GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Erythrobacter marinus HWDM-33

Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate WP_047093417.1 AAV99_RS07600 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::P75682
         (302 letters)



>NCBI__GCF_001013305.1:WP_047093417.1
          Length = 293

 Score =  106 bits (265), Expect = 6e-28
 Identities = 72/241 (29%), Positives = 113/241 (46%), Gaps = 6/241 (2%)

Query: 6   LFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIA 65
           +F+G IP ++T F  +   D+      ID  I  G  GL   G+ GE + L  +E   + 
Sbjct: 1   MFSGSIPALATPFRGEA-FDESAYRQFIDWQIDNGTSGLVPCGTTGESATLDNDEHHRVI 59

Query: 66  RFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFE 125
               +    RVPV+ G G  + R  +  ++ AQ AGAD ++++ PYY + S+A L+ +F 
Sbjct: 60  AVCAEQAAGRVPVIAGAGSNDTRTALWHAKEAQIAGADALLLVAPYYNRPSQAGLLAHFS 119

Query: 126 QVADSVTLPVMLYNFPALTGQDLTPALVKTL-ADSRSNIIGIKDTIDSVAHLRSMIHTVK 184
            +A+   LP++LYN P  T  D+ P  V  L       I+ +KD    +    S + T +
Sbjct: 120 YLAERTDLPIVLYNVPGRTVTDILPETVVELHRRFPEKIVALKDASGDL----SRVVTHR 175

Query: 185 GAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQT 244
              P    L G D  +     +G  G IS + N AP++      A   GD A A   ++ 
Sbjct: 176 MGAPALCQLSGDDPLVLGGYAMGQVGCISVTANVAPKLCAEFHAAAASGDFAAAREINEK 235

Query: 245 L 245
           L
Sbjct: 236 L 236


Lambda     K      H
   0.320    0.138    0.407 

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: 193
Number of extensions: 7
Number of successful extensions: 2
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: 302
Length of database: 293
Length adjustment: 26
Effective length of query: 276
Effective length of database: 267
Effective search space:    73692
Effective search space used:    73692
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 (21.8 bits)
S2: 48 (23.1 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