GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Marinobacter adhaerens HP15

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF856 HP15_835 secreted protein containing glucose sorbosone dehydrogenase domain

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Marino:GFF856
          Length = 373

 Score =  207 bits (526), Expect = 5e-58
 Identities = 127/343 (37%), Positives = 186/343 (54%), Gaps = 37/343 (10%)

Query: 22  RVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRL-----STYAELPVYHRGESG 76
           R+E +  GLE PW+LAFLPDG ML+ ER GR+R+ R G L     S   EL V   G+ G
Sbjct: 34  RLETIAQGLEHPWSLAFLPDGSMLVTEREGRLRMIRNGALLSTPISGLPELVV--SGQGG 91

Query: 77  LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGERGVLDRVVLDGIPARPHGLH 135
           LL + LHP F +   ++ +Y      G+  +V R R  GER     V+ + +P      H
Sbjct: 92  LLDVILHPEFEQNQILFLSYAHRNRDGMTTRVARARLDGERLTGVDVIFEALPRSNTSRH 151

Query: 136 SGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPE 195
             GR+ F  +G LY++ G+  E + AQ+     G + R+T +G PAPGNPFL   G    
Sbjct: 152 FAGRMEFDREGNLYISVGDRGEMDRAQNNGDDAGGVHRITTDGGPAPGNPFLDTSGVNDT 211

Query: 196 VYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV---VGRG 252
            Y+ G+RN QG+  HP+TGE++S EHGP      G DE+N+I  G +YGWP +   +   
Sbjct: 212 FYTTGNRNIQGMTIHPETGEIWSHEHGPR-----GGDEINIIRAGTDYGWPTITFGIDYS 266

Query: 253 NDPRYRD--------PLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLE 296
             P   D        PL++W     P  +AF+        +GDL+V  L+ + L+RL ++
Sbjct: 267 GLPITDDTEKEGMAQPLHYWDPSIAPSGMAFYTGDLFPEWQGDLFVGALKMRKLVRLRIQ 326

Query: 297 GERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338
                 +V   E  L+  G R+R+V++GPDGAL++ T +  G+
Sbjct: 327 D----GKVTEEEDLLTDLGERIRDVRMGPDGALWLLTDSPRGK 365


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: 516
Number of extensions: 48
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: 373
Length adjustment: 29
Effective length of query: 323
Effective length of database: 344
Effective search space:   111112
Effective search space used:   111112
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