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_085218047.1 B9N75_RS06390 acetoacetyl-CoA reductase

Query= BRENDA::B8H1Z0
         (248 letters)



>NCBI__GCF_900177405.1:WP_085218047.1
          Length = 240

 Score = 98.2 bits (243), Expect = 1e-25
 Identities = 76/237 (32%), Positives = 110/237 (46%), Gaps = 11/237 (4%)

Query: 15  VITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCDLMNLE- 73
           ++TGG  GIG  ++     +G  V      +E+      E  G      YK  D+ + E 
Sbjct: 6   IVTGGTRGIGEAISLALRDKGLTVAANYAGNEEKAKAFTEKTGIK---AYK-WDVADFEG 61

Query: 74  ---AIKAVFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQAVAPGM 130
              A+K + A++G VDVLVNNAG      +  +    WD+ I+VNL       +AV  GM
Sbjct: 62  CVAAVKQIEADLGAVDVLVNNAGITRDGTMKRMDRNAWDDVIDVNLGGCFNMAKAVWEGM 121

Query: 131 KKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVVPGNVK 190
            +R  G ++N GSI+   G    V Y  AK+GI G T+ALA+E     I V  + PG + 
Sbjct: 122 SERKYGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGARAGITVNAIAPGYID 181

Query: 191 TKRQEKWYTPEGEAQIVAAQCLKGRI-VPENVAALVLFLASDDASLCTGHEYWIDAG 246
           T        P    Q + A+   GR+     +A  V FL ++D    TG    I+ G
Sbjct: 182 TDMVAA--VPADVLQKIVAKIPVGRLGQASEIARGVTFLCAEDGGFITGSTLSINGG 236


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: 155
Number of extensions: 13
Number of successful extensions: 2
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: 240
Length adjustment: 24
Effective length of query: 224
Effective length of database: 216
Effective search space:    48384
Effective search space used:    48384
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.

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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