GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Dinoroseobacter shibae DFL-12

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate 3608476 Dshi_1872 hypothetical protein (RefSeq)

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Dino:3608476
          Length = 422

 Score =  143 bits (360), Expect = 9e-39
 Identities = 97/271 (35%), Positives = 140/271 (51%), Gaps = 41/271 (15%)

Query: 16  ARGQGLRVEEVVGGLEVPWALAFLPDGGMLIAER---------PGRIR--LFREGRLSTY 64
           A    L  E V+ GLE PW +AFL DG M   E+          G +   L  +G    Y
Sbjct: 26  ANTTSLSHEIVLEGLENPWDVAFLEDGTMFFTEKCLGLSVRLPDGSVNKLLGMKGTDDDY 85

Query: 65  AELP--VYHRGESGLLGLALHPRFPEAPYVYAYRT---VAEGGLRNQVVRLRHLGE--RG 117
           A     ++  G++G+ G+A+ P F E   +Y Y T    A G   N+++R+  +GE    
Sbjct: 86  ASTAEDLFCEGQAGMQGVAVDPDFAENRQIYVYSTSDLTAPGS--NRLLRMT-VGEDLAS 142

Query: 118 VLDRV-VLDGIPARPH---------GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASL 167
           V DR  +++ +P +P          G H+GGR+ FGPDG +Y+TTG+ +  E  Q    L
Sbjct: 143 VADRTDIVEDVPYKPAATDHPFGGPGAHNGGRVRFGPDGFIYLTTGDTHNGEGPQSPTLL 202

Query: 168 GGKILRLTPEGEPAPGNPFLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQ 227
            GK+LR+  +G  A GN      G  P +Y+ GHRN QG+ +HP+TG   ++EHGP    
Sbjct: 203 AGKVLRIDRDGNAAEGN--APPEGFDPRIYTYGHRNTQGITFHPETGAAITAEHGP---- 256

Query: 228 GYGHDEVNLIVPGGNYGW---PRVVGRGNDP 255
            +  DE+ ++  GGN GW   P V GRG  P
Sbjct: 257 -WHSDEITVLQNGGNAGWDPRPNVGGRGECP 286



 Score = 24.6 bits (52), Expect = 0.005
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 320 VQVGPDGALYVTTSN-RDGRGQVRP 343
           V+ GPDG +Y+TT +  +G G   P
Sbjct: 175 VRFGPDGFIYLTTGDTHNGEGPQSP 199


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: 540
Number of extensions: 35
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 352
Length of database: 422
Length adjustment: 30
Effective length of query: 322
Effective length of database: 392
Effective search space:   126224
Effective search space used:   126224
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