GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N2E2

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Pf6N2E2_801 Soluble aldose sugar dehydrogenase, PQQ-dependent (EC 1.1.5.-)

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_801
          Length = 382

 Score =  179 bits (453), Expect = 1e-49
 Identities = 125/347 (36%), Positives = 180/347 (51%), Gaps = 39/347 (11%)

Query: 21  LRVEEVVGGLEVPWALAFLP-DGGMLIAERPGRIRLFR-EGRLST-YAELP-VYHRGESG 76
           L V  VV GLE PW++AFLP   GML+ ERPG +R+   +G+LS   + +P V+ +G+ G
Sbjct: 37  LEVTTVVKGLEHPWSVAFLPGQQGMLVTERPGNLRVVSADGQLSAPLSGVPEVWAKGQGG 96

Query: 77  LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE--RGVLD-RVVLDGIPARPH 132
           LL + L P F +   VY +Y      G     V    L E  + + +  V+   +P    
Sbjct: 97  LLDVVLSPDFKQDRTVYLSYAEAGADGKAGTAVGRGQLSEDLKSLKNFDVIFRQLPKLST 156

Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192
           G H G R+ F  DG L++T GE  ER  AQDL  L GKI+R+ P+G+    NPF+G++  
Sbjct: 157 GNHFGSRLVFDRDGYLFITLGENNERPTAQDLDKLQGKIVRIYPDGKVPDDNPFVGQKNV 216

Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWP------ 246
           RPE++S G RNPQG A +P  G L+ +EHGP      G DE+N+I  G NYGWP      
Sbjct: 217 RPEIWSYGMRNPQGAALNPWNGTLWENEHGPK-----GGDEMNIIERGKNYGWPLATHGI 271

Query: 247 ------------RVVGRGNDPRY---RDPLYFWPQGFPPGNLAFFRGDLYVAGLRGQALL 291
                       + V  G DP +     P       +  G    ++ ++++  L    L+
Sbjct: 272 NYSGAPIPEAQGKTVEGGLDPHHVWQVSPGLSGMAFYDHGRFKAWQHNVFIGALVPGELI 331

Query: 292 RLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337
           RL L+ +    +++  E  L     R+R+V+ GPDG LYV T   DG
Sbjct: 332 RLQLQDD----KIVHEERLLGELKARIRDVRQGPDGYLYVLTDEDDG 374


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: 493
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: 382
Length adjustment: 30
Effective length of query: 322
Effective length of database: 352
Effective search space:   113344
Effective search space used:   113344
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