GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Methylocystis bryophila S285

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  130 bits (327), Expect = 3e-35
 Identities = 78/241 (32%), Positives = 129/241 (53%), Gaps = 1/241 (0%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDI 69
           F++T K A+VTGA+SG+G A+A    + GA V L   + +  +  A     R   L  ++
Sbjct: 2   FDLTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCNL 61

Query: 70  TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129
           + +   +K++   +     +DIL N+AG+        + +E WD  + +NL  +F +++ 
Sbjct: 62  SDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSRA 121

Query: 130 IGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAIS 189
           + R M+    G+I+N+ S A  +       Y A+KA +  MT+ LA E A   + VN ++
Sbjct: 122 VLRGMMRKRHGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCVA 181

Query: 190 PTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIIDG 249
           P VI + + +     Q  E + KLIP  RFG  +E+ A  L+L SD A+ ITG+ L I+G
Sbjct: 182 PGVIESPMTQVLNEAQ-RERLLKLIPMERFGSADEIGAAVLYLASDEAAFITGQTLHING 240

Query: 250 G 250
           G
Sbjct: 241 G 241


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: 114
Number of extensions: 6
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: 246
Length adjustment: 24
Effective length of query: 230
Effective length of database: 222
Effective search space:    51060
Effective search space used:    51060
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: 46 (22.3 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