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Table 1 YM001-specific genetic variations compared to HN016

From: Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016

YM001 position

HN016 position

Gene product

Biological function

Variation

Effect on YM001 coding

Carbohydrate metabolism

 136826

142595

Fructose-bisphosphate aldolase

Fructose and mannose metabolism

SNV

K259N substitution

 780441

786056

Phosphoenolpyruvate carboxylase

Microbial metabolism in diverse environments and Carbon metabolism

SNV

I181I substitution

 868738

874444

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

Biosynthesis of the bacterial cell wall and is critical for bacterial survival

SNV

H126R substitution

 1403613

1420411

glycosyl transferase family 8

glycosyl synthesis

SNV

T383I substitution

 1534895

1551880

metallophosphoesterase

hydrolysis of phosphate

SNV

Y64C substitution

Lipid metabolism

 1805677

1822388

Phosphatidate cytidylyltransferase

Glycerophospholipid metabolism

SNV

P239L substitution

Nucleotide metabolism

 83930

89762

DNA-directed RNA polymerase subunit alpha

Primary transcript RNA production and RNA chains construction

SNV

V258A substitution

 192012

197717

DNA-directed RNA polymerase subunit beta

Primary transcript RNA production and RNA chains construction

SNV

P360A substitution

 1515764

1532749

Thymidylate kinase

dTDP Biosynthesis

SNV

D35D substitution

Amino acid metabolism

 2033153

2049866

Arginine deiminase

Acid tolerant

SNV

V362I substitution

Environmental information processing

 1858831

1875542

Sensor histidine kinase

Peptidoglycan metabolism

SNV

R126H substitution

Translation

 393841

399503

Transcription elongation factor NusA

RNA polymerase-associated protein

SNV

E116G substitution

 407665

413327

FUR family transcriptional regulator

Peroxide stress response regulator

SNV

S42I substitution

 755561

761176

S1 RNA-binding protein

Post-transcriptional control of RNAs

SNV

R460S substitution

 949470

955242

chloramphenicol acetyltransferase

Hexapeptide repeat-containing transferase

SNV

G43Y substitution

 1264942

1270622

TetR family transcriptional regulator

Transcriptional regulator

SNV

W122R substitution

 1967217

1983929

Arginine repressor ArgR

Transcriptional regulator of arginine metabolism

SNV

117-aa C-terminal deletion

DNA repair and recombination proteins

 1022277

1028049

DNA topoisomerase I

Regulation of supercoiling and maintenance of genetic stability

SNV

T644K substitution

Transport

 253283

258943

amino acid ABC transporter permease

Membrane transport

SNV

G147E substitution

297760..297761

303421

PTS system transporter subunit IIC

Starch and sucrose metabolism

Deletion

10-aa C-terminal extension,102-aa C-terminal deletion

 364407

370068

MarR family transcriptional regulator

Regulate multiple antibiotic resistance and the oxidative stress response

SNV

H106N substitution

 970865

976637

Sugar ABC transporter permease

simple sugar transport system permease protein

SNV

T5T substitution

 1635394

1652379

Multidrug transporter

Drug efflux proteins

SNV

M126V substitution

 1663151

1680136

Glycerol uptake facilitator protein

glycerol-uptake facilitator

SNV

I44I substitution

 1761614

1778325

PTS system ascorbate-specific transporter subunit IIC

Microbial metabolism in diverse environments

SNV

D327J substitution

 1828308

1845019

PTS system transporter subunit IIB

Galactose metabolism

SNV

M1T substitution

 2020460

2037173

Cobalt transporter ATP-binding subunit

energy-coupling factor transport system ATP-binding protein

SNV

E79K substitution

Folding, sorting and degradation

 743279..743280

748941

Recombinase RecF

Manipulate the structure of genomes

Deletion

6-aa C-terminal extension,855-aa C-terminal deletion

Unknown function

 1271532..1271533

1277212

Hypothetical protein

Unknown function

Deletion

Y63N substitution, 5-aa C-terminal extension,81-aa C-terminal deletion