GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pedobacter sp. GW460-11-11-14-LB5

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate CA265_RS03100 CA265_RS03100 glucose dehydrogenase

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Pedo557:CA265_RS03100
          Length = 403

 Score =  176 bits (447), Expect = 7e-49
 Identities = 121/335 (36%), Positives = 177/335 (52%), Gaps = 39/335 (11%)

Query: 30  LEVPWALAFLPDGGMLIAERPGR-IRLFREGRLST-YAELP-VYHRGESGLLGLALHPRF 86
           LE PWA++ LP+GG LI ++ G  + L  +G+LS     LP V   G+ GLL + L P F
Sbjct: 69  LENPWAISVLPNGGFLITQKQGTMVILTPDGKLSKKITGLPKVDPSGQGGLLDVTLDPNF 128

Query: 87  PEAPYVY-AYRTVAEGGLRNQVVRLRHLGERGVLDR--VVLDGIPARPHGLHSGGRIAFG 143
            +   +Y AY    + G+   + + +       ++   ++    PA    L  G RI F 
Sbjct: 129 AKNRMIYWAYSEPQDKGVLLAIAKGKLAANETTIENQSIIYRATPAYGGKLQYGSRIVFD 188

Query: 144 PDGMLYVTTGEVYEREL---AQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVYSLG 200
            +G L+V+TGE    ++   AQ L S  GKIL LT +G+     PF G+  A+PE+Y+ G
Sbjct: 189 KNGNLFVSTGERSGSDIRIQAQYLNSSLGKILHLTTDGKAVANGPFAGKADAKPEIYAYG 248

Query: 201 HRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWP----------RVVG 250
            RNP GLA +P TG+L+ +E GP      G DEVN+I PG NYGWP          + VG
Sbjct: 249 LRNPDGLAINPLTGDLWEAEFGPK-----GGDEVNIIKPGKNYGWPIITYGTEYSGKKVG 303

Query: 251 RGNDPR--YRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLEGERG 300
            G   +     P+Y+W     PG +AF+        +G+L+V GL G  ++RLV++ +  
Sbjct: 304 DGIQQKEGMEQPVYYWNPSISPGCIAFYNSSSIAEWKGNLFVGGLGGSHIIRLVIKDD-- 361

Query: 301 RWRVLRVETALSGFG-RLREVQVGPDGALYVTTSN 334
             +++  E  L G G R R++  G DGALY  T N
Sbjct: 362 --KIVGEERLLEGKGERFRDMVEGKDGALYSVTDN 394


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: 471
Number of extensions: 43
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: 403
Length adjustment: 30
Effective length of query: 322
Effective length of database: 373
Effective search space:   120106
Effective search space used:   120106
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: 50 (23.9 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