GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Nocardiopsis gilva YIM 90087

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_094932674.1 CDO52_RS22395 PQQ-dependent sugar dehydrogenase

Query= BRENDA::I7A144
         (352 letters)



>NCBI__GCF_002263495.1:WP_094932674.1
          Length = 382

 Score =  252 bits (644), Expect = 1e-71
 Identities = 153/337 (45%), Positives = 198/337 (58%), Gaps = 31/337 (9%)

Query: 25  EVVGGLEVPWALAFLPDGGMLIAERPGR--IRLFREGRLSTYAELPVYH-RGESGLLGLA 81
           +V   LEVPW +AFLPDG  L+ ER     +R+   G ++    +     RGE GLLGLA
Sbjct: 63  DVATDLEVPWDIAFLPDGAALVTERDSARIVRVEPGGEVTEVGTVDAAAPRGEGGLLGLA 122

Query: 82  LHPRFPEAPYVYAYRTVAEGGLRNQVVRLRHLGERGVLD-RVVLDGIPARPHGLHSGGRI 140
           +HP +P  P +Y Y T A+    N+++R+ +  + G+ +  VVLDGIP     +H+GGRI
Sbjct: 123 VHPHYPADPAIYVYVTAADD---NRILRMSYAADSGLGEPEVVLDGIPKA--AVHNGGRI 177

Query: 141 AFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVYSLG 200
           AFGPDG+LY +TG+  E   AQD  SLGGKILR+TP+G+    NPF         VYS G
Sbjct: 178 AFGPDGLLYASTGDATEGSTAQDTGSLGGKILRMTPDGKAPDDNPFGNL------VYSYG 231

Query: 201 HRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGNDPRYRDP 260
           HRN QGLAW  + G LF++E G        +DE+N+I PG NYGWP V G G D RY +P
Sbjct: 232 HRNVQGLAWDDE-GRLFATEFGQD-----TYDEINVIEPGDNYGWPEVEGIGGDDRYTEP 285

Query: 261 LYFW-PQGFPPGNLAFFRGDLYVAGLRGQALLRLVLEGER----GRWRVLRVETALSGFG 315
           +  W P    P   A   G L+VA LRG+ L ++ L G+     G    L VE     +G
Sbjct: 286 VVVWRPAEASPSGGAIAGGALWVAALRGERLWKVPLTGDADDPVGDPEALYVER----YG 341

Query: 316 RLREVQVGPDGA-LYVTTSNRDGRGQVRPGDDRVLRL 351
           RLR V   P G  L+V TSNRDGRG    GDDR+LR+
Sbjct: 342 RLRSVTTAPGGTELWVGTSNRDGRGSPASGDDRILRV 378


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: 635
Number of extensions: 47
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: 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 24 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