GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Desulfovibrio vulgaris Hildenborough

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 207334 DVU1868 dihydrodipicolinate synthase

Query= SwissProt::P75682
         (302 letters)



>MicrobesOnline__882:207334
          Length = 292

 Score =  149 bits (376), Expect = 8e-41
 Identities = 91/290 (31%), Positives = 158/290 (54%), Gaps = 6/290 (2%)

Query: 7   FTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIAR 66
           FTG    + T F  +G++D+     LI+  I+ G++GL   G+ GE + L  +E + + R
Sbjct: 3   FTGAFTAIVTPFR-NGRVDEERFRELIEWQIEQGINGLVPCGTTGESATLSHDEHRDVIR 61

Query: 67  FAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQ 126
             ++ V  R+PVL G G  N RE I+L++ A++AGADG ++I PYY K ++  L  +F+ 
Sbjct: 62  ICVEQVKGRIPVLAGAGSNNTREAIDLTRFAKEAGADGALLITPYYNKPTQEGLYLHFKA 121

Query: 127 VADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGA 186
           +A  V++P ++YN P+ TG ++ P  +  L      ++G+K   ++  +L  +   ++  
Sbjct: 122 IASEVSMPFIVYNVPSRTGTNICPETLARLNRDIPEVVGVK---EATGNLIQVSEILEYC 178

Query: 187 HPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLL 246
              F VL G D  +   L +GG G IS + N  P    ++ +A++ GD+A A   H  L 
Sbjct: 179 GTDFQVLSGDDFTVLPLLSVGGCGVISVTSNVVPAKMSDMCRAFKAGDLATARRLHFELS 238

Query: 247 QIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLL 296
            I +   L+T  + V K A+ L GR +   +  P  PL +  +++L+ +L
Sbjct: 239 PINRAMFLETNPIPV-KTALALMGR-IDLEMRLPLCPLQQVNQSRLRDIL 286


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: 204
Number of extensions: 11
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: 292
Length adjustment: 26
Effective length of query: 276
Effective length of database: 266
Effective search space:    73416
Effective search space used:    73416
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 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