GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas stutzeri RCH2

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2859 Psest_2915 Glucose/sorbosone dehydrogenases

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__psRCH2:GFF2859
          Length = 382

 Score =  186 bits (472), Expect = 9e-52
 Identities = 129/348 (37%), Positives = 182/348 (52%), Gaps = 43/348 (12%)

Query: 23  VEEVVGGLEVPWALAFLPDGG-MLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLL 78
           V E+  G E PWALAFLPDG  ML+ ERPGR+RL   +G  S   E +P V+ + + GLL
Sbjct: 37  VREIAAGFENPWALAFLPDGEHMLVTERPGRLRLVGLDGSRSKPLEGVPEVFAQAQGGLL 96

Query: 79  GLALHPRFPEAPYVYAYRTVAEGGLRNQ----VVRLRHLGERGVLDR--VVLDGIPARPH 132
            + L P F     VY   T AE G + +    V R R   +   L+   V+   +P    
Sbjct: 97  DVRLSPDFESDRLVYL--TYAEAGEQGKAGTAVGRGRLSDDHSKLENFEVIFRQLPKLST 154

Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192
           G+H G R+ F  DG L+V  GE  +R  +QDL    GK++R+  +G     NPF+G+ G 
Sbjct: 155 GIHFGSRLVFDNDGHLFVALGENNQRPTSQDLDKHQGKVVRIGLDGSVPDDNPFIGQEGV 214

Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRG 252
           RPE++S GHRN QG A +P +G L+++EHGP      G DEVN+   G NYGWP      
Sbjct: 215 RPEIWSYGHRNQQGAALNPWSGVLWTNEHGPR-----GGDEVNIPQAGKNYGWPLATHGI 269

Query: 253 NDPRY-------------RDPLYFWPQGFPPGNLAFFRGD--------LYVAGLRGQALL 291
           N                   P + W +      +AF+ G+        L++  L  Q+L+
Sbjct: 270 NYSMLPIPEAKGKAVEGTEQPHHVWGKSPGVSGMAFYDGERFAAWQHSLFIGALVDQSLI 329

Query: 292 RLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338
           RL L+G+    R++  E  L   G R+R+V+VGPDG +Y+ T   DG+
Sbjct: 330 RLRLDGD----RIVGEERLLKDLGARIRDVRVGPDGYVYLLTDAGDGK 373


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: 459
Number of extensions: 39
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: 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