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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].