GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas simiae WCS417

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2578 PS417_13140 oxidoreductase

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__WCS417:GFF2578
          Length = 385

 Score =  192 bits (488), Expect = 1e-53
 Identities = 132/345 (38%), Positives = 187/345 (54%), Gaps = 44/345 (12%)

Query: 26  VVGGLEVPWALAFLPDG-GMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLGLA 81
           +  GL+ PWA+AFLPD  G L+ ERPG +R    +G+LS   + +P V+ +G+ GLL + 
Sbjct: 42  IAKGLDHPWAVAFLPDKQGFLVTERPGHLRFVSPDGKLSAPLKGVPEVWAKGQGGLLDVV 101

Query: 82  LHPRFPEAPYVYAYRTVAEGGLRN-----QVVRLRHLGE-RGVLD-RVVLDGIPARPHGL 134
           L P F E   VY   + AEGG ++      V R R   +  G+ D +V+L   P    G 
Sbjct: 102 LSPDFKEDRTVYL--SYAEGGGKDGTAGTAVGRGRLAADLSGLTDFKVILRQEPKLSTGN 159

Query: 135 HSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARP 194
           H G R+AF  DG L+VT GE  +R  AQDL  L GK++R+ P+G     NPF+G++G RP
Sbjct: 160 HFGSRLAFDRDGYLFVTLGENNDRPTAQDLDKLQGKVVRIYPDGRVPDDNPFVGQQGVRP 219

Query: 195 EVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGN- 253
           E++S G RNPQGLA +P +G ++ +EHGP      G DE+N+I  G NYGWP      N 
Sbjct: 220 EIWSYGQRNPQGLALNPWSGTIWENEHGPR-----GGDEINIIERGKNYGWPLATHGINY 274

Query: 254 ----DPRYR--------DPLYFWPQGFPPGNLAFFRGD--------LYVAGLRGQALLRL 293
                P  +         P + W +      +AF+  D        +++  L  Q L+RL
Sbjct: 275 SLTPIPEAKGKTVEGTVPPHHVWEKSPGISGMAFYDADRFKPWQHNVFIGALATQELIRL 334

Query: 294 VLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337
             +G+    +V+  E  L G   R+R+V+ GPDG LYV T   DG
Sbjct: 335 QFDGD----KVIHEERLLGGLKARIRDVRQGPDGFLYVLTDEEDG 375


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: 42
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: 385
Length adjustment: 30
Effective length of query: 322
Effective length of database: 355
Effective search space:   114310
Effective search space used:   114310
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