Scenario 2 Anotation: Gene of which something known

Scenario 2 Anotation: Gene of which something known

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 begin: 1. Click on Slide Show, (on the upper toolbar) 2. Click View Show 3. Click Continue button Continue Main Menu Annotate Anabaena PCC 7120: alr1152 Options History Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 1357843 (stop) Length = 293 amino acids Human A Experiment Human A Activity: Modification: N4-methylcytosine (inner cytosine of GGCC) Protects against: HaeIII In vivo activity: exists Experiment Experiment Experiment A

Expression: no data Syny6803:sll1330: (click to expand) Experiment Strand: Direct Gene name(s): dmtB, avaVIIM, dmnB Function: solitary Type II DNA methyltransferase (GGCC-specific) Classification: Type II alpha (N4) Mutant: Knockout loses GGCC methylation. Otherwise no known difference from wild-type This is an example of an orf that has substantial human annotation. Experiment Cyanobacterial Syny6803.C:sll0729 The sourceorthologs: of each assertion is given atNostPunc.352:003 the right. Press Continue . Continue A A A A Main Menu Annotate Anabaena PCC 7120: alr1152 Options History Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 1357843 (stop) Length = 293 amino acids Human

A Experiment Human A Activity: Modification: N4-methylcytosine (inner cytosine of GGCC) Protects against: HaeIII In vivo activity: exists Experiment Experiment Experiment A Expression: no data Syny6803:sll1330: (click to expand) Experiment Strand: Direct Gene name(s): dmtB, avaVIIM, dmnB Function: solitary Type II DNA methyltransferase (GGCC-specific) Classification: Type II alpha (N4) Mutant: Knockout loses GGCC methylation. Otherwise no known difference fromMouse wild-type over* to Experiment to the right of the Function Cyanobacterial orthologs: NostPunc.352:003 specification line to Syny6803.C:sll0729 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. Experiment A A A

A Main Menu Annotate Anabaena PCC 7120: alr1152 Options History Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 1357843 (stop) Length = 293 amino acids Strand: Direct Gene name(s): dmtB, avaVIIM, dmnB Function: solitary Type II DNA methyltransferase (GGCC-specific) Classification: Type II alpha (N4) Human A IDA: Matveyev et al (2001) Experiment Human A Activity: Modification: N4-methylcytosine (inner cytosine of GGCC) Protects against: HaeIII In vivo activity: exists Experiment Experiment Experiment A Expression: no data Syny6803:sll1330: (click to expand) Experiment Mutant: Knockout loses GGCC methylation. Otherwise no known difference from IDAwild-type

(Inferred from Direct Assay) is a standard Cyanobacterial orthologs: Syny6803.C:sll0729 Gene Ontology Consortium descriptor,NostPunc.352:003 useful for searching (see Scenario 3 for more). Evidently theres some hard evidence for the assertion. To learn more, click on Experiment. Experiment A A A A Back to Annotation page Nucleic Acids Research (2001) 151:1491-1506 Full text article at nar.oupjournals.orf PubMed Central access FREE full text articles 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 theAnnotations former. The solitary MTases, appear to be are linked to references

at of ancient origin within cyanobacteria, while the restriction MTases appear to have arrived by recent horizontal transfer as did five now inactive PubMed and from there (sometimes) to Type I restriction systems. One MTase, M.AvaV, cannot reliably be classified as either a full length articles. Click on button to solitary or restriction MTase. It is structurally unusual and along with a few proteins of return to annotation prokaryotic and eukaryotic originpage. defines a structural class of MTases distinct from all previously described. Main Menu Annotate Anabaena PCC 7120: alr1152 Options History Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 1357843 (stop) Length = 293 amino acids Human A Experiment Human A Experiment Experiment Experiment A Strand: Direct Gene name(s): dmtB, avaVIIM, dmnB Function: solitary Type II DNA methyltransferase (GGCC-specific) Classification: Type II alpha (N4) Activity: Modification: (inner cytosine of GGCC)

The human N4-methylcytosine annotations are propagated Protects against: HaeIII throughout all cyanobacterial orthologs. Click In vivo activity: exists on Syny6803.C:sll0729 to see how this works. Expression: no data Syny6803:sll1330: (click to expand) Mutant: Knockout loses GGCC methylation. Otherwise no known difference from wild-type Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003 A A A Experiment Experiment A Main Menu Annotate Synechocystis PCC 6803: sll0729 Options History Replicon: Chromosome Coordinates: 3424667 (stop) <- 3425524 (start) Length = 285 amino acids System Strand: Complement Function: probable DNA methyltransferase System Anab7120.C:alr1152: solitary Type II DNA methyltransferase (GGCC-specific)

Experiment Motifs: pfm:MethyltransfD12: D12 class N6 adenine-specific DNA methyltransferase ps:N6_MTASE: N-6 Adenine-specific DNA methylases signature. System System Expression: (click to expand) Mutant: none Anab7120.C:alr1152: Knockout loses GGCC methylation. Otherwise no known difference from wild-type Experiment Experiment Cyanobacterial orthologs: Anab7120.C:alr1152 NostPunc.352:003 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. A End A Scenario 2 Anotation: Gene of which something known Summary 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.

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