GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Maridesulfovibrio zosterae DSM 11974

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_000425265.1:WP_027723082.1
          Length = 240

 Score =  115 bits (288), Expect = 8e-31
 Identities = 78/242 (32%), Positives = 132/242 (54%), Gaps = 13/242 (5%)

Query: 15  KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED---VKDVAAQINP--SRTLALQVDI 69
           K+A++TGA+ GIG A+A   +E G Y + L+ + D       A QI     +   L+ D+
Sbjct: 3   KIALITGASKGIGAAIAVQLAEDG-YDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDV 61

Query: 70  TKKENIEKVVAEI-KKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128
           T ++ +E+ ++ + +K  P I  + N+AG         +    W+K ++++L G F + +
Sbjct: 62  TDEKAVEENLSSLLEKKVPYI--VVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTK 119

Query: 129 IIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188
            +   M+    G+I+N+AS +    +     YCA+KA ++  T+ LAME A  NI VNA+
Sbjct: 120 PVVSRMLRKRTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAV 179

Query: 189 SPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIID 248
           +P  I T++  +       +++K  IP  R G P+EVA    FL SD AS ITG+ + ++
Sbjct: 180 TPGFIDTDMLSELPV----DEIKNTIPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAVN 235

Query: 249 GG 250
           GG
Sbjct: 236 GG 237


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: 133
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: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
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