GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruD in Desulfovibrio vulgaris Hildenborough

Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202) (characterized)
to candidate 207082 DVU1630 PTS system, IIA component

Query= BRENDA::Q8DWE6
         (150 letters)



>MicrobesOnline__882:207082
          Length = 149

 Score = 64.7 bits (156), Expect = 6e-16
 Identities = 42/143 (29%), Positives = 76/143 (53%), Gaps = 1/143 (0%)

Query: 2   IDENLIKINLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAIP 61
           + ++LI   +   +++EV   L   V       +  + ++ L  RE  GTTG+ +G AIP
Sbjct: 7   LSKDLIIHEISASTKEEVLAELVNAVCRAHPEVDGRAALKVLHEREQLGTTGIGDGIAIP 66

Query: 62  HAKDKSIVKPSIAILKLKTGVEWHSMDGQLINNVIALFIPEKEAGTTHLKVLSQIARLLV 121
           H K   + +  +++ +   G  + S+DG+ ++ V  +  PE  AG  HL+VL+ I+RLL 
Sbjct: 67  HGKLSDLGRIVLSVGRSSAGFGFDSLDGKPVHIVFLVLAPEHVAG-MHLRVLAHISRLLK 125

Query: 122 NKTFKEKIKEADTILELKELLTE 144
           +  F+  + EA     + ELL++
Sbjct: 126 DVAFRRALIEAPDANAMWELLSK 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: 46
Number of extensions: 4
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: 149
Length adjustment: 16
Effective length of query: 134
Effective length of database: 133
Effective search space:    17822
Effective search space used:    17822
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: 42 (20.8 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