GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Acidovorax sp. GW101-3H11

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Ac3H11_2201 PQQ-dependent oxidoreductase, gdhB family

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2201
          Length = 383

 Score =  182 bits (463), Expect = 1e-50
 Identities = 132/351 (37%), Positives = 174/351 (49%), Gaps = 40/351 (11%)

Query: 18  GQGLRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFRE-GRL--STYAELPVYHRGE 74
           G  + +  V  GL  PWALAFLPDG  L+ ERPGR+R+    G+L  +     PV   G+
Sbjct: 36  GPAVSLVPVATGLANPWALAFLPDGQFLLTERPGRMRVVSATGQLGPALAGVPPVAAGGQ 95

Query: 75  SGLLGLALHPRFPEAPYVY-AYRTVAEGGLRN--QVVRLRHLGERGVLD--RVVLDGIPA 129
            GLL +     F     +Y  +  +A  G  N   V R     +   L   RVV    P 
Sbjct: 96  GGLLDVVTDADFARNRRIYFCFSELATSGAGNGTAVARATLAADAKSLQDVRVVFSQRPK 155

Query: 130 RPHGLHSGGRIAFGPDGMLYVTTGEVYER-ELAQDLASLGGKILRLTPEGEPAPGNPFLG 188
               LH G RI   PDG L+V  GE Y R + AQ L +  GK++R+TP+G   PGNPF  
Sbjct: 156 VESALHFGCRIVQAPDGNLFVALGERYHRKDDAQKLDNHHGKVIRITPDGAVPPGNPFTN 215

Query: 189 RRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV 248
           + G  PE++S GHRNPQG    P  G+L+  EHGP      G DE+NL  PG NYGWP +
Sbjct: 216 QPGTLPEIWSYGHRNPQGATIGP-DGKLWMHEHGPQ-----GGDEINLPQPGRNYGWPVI 269

Query: 249 ----------VGRGN-DPRYRDPLYFWPQGFPPGNLAF---------FRGDLYVAGLRGQ 288
                     +G G        PL+ W     P  +AF         ++G L+V  L+  
Sbjct: 270 TYGENYGGGKMGEGTARAGMEQPLHHWTPSLAPSGMAFLTSTRYGAAWQGSLFVGSLKFG 329

Query: 289 ALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338
            L RL + G     ++ R E  L G G R+R+V+ GPDG LY+ T +  GR
Sbjct: 330 TLHRLEVAG----GKLQREEKLLQGNGERIRDVRQGPDGLLYMVTDSPQGR 376


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: 579
Number of extensions: 50
Number of successful extensions: 8
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: 383
Length adjustment: 30
Effective length of query: 322
Effective length of database: 353
Effective search space:   113666
Effective search space used:   113666
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