GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaK in Klebsiella michiganensis M5al

Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate BWI76_RS24610 BWI76_RS24610 dihydroxyacetone kinase

Query= SwissProt::Q9CIV8
         (332 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS24610 BWI76_RS24610
           dihydroxyacetone kinase
          Length = 549

 Score =  188 bits (478), Expect = 2e-52
 Identities = 117/328 (35%), Positives = 186/328 (56%), Gaps = 11/328 (3%)

Query: 8   NQPQDVVSEMLDGLTYA--YGDL--IEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHA 63
           NQ  ++V+++++G   A  + +L  +E  P   ++ R+      VA++SGGGSGH+PAHA
Sbjct: 7   NQRANLVNDVIEGTIIASPWNNLARLESDPAIRVVVRRDLDKNNVAVISGGGSGHEPAHA 66

Query: 64  GFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAE 123
           GFVG+GML+AAVCG +F SP+ D +  AI++    AG LLI+KNY GD +NF +A E A 
Sbjct: 67  GFVGKGMLTAAVCGDLFASPSVDAVLTAIQAVTGDAGCLLIVKNYTGDRLNFGLAAEKAR 126

Query: 124 MEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVV 183
                VE +IV DDI++ ++ +    RG+AGT+LVHK+ G  A +  +L  +   A    
Sbjct: 127 RMGYNVEMLIVGDDISLPDNKHP---RGIAGTILVHKVAGYFAERGHNLATVLREAQYAA 183

Query: 184 KNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGK 243
            +  ++GLAL++  +P+  +       ++ E G+GIH EPG      + S E+ T +  K
Sbjct: 184 GHTFSLGLALASCHLPQDAETAPRHHADQAELGMGIHGEPGASVIATQNSAEIVTLMAEK 243

Query: 244 LKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDM 303
           L      E G +  +++N +G   + E  I   ++A    ++ I+ L     + +T++DM
Sbjct: 244 LSAALP-ETG-RLAVMINNLGGVSIAEMAILTRELAHTPLQQRIDWLIGP-ASLVTALDM 300

Query: 304 AGLSLTMIKLEDDQWLKNLNEDVKTISW 331
            G SLT I LE +   K L   V+T  W
Sbjct: 301 KGFSLTAIVLE-ESIEKALLSAVETAGW 327


Lambda     K      H
   0.315    0.135    0.375 

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: 389
Number of extensions: 19
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: 332
Length of database: 549
Length adjustment: 32
Effective length of query: 300
Effective length of database: 517
Effective search space:   155100
Effective search space used:   155100
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: 42 (22.0 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 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