GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Sphingomonas koreensis DSMZ 15582

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Ga0059261_0844 Ga0059261_0844 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__Korea:Ga0059261_0844
          Length = 254

 Score =  127 bits (319), Expect = 2e-34
 Identities = 82/253 (32%), Positives = 135/253 (53%), Gaps = 7/253 (2%)

Query: 8   KDFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKD-VAAQINPSR----T 62
           K F++T KVA+VTG++ GIGKA AE  ++ GA VV+   K+D  D VAA IN        
Sbjct: 2   KLFDLTGKVAIVTGSSRGIGKASAEALADHGAKVVISSRKQDACDEVAAAINAKHGAGTA 61

Query: 63  LALQVDITKKENIEKVVAEIKKVYPKIDIL-ANSAGVALLEKAEDLPEEYWDKTMELNLK 121
           +A+   I+ K  ++ +V E ++ + +IDIL  N+A          + ++ + K ++ N+ 
Sbjct: 62  IAVAASISDKAALQNLVDETRRAFGRIDILVCNAASNPYYGPLAGIEDDQFRKILDNNII 121

Query: 122 GSFLMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPY 181
            +  + Q+   EM     G IV ++S   +       AY  SKAA   + +  A+E+ P 
Sbjct: 122 SNHWLIQMTAPEMRERKDGAIVIVSSIGGLRGSPVIGAYNVSKAADFQLARNYAVEYGPD 181

Query: 182 NINVNAISPTVILTELGKKAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLI 240
           N+ VN I+P +I T+  +  W     E  + +  P  R G PE++A   ++L S A   +
Sbjct: 182 NVRVNCIAPGLIRTDFARALWEDPAAEKRVNQGTPLRRLGEPEDIAGAVVYLASPAGRYM 241

Query: 241 TGENLIIDGGYTI 253
           TG+ +++DGG TI
Sbjct: 242 TGQAMVVDGGVTI 254


Lambda     K      H
   0.316    0.133    0.369 

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: 148
Number of extensions: 10
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: 254
Length of database: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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: 47 (22.7 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