GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaK in Klebsiella michiganensis M5al

Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate BWI76_RS24595 BWI76_RS24595 dihydroxyacetone kinase subunit DhaK

Query= BRENDA::P76015
         (356 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS24595 BWI76_RS24595
           dihydroxyacetone kinase subunit DhaK
          Length = 356

 Score =  646 bits (1667), Expect = 0.0
 Identities = 316/356 (88%), Positives = 334/356 (93%)

Query: 1   MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH 60
           MKKLIN V+DVL EQLAGLAKAHP L LHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH
Sbjct: 1   MKKLINRVEDVLSEQLAGLAKAHPELRLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH 60

Query: 61  CGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELL 120
           CGYIGQGMLSGACPGEIFTSPTPDK+FECAM +DGGEGVLLIIKNYTGDILNFETATELL
Sbjct: 61  CGYIGQGMLSGACPGEIFTSPTPDKMFECAMNIDGGEGVLLIIKNYTGDILNFETATELL 120

Query: 121 HDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKL 180
           H+SGVKVTTVV+DDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSL++CAELGRKL
Sbjct: 121 HESGVKVTTVVVDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLESCAELGRKL 180

Query: 181 NNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFD 240
           NN GHSIGIALGACTVPAAG+PSF L D+EMEFGVGIHGEPGIDRR F+SLD+TVDEMFD
Sbjct: 181 NNLGHSIGIALGACTVPAAGQPSFELQDDEMEFGVGIHGEPGIDRRRFTSLDRTVDEMFD 240

Query: 241 TLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRL 300
           TLL NG+Y RTLR WD  +G+WQE  QTKQ LQ GDRVIALVNNLGATPLSELYGVYNRL
Sbjct: 241 TLLENGAYSRTLRHWDNVKGAWQEVAQTKQALQKGDRVIALVNNLGATPLSELYGVYNRL 300

Query: 301 TTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
           T RC++ G+ IERNLIG+YCTSLDM GFSITLLKVDDETLALWDAPVHTPALNWGK
Sbjct: 301 TQRCEETGIVIERNLIGSYCTSLDMVGFSITLLKVDDETLALWDAPVHTPALNWGK 356


Lambda     K      H
   0.317    0.136    0.406 

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: 534
Number of extensions: 12
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: 356
Length of database: 356
Length adjustment: 29
Effective length of query: 327
Effective length of database: 327
Effective search space:   106929
Effective search space used:   106929
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: 49 (23.5 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 paper from 2022 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