GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntK in Pseudomonas fluorescens FW300-N2E2

Align gluconokinase (EC 2.7.1.12) (characterized)
to candidate Pf6N2E2_2864 Gluconokinase (EC 2.7.1.12)

Query= BRENDA::Q8NMT0
         (167 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2864
          Length = 177

 Score =  123 bits (308), Expect = 2e-33
 Identities = 72/162 (44%), Positives = 98/162 (60%), Gaps = 9/162 (5%)

Query: 9   IVVMGVSGCGKSSVGKALAAELGIEYKDGDELHPQENIDKMASGQALDDDDRAWWLVQVG 68
           +V+MGV+GCGK+ V +AL    G    +GD  HP  NI KM++G  L+DDDRA WL  + 
Sbjct: 8   LVIMGVAGCGKTCVSQALCELSGATAIEGDTFHPAANIQKMSAGIPLNDDDRAGWLDSLC 67

Query: 69  KWLR------DRPSGVIACSALKRSYRDLLRTKCPGTVFVHLHGDYDLLLSRMKAREDHF 122
             LR      +RP  V+ CSALK SYR+ LR+  PG  FV L    ++   R+  R  HF
Sbjct: 68  DELRRVDAMGERP--VLTCSALKHSYRERLRSALPGLGFVFLELTPEVAADRVSHRPGHF 125

Query: 123 MPSTLLDSQFATLE-PLEDDEDGKVFDVAHTISELAAQSAEW 163
           MPSTL+DSQFATL+ P+ +     +   +H++ ELA Q+  W
Sbjct: 126 MPSTLIDSQFATLQSPVGEPLTLALDASSHSVEELAHQAYVW 167


Lambda     K      H
   0.318    0.134    0.406 

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: 89
Number of extensions: 8
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: 167
Length of database: 177
Length adjustment: 18
Effective length of query: 149
Effective length of database: 159
Effective search space:    23691
Effective search space used:    23691
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: 44 (21.6 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