GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Dinoroseobacter shibae DFL-12

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 3607131 Dshi_0553 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__Dino:3607131
          Length = 255

 Score =  174 bits (442), Expect = 1e-48
 Identities = 97/247 (39%), Positives = 151/247 (61%), Gaps = 4/247 (1%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED-VKDVAAQINPS--RTLALQ 66
           F++ DK A+VTGA+SGIG+A+AE+F++ GA +V      D + D+ AQI  +  +  A+ 
Sbjct: 7   FSLQDKTALVTGASSGIGRAIAEVFADAGADIVGQGRDLDRLTDLGAQIKTTGRQFAAIT 66

Query: 67  VDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLM 126
            D+   +  + V       + KIDIL NSAG+A+     +   + W +T+ +NL   F++
Sbjct: 67  GDLADPDQTQNVADRALAAFGKIDILVNSAGIAVTGPVTNYDLDDWQRTLAVNLTAPFIL 126

Query: 127 AQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVN 186
           ++ +   M+    GKI+N++SQ  VIAL  H AY  SK  + ++T+ L  E AP+N+ VN
Sbjct: 127 SKAVMPGMMQRKQGKIINISSQTGVIALKDHAAYATSKGGLNALTKSLMTEAAPHNVQVN 186

Query: 187 AISPTVILTELGKKAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLITGENL 245
           AI PTV+LTE+GK+ W+    +D      P GRFG P E+A  AL+L S A+ L+ G  +
Sbjct: 187 AICPTVVLTEMGKELWSAPERKDPFIARTPLGRFGEPIEIADMALYLASPASDLVNGAVM 246

Query: 246 IIDGGYT 252
           +I+GGY+
Sbjct: 247 MIEGGYS 253


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: 169
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: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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 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