GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Pandoraea thiooxydans ATSB16

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_047212941.1 PATSB16_RS05105 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::P75682
         (302 letters)



>NCBI__GCF_001931675.1:WP_047212941.1
          Length = 299

 Score =  140 bits (353), Expect = 4e-38
 Identities = 89/278 (32%), Positives = 141/278 (50%), Gaps = 6/278 (2%)

Query: 21  DGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLI 80
           +  LD      LID  I  G DG+  +G+ GE   +  EE   + + A+D   +RVP++ 
Sbjct: 23  EASLDHDALRKLIDWHIAEGTDGIVIVGTSGESPTVSVEEHCELVKLAVDQAAKRVPIIA 82

Query: 81  GTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNF 140
           GTGG +  E IEL+++A++ GAD  + + PYY K ++  + R+F  +A+ V LPV+LYN 
Sbjct: 83  GTGGNSTAEAIELTEYARKVGADATLQVVPYYNKPTQEGIYRHFRSIAEHVDLPVILYNV 142

Query: 141 PALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHL 200
           P  T  D +   +  LA     I+G+K   D+  +L      +K A  HF V  G D   
Sbjct: 143 PGRTVADASNETLLRLAQV-PGIVGVK---DATGNLDRGAQLIKDAPEHFAVYSGDDLTA 198

Query: 201 FNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVN 260
              +L+GG G IS + N AP+    L +A   GD   A   H  LL + +   ++ P   
Sbjct: 199 VMLMLMGGKGNISVTANVAPRAMHELCEAAMRGDAVAARDMHFKLLNLHRAMFVE-PNPI 257

Query: 261 VIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQ 298
            +K A+   G+ +   +  P +PL +P    + T L++
Sbjct: 258 PVKWALQQMGK-IQGGIRLPLTPLAKPYHDAVLTALRE 294


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: 224
Number of extensions: 12
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: 299
Length adjustment: 27
Effective length of query: 275
Effective length of database: 272
Effective search space:    74800
Effective search space used:    74800
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