GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Burkholderia phytofirmans PsJN

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS01820 BPHYT_RS01820 sugar ABC
           transporter ATP-binding protein
          Length = 544

 Score =  403 bits (1036), Expect = e-117
 Identities = 210/500 (42%), Positives = 320/500 (64%), Gaps = 2/500 (0%)

Query: 4   KNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGS 63
           ++P++ M+ I I F GV AL   +L++  GEVHAL+G+NGAGKSTMIK LTG Y+  +GS
Sbjct: 15  RSPLLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGS 74

Query: 64  IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA 123
           +  +G+   F     A+ AGI+T+YQE+NL    SV EN+ LG E R    IDW    + 
Sbjct: 75  VRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWHAVQQR 134

Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183
           A   L   GL+ ID   P+   S A+QQ+VA+ARA+  +AK++I+DE TSSLD  EV  L
Sbjct: 135 AAALLESFGLQ-IDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELL 193

Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243
           F ++RK+RD G A++FVSH LD++Y + DR+T++R+GQ + +    D  + +L+  M+G+
Sbjct: 194 FTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTTMLGR 253

Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
           + A + Q  A+     +    K ++    L     ++ V ++++ GE VG AGLLGSGRT
Sbjct: 254 TLAAVVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLGSGRT 313

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           E  RL++GAD  + G+ ++ G+ V +  P  A+   +AY TE+R+ EGI+ +L+VR N+ 
Sbjct: 314 ETMRLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVRDNLT 373

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           +    T      +  K+  AIVD+++  L ++    D+P++ LSGGNQQKVL+ RWLA  
Sbjct: 374 LVCLRTLAKNGVVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAE 433

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483
           P LL+LDEPTRGID+GAKAE+ ++V +L   G+ V+  +SELEE+  ++D   V++D   
Sbjct: 434 PSLLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIRDGRT 493

Query: 484 IAEIENDDTVSQATIVETIA 503
           +AE+   D +S+  I++ IA
Sbjct: 494 VAELNGAD-MSETAIMDAIA 512


Lambda     K      H
   0.316    0.135    0.376 

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: 671
Number of extensions: 29
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: 513
Length of database: 544
Length adjustment: 35
Effective length of query: 478
Effective length of database: 509
Effective search space:   243302
Effective search space used:   243302
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: 52 (24.6 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