GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Sphingomonas indica Dd16

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_085218502.1 B9N75_RS09070 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::B8H1Z0
         (248 letters)



>NCBI__GCF_900177405.1:WP_085218502.1
          Length = 258

 Score = 77.0 bits (188), Expect = 3e-19
 Identities = 58/181 (32%), Positives = 87/181 (48%), Gaps = 5/181 (2%)

Query: 15  VITGGGSGIGAGLTAGFARQGAEVIFL-DIADEDSRALEAELAGSPIPPVYKRCDLMNLE 73
           ++TG  +GIG  L    A  G ++I   D A+ +S A      G  + PV  + DL   +
Sbjct: 8   IVTGASTGIGFELAKCCAADGYDLIIAADEAEIESAAETLRATGVWVQPV--QADLGTPD 65

Query: 74  AIKAVFAEIGD--VDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQAVAPGMK 131
            +  + AEIGD  VD L+ NAG    H   D         I VN+   +   Q V  GM+
Sbjct: 66  GVDKLIAEIGDRPVDALLANAGRGLGHAFLDQDFDEIAAVIGVNVTGTVALVQQVGRGMR 125

Query: 132 KRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVVPGNVKT 191
            R  G ++  GSI+ +L      +Y   KA ++  + AL  EL   +I VTC++PG  +T
Sbjct: 126 DRNKGRILITGSIAGYLPGSFQAVYNGTKAFLDSFSYALGNELKDTEITVTCLMPGATET 185

Query: 192 K 192
           +
Sbjct: 186 E 186


Lambda     K      H
   0.319    0.137    0.416 

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: 136
Number of extensions: 5
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: 248
Length of database: 258
Length adjustment: 24
Effective length of query: 224
Effective length of database: 234
Effective search space:    52416
Effective search space used:    52416
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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