GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Phaeobacter inhibens BS107

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3871 PGA1_78p00350 FAD dependent oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>FitnessBrowser__Phaeo:GFF3871
          Length = 445

 Score =  152 bits (384), Expect = 2e-41
 Identities = 134/430 (31%), Positives = 203/430 (47%), Gaps = 36/430 (8%)

Query: 16  YAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQL-V 74
           YAP   L + +T +  V+GGGYTGLS+AL LAEAG DVV+L+A R G+GASGRNGG + V
Sbjct: 31  YAP---LQDEVTAEFAVIGGGYTGLSAALTLAEAGADVVLLDAQRPGWGASGRNGGLVSV 87

Query: 75  NSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCD-YRPGGLFVAMNDKQ 133
            S     D I + YG   A    +      +++   ++R  ++ D +  G  FVA    +
Sbjct: 88  GSAKLADDAILRRYGQADAEQFFAAERAAVDLVETYVERLALEVDRHSRGYTFVAHRPDR 147

Query: 134 LATLEEQ-KENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEAD 192
           L  L +  +E   RYG     +         + S  + GA+    G  ++P+   +G   
Sbjct: 148 LTELHDYGQEYTRRYGLSYEFIPKEEMAAHGLNSPEFHGAVNLPVGFALNPMKFVLGLTR 207

Query: 193 AIRLNGGRVYELSAVTQIQHTTPA----VVRTAKGQVTAKYVIVAGNAYLGDKVEPELAK 248
           A+   G R++   + T +Q  TPA    +++   GQV A+++++A N Y  D +   LA 
Sbjct: 208 AVEAAGVRMF---SDTPVQAITPAAGGYLLQGPAGQVRARHLLIATNGYSSDDLPQALAG 264

Query: 249 RSMPCGTQVITTERLSE-DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYG--GGV--- 302
           R +P  + ++ T  LSE ++A         V D   LL Y RL  D RLL G  G V   
Sbjct: 265 RYLPVQSNIMVTRPLSEAEIADQGWWSEQMVCDSRTLLHYLRLLPDRRLLLGLRGSVRVS 324

Query: 303 -----VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD--T 355
                V  AR   D +R+        FP  + V+  + W+G   +T + +P  G +    
Sbjct: 325 EENIAVTKARARADFDRM--------FPAWRAVETAHFWSGLICMTRNLVPFAGAIPGMK 376

Query: 356 NIYYMQGYSGHGVTCTHLAGRLIAELLRGDAER-FDAFANLPHYPFPGGRTLRVPFTAMG 414
           N +   GY G GV     AG LIA+   G  +R        P   F  GR  R+    + 
Sbjct: 377 NAWAALGYHGSGVCMAPYAGALIADQALGRHQRPHPDLMQRPLRRFELGRWRRLSL-PLA 435

Query: 415 AAYYSLRDRL 424
             +Y ++DR+
Sbjct: 436 FGWYHIKDRI 445


Lambda     K      H
   0.320    0.138    0.411 

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: 447
Number of extensions: 20
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: 426
Length of database: 445
Length adjustment: 32
Effective length of query: 394
Effective length of database: 413
Effective search space:   162722
Effective search space used:   162722
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