GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N2C3

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate AO356_30165 AO356_30165 hypothetical protein

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30165
          Length = 357

 Score =  167 bits (422), Expect = 5e-46
 Identities = 124/348 (35%), Positives = 173/348 (49%), Gaps = 39/348 (11%)

Query: 21  LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLF-REGRLSTYAE-LP-VYHRGESGL 77
           +R E V  GLE PWA+AFLP    L+ ERPGR+R+   +G +    E LP +   G+ GL
Sbjct: 12  VRAERVATGLENPWAVAFLPAHRYLVTERPGRLRVVGADGSIGPPVEGLPAIAAGGQGGL 71

Query: 78  LGLALHPRFPEAPYVY-AYRTVAEGGLRNQ--VVRLRHLGERGVLD--RVVLDGIPARPH 132
           L +     F     VY  +   A GG  N   V R         LD  +V+    P    
Sbjct: 72  LDVVTDSAFDVNRMVYFCFSEPAAGGAGNSTAVARATLSSNMVRLDNLQVIFSQRPKVSS 131

Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYER-ELAQDLASLGGKILRLTPEGEPAPGNPFLGRRG 191
             H G RI    DG L+VT GE Y R E AQ+L +  GK++R+  +G     NPF+GR G
Sbjct: 132 SAHFGCRIVEAKDGTLFVTLGERYSRKEDAQELDNHLGKVVRIQKDGVVPTDNPFVGRPG 191

Query: 192 ARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV--- 248
           A PE++S GHRN QG    P  G L+ ++HGP      G DE+N+ + G NYGWP +   
Sbjct: 192 ALPEIWSYGHRNSQGATLGP-DGRLWMNDHGPQ-----GGDEINVPLAGRNYGWPVITYG 245

Query: 249 -------VGRGNDPR--YRDPLYFWPQGFPPGNLAF---------FRGDLYVAGLRGQAL 290
                  +G G   +     PL++W     P  +AF         ++G+L+V  L+   L
Sbjct: 246 ENYGGGKIGDGLTAKDGMEQPLHYWVPSIAPSGMAFLTSDRYGPAWKGNLFVGSLKFGYL 305

Query: 291 LRLVLEGERGRWRVLRVETALSGFGRLREVQVGPDGALYVTTSNRDGR 338
            R+ L+  +    V   +    G  R+R+V+ GPDG LYV T  +DG+
Sbjct: 306 DRIELKDGK---VVAEHKLLEDGHARVRDVRQGPDGLLYVLTDEQDGK 350


Lambda     K      H
   0.322    0.146    0.460 

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: 510
Number of extensions: 36
Number of successful extensions: 7
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: 352
Length of database: 357
Length adjustment: 29
Effective length of query: 323
Effective length of database: 328
Effective search space:   105944
Effective search space used:   105944
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: 49 (23.5 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