GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaK' in Escherichia coli BW25113

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 15322 b1200 putative dihydroxyacetone kinase (EC 2.7.1.2) (VIMSS)

Query= BRENDA::Q3LXA3
         (575 letters)



>lcl|FitnessBrowser__Keio:15322 b1200 putative dihydroxyacetone
           kinase (EC 2.7.1.2) (VIMSS)
          Length = 356

 Score =  225 bits (574), Expect = 2e-63
 Identities = 144/356 (40%), Positives = 194/356 (54%), Gaps = 26/356 (7%)

Query: 4   KKLVNSVAGCADDALAGLVACNPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63
           KKL+N V    D+ LAGL   +P+L L Q      R+D   + G+VALLSGGGSGHEP H
Sbjct: 2   KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAP-VAGKVALLSGGGSGHEPMH 60

Query: 64  AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123
            G+IG+GML+G   G +FTSP    I     A+   G  G LLI+KNYTGD LNF  A E
Sbjct: 61  CGYIGQGMLSGACPGEIFTSPTPDKIFEC--AMQVDGGEGVLLIIKNYTGDILNFETATE 118

Query: 124 QARAEGIPVEMVVIGDDSAF-TVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVN 182
                G+ V  VVI DD A    L  AGRRG+  TVLI K+ GA AE G  L+  A+   
Sbjct: 119 LLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGR 178

Query: 183 VVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKLM 241
            +     ++G++L +C+VP + KP+F L+ +E+E G+GIHGE G+ R   ++ D+ V  M
Sbjct: 179 KLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEM 238

Query: 242 LD--------HMT-----------NTTNASHVPVQPGSSVVMMVNNLGGLSFLELGIIAD 282
            D        H T                +  P+Q G  V+ +VNNLG     EL  + +
Sbjct: 239 FDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYN 298

Query: 283 ATVRSLEGRGVKIARALVGTFMSALEMPGISLTLLLVDEPLLKLIDA--ETTAAAW 336
                 +  G+ I R L+G + ++L+M G S+TLL VD+  L L DA   T A  W
Sbjct: 299 RLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNW 354


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: 463
Number of extensions: 17
Number of successful extensions: 6
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: 356
Length adjustment: 33
Effective length of query: 542
Effective length of database: 323
Effective search space:   175066
Effective search space used:   175066
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 Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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