GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Bacteroides thetaiotaomicron VPI-5482

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 350423 BT0895 dihydrodipicolinate synthase (NCBI ptt file)

Query= SwissProt::P75682
         (302 letters)



>FitnessBrowser__Btheta:350423
          Length = 297

 Score =  129 bits (324), Expect = 8e-35
 Identities = 73/240 (30%), Positives = 121/240 (50%), Gaps = 3/240 (1%)

Query: 16  TIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRR 75
           T F  D  +D      L+D L++   D L  LG+  E   L  EE+K I +  ID V+ R
Sbjct: 15  TPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKMVIDRVNGR 74

Query: 76  VPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPV 135
           +P+L+G GG N R  +E  ++    G D I+ + PYY K S+  + ++++ ++++  LP+
Sbjct: 75  IPILLGVGGNNTRAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAISEATELPI 134

Query: 136 MLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCG 195
           +LYN P  TG ++T      +A + SN+I IK+   ++  +  +I   K    +F V+ G
Sbjct: 135 VLYNVPGRTGVNMTAETTLRIARNFSNVIAIKEASGNITQMDDII---KNKPDNFNVISG 191

Query: 196 YDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLD 255
            D   F  + LG  G IS  GN  P+    + +    GD A A   H    ++  +  +D
Sbjct: 192 DDGITFPLITLGAVGVISVIGNAFPREFSRMTRLALQGDFANALTIHHRFTELFDLLFVD 251


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: 192
Number of extensions: 7
Number of successful extensions: 1
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: 297
Length adjustment: 27
Effective length of query: 275
Effective length of database: 270
Effective search space:    74250
Effective search space used:    74250
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.

Links

Downloads

Related tools

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