GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Shewanella loihica PV-4

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__PV4:5209125
          Length = 248

 Score =  135 bits (340), Expect = 8e-37
 Identities = 81/242 (33%), Positives = 131/242 (54%), Gaps = 1/242 (0%)

Query: 9   DFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVD 68
           + ++T KVA+VTGA+ GIG+A+AE   E GA V+     E       +    +   L ++
Sbjct: 4   NLDLTGKVALVTGASRGIGRAVAETLVEAGALVIGTATSERGAAAIQEYLGDKGHGLVLN 63

Query: 69  ITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128
           +T  E+I+ + A IK+   ++DIL N+AG+        + E+ W   ++ NL   +  ++
Sbjct: 64  VTDSESIDHLFASIKEKVGEVDILVNNAGITRDNLLMRMKEDEWTDIIDTNLTSLYRTSK 123

Query: 129 IIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188
            + R M+    G+I+N+ S    +       YCA+KA ++  T+ LA E A   I VNAI
Sbjct: 124 QVLRAMMKKRSGRIINIGSVVGTMGNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAI 183

Query: 189 SPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIID 248
           +P  I T++  +    Q    M + +P  R G P+E+A   LFL SD+A+ ITGE L ++
Sbjct: 184 APGFIQTDMTDELTEEQQKGIMSQ-VPMERLGQPQEIANAVLFLASDSAAYITGETLHVN 242

Query: 249 GG 250
           GG
Sbjct: 243 GG 244


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: 142
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: 248
Length adjustment: 24
Effective length of query: 230
Effective length of database: 224
Effective search space:    51520
Effective search space used:    51520
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 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