GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Azospirillum brasilense Sp245

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate AZOBR_RS31355 AZOBR_RS31355 putative glucose dehydrogenase precursor

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__azobra:AZOBR_RS31355
          Length = 386

 Score =  186 bits (471), Expect = 1e-51
 Identities = 131/357 (36%), Positives = 182/357 (50%), Gaps = 55/357 (15%)

Query: 23  VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLG 79
           V+ V  GL  PW LAFLPDG ML+ E+ GR+R+   +G +S   + +P V  RG+ GLL 
Sbjct: 38  VKTVASGLSHPWGLAFLPDGRMLVTEKDGRLRIVAPDGTVSAPVKGVPKVDDRGQGGLLD 97

Query: 80  LALHPRFPEAPYVYAYRTV--AEGGLRNQVVRLRHLGERGVLD---------RVVLDGIP 128
           +AL P F +  +VY   +    E G  +  V       RGVL+         RV+    P
Sbjct: 98  VALDPEFAQNRFVYLSFSEPGTEDGTNSTAVA------RGVLNADETALTDVRVIFSQKP 151

Query: 129 ARPHGLHSGGRIAFGPDGMLYVTTGE---VYERELAQDLASLGGKILRLTPEGEPAPGNP 185
                +H G R+ F   G LYVT GE      R  AQDL S  GK++R+  +G     NP
Sbjct: 152 KVESRMHYGSRLVFDRQGHLYVTLGERSLEQFRTQAQDLDSHLGKVVRINRDGSVPADNP 211

Query: 186 FLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGW 245
           F+ + GA PE++S GHRN QG A +P+TG L+ +EHGP      G DEVN+  PG NYGW
Sbjct: 212 FVNQSGALPEIWSYGHRNIQGAALNPQTGALWINEHGPR-----GGDEVNVPEPGKNYGW 266

Query: 246 PRV------------VGRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGL 285
           P V             G+ + P   +P+Y W        + F+        +G L+  GL
Sbjct: 267 PVVSYGVNYNGTPIGTGKSSAPGMEEPVYQWTPVIGSSGMTFYTADTLPGWKGSLFNGGL 326

Query: 286 RGQALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGRGQV 341
             + ++RL L+G     +V   E      G R+R+V  GPDGALY+ T   + RG++
Sbjct: 327 ATKEVVRLELDGN----KVKHEERMFRDLGKRIRQVSQGPDGALYLLTD--ENRGEI 377



 Score = 29.3 bits (64), Expect = 2e-04
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 12/42 (28%)

Query: 139 RIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEP 180
           +++ GPDG LY+ T E              G+ILR+TP G+P
Sbjct: 357 QVSQGPDGALYLLTDENR------------GEILRVTPAGKP 386


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: 484
Number of extensions: 41
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 352
Length of database: 386
Length adjustment: 30
Effective length of query: 322
Effective length of database: 356
Effective search space:   114632
Effective search space used:   114632
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