GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Shewanella amazonensis SB2B

Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 6937235 Sama_1405 fructokinase (RefSeq)

Query= curated2:Q4QP08
         (304 letters)



>FitnessBrowser__SB2B:6937235
          Length = 310

 Score =  223 bits (567), Expect = 6e-63
 Identities = 123/298 (41%), Positives = 175/298 (58%), Gaps = 6/298 (2%)

Query: 4   GLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTVGLG 63
           G+D+GGTKIEL   NE+ E+++ +RVPTPK DY   L  +  LV+ ++++ G+V +VG+G
Sbjct: 5   GIDLGGTKIELVTLNEKGEEVFRKRVPTPK-DYRATLEAVAGLVHDSEKETGQVSSVGIG 63

Query: 64  VPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQQYP 123
           +PG V+  TG  + +N    + +P+ +DL   LGREVR  NDANCFA+SE+ D       
Sbjct: 64  IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123

Query: 124 TVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDNAPIYQCGCGNK 183
            V G ILGTG G G  +N KVH G  G+ GE GH     + L  +  D     +C CGN 
Sbjct: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGH-----NPLPWMTADEFNSTRCFCGNA 178

Query: 184 ACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGNIIT 243
            C++ ++SG GF   +R   GE  S  EI+ L  +G   A      F++  A ++ ++I 
Sbjct: 179 DCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVIN 238

Query: 244 AFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAALF 301
             DP +IVLGGG+SN D +YE LP  LP +++       + K  HG S GVRGAA L+
Sbjct: 239 LLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296


Lambda     K      H
   0.319    0.140    0.421 

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: 265
Number of extensions: 13
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: 304
Length of database: 310
Length adjustment: 27
Effective length of query: 277
Effective length of database: 283
Effective search space:    78391
Effective search space used:    78391
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 (21.7 bits)
S2: 48 (23.1 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