GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Desulfovibrio vulgaris Miyazaki F

Align BadH (characterized)
to candidate 8502147 DvMF_2858 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__Miya:8502147
          Length = 245

 Score =  124 bits (312), Expect = 1e-33
 Identities = 80/245 (32%), Positives = 118/245 (48%), Gaps = 8/245 (3%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65
           + A++TGG  GIG A   R AQ+G  + V +  N  AA +V  AI   GG A AV  D+ 
Sbjct: 6   RNAIVTGGSRGIGRAIALRLAQDGFCVVVNYASNAPAALEVVDAIARTGGQAVAVPADVG 65

Query: 66  DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAV 125
           +   V+   A      G V ++VN+AG     P    +   +E+++  NLTG  ++    
Sbjct: 66  ETGDVEGLFAAAHDAFGQVGVVVNSAGIMPMLPIAGGDTAAFEKVLRTNLTGTFNVLSRA 125

Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185
              +     GRI+ +++        G   Y A K G+    + LA E     ITVN V P
Sbjct: 126 ANALT--AGGRIIALSTSVIAKPFPGYGPYIASKAGVEGLVRVLANELRGRSITVNAVAP 183

Query: 186 GPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVL 245
           GP  T L  +        E+ I A  K  PL RLG P+++AG ++F    + G+I  QV+
Sbjct: 184 GPVATDLFLN-----GKTEEQIAAIGKLAPLERLGTPEEIAGVVSFLVGPEGGWINAQVV 238

Query: 246 SVSGG 250
            V+GG
Sbjct: 239 RVNGG 243


Lambda     K      H
   0.318    0.135    0.398 

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: 176
Number of extensions: 15
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
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 (21.7 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