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Scenario 3
Anotation Process
What follows is a simulation of the process of annotating,
using 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 3
Anotation Process
You find yourself annotating a set of genes that includes
all1290 from Anabaena PCC 7120.
You want to assess the validity of the automated annotation,
particularly the assertion of function and start codon.
If there are any problems, you want to fix them.
Continue
Main Menu
Options
Annotate
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Evidently no human has touched this annotation (System is given as
the only source). Is the functional annotation sound? Mouse over* to
the blue motif bar above the graphical representation of all1290.
*In real life, information will pop up when you mouse to an informative position. In this
simulation you’ll also need to click.
System
Main Menu
Options
Annotate
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
N6,N4 DNA methyltransferase
(PF01515): 2e-18
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Pfam found a motif consistent with the annotation with a good
expectation value. Curiously, the motif extends beyond the start of
the gene. Mouse away from the bar.*
*In real life, information will go away when you mouse away from an informative
position. In this simulation you’ll also need to click anywhere..
System
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
System
Cyanobacterial orthologs: none
PvuIIM: DNA methyltransferase
(NP_072082): 8e-64
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Mouse over to the first aligned gene, from Proteus vulgaris.
Again, good support, and again, the gene extends beyond
the annotated start codon of the Anabaena orf.
*Remember to click to view the popup and click to make it disappear.
Main Menu
Annotate
Options
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
You begin to suspect the annotated start codon. To
visualize alternatives, click on the OptionsOptions
button,
then click on Show alternate starts.
History
View: graphic
Show all
Show hits: <1e-6
Predicted
Show neighbors:
+/- 1
Show motifs
Show alternate starts
Show annotated features
Predicted
Show predicted features
Show transposon ends
Show tandem repeats
Show inverted repeats
Show dispersed repeats
Show private set
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Mouse over to the annotated start site* and you
see the sequence preceding it: a plausible
ribosome binding site. Mouse over to the most
distant start site. Not as good.
*Click to show, click to disappear
System
1533628
and upstream:
1533931
and upstream:
CTTCCGGGAAATCCTGTG
TAACTTAAATGTCGCTTG
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Nonetheless, the position of the distant site
relative to the other sequences makes it a
reasonable candidate. Click on it to
provisionally change the start site.
System
Main Menu
Annotate
Options
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Length = 200 amino acids
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
History
View:View
graphic
Show all
Show hits: <1e-6
System
Show neighbors:
+/- 1
Show motifs
Show alternate starts
Show annotated features
System
Show predicted features
Show transposon ends
Show tandem repeats
Show inverted repeats
Show dispersed repeats
Show private set
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
Much better! More similarity and more sequences that are similar (and
Neisseria
better meningitidis
E-values, too, if you were to look). However, it is always a good
practice to check the alignment before accepting the conclusions of a
More and then on View.
similarity search, so click on Options
button.
Main Menu
Annotate
Options
Anabaena PCC 7120:
Graphicall1290
Genome
Alignment with homologs
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Alignment with motif
Replicon: Chromosome
Length = 200 amino acids
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
Click on Alignment with motif to see
Neisseria
meningitidis
how All1120
compares to other
protein that make up the Pfam motif
represented by the motif bar.
More
History
View
Show all
Show hits: <1e-6
System
Show neighbors:
+/- 1
Show motifs
Show alternate starts
Show annotated features
System
Show predicted features
Show transposon ends
Show tandem repeats
Show inverted repeats
Show dispersed repeats
Show private set
Conserved Domain Database
PubMed
Nucleotide
Protein
CD: Pfam01555.5, N6_N4_Mtase
Structure
CDD
Taxonomy
Help
Source: Pfam[US], Pfam[UK]
PSSM-Id: 8054
Description: DNA methylase. Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA
methylases and N-6 Adenine-specific DNA methylases.
Taxa: root
Status: Alignment from source
Created: 13-Jun-2002
Aligned: 52 rows
PSSM: 199 columns
Representative: Consensus
Proteins: [Click here for CDART summary of Proteins containing pfam01555]
View 3D Structure
Subset Rows
with Cn3D
up to 10
All1290
consensus
Pvuii Dna Methyltransfer
Modification methylase S
BglI modification methyl
adenine specific DNA met
adenine specific DNA met
Modification methylase M
Modification methylase M
Modification methylase B
gi_3257411
78
1
77
119
92
174
131
133
178
134
123
using Virtual Bonds
(To display structure, download Cn3D)
of the most diverse members
10
20
30
40
50
60
....*....|....*....|....*....|....*....|....*....|....*....|
KRVLTENGSFILDLGgaylpgnp----VRSIYQYELLVKLCKEVGFFL----------- 122
ARRVLKPDGSIFIFGG------------NKSQKNIFRFIDILIEKGFKF----------- 37
DGSFVVDFGGAYMKGVp-----------ARSIYNFRVLIRMIDEVGFFL----------114
This
is
output
from
NCBI
showing
the
PRTGWKRNKQLSLVP--------------------FRVALALQDDGWWI----------- 147
alignment that went into making Pfam
FQAVNLKKHRVSVTREd----------iLNALKLEPELTKYQLAKKFNCs---------e
132
ARDLLKEDGVIFISIDdnecan-lkilcDEIFGEDNFVGDFIRKTKSTTndakiglnyqh
232
motif
01555...
but
it
was
intercepted
by
ILRTLLPIYARALKDLmrt------iknVFKQKGQAQAQLVLKEQIKELs---------q 175
the interface in order to incorporate
IIDPFMGSGTTLVQCMem--------giNSIGIDISPFNCLIAEVKLQKydi------qk
178
LSRCNLKDGDYILDPFagtgttgavvkkMKYQLYPKDLNVILIEKGKKF----------226
the
sequence
of
All1290
for
SHIAFEPKSFIFEYNLeeldraykeiyeISPTKIEQKFNHLSITEGAFPeete----ndl 189
comparison. Click on
ANTYAMPSELILKGFP-------------KVKDVVLLFVDDKVLVGETVr---------159
More to
get to the best part of the alignment.
More
Back to Annotation
Conserved Domain Database
PubMed
Nucleotide
All1290
consensus
Pvuii Dna Methyltransfer
Modification methylase S
BglI modification methyl
adenine specific DNA met
adenine specific DNA met
Modification methylase M
Modification methylase M
Modification methylase B
gi_3257411
All1290
consensus
Pvuii Dna Methyltransfer
Modification methylase S
BglI modification methyl
adenine specific DNA met
adenine specific DNA met
Modification methylase M
Modification methylase M
Modification methylase B
gi_3257411
Protein
Structure
CDD
Taxonomy
Help
228
131
223
339
238
367
279
329
464
319
255
310
320
330
340
350
360
....*....|....*....|....*....|....*....|....*....|....*....|
rrcKAAGVKPHPARFPQGFAEFFIKFLTD-------------------EGDLVLDPFAGS
---NLKGKKKHPTQKPEALLERIILESSN-------------------EGDLVLDPFAGS
ancKLMGIKAHPARFPAKLPEFFIRMLTE-------------------PDDLVVDIFGGS
sipTAPSGANHFAVMPRKLAHFALKATLP-------------------MNGSCLDPFMGS
---SVRKNDDHEAKFPLLLPQRLIKLLTQ-------------------KGDTVLDCFMGS
ellNLGMGEYFTYPKGVEFMKKIILHSTTp-----------------nEGDIILDFFAGS
----LGLKGLFKTPKPVALIKYLLLCSTP-------------------KDSIILDFFAGS
vfdPYYCYKHKKICRPVQTILRHLEEYTNdvisri-------eefskiRKDAYYLIINGD
icyNCQKEIYGKNSLPILKESKEIIESLEsvengeyqvgenikpqyqkRCKESKSKFAGM
tspPYCNRYDYTRTYALELAYLGVDEKKIrelrqa-------qlsctvENKSKLKQLKDY
---KVCDVRRLRKCFPRTRFDAIITEPYM-------------------GKPLKYKPSRGE
269
169
264
380
276
410
316
382
524
372
293
370
380
390
400
410
....*....|....*....|....*....|....*....|....*....|....*.
NTTGFVAETW-----------QRRWIAVEINQDYVLGS--------------RYRF 299
GTTAAAAKEL-----------GRKFIGIEINEEYVKLA--------------KKRL 199
Note that All1290 matches
the
NTTGLVAERE-----------SRKWISFEMKPEYVAAS--------------AFRF
294
GTTGRVVREL-----------GGRFVGVDVNEHYMTDY--------------LVES
410most
alignment in almost all of the
GTTAVAALSE-----------SRNFIGIEKEPKYIQLS--------------NKNV 306
informative positions (in 452
red),
GTTVHAVMELnae-----dkgNREFILVQIDEEIKEDEsay--------dfcKKEL
GTTAQAVIEV-----------NRDYCLNWSFYLCQKEE--------------KIKN
346
those presumably related
to
SRTVDIEEELkkhpnfyelykNKKIDGIFTSPPYLGQIdyheqhayayelfdIPRL 437
common function. Click554
on
ERMNWGASPG-----------ARKTIIGDSFSKMRLYR--------------LDQP
YHSLFLESRYae--------iERLVTGNEVLNEINYAL--------------RKRW 405
Back to Annotation
AIKIAKGLDR------------LYYQAFESFADVLKRGs-------------IIVF 323
More
Back to Annotation
268
168
263
379
275
409
315
381
523
371
292
Main Menu
Annotate
Options
Anabaena PCC 7120:
Graphicall1290
Genome
Alignment with homologs
Coordinates: 1533026 (stop) <- 1533628 (start-GTG)
Alignment with motif
Replicon: Chromosome
Length = 200 amino acids
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
Since the motif does not extend to the beginning of the
Neisseria
protein, meningitidis
it might be a good idea to check alignment with
the full length of protein identified by the similarity
search. Click on button then
on View,More
and finally
Options
on Alignment with homologs.
History
View:View
graphic
Show all
Show hits: <1e-6
System
Show neighbors:
+/- 1
Show motifs
Show alternate starts
Show annotated features
System
Show predicted features
Show transposon ends
Show tandem repeats
Show inverted repeats
Show dispersed repeats
Show private set
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
NmeSIM (Neisseria)
ScaIM (Streptomyces)
All1290 (Anabaena)
PvuIIM (Proteus)
SptAIM (Salmonella)
SpcM (Streptomyces)
SpcG (Streptomyces)
BglIIM (Bacillus)
MJ1498 (Methanococcus)
CfrBIM (Citrobacter)
BamHIM (Bacillus)
3
6
1
6
1
1
1
5
1
66
68
---TISSIMSLEN---------------FQLIKTQLGVPSYEND--RVAIYQGDCIQLMD
FGYVIQSSAALWNRLSTFSQRGKALDTRLADIKKALGKPYYETS--DVLLYHGDSLELLK
LNSQQTTTIKLTN-----------------------FIPSYTQQ--HGAVYLGDCLEIIK
LQTMSSNDMLNFG-----------------------KKPAYTTS--NGSMYIGDSLELLE
--------MMFDD-----------------------KKPAYKTD--LGAMYIADSLEMLE
----MTESTTAAG-----------------------DRRALGAE--HGSYHWGDSLALLE
----MTELT-PTE-----------------------DRCPLEAE--HGSYHWGNSLELMK
QYKQIKLHLGMED---D-----------NEDLPNHIPSSFPKQH--LNKIYNGDTMNMLL
------------------------------------------ME--INKIYCMDCLEGMK
VINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKKIISKSPLNNMLLQGNCAETLK
KILENKNSVKLNEFN-----------------SIQEIKPYFYTD--LGKLYNGDCLELFK
NmeSIM (Neisseria)
43 KISKGSFQMTITSPPYNIGKEYES----ILDLEHYLEWCERWMQSIHHLTEDSGCFWLNL
ScaIM (Streptomyces)
64 SMPQQIFDLTVTSPPYNIGKEYEG----VLSIEEYISWCETWMSRVHRATSAGGAFWLNV
All1290 (Anabaena)
36 SIPDNSVNLILTSPPFALTRKKEYG---NESAEKYIEWFLPFADEFKRVLTENGSFILDL
PvuIIM (Proteus)
41 SFPDESISLVMTSPPFALQRKKEYG---NLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDF
SptAIM (Salmonella)
28 SMPDNSLNLVMTSPPFALQRKKEYG---NHDQEQYIDWFLKFGELVFKKLKDDGSFVVDF
SpcM (Streptomyces)
32 GVPDGSVRAVVCSPPFEGPQLIADE---DRAGACSSDWLMPFFGQFERVLRPDGCVAFEL
SpcG (Streptomyces)
32 GIPDASVDAVVCSPPFEGDALISDE---GRRGDAFVAWIEPFFRQFQRVLRPAGCVAFEL
BglIIM (Bacillus)
49 DIPDNSVDLVVTSPPYNINKFKND----RRPLEEYLKWQTEIIEQCHRVLKPSGSIFWQV
MJ1498 (Methanococcus) 17 QLKDKTVDVVVTSPPYNIGIKYNKYSD-NLSREDYLNWIEEVVKEIKRVLKDDGSFFINV
CfrBIM (Citrobacter)
126 KLPDESVNLVFTSPPYYNAKPEYS--E-YHTYDEYLSLLRSVIKECHRVLSEGRFFVINV
BamHIM (Bacillus)
68 QVPDENVDTIFADPPFNLDKEYDEGVTDKNSFSGYLDWYYKWIDECIRVLKPGGSLFIYN
To one knowledgeable on DNA methyltransferases, the identity
of All1290 at positions 48-51 (SPPF) is particularly striking, as
that is part of the AdoMet binding site and one of the signatures
of N4-cytosine methyltransferases. Press Continue .
Continue
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
NmeSIM (Neisseria)
ScaIM (Streptomyces)
All1290 (Anabaena)
PvuIIM (Proteus)
SptAIM (Salmonella)
SpcM (Streptomyces)
SpcG (Streptomyces)
BglIIM (Bacillus)
MJ1498 (Methanococcus)
CfrBIM (Citrobacter)
BamHIM (Bacillus)
3
6
1
6
1
1
1
5
1
66
68
---TISSIMSLEN---------------FQLIKTQLGVPSYEND--RVAIYQGDCIQLMD
FGYVIQSSAALWNRLSTFSQRGKALDTRLADIKKALGKPYYETS--DVLLYHGDSLELLK
LNSQQTTTIKLTN-----------------------FIPSYTQQ--HGAVYLGDCLEIIK
LQTMSSNDMLNFG-----------------------KKPAYTTS--NGSMYIGDSLELLE
--------MMFDD-----------------------KKPAYKTD--LGAMYIADSLEMLE
----MTESTTAAG-----------------------DRRALGAE--HGSYHWGDSLALLE
----MTELT-PTE-----------------------DRCPLEAE--HGSYHWGNSLELMK
QYKQIKLHLGMED---D-----------NEDLPNHIPSSFPKQH--LNKIYNGDTMNMLL
------------------------------------------ME--INKIYCMDCLEGMK
VINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKKIISKSPLNNMLLQGNCAETLK
KILENKNSVKLNEFN-----------------SIQEIKPYFYTD--LGKLYNGDCLELFK
NmeSIM (Neisseria)
43 KISKGSFQMTITSPPYNIGKEYES----ILDLEHYLEWCERWMQSIHHLTEDSGCFWLNL
ScaIM (Streptomyces)
64 SMPQQIFDLTVTSPPYNIGKEYEG----VLSIEEYISWCETWMSRVHRATSAGGAFWLNV
All1290 (Anabaena)
36 SIPDNSVNLILTSPPFALTRKKEYG---NESAEKYIEWFLPFADEFKRVLTENGSFILDL
PvuIIM (Proteus)
41 SFPDESISLVMTSPPFALQRKKEYG---NLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDF
SptAIM (Salmonella)
28 SMPDNSLNLVMTSPPFALQRKKEYG---NHDQEQYIDWFLKFGELVFKKLKDDGSFVVDF
SpcM (Streptomyces)
32 GVPDGSVRAVVCSPPFEGPQLIADE---DRAGACSSDWLMPFFGQFERVLRPDGCVAFEL
SpcG (Streptomyces)
32 GIPDASVDAVVCSPPFEGDALISDE---GRRGDAFVAWIEPFFRQFQRVLRPAGCVAFEL
BglIIM (Bacillus)
49 DIPDNSVDLVVTSPPYNINKFKND----RRPLEEYLKWQTEIIEQCHRVLKPSGSIFWQV
MJ1498 (Methanococcus) 17 QLKDKTVDVVVTSPPYNIGIKYNKYSD-NLSREDYLNWIEEVVKEIKRVLKDDGSFFINV
CfrBIM (Citrobacter)
126 KLPDESVNLVFTSPPYYNAKPEYS--E-YHTYDEYLSLLRSVIKECHRVLSEGRFFVINV
BamHIM (Bacillus)
68 QVPDENVDTIFADPPFNLDKEYDEGVTDKNSFSGYLDWYYKWIDECIRVLKPGGSLFIYN
The substantial agreement between All1290, PvuIIM,
and SptAIM turns out to extend through the DNA
recognition domain. That’s good enough for me! Let’s
start making this public by clicking Annotate .
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Coordinates
Start site
Replicon: Chromosome
Gene name
Coordinates: 1533026
(stop) <- 1533628 (start-GTG)
Function
Length = 200
amino acids
Comment
Internal note
Strand: Complementary
Remove orf
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
That click gets you back to the annotation
Neisseria
meningitidis
page. Let’s
begin by changing the start site.
Click Start site..
More
System
System
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533628
1533628 (start-GTG)
Length = 200 amino acids
System
Strand: Complementary
Function: PvuII DNA methyltransferase
System
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
You could type in the new
Neisseria
meningitidis
coordinate,
but it’s easier just to
click on the new start site.
More
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533931
1533628 (start-TTG)
Length = 301 amino acids
IC: Inferred by curator
Use this when your assertion is
based on your own judgement
Function: PvuII DNA methyltransferaseof sequence similarity or other
information, when there is no
direct experimental data.
Cyanobacterial orthologs: none
Strand: Complementary
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
Every assertion must be accompanied by a
Neisseria
meningitidis
justification.
The codes are standard from the Gene
Ontology Consortium and facilitate searching.
More
Mouse over to IC to find out what it’s used
for.
Justification
Predicted
IC: Inferred by curator
IDA: Inferred by direct assay
IEP: Inferred from expression pattern
IGI: Inferred from genetic
interaction
Predicted
IMP: Inferred from mutant phenotype
IPI: Inferred from physical interaction
TAS: Traceable author statement
NAS: Nontraceable author statement
ND: No biological data available
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533931
1533628 (start-TTG)
Length = 301 amino acids
Strand: Complementary
Function: PvuII DNA methyltransferase
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
Inferred by curator seems to fit
Neisseria
the meningitidis
situation. Click on it.
More
Justification
Predicted
IC: Inferred by curator
IDA: Inferred by direct assay
IEP: Inferred from expression pattern
IGI: Inferred from genetic
interaction
Predicted
IMP: Inferred from mutant phenotype
IPI: Inferred from physical interaction
TAS: Traceable author statement
NAS: Nontraceable author statement
ND: No biological data available
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533931
1533628 (start-TTG)
Length = 301 amino acids
Comment
Human
Strand: Complementary
Function: PvuII DNA methyltransferase
Predicted
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
You would now fill in the reasons
Neisseria
meningitidis
leading
you to your assertion
regarding the start codon. For
now, just press the Enter key.
More
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533931 (start-TTG)
Length = 301 amino acids
Human
Strand: Complementary
Function: PvuII DNA methyltransferase
System
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella paratyphi
Streptomyces spectabilis
Streptomyces netropsis
The start codon has been changed. In a like fashion, a name is
Neisseria
given tomeningitidis
the orf, and functional annotation added. Now that the
activity seems real, I’m inspired to look through the literature,
More
and... it turns out that Bancroft et al (1989)
described in vivo
protection of Anabaena DNA against PvuII! Press Continue .
Continue
A
Main Menu
Annotate
Options
History
Anabaena PCC 7120: all1290
Replicon: Chromosome
Coordinates: 1533026 (stop) <- 1533931 (start-TTG)
Length = 301 amino acids
Human
A
Human
Human
A
Experiment
Experiment
A
Strand: Complementary
Gene name(s): avaXM
Function: Putative type II DNA cytosine methyltransferase (CAGCTG-specific)
Classification: Type II beta (N4)
Activity:
Protects against: PvuII
In vivo activity: exists
Cyanobacterial orthologs: none
Anab7120
Proteus vulgaris
Salmonella
paratyphi
That’s how
the annotation ends up. Now anyone clicking on
Human or Experiment will find the annotations you made, and
Streptomyces spectabilis
anyone mousing over one of the annotator icons ( ) willA get
More
to your name, and your e-mail address.
End
A
A
Scenario 3
Anotation Process
Summary
• Each assertion is accompanied by a justification linked to the
annotator
• Interface provides tools for trying out different start codons
and assessing their validity
• Interface provides different alignments for the assessment
of orf function
• In the end, human expertise is required to recognize the
critical information
There are no new tools here, just a comprehensive interface to
put these tools at the service of human annotators who prefer
to do science rather than click keys. The proposal seeks
resources to support the development of this interface.
To quit, right click, then click End Show.