GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS15450 CA265_RS15450 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__Pedo557:CA265_RS15450
          Length = 247

 Score =  121 bits (304), Expect = 1e-32
 Identities = 76/242 (31%), Positives = 123/242 (50%), Gaps = 8/242 (3%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLN----GDALAATQAEIDATHVVAL--D 63
           G+ A+VTG + G+G+++A +   +G  VA   L+    G+AL   + +   T V     D
Sbjct: 6   GKTALVTGASKGIGRKIAEKFAEQGANVAFTYLSSVEKGEALEQ-ELQSFGTKVKGYRSD 64

Query: 64  VSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCN 123
            S  A       D  A  G +DI++ +AGIT   + +     +++  VI+INL  +F   
Sbjct: 65  ASKFAEAEQLINDIVAEFGTIDIVVNNAGITKDGL-LMRMSEENWDDVININLKSIFNVT 123

Query: 124 REVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANA 183
           +     M++   G  +N+ S+ G  GN   + Y+ASKAG+IGFTKS+ KEL  + + AN 
Sbjct: 124 KAASKVMMKARKGVFINMGSIVGTTGNGGQANYAASKAGIIGFTKSIAKELGSRNIRANV 183

Query: 184 LTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTS 243
           + P    + + D L    V+     IP+ R G  E+ A +  F+AS+  ++ T  T    
Sbjct: 184 VAPGFIRTEMTDILDPKVVEGWEKDIPLKRAGETEDIANVCVFLASDMSAYVTGQTLSVC 243

Query: 244 GG 245
           GG
Sbjct: 244 GG 245


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: 137
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: 247
Length adjustment: 24
Effective length of query: 225
Effective length of database: 223
Effective search space:    50175
Effective search space used:    50175
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