GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Shewanella loihica PV-4

Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 5208927 Shew_1428 fructokinase (RefSeq)

Query= curated2:Q4QP08
         (304 letters)



>FitnessBrowser__PV4:5208927
          Length = 296

 Score =  219 bits (559), Expect = 5e-62
 Identities = 122/301 (40%), Positives = 176/301 (58%), Gaps = 6/301 (1%)

Query: 1   MYYGLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTV 60
           M  G+D+GGTKIEL   +E  ++L+ +R+PTP+ +Y+  L+ I  LVN A+   G+ GTV
Sbjct: 2   MRMGVDLGGTKIELVALSEAGKELFRKRIPTPR-EYKATLDAIEALVNEAESTLGQKGTV 60

Query: 61  GLGVPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQ 120
           G+G+PG ++  +GL +  N    +  P+  DL  RL REVR  NDANCFA+SEA D    
Sbjct: 61  GVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAVDGAAA 120

Query: 121 QYPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDNAPIYQCGC 180
               V G+I+GTG GGG  +NGKVH G  G+ GE GH     + L  +  D     +C C
Sbjct: 121 GKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGH-----NPLPWMTPDEFNSTECFC 175

Query: 181 GNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGN 240
           GNK C++ ++SG GF   Y+   G+  S  EI     QG   A      +++  A S+ +
Sbjct: 176 GNKDCIETFISGTGFVRDYKAAGGDAPSGIEIARRMEQGEALATAAFERYIDRLARSLAH 235

Query: 241 IITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAAL 300
           +I   DP +IVLGGG+SN + +Y  LP+AL  +++      P+ +  +G S GVRGAA L
Sbjct: 236 MINMLDPDIIVLGGGVSNIEAIYPRLPEALSKYVLGGECRTPVVQNMYGGSSGVRGAAWL 295

Query: 301 F 301
           +
Sbjct: 296 W 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: 250
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: 296
Length adjustment: 27
Effective length of query: 277
Effective length of database: 269
Effective search space:    74513
Effective search space used:    74513
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