWAHLERAAQL-MFPQLRGTEYEFRWAGRIAITRNFLPHVHMPAKGMTI 366

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418
           + G +G G+      GK LA  L G A+        P  P P   L R   +A  AWY
Sbjct: 367 ALGYNGRGIAMATTLGKHLAAYLGGAAKGL-PLPPTPIEPVPLHALQRFYISAGVAWY 423


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: 507
Number of extensions: 33
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: 430
Length adjustment: 32
Effective length of query: 395
Effective length of database: 398
Effective search space:   157210
Effective search space used:   157210
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