GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaK' in Sinorhizobium fredii NGR234

Align triokinase (EC 2.7.1.28); glycerone kinase (EC 2.7.1.29); FAD-AMP lyase (cyclizing) (EC 4.6.1.15) (characterized)
to candidate WP_012706475.1 NGR_RS02025 dihydroxyacetone kinase subunit DhaK

Query= BRENDA::Q3LXA3
         (575 letters)



>NCBI__GCF_000018545.1:WP_012706475.1
          Length = 331

 Score =  213 bits (541), Expect = 1e-59
 Identities = 136/338 (40%), Positives = 194/338 (57%), Gaps = 15/338 (4%)

Query: 4   KKLVNSVAGCADDALAGLVACNPNLQLL--QGHRVALRSDLDSLKGRVALLSGGGSGHEP 61
           KK +N       ++LAGLV+ +  L      G  V  RS      G+V+L+SGGG+GHEP
Sbjct: 2   KKFMNRAETLVAESLAGLVSAHERLVTFGADGKFVRRRS---LRPGKVSLISGGGAGHEP 58

Query: 62  AHAGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLA 121
            H GF+G+GML     G VFTSP    I+AAIR   +    G LLIVKNY GD +NF +A
Sbjct: 59  MHVGFVGRGMLDAACTGHVFTSPTPDQIVAAIRETDRGE--GCLLIVKNYDGDVMNFEMA 116

Query: 122 REQARAEGIPVEMVVIGDDSAFTVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQV 181
            E   AE     +VV  D       +  GRRG+ GTV++ K+ GA AEAG  L+E++   
Sbjct: 117 AELVAAEHRIATVVVRDDVDPGGSKRSQGRRGVAGTVVMEKLLGAAAEAGWRLDELSALG 176

Query: 182 NVVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKL 240
             +   + T+GVSL   +VP + + TF L  DE+E+G+GIHGE G  R+K ATADEIV+ 
Sbjct: 177 ESLNGRIRTMGVSLRGVTVPDTERETFVLPEDEMEIGVGIHGEPGRARVKFATADEIVET 236

Query: 241 MLDHMTNTTNASHVPVQPGSSVVMMVNNLGGLSFLELGIIADATVRSLEGRGVKIARALV 300
           ML+ +        +  +   +++M +N  GG    EL ++ ++     E  G+ IAR LV
Sbjct: 237 MLEAI-----LGELASERDENLLMFINGYGGTPASELYLVYNSAKAQCERLGLTIARPLV 291

Query: 301 GTFMSALEMPGISLTLLLVDEPLLKLIDA--ETTAAAW 336
           GT++++L+M G+S+T+  + E  L L DA  +T A  W
Sbjct: 292 GTYVTSLDMAGLSITVARLAERELSLWDAPVDTAALRW 329


Lambda     K      H
   0.315    0.130    0.365 

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: 448
Number of extensions: 21
Number of successful extensions: 4
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: 575
Length of database: 331
Length adjustment: 32
Effective length of query: 543
Effective length of database: 299
Effective search space:   162357
Effective search space used:   162357
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 (21.6 bits)
S2: 51 (24.3 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