GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1276 Echvi_1276 Dihydrodipicolinate synthase/N-acetylneuraminate lyase

Query= SwissProt::Q6KZI8
         (266 letters)



>FitnessBrowser__Cola:Echvi_1276
          Length = 308

 Score =  103 bits (257), Expect = 4e-27
 Identities = 68/213 (31%), Positives = 112/213 (52%), Gaps = 7/213 (3%)

Query: 1   MITPLDAHGNIDYNATNILIKYLEGINVDYLFPMGSTGVFPYFTLKERKDFLKFVRE--N 58
           MITPL     +D      LI ++    V  LF +G+TG     +   R + +K      N
Sbjct: 18  MITPLADENQLDIPGLERLINHIIAGGVHGLFILGTTGESTSLSYDIRHELVKRTCAIVN 77

Query: 59  SKKPIMAGVGSSSINEVNELMKFSMDIGIEAAVLMPPYYIKLNQEAIYHYYKEILSSNDM 118
            + P++ G+  ++  E   L   +   G  A V  PPYY  L Q  +  YY+ ++    +
Sbjct: 78  GRVPVLVGITDTAATESLRLADTAAKEGAAAVVAAPPYYFSLGQPELIEYYEYLVERLSL 137

Query: 119 DLLIYNIPQFTN-KIDPETVKNLKSEFSSVKGVKDSSADIRGFMEMLSLSDD--DFAVFQ 175
            L +YN+P  T   I+P+TVK L S++ ++ G+KDSSA+   F ++++   D  DF++F 
Sbjct: 138 PLFLYNMPSHTKIVIEPDTVKTL-SQYDNIVGLKDSSANNAYFNKVMAKMKDRQDFSLFV 196

Query: 176 GQDDLLFTSLELGASGGVCGTTN-FSDGIVRLY 207
           G ++++  ++ LGA GGV G  N F +  V+LY
Sbjct: 197 GPEEIMAETVLLGAHGGVNGGANMFPELYVKLY 229


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: 235
Number of extensions: 12
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: 308
Length adjustment: 26
Effective length of query: 240
Effective length of database: 282
Effective search space:    67680
Effective search space used:    67680
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