GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruD in Dechlorosoma suillum PS

Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202) (characterized)
to candidate Dsui_0702 Dsui_0702 PTS IIA-like nitrogen-regulatory protein PtsN

Query= BRENDA::Q8DWE6
         (150 letters)



>FitnessBrowser__PS:Dsui_0702
          Length = 161

 Score = 65.9 bits (159), Expect = 3e-16
 Identities = 40/138 (28%), Positives = 73/138 (52%), Gaps = 2/138 (1%)

Query: 7   IKINLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAIPHAKDK 66
           I ++L   S+   F   A L+ +N       +V  +L  RE  G+TG+ +G AIPH + K
Sbjct: 13  ILLDLEASSKKRAFEQ-AGLLFENNLGIARATVFDSLFAREKLGSTGLGQGVAIPHGRIK 71

Query: 67  SIVKPSIAILKLKTGVEWHSMDGQLINNVIALFIPEKEAGTTHLKVLSQIARLLVNKTFK 126
            + + + A ++L   V + S DG+ +  +  L +PE +A   HL++LS++A+   ++ F+
Sbjct: 72  GLKEAAGAFMRLSAPVPFDSPDGKPVGLMFVLLVPE-QATEQHLQILSELAQRFSDRAFR 130

Query: 127 EKIKEADTILELKELLTE 144
           E +   D   +   L T+
Sbjct: 131 EALGACDNTDDAHRLFTD 148


Lambda     K      H
   0.315    0.133    0.358 

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: 47
Number of extensions: 3
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: 150
Length of database: 161
Length adjustment: 17
Effective length of query: 133
Effective length of database: 144
Effective search space:    19152
Effective search space used:    19152
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 (21.6 bits)
S2: 43 (21.2 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