GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Escherichia coli BW25113

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Keio:1937256
          Length = 500

 Score =  444 bits (1143), Expect = e-129
 Identities = 230/481 (47%), Positives = 334/481 (69%), Gaps = 5/481 (1%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           I+  +G++  FPGVKALD VD +L  GE+ AL+GENGAGKST+IKALTGVY  + G+I +
Sbjct: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126
           +G+      T  AQ  GI TVYQEVNL  N+SV +N+ +G E +    +  K+  + A +
Sbjct: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
            +A  G  S+D   PL+  S+AMQQ+VAI RA+ ++AKVLILDEPT+SLD  EV  LF +
Sbjct: 129 LMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246
           MR++RD GV+++FV+HFLDQ+Y+++DR+T+LRNG F+    T + P+ EL+ MM+G+   
Sbjct: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR--- 244

Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELG 306
           EL     ++A R +   +KP+   K  GKKGTI P D+++  GE+VG AGLLGSGRTE  
Sbjct: 245 ELDTHALQRAGRTLL-SDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303

Query: 307 RLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIAL 366
            +++G    DSGT  + GK  N+  P+ A    I +  E+R+ +GII   +VR+NI++AL
Sbjct: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363

Query: 367 QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426
           QA RG  +PI +KE   I ++++++L +R    ++P++ LSGGNQQKVL+ RWL T P+ 
Sbjct: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423

Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486
           LILDEPTRGID+GA AEI +++  L + G+ ++ ISSELEE+V  +D + +++DR ++AE
Sbjct: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483

Query: 487 I 487
           I
Sbjct: 484 I 484


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: 667
Number of extensions: 29
Number of successful extensions: 7
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: 500
Length adjustment: 34
Effective length of query: 479
Effective length of database: 466
Effective search space:   223214
Effective search space used:   223214
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:

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