GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Haloglycomyces albus DSM 45210

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_025272126.1 HALAL_RS0100575 SDR family NAD(P)-dependent oxidoreductase

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_000527155.1:WP_025272126.1
          Length = 290

 Score =  106 bits (265), Expect = 5e-28
 Identities = 75/253 (29%), Positives = 132/253 (52%), Gaps = 17/253 (6%)

Query: 11  NITDKVAVVTGAAS--GIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVD 68
           ++  K A+VTGA +  GIG A+A      GA + L+   + + + A +++    +    D
Sbjct: 45  SLIGKTALVTGAGADDGIGMAIATRLRLAGARLALVSTTKRIHERANELD---AVGFVAD 101

Query: 69  ITKKENIEKVVAEIKKVYPKIDILANSAGV------ALLEKAEDLPEEYWDKTMELNLKG 122
           +T +  +  +   + +   ++DI+ N+AG+      A+ +    L  + W+  +  NL  
Sbjct: 102 LTDEAEVAGLGDAVTEGLGEVDIVVNNAGMTSKTAPAVTKPVAQLGFDDWEAEITRNLHS 161

Query: 123 SFLMAQIIGREMIATGGGKIVNMASQASVIA-LDKHVAYCASKAAIVSMTQVLAMEWAPY 181
           +FL+++   + M  +G G+IVN+++ A V + +    AY ++KA +  +T+ LA E    
Sbjct: 162 TFLVSRYFVQSMAESGWGRIVNVSATAGVSSVMPAEAAYASAKAGVAGLTRALATEVVAD 221

Query: 182 NINVNAISPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLIT 241
            + VNA++P +I T         Q G D     P GR G PEEVAA   F  S +AS +T
Sbjct: 222 GVTVNAVAPGLIHTGSSTVPEL-QRGVDS----PLGRPGTPEEVAAAVAFFCSPSASYVT 276

Query: 242 GENLIIDGGYTIK 254
           G+ L++DGG  I+
Sbjct: 277 GQTLVVDGGNGIR 289


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: 156
Number of extensions: 11
Number of successful extensions: 4
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: 290
Length adjustment: 25
Effective length of query: 229
Effective length of database: 265
Effective search space:    60685
Effective search space used:    60685
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 Apr 09 2024. 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