GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Bacteroides thetaiotaomicron VPI-5482

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate 352326 BT2799 putative PfkB family carbohydrate kinase (NCBI ptt file)

Query= BRENDA::Q6VWJ5
         (386 letters)



>FitnessBrowser__Btheta:352326
          Length = 329

 Score = 77.8 bits (190), Expect = 4e-19
 Identities = 74/247 (29%), Positives = 113/247 (45%), Gaps = 16/247 (6%)

Query: 96  APGGAPANVAVGISRLGGSSAFIGKVGEDEFGYMLAEILKENNVNSDGMRFDPGARTALA 155
           A GG+  N  +G++ LG  + FIGKVG D +G    + L++NN+  D +       + +A
Sbjct: 57  ATGGSAGNAILGLACLGAGTGFIGKVGNDHYGDFFRKNLQKNNI-EDNLLTSEQLPSGVA 115

Query: 156 FVTLRKDGEREFMFYRNPSADMLLQEDELDLELIRKAKVFHYGSISLITEPCKSAHIAAA 215
              + +DGER F  Y   +A   L+ ++L LE+    K + Y  I           + A 
Sbjct: 116 STFISQDGERTFGTYLGAAAS--LKAEDLTLEMF---KGYAYLFIEGYLVQDHEMILHAI 170

Query: 216 KAAKDAGVILSYDPNLRLPLWPSAESAREGI-LSIWNTADIIKISEEEISFLTQGEDPYD 274
           + AK+AG+ +  D    +  +   E+  E   L I    DI+  +EEE    T GE+P +
Sbjct: 171 ELAKEAGLQICLD----MASYNIVENDLEFFSLLINKYVDIVFANEEEAKAFT-GEEPEE 225

Query: 275 DNVVRKLYHPNLKLLLVTEGPEGCRYYTKDFSGRVKGIKVDAV-DTTGAGDAFVAGILSQ 333
                ++      + +V  G  G          +V  I V+ V DTTGAGD F AG L  
Sbjct: 226 ---ALRVIAKKCSIAIVKVGANGSYIRKGTEEIKVSAIPVEKVLDTTGAGDYFAAGFLYG 282

Query: 334 LASDVSL 340
           L    SL
Sbjct: 283 LTCGYSL 289


Lambda     K      H
   0.317    0.134    0.382 

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: 191
Number of extensions: 7
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: 386
Length of database: 329
Length adjustment: 29
Effective length of query: 357
Effective length of database: 300
Effective search space:   107100
Effective search space used:   107100
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 (21.7 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:

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