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Table 2 Distribution of mitochondrial porin motifs in the sequences in the current analysis and public protein sequence databases.

From: The evolutionary history of mitochondrial porins

Motif

Total Sequences Analyzed (this work)

Hits

Misses

Insufficient sequence data

Hits in Swiss-Prot TrEMBL and PDB a

Expected random matches b

Animal Motif c

93 animal

76

4

13

81 (including 7 splice variants)

2.9 d (84)

Plant Motif e

105 plant

90

11

4

43 (splice variants not identified)

2.1e-14

Fungal Motif f

38 fungal

33

1

4

18 (splice variants not identified)

4.4 d (26)

Totals for this work

236

199

16

21

142

 

PS00558 g

93 animal

42

41

10

61 animal sequences

6.3e-02

PS00558

105 plant

59

35

11

30 plant sequences

as above

PS00558

38 fungal

20

15

3

11 fungal sequences

as above

PS00558

5 stramenopiles

0

1

4

0 stramenopile sequences

as above

Totals for PS00558

241

121

92

28

102 (94 without splice variants)

 

GLK

93 animal

82

11 (2 GXK/Rh)

0

28i

17478

GLK

105 plant

74

30 (11 GXK/R) 15 SXK

1

14

as above

GLK

38 fungal

30

8 (6 GXK/R)

0

2

as above

GLK

5 stramenopiles

5

0

0

0

as above

Totals for GLK

241

192

47 (19 GXK/R)

1

44 (of 50 VDAC sequences) j

 
  1. a sequences in UniProtKB/Swiss-Prot (release 50.6), UniProtKB/TrEMBL (release 33.6), PDB (14-Sep-2006) databases
  2. bapproximate number of expected random matches in Swiss-Prot release 41 (122564 sequences)
  3. c animal motif: <-X(0,30)-[PTSA]-X(1,2)-[YF]-X-[DE]-[ILVF]-[AG]-[KR]-X-[AST]-[KR]-[DE]-[ILV]-[FYST].; was not found in any plant or fungal VDAC sequences
  4. d expected random matches could not be calculated for constrained patterns; value was obtained using the unconstrained motif; in parentheses is the number of hits using the unconstrained motif
  5. e plant motif derived for Viridiplantae: [YF]-X-[DE]-[ILV]-G-[KR]-[KR]-[APST]-[KR]-D-[IL]-L-X-[KR]-D-[FHY]-X(4)-K-[FL]-[CNST]-X(4)-[ANST]-X(2)-G-X(2)-[FILV]-X-[ASTV]-[AST]-[AGS]-X(3)-[ADGNS].; was not found in any animal or fungal VDAC sequences
  6. f fungal motif: <-X(0,10)-[STIMLQ]-X(1,3)-[PL]-X(1,3)-[WYF]-X-[DEAG]-[ILV]-X-[RK]-X(3)-[DG]-X(0,1)-[ILV]-X(48,53)-[ILV]-X(2)-[ST]-Q-.96-[WL].; was not found in any plant or animal VDAC sequences
  7. g PS00558 (EUKARYOTIC_PORIN) [PROSITE (release 19.29)] motif: [YH]-x(2)-D-[SPCAD]-x-[STA]-x(3)-[TAG]-[KR]-[LIVMF]-[DNSTA]-[DNS]-x(4)-[GSTAN]-[LIVMA]-x-[LIVMY]
  8. h where X represents any amino acid
  9. i GXK/GXR included in total
  10. j the description (DE) filter VDAC was used due to the common occurrence of short sequences (G-L-K); this filter does not work on PDB sequence data, so only the Swiss-Prot and TrEMBL databases were searched