Anotation: Gene of which something known

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Scenario 2
Anotation Gene of which something known
What follows is a simulation of an orf page in
the proposed graphical interface. The interface
does not yet exist. As you go through the
simulation please consider what capabilities you
would want to serve your research and annotation
interests. A narrative to help you go through the
simulation appears in a red-bordered box, such as
the one below.
To begin1. Click on Slide Show, (on the upper
toolbar)2. Click View Show3. Click Continue
button
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Annotate
History
Anabaena PCC 7120 alr1152
Replicon Chromosome Coordinates 1356962
(start-ATG) -gt 1357843 (stop) Human Length
293 amino acids Strand Direct Gene name(s)
dmtB, avaVIIM, dmnB Function solitary Type II
DNA methyltransferase (GGCC-specific) Experiment
Classification Type II alpha (N4) Human
Activity Modification N4-methylcytosine
(inner cytosine of GGCC) Experiment
Protects against HaeIII Experiment
In vivo activity exists Experiment
Expression no data Syny6803sll1330
(click to expand) Experiment Mutant Knockout
loses GGCC methylation. Otherwise no known
difference Experiment from
wild-typeCyanobacterial orthologs
Syny6803.Csll0729 NostPunc.352003
A
A
A
A
A
A
A
This is an example of an orf that has substantial
human annotation. The source of each assertion is
given at the right. Press .
Continue
Continue
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History
Anabaena PCC 7120 alr1152
Replicon Chromosome Coordinates 1356962
(start-ATG) -gt 1357843 (stop) Human Length
293 amino acids Strand Direct Gene name(s)
dmtB, avaVIIM, dmnB Function solitary Type II
DNA methyltransferase (GGCC-specific) Experiment
Classification Type II alpha (N4) Human
Activity Modification N4-methylcytosine
(inner cytosine of GGCC) Experiment
Protects against HaeIII Experiment
In vivo activity exists Experiment
Expression no data Syny6803sll1330
(click to expand) Experiment Mutant Knockout
loses GGCC methylation. Otherwise no known
difference Experiment from
wild-typeCyanobacterial orthologs
Syny6803.Csll0729 NostPunc.352003
A
A
A
A
A
A
A
Mouse over to Experiment to the right of the
Function specification line to see where the
assertion comes from. In real life, information
will pop up when you mouse to an informative
position. In this simulation youll also need to
click.
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Annotate
History
Anabaena PCC 7120 alr1152
Replicon Chromosome Coordinates 1356962
(start-ATG) -gt 1357843 (stop) Human Length
293 amino acids Strand Direct Gene name(s)
dmtB, avaVIIM, dmnB Function solitary Type II
DNA methyltransferase (GGCC-specific) Experiment
Classification Type II alpha (N4) Human
Activity Modification N4-methylcytosine
(inner cytosine of GGCC) Experiment
Protects against HaeIII Experiment
In vivo activity exists Experiment
Expression no data Syny6803sll1330
(click to expand) Experiment Mutant Knockout
loses GGCC methylation. Otherwise no known
difference Experiment from
wild-typeCyanobacterial orthologs
Syny6803.Csll0729 NostPunc.352003
A
IDA Matveyev et al (2001)
A
A
A
A
A
A
IDA (Inferred from Direct Assay) is a standard
Gene Ontology Consortium descriptor, useful for
searching (see Scenario 3 for more). Evidently
theres some hard evidence for the assertion. To
learn more, click on Experiment.
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Back to Annotation page
Nucleic Acids Research (2001) 1511491-1506 DNA
methyltransferases of the cyanobacterium Anabaena
PCC 7120 Andrey Matveyev, Kathryn T Young, Andrew
Meng, and Jeff Elhai Dept. of Biology, University
of Richmond, Richmond VA USA From the
characterization of enzyme activities and the
analysis of genomic sequences, the complement of
DNA methyltransferases (MTases) possessed by the
cyanobacterium Anabaena PCC 7120 has been
deduced. Anabaena has nine DNA MTases. Four are
associated with Type II restriction enzymes
(AvaI, AvaII, AvaIII and the newly recognized
inactive AvaIV), and five are not. Of the latter,
four may be classified as solitary MTases, those
whose function lies outside of a
restriction/modification system. The group is
defined here based on biochemical and genetic
characteristics. The four solitary MTases,
DmtA/M.AvaVI, DmtB/M.AvaVII, DmtC/M.AvaVIII and
DmtD/M.AvaIX, methylate at GATC, GGCC, CGATCG and
rCCGGy, respectively. DmtB methylates cytosines
at the N4 position, but its sequence is more
similar to N6-adenine MTases than to
cytosine-specific enzymes, indicating that it may
have evolved from the former. The solitary
MTases, appear to be of ancient origin within
cyanobacteria, while the restriction MTases
appear to have arrived by recent horizontal
transfer as did five now inactive Type I
restriction systems. One MTase, M.AvaV, cannot
reliably be classified as either a solitary or
restriction MTase. It is structurally unusual
and along with a few proteins of prokaryotic and
eukaryotic origin defines a structural class of
MTases distinct from all previously described.
Full text article atnar.oupjournals.orf
PubMed Centralaccess FREE full text articles
Annotations are linked to references at PubMed
and from there (sometimes) to full length
articles. Click on button to return to annotation
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Anabaena PCC 7120 alr1152
Replicon Chromosome Coordinates 1356962
(start-ATG) -gt 1357843 (stop) Human Length
293 amino acids Strand Direct Gene name(s)
dmtB, avaVIIM, dmnB Function solitary Type II
DNA methyltransferase (GGCC-specific) Experiment
Classification Type II alpha (N4) Human
Activity Modification N4-methylcytosine
(inner cytosine of GGCC) Experiment
Protects against HaeIII Experiment
In vivo activity exists Experiment
Expression no data Syny6803sll1330
(click to expand) Experiment Mutant Knockout
loses GGCC methylation. Otherwise no known
difference Experiment from
wild-typeCyanobacterial orthologs
Syny6803.Csll0729 NostPunc.352003
A
A
A
The human annotations are propagated throughout
all cyanobacterial orthologs. Click on
Syny6803.Csll0729 to see how this works.
A
A
A
A
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Annotate
History
Synechocystis PCC 6803 sll0729
Replicon Chromosome Coordinates 3424667 (stop)
lt- 3425524 (start) System Length 285
amino acids Strand Complement Function probable
DNA methyltransferase System
Anab7120.Calr1152 solitary Type II DNA
methyltransferase (GGCC-specific) Experiment
Motifs pfmMethyltransfD12 D12 class N6
adenine-specific DNA methyltransferase System
psN6_MTASE N-6 Adenine-specific DNA
methylases signature. System Expression
(click to expand) Experiment Mutant none
Anab7120.Calr1152 Knockout loses GGCC
methylation. Otherwise no known Experiment
difference from wild-typeCyanobacterial
orthologs Anab7120.Calr1152 NostPunc.352003
A
A
The annotation for the Anabaena gene appears
automically on the annotation page of its
orthologs. This gives a hint to visitors to the
Synechocystis page that the systems suggestion
that Sll0729 is an adenine methyltransferase may
be and is wrong.
End
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Scenario 2
Anotation Gene of which something knownSummary

• Each assertion is linked to a justification.
• Justifying references are made available
  on-line.
• Annotations of an orf in one organism are
  propagated through orthologs to other
  cyanobacteria.

The integration of annotation across all
cyanobacterial genomes makes possible the ideal
of consideration of each gene by a person expert
in the field. This is achieved by dividing genes
vertically, by function, rather than
horizontally, by species.