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Table 2 Conserved domains found more than once among the toxic in-frame ORF fragments

From: Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae

Domain reference

Domain name

S. cerevisiae

Toxic inserts

Mean

95% confidence interval

Result

Domain description

Transport-specific domains

COG0471

CitT

4

4

0.21

0.17-1.25

+

Di-and tricarboxylate transporter

pfam03169

OPT

3

3

0.16

0.11-1.17

+

Oligopeptide transporter protein

COG1953

FUI1

9

3

0.48

0.44-1.56

+

Nucleotide transporter

pfam00324

aa_permeases

22

7

1.16

1.04-2.22

+

Amino acid permease

pfam00153

mito_carr

97

24

5.13

5.07-6.45

+

Mitochondrial carrier protein

COG0531

PotE

26

5

1.38

1.28-2.48

+

Amino acid transporter

COG0474

MgtA

23

4

1.22

1.12-2.30

+

Cation transport ATPase

cd00267

ABC_ATPase

58

6

3.07

2.93-4.22

+

ABC transporter nucleotide-binding domain

pfam00664

ABC_membrane

14

2

0.74

0.68-1.82

+

ABC transporter transmembrane region

COG0842

COG0842

6

3

0.32

0.29-1.38

+

ABC-type multidrug transport system, permease component

COG1131

CcmA

54

4

2.86

2.74-4.01

NS

ABC-type multidrug transport system, ATPase component

pfam00083

Sugar_tr

58

5

3.07

2.94-4.23

+

Sugar (and other) transporter

RNA-and DNA-binding domains

pfam00076

rrm

72

11

3.81

3.62-4.95

+

RNA recognition motif (transcription)

COG5099

(PUF)

9

5

0.48

0.44-1.56

+

Pumilio family RNA-binding repeat (translational repression)

smart00322

KH

11

4

0.58

0.54-1.66

+

K homology: RNA-binding domain (transcription, RNA metabolism)

smart00356

ZnF_C3H1

5

4

0.26

0.21-1.30

+

Zinc finger, C3H1 type (transcription)

COG5048

C2H2-type Zn_finger

15

4

0.79

0.74-1.89

+

Zn-finger (C2H2-type) (transcription)

COG0210

UvrD

4

2

0.21

0.17-1.24

+

DNA and RNA helicases, superfamily I (DNA replication, recombination, repair)

cd00086

Homeodomain

9

2

0.48

0.45-1.57

+

DNA binding domain (eukaryotic development)

pfam00249

myb_DNA-binding

13

2

0.69

0.66-1.80

+

Myb-like DNA-binding domain (transcription)

pfam00170

bZIP

4

2

0.21

0.17-1.25

+

Basic-leucine zipper DNA binding and dimerization domains (transcription)

smart00066

GAL4

48

2

2.54

2.44-3.72

NS

GAL4-like Zn(II)2Cys6 DNA-binding domain (fungal) (transcription)

pfam04082

Fungal_trans

26

2

1.38

1.29-2.48

NS

Fungal specific transcription factor domain.

pfam00270

DEAD

48

3

2.54

2.38-3.63

NS

DEAD/DEAH box helicase (replication, repair, transcription)

cd00079

HELICc

60

2

3.18

3.08-4.34

_

Helicase superfamily, C-ter domain (replication, repair, transcription)

Domains involved in Interactions with peptides, proteins or phospholipids

cd00200

WD40

327

29

17.31

16.87-18.54

+

Tandem repeats of about 40 residues interacting with peptides

pfam01602

Adaptin_N

9

2

0.48

0.43-1.54

+

N-ter region of adaptor proteins (clathrin-coated pits and vesicles)

pfam00786

PBD

4

2

0.21

0.20-1.27

+

P21-Rho-binding domain (or CRIB)

pfam00169

PH

11

3

0.58

0.55-1.67

+

PH: pleckstrin homology. binds phosphoinositides or other ligands (signalling)

COG5271

MDN1

16

3

0.85

0.78-1.93

+

AAA : ATPase with von Willebrand factor type A domain (multiprot. complexes)

smart00268

ACTIN

14

2

0.74

0.67-1.82

+

ACTIN, cytoskeleton/motor protein

COG5022

Myosin heavy chain

7

5

0.37

0.33-1.43

+

ATPase, molecular motor

COG5043

MRS6

4

2

0.21

0.17-1.24

+

Vacuolar protein sorting-associated protein

KOG0446*

Dynamin

3

3

0.16

0.13-1.20

+

GTPase that mediates vesicle trafficking

Metabolism-related domains

pfam03901

PMP

5

2

0.21

0.21-1.29

+

Mannosyltransferase

COG1928

PMT1

7

4

0.37

0.30-1.40

+

Mannosyltransferase

pfam00561

Abhydrolase

18

3

0.95

0.88-2.05

+

Abhydrolase, alpha/beta hydrolase fold (catalytic domain)

pfam00107

ADH_zinc_N

21

2

1.11

1.01-2.19

NS

Zinc-binding dehydrogenase

pfam00501

AMP-binding

11

2

0.58

0.51-1.64

+

AMP-binding synthetase

Other domains

pfam00674

DUP

35

3

1.85

1.81-3.03

NS

DUP family (proteins of unknown functions)

COG5384

Mpp10

1

2

0.05

0.03-1.07

+

M phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein component)

COG5032

TEL1

8

4

0.42

0.34-1.44

+

PI kinase and protein kinases of the PI kinase family

COG1025

Ptr

5

2

0.26

0.22-1.31

+

Zn-dependent peptidases (secreted/periplasmic, insulinase-like)

pfam02902

Peptidase_C48

2

2

0.11

0.08-1.13

+

Ulp1 protease family, C-terminal catalytic domain

pfam00004

AAA

43

3

2.28

2.15-3.39

NS

AAA, ATPase family associated with various cellular activities (AAA)

smart00220

S_TKc

125

4

6.52

6.31-7.72

-

Serine/threonine protein kinases, catalytic domain

  1. Peptide sequences of toxic natural ORF fragments were searched for domains (see text), and the frequency of domains found more than once was compared to the frequency in the whole proteome. References and names of domains are in the first two columns; occurrences in the whole genome (S. cerevisiae) and in the toxic inserts are in the third and fourth columns, respectively. The next three columns show the statistical analysis performed as follows: 1,000 random selections of 843 domains (total number of occurrences in the toxic inserts) were made from the set of 15,925 domains identified in S. cerevisiae (see Materials and methods); mean (column 5) represents the mean number of occurrences of each domain among the toxic inserts; the 95% confidence interval (column 6) was calculated using the SD of the 1,000 random drawings; column 7 shows the result of this analysis for each domain: NS, not significant; +, domain over-represented in toxic inserts; -, domain under-represented in toxic inserts. The last column gives a brief description of domains from NCBI Conserved Domain Database [65]. *KOG0446 was found using cdd.v1.63 of NCBI CD-Search [64].
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Genome Biology

ISSN: 1474-760X

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