MaGe - MicroScope - Web Interface System & Specialized Databases for (re)Annotation and Analysis of Microbial Genomes

Genome Browser interface provides an user-friendly way to visualize and explore a replicon content (cartographic map of the genome), together with the similarity results (synteny maps) obtained with other bacterial genomes available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). Artemis tool can be launched at this level to examine more precisely the nucleotidic/proteic sequences (a useful interface to correct translational start codon positions if necessary). For genomic objects drawn in part of the chromosome visualized in the cartographic map, additional information is listed in a table.

Label	Type	Gene	Begin	End	Length	Frame	Product	Matrix	Evidence	AMIGene Status	Mutation	GC Content	GC3 Content	CAI	Mw (Da)	pI
PP_0001	CDS	parB	147	1019	873	-3	probable chromosome-partitioning protein	1	validated/finished	COMMON	no	0.6254	0.7388	0.60	32388.82	6.12
PP_0002	CDS	parA	1029	1820	792	-3	probable chromosome partition protein	2	validated/finished	COMMON	no	0.6010	0.7576	0.60	28918.21	6.21
PP_0003	CDS	rsmG	1839	2489	651	-3	16S RNA methyltransferase	2	validated/finished	COMMON	no	0.5899	0.7327	0.58	24044.62	6.59
PP_0004	CDS	trmF	2486	4381	1896	-1	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	1	validated/finished	COMMON	no	0.6145	0.7579	0.65	69533.33	6.03
PP_0005	CDS	trmE	5012	6382	1371	-1	GTPase	1	validated/finished	COMMON	no	0.6273	0.7309	0.52	48961.52	5.15
PP_0006	CDS	oxaA	6471	8153	1683	-3	probable membrane protein insertase	2	validated/finished	COMMON	no	0.5859	0.7701	0.75	61917.12	8.81
PP_0007	CDS	yidD	8156	8401	246	-1	conserved hypothetical protein	2	validated/finished	COMMON	no	0.5569	0.5488	0.44	9213.26	9.13
PP_0008	CDS	rnpA	8394	8798	405	-3	ribonuclease P protein component	2	validated/finished	COMMON	no	0.5728	0.6667	0.42	14988.84	11.15
PP_0009	CDS	rpmH	8812	8946	135	-2	50S ribosomal protein L34	1	validated/finished	COMMON	no	0.5852	0.5556	0.80	5137.96	13.00
PP_0010	CDS	dnaA	9542	11062	1521	+2	chromosomal replication initiator protein	1	validated/finished	COMMON	no	0.5832	0.6943	0.57	56439.30	7.78
PP_0011	CDS	dnaN	11103	12206	1104	+3	DNA polymerase III subunit beta	2	validated/finished	COMMON	no	0.5870	0.7337	0.66	40717.13	5.16
PP_0012	CDS	recF	12222	13325	1104	+3	DNA replication and repair protein	2	validated/finished	COMMON	no	0.5888	0.6712	0.44	41793.22	8.72
PP_0013	CDS	gyrB	13330	15750	2421	+1	DNA gyrase subunit B	1	validated/finished	COMMON	no	0.5746	0.7460	0.74	90027.30	5.64
PP_5421	CDS		16589	17227	639	+2	conserved protein of unknown function	2	validated/finished	UNIQUE_AMIGA	no	0.5571	0.6338	0.39	24464.18	9.13
PP_0014	CDS		17208	19166	1959	+3	putative transposase	2	validated/finished	COMMON	no	0.5354	0.6091	0.38	76982.93	9.44
PP_0015	CDS		19163	20122	960	+2	putative transposon protein	2	validated/finished	COMMON	no	0.5240	0.6125	0.39	36302.25	5.62

Sequence

Label

Type

Gene

Begin

End

Length

Frame

Product

Matrix

Evidence

AMIGene Status

Mutation

GC Content

GC3 Content

CAI

Mw (Da)

History

PP_0001

CDS

parB

147

1019

873

-3

probable chromosome-partitioning protein

validated/finished

COMMON

0.6254

0.7388

0.60

32388.82

6.12

PP_0002

CDS

parA

1029

1820

792

-3

probable chromosome partition protein

validated/finished

COMMON

0.6010

0.7576

0.60

28918.21

6.21

PP_0003

CDS

rsmG

1839

2489

651

-3

16S RNA methyltransferase

validated/finished

COMMON

0.5899

0.7327

0.58

24044.62

6.59

PP_0004

CDS

trmF

2486

4381

1896

-1

tRNA uridine 5-carboxymethylaminomethyl modification enzyme

validated/finished

COMMON

0.6145

0.7579

0.65

69533.33

6.03

PP_0005

CDS

trmE

5012

6382

1371

-1

GTPase

validated/finished

COMMON

0.6273

0.7309

0.52

48961.52

5.15

PP_0006

CDS

oxaA

6471

8153

1683

-3

probable membrane protein insertase

validated/finished

COMMON

0.5859

0.7701

0.75

61917.12

8.81

PP_0007

CDS

yidD

8156

8401

246

-1

conserved hypothetical protein

validated/finished

COMMON

0.5569

0.5488

0.44

9213.26

9.13

PP_0008

CDS

rnpA

8394

8798

405

-3

ribonuclease P protein component

validated/finished

COMMON

0.5728

0.6667

0.42

14988.84

11.15

PP_0009

CDS

rpmH

8812

8946

135

-2

50S ribosomal protein L34

validated/finished

COMMON

0.5852

0.5556

0.80

5137.96

13.00

PP_0010

CDS

dnaA

9542

11062

1521

chromosomal replication initiator protein

validated/finished

COMMON

0.5832

0.6943

0.57

56439.30

7.78

PP_0011

CDS

dnaN

11103

12206

1104

DNA polymerase III subunit beta

validated/finished

COMMON

0.5870

0.7337

0.66

40717.13

5.16

PP_0012

CDS

recF

12222

13325

1104

DNA replication and repair protein

validated/finished

COMMON

0.5888

0.6712

0.44

41793.22

8.72

PP_0013

CDS

gyrB

13330

15750

2421

DNA gyrase subunit B

validated/finished

COMMON

0.5746

0.7460

0.74

90027.30

5.64

PP_5421

CDS

16589

17227

639

conserved protein of unknown function

validated/finished

UNIQUE_AMIGA

0.5571

0.6338

0.39

24464.18

9.13

PP_0014

CDS

17208

19166

1959

putative transposase

validated/finished

COMMON

0.5354

0.6091

0.38

76982.93

9.44

PP_0015

CDS

19163

20122

960

putative transposon protein

validated/finished

COMMON

0.5240

0.6125

0.39

36302.25

5.62

Pseudomonas putida KT2440 - chromosome AE015451.2 Public

(sequence length : 6181873 bases)