GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaK in Burkholderia phytofirmans PsJN

Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate BPHYT_RS32475 BPHYT_RS32475 dihydroxyacetone kinase

Query= SwissProt::Q9CIV8
         (332 letters)



>FitnessBrowser__BFirm:BPHYT_RS32475
          Length = 567

 Score =  263 bits (673), Expect = 6e-75
 Identities = 142/332 (42%), Positives = 208/332 (62%), Gaps = 6/332 (1%)

Query: 4   EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKS----GKVALVSGGGSGHK 59
           +K+IN+   VV +MLDGL  A    +  +    I+ R   ++    G+VAL+SGGGSGH+
Sbjct: 2   KKLINEVSAVVPDMLDGLA-ALNPNLSLLQGGTIVVRADAEAAAARGEVALISGGGSGHE 60

Query: 60  PAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAR 119
           PAH G+VG GMLSAAV G +FTSP+ D + +AI++    AG LLI+KNY GD  NF +A 
Sbjct: 61  PAHGGYVGSGMLSAAVAGEVFTSPSTDAVLDAIRAVAGAAGALLIVKNYTGDRFNFGLAA 120

Query: 120 EMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLA 179
           E+A  E I  E +IV DD+A+  S    GRRG+AGTVL+HKI GAAA     L E+  +A
Sbjct: 121 EIARAEGIPTEMVIVADDVALTASGDHAGRRGLAGTVLIHKIAGAAAAAGRPLGEVAQIA 180

Query: 180 DKVVKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATE 239
             V  ++ T+G+AL+A TVP  GKPGF L D EIE+G+GIH EPG  R  ++ +  +  +
Sbjct: 181 RDVAASLGTMGVALTACTVPAAGKPGFELADGEIEWGLGIHGEPGVERGALEPADAIVEK 240

Query: 240 LVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMT 299
           L+ K+  +   + G++  +LVN +G TP  E  I      + L +  IE+     G +++
Sbjct: 241 LLAKIVGDLSLQTGERVALLVNNLGGTPSSELSIVAGSALRYLAKRGIEVERAWAGTFLS 300

Query: 300 SIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
           +++MAG+SLT++++ DD+ L  L+    T +W
Sbjct: 301 ALEMAGVSLTLLRV-DDERLAWLDAATHTSAW 331


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: 444
Number of extensions: 19
Number of successful extensions: 2
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: 567
Length adjustment: 32
Effective length of query: 300
Effective length of database: 535
Effective search space:   160500
Effective search space used:   160500
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.

Links

Downloads

Related tools

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