GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruD in Photobacterium jeanii R-40508

Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202) (characterized)
to candidate WP_068336976.1 A3K86_RS18055 PTS transporter subunit EIIA

Query= BRENDA::Q8DWE6
         (150 letters)



>NCBI__GCF_001650345.1:WP_068336976.1
          Length = 622

 Score = 76.3 bits (186), Expect = 8e-19
 Identities = 43/144 (29%), Positives = 84/144 (58%), Gaps = 1/144 (0%)

Query: 1   MIDENLIKINLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAI 60
           +I+  +I ++L   ++++V   L  L+   G   +    +  +  RE  G TG  EG AI
Sbjct: 6   LIESEIICLDLKATNKEDVLAELTDLLDAAGKLVDKTQFLADVWKREEIGNTGFEEGIAI 65

Query: 61  PHAKDKSIVKPSIAILKLKTGVEWHSMDGQLINNVIALFIPEKEAGTTHLKVLSQIARLL 120
           PHAK  ++ KP++A+   ++G+++ + DG+L +    L  P+ +    H++VL+Q++  L
Sbjct: 66  PHAKSGAVAKPAVAVGISRSGIDYGAEDGELSDVFFMLASPDGQ-DHHHIEVLAQLSTKL 124

Query: 121 VNKTFKEKIKEADTILELKELLTE 144
           + ++F  K+K A+++ E  ELLT+
Sbjct: 125 IEESFITKLKGAESVEEALELLTD 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: 172
Number of extensions: 12
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: 622
Length adjustment: 26
Effective length of query: 124
Effective length of database: 596
Effective search space:    73904
Effective search space used:    73904
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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