GapMind for catabolism of small carbon sources

 

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

Align 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; 2-dehydro-3-deoxy-galactonate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase; EC 4.1.2.14; EC 4.1.2.51; EC 4.1.2.-; EC 4.1.2.21 (characterized)
to candidate CA265_RS02050 CA265_RS02050 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::Q6KZI8
         (266 letters)



>FitnessBrowser__Pedo557:CA265_RS02050
          Length = 295

 Score =  112 bits (280), Expect = 9e-30
 Identities = 61/194 (31%), Positives = 103/194 (53%), Gaps = 3/194 (1%)

Query: 1   MITPLDAHGNIDYNATNILIKYLEGINVDYLFPMGSTGVFPYFTLKERKDFLKFVRE--N 58
           ++TP +  G++DYN    LI +L    +DYL  +G+TG     T  E+K    +  E  N
Sbjct: 11  LVTPFNTDGSVDYNGLKNLINHLVDGGIDYLVSLGTTGETATMTKDEKKKVWAYTAEINN 70

Query: 59  SKKPIMAGVGSSSINEVNELMKFSMDIGIEAAVLMPPYYIKLNQEAIYHYYKEILSSNDM 118
           ++ P++AG+G ++   V E +K     G  A + + PYY K  QE IY +YK +   + +
Sbjct: 71  NRLPLVAGIGGNNTLAVAEDIKSLDAAGYSAILSVSPYYNKPTQEGIYQHYKYLAEISPL 130

Query: 119 DLLIYNIPQFT-NKIDPETVKNLKSEFSSVKGVKDSSADIRGFMEMLSLSDDDFAVFQGQ 177
           DL++YN+P  T + + PET   L  +F ++   K++S     F +++     DF +  G 
Sbjct: 131 DLILYNVPGRTGSNMSPETTCRLAHDFKNIIATKEASGSFDQFNQIMRDKPADFLLISGD 190

Query: 178 DDLLFTSLELGASG 191
           D +    + LGA+G
Sbjct: 191 DPVTLPMIALGAAG 204


Lambda     K      H
   0.319    0.139    0.400 

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: 206
Number of extensions: 13
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: 266
Length of database: 295
Length adjustment: 26
Effective length of query: 240
Effective length of database: 269
Effective search space:    64560
Effective search space used:    64560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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