GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Dechlorosoma suillum PS

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Dsui_2448 Dsui_2448 3-oxoacyl-(acyl-carrier-protein) reductase

Query= reanno::Korea:Ga0059261_1894
         (259 letters)



>FitnessBrowser__PS:Dsui_2448
          Length = 246

 Score =  120 bits (300), Expect = 3e-32
 Identities = 92/247 (37%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 16  LKGKRVLVTGGGSGIGAGIVEGFARQGADV----TFFDIAGAESQLLVERLSADGHKACF 71
           L+G+  LVTG   GIG  +    AR GA V    T  D AG  S  L E   A G  A  
Sbjct: 2   LQGQIALVTGASRGIGKAVALELARLGATVVGTATSDDGAGKISAYLAEA-GAKGRGALL 60

Query: 72  ERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIF 131
           E   + D A + A+IA L K  G   ILVNNA     +    + +  WD  +  NLK +F
Sbjct: 61  E---VRDQAQVDALIAALEKEFGAVSILVNNAGITRDNLAMRMKDDEWDAVIDTNLKAVF 117

Query: 132 FCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIR 191
             ++AV+  M     G I+N+ S+  H G      Y   KA + G+TRSLAR+LG   I 
Sbjct: 118 RLSKAVMRGMMKARAGRIINITSVVGHAGNPGQANYCAAKAGVSGMTRSLARELGSRNIT 177

Query: 192 ATCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRL-APEDVAAMVLFLASDDARLVTGH 250
             CV PG + T   +     + + E +      GRL +PED+AA V FLAS  A  VTG 
Sbjct: 178 VNCVAPGFIDT--DMTKALDDKQKEGLLGNIPLGRLGSPEDIAAAVAFLASPAAGYVTGS 235

Query: 251 SYFVDAG 257
           +  V+ G
Sbjct: 236 TIHVNGG 242


Lambda     K      H
   0.321    0.137    0.409 

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: 144
Number of extensions: 7
Number of successful extensions: 3
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: 259
Length of database: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
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 (21.9 bits)
S2: 46 (22.3 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