GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Collinsella tanakaei YIT 12063

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate WP_009141415.1 HMPREF9452_RS06915 carbohydrate kinase

Query= SwissProt::Q53W83
         (309 letters)



>NCBI__GCF_000225705.1:WP_009141415.1
          Length = 322

 Score =  109 bits (272), Expect = 1e-28
 Identities = 92/304 (30%), Positives = 137/304 (45%), Gaps = 29/304 (9%)

Query: 24  GKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAP 83
           G+++ E   GGA  NV VA  +LG    F+G+VG+D  G  + + L  EGVD T     P
Sbjct: 26  GQKMFERNPGGAPANVLVAARKLGATTAFIGKVGDDMHGTFLRDTLAGEGVDTTGLILDP 85

Query: 84  G-FTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEA 142
             FT L        G+    + RK  A + L         ++  R  H+  ++    P A
Sbjct: 86  NVFTTLAFVALDERGERAFSFARKPGADTCLNARELALGVIDATRVFHVGSLSLTNEP-A 144

Query: 143 RAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPG-VDLLFLSEEEAELLF 201
           R  +L A++ A+  G  +S D NYR +LW+  +      R++   +DL+ +S+EE ELL 
Sbjct: 145 RGATLAALDRAREAGCVLSYDPNYRSSLWASAQVAQLQMRSIVNRMDLMKISDEECELLT 204

Query: 202 GRVEEALRALSAPEVVLKRGAK-------GAWAFV----DGRRVEGSAFAVEAVDPVGAG 250
           G          A E +L++G K       GA A+V     G  VEG  F  + VD  GAG
Sbjct: 205 G----TRHPEKAAETLLEKGVKVAVVTLGGAGAYVRCAQGGAYVEG--FPTDIVDTTGAG 258

Query: 251 DAFAAGYLAG------AVWGLPVEER---LRLANLLGASVAASRGDHEGAPYREDLEVLL 301
           D+F  G+L            + +E+     R  N + +     RG     P R ++E LL
Sbjct: 259 DSFWGGFLTAFCESGVDAADVTLEQACGFARFGNAVASLCVRGRGAIPSMPTRGEVEALL 318

Query: 302 KATQ 305
              Q
Sbjct: 319 AQQQ 322


Lambda     K      H
   0.320    0.139    0.407 

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: 271
Number of extensions: 15
Number of successful extensions: 3
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: 309
Length of database: 322
Length adjustment: 27
Effective length of query: 282
Effective length of database: 295
Effective search space:    83190
Effective search space used:    83190
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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