GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Phaeobacter inhibens BS107

Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate GFF3849 PGA1_78p00130 putative oxidoreductase, GFO/IDH/MOCA family

Query= BRENDA::D4GP30
         (325 letters)



>FitnessBrowser__Phaeo:GFF3849
          Length = 374

 Score = 73.9 bits (180), Expect = 6e-18
 Identities = 66/220 (30%), Positives = 99/220 (45%), Gaps = 25/220 (11%)

Query: 28  AAIASRDEARASAVADELGIPT--AYGSYEALLA-----DDSLDAVYIPLPNGLHADWVR 80
           A   S D ARASA A ELGI    +Y S+  +       +D +DAV I  PN LHA    
Sbjct: 40  AGALSSDPARASASAAELGIDPDRSYASFAEMAEAEAAREDGIDAVAIVTPNHLHAGPSI 99

Query: 81  AAADRGLHVLCEKPLTASADETAAVFDYCEDAGVTLMEAFMYRFHPLTERAAELVA-SEL 139
           A  + G+HV+C+KPL AS  E  A+ D    +         Y  +PL  +A  +VA  +L
Sbjct: 100 AFLNAGIHVICDKPLAASVAEAEAIKDAARSSSARFFLTHNYTGYPLLRQARAMVARGDL 159

Query: 140 GAVVSVTSNFSFRLPDGADDI-----------RIDPDLAG-GSVMDVGCYAVSAARLFLG 187
           G +  V + ++    D   ++           R DP  +G G++ D+G +A + A    G
Sbjct: 160 GRIRLVQAEYA---QDWLTNVIEQEGHKQAAWRTDPAQSGAGAIGDIGTHAFNIACFVSG 216

Query: 188 TPDRVYATTTDTRDCG--VDTRMSGVLEYDSGATARVESS 225
              +  +    +   G  VD     +L Y  GA   + +S
Sbjct: 217 LAPQALSAELHSFGPGRQVDDNAHILLRYAEGARGMLWAS 256


Lambda     K      H
   0.316    0.131    0.371 

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: 278
Number of extensions: 13
Number of successful extensions: 1
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: 325
Length of database: 374
Length adjustment: 29
Effective length of query: 296
Effective length of database: 345
Effective search space:   102120
Effective search space used:   102120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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