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_047212687.1 PATSB16_RS03670 dihydrodipicolinate synthase family protein

Query= SwissProt::P75682
         (302 letters)



>NCBI__GCF_001931675.1:WP_047212687.1
          Length = 300

 Score =  123 bits (308), Expect = 6e-33
 Identities = 75/249 (30%), Positives = 123/249 (49%), Gaps = 9/249 (3%)

Query: 9   GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68
           G+ P ++T    D  LD       ++ LI +GV G+  +G  GE + L  +E++ + R A
Sbjct: 7   GVFPAITTKLKVDETLDPEAIRTGLERLIASGVGGVVMMGMVGENASLTPDEKRTVLRIA 66

Query: 69  IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128
           +  V  RVPV+ G   TN    +  ++ A+Q G  G+++     +K      + ++  VA
Sbjct: 67  VQTVAGRVPVVAGVAETNTANAMLFARDAEQIGVSGLMLFPALTYKSDARETVAFYRSVA 126

Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAH- 187
            +  LP+M+YN P   G DLTPAL+  LA+  + +   ++T D+     + +  + G   
Sbjct: 127 RASGLPIMMYNNPRGYGVDLTPALLAELAEEPTLVCIKEETYDT-----TRVTDIYGRFG 181

Query: 188 PHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQ 247
             FTV CG DD +  ++ LG  G +S   N  P  SV L    + GD   A   ++ L+ 
Sbjct: 182 DRFTVFCGVDDLVLESIALGVSGWVSGMANALPVESVKLFDLAKQGDFPAARELYRALI- 240

Query: 248 IPQMYQLDT 256
              +Y LDT
Sbjct: 241 --DLYHLDT 247


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: 186
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: 300
Length adjustment: 27
Effective length of query: 275
Effective length of database: 273
Effective search space:    75075
Effective search space used:    75075
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