1. 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 Scenario 2

2. Anabaena PCC 7120: alr1152 Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 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: existsExperiment Expression: no data Syny6803:sll1330: (click to expand)Experiment Mutant: Knockout loses GGCC methylation. Otherwise no known differenceExperiment from wild-type Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003 OptionsAnnotateHistory Main Menu 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

3. Anabaena PCC 7120: alr1152 Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 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: existsExperiment Expression: no data Syny6803:sll1330: (click to expand)Experiment Mutant: Knockout loses GGCC methylation. Otherwise no known differenceExperiment from wild-type Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003 OptionsAnnotateHistory Main Menu 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 you’ll also need to click. A

4. Anabaena PCC 7120: alr1152 Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 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: existsExperiment Expression: no data Syny6803:sll1330: (click to expand)Experiment Mutant: Knockout loses GGCC methylation. Otherwise no known differenceExperiment from wild-type Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003 OptionsAnnotateHistory Main Menu 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 there’s some hard evidence for the assertion. To learn more, click on Experiment. IDA: Matveyev et al (2001) A

5. Nucleic Acids Research (2001) 151:1491-1506 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 at nar.oupjournals.orf PubMed Central access FREE full text articles Back to Annotation page Annotations are linked to references at PubMed and from there (sometimes) to full length articles. Click on button to return to annotation page.

6. Anabaena PCC 7120: alr1152 Replicon: Chromosome Coordinates: 1356962 (start-ATG) -> 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: existsExperiment Expression: no data Syny6803:sll1330: (click to expand)Experiment Mutant: Knockout loses GGCC methylation. Otherwise no known differenceExperiment from wild-type Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003 OptionsAnnotateHistory Main Menu A A A A A A The human annotations are propagated throughout all cyanobacterial orthologs. Click on Syny6803.C:sll0729 to see how this works. A

7. Synechocystis PCC 6803: sll0729 Replicon: Chromosome Coordinates: 3424667 (stop) < - 3425524 (start)System Length = 285 amino acids 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 System ps:N6_MTASE: N-6 Adenine-specific DNA methylases signature. System Expression: (click to expand)Experiment Mutant: none Anab7120.C:alr1152: Knockout loses GGCC methylation. Otherwise no known Experiment difference from wild-type Cyanobacterial orthologs: Anab7120.C:alr1152 NostPunc.352:003 OptionsAnnotateHistory Main Menu 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 system’s suggestion that Sll0729 is an adenine methyltransferase may be [and is] wrong. End

8. 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. Scenario 2 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.