GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Flavobacterium sp. LM5

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_002017945.1:WP_024981780.1
          Length = 248

 Score =  119 bits (298), Expect = 6e-32
 Identities = 77/244 (31%), Positives = 124/244 (50%), Gaps = 6/244 (2%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVAL-WDLNGDALAATQAEIDATHVVALDVSDHA 68
           G+ AI+TG + G+GK +A      G  +A  +  + ++  A + E++   + A     +A
Sbjct: 6   GKVAIITGASRGIGKGIAEVFAKHGANIAFTYSSSVESALALENELNTMGIKAKGYQSNA 65

Query: 69  AVAAAAKDSAAAL----GKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNR 124
           A    A+    A+    G VDILI +AGIT   + +     D F +VID+NL  +F   +
Sbjct: 66  ADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMMRMSEAD-FDQVIDVNLKSVFNMTK 124

Query: 125 EVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANAL 184
            +    L+   G I+N++SV G +GN   + Y+ASKAGVIGF+KS+  EL  + +  N +
Sbjct: 125 AIQKTFLKQRAGSIINMSSVVGVKGNAGQTNYAASKAGVIGFSKSVALELGSRNIRCNVI 184

Query: 185 TPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSG 244
            P   E+ +  +L    V   R  IP+ R G  ++ A    F AS+  ++ T    +  G
Sbjct: 185 APGFIETEMTAKLSDDVVKGWREGIPLKRGGSTDDVANACLFFASDMSAYVTGQVLNVCG 244

Query: 245 GRTT 248
           G  T
Sbjct: 245 GMLT 248


Lambda     K      H
   0.318    0.132    0.381 

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: 131
Number of extensions: 7
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: 249
Length of database: 248
Length adjustment: 24
Effective length of query: 225
Effective length of database: 224
Effective search space:    50400
Effective search space used:    50400
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 24 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