GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaL in Sinorhizobium fredii NGR234

Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate WP_012706470.1 NGR_RS02000 dihydroxyacetone kinase subunit DhaL

Query= BRENDA::P76014
         (210 letters)



>NCBI__GCF_000018545.1:WP_012706470.1
          Length = 207

 Score =  125 bits (315), Expect = 4e-34
 Identities = 74/183 (40%), Positives = 104/183 (56%), Gaps = 12/183 (6%)

Query: 15  CGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLS 74
           C +  +  +++L+ LDR IGD DHG+NM RG   V  +   +A+  +   L+  G+TL+ 
Sbjct: 18  CREAIAANADHLSELDRAIGDGDHGINMRRGLEAVYAERNRLAELALPKALEEIGLTLVM 77

Query: 75  SVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVW 134
           SVGGA+GPL+GT  I  A   Q   +   ++  +      D V  RG+A PGDKT+ DV 
Sbjct: 78  SVGGAAGPLYGTLLI--AIGRQLGGANGQQDFARALEHAIDAVARRGRASPGDKTLLDVL 135

Query: 135 VPV-VESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPG 193
            PV  E +R++          L   S  AE AA  T  M+A +GRA++LG+RSIGH DPG
Sbjct: 136 YPVHAEVVRRA---------GLAGISEQAERAASLTFGMRAMRGRAAFLGDRSIGHVDPG 186

Query: 194 ATS 196
           A S
Sbjct: 187 AKS 189


Lambda     K      H
   0.316    0.130    0.364 

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: 112
Number of extensions: 7
Number of successful extensions: 3
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: 210
Length of database: 207
Length adjustment: 21
Effective length of query: 189
Effective length of database: 186
Effective search space:    35154
Effective search space used:    35154
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 09 2024. 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