GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas putida KT2440

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate PP_2198 PP_2198 aldose sugar dehydrogenase

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Putida:PP_2198
          Length = 381

 Score =  191 bits (484), Expect = 3e-53
 Identities = 131/348 (37%), Positives = 182/348 (52%), Gaps = 41/348 (11%)

Query: 21  LRVEEVVGGLEVPWALAFLPDG-GMLIAERPGRIRLFR-EGRLS-TYAELP-VYHRGESG 76
           L V+ +  GL  PWALAFLP G  ML+ ER G +RL   EG++  + + +P V+  G+ G
Sbjct: 35  LIVDTLADGLRNPWALAFLPGGKDMLVTERAGNLRLVNAEGKVGPSISGVPKVWAEGQGG 94

Query: 77  LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE-RGVLDR--VVLDGIPARPH 132
           LL +AL P F +   VY +Y      G     V    L E R  L+   V+    P    
Sbjct: 95  LLDVALSPEFGKDRTVYLSYAEEGSDGKAGTAVGRGQLSEDRARLENFTVIFRQQPKLSV 154

Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192
           G H G R+ F  DG L++  GE  +R  AQDL  L GK++R+ P+GE    NPF+G+   
Sbjct: 155 GNHFGSRLVFDRDGYLFIALGENNQRPTAQDLDKLQGKVVRILPDGEVPKDNPFVGKDNV 214

Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGW------- 245
           RPE++S GHRN QG A +P TG+L++ EHGP      G DE+N+  PG NYGW       
Sbjct: 215 RPEIWSYGHRNQQGAALNPWTGQLWTHEHGPR-----GGDEINIPKPGKNYGWPIATHGI 269

Query: 246 -------PRVVGRGNDPRYRDPLYFWPQGFPPGNLAFFRG--------DLYVAGLRGQAL 290
                  P   G   D    DP + W +      +AF+          +L++  L  Q L
Sbjct: 270 NYSLLPIPEAKGEHVDGMV-DPHHVWEKSPGISGMAFYDSPTFKAWDHNLFIGALATQEL 328

Query: 291 LRLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337
           +RL L+G+    +V+  E  L     R+R+V+VGPDG LYV T ++DG
Sbjct: 329 IRLQLDGD----KVVHEERLLGDLKARIRDVRVGPDGYLYVLTDDKDG 372


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: 498
Number of extensions: 33
Number of successful extensions: 6
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: 381
Length adjustment: 30
Effective length of query: 322
Effective length of database: 351
Effective search space:   113022
Effective search space used:   113022
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