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Table 3 27 cases of functionally-related TM helices in single-spanning membrane proteins

From: Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

Section

Description of match

Gene name

Seed UniProtID

x c

x φ

z-score

Orthologues of seed

A

Cases of 19 complete matches between full length and TM-only sequence

FGFR2

FGFR2_HUMAN

2.39

1.26

-0.10

FGFR2_CHICK;FGFR2_MOUSE; FGFR2_NOTVI;FGFR2_PLEWA; FGFR2_DANRE;FGFR2_XENLA

  

ectodysplasin

EDA_HUMAN

2.27

1.61

-0.45

EDA_BOVIN;EDA_MOUSE

  

TCR-α

TCA_HUMAN

2.29

1.85

-0.46

TCA_MOUSE

  

Ig-α

CD79A_HUMAN

2.29

2.15

-0.56

CD79A_CANFA;CD79A_BOVIN; CD79A_MOUSE

  

TREM-1

TREM1_HUMAN

2.18

1.00

-0.73

TREM1_PONAB;TREM1_PIG; TREM1_BOVIN;TREM1_MOUSE

  

caveolin-3

CAV3_HUMAN

2.26

3.86

-1.72

CAV3_BOVIN;CAV3_PIG; CAV3_RAT;CAV3_MOUSE

  

CD3-γ

CD3G_HUMAN

2.09

2.62

-1.89

CD3G_MACFA;CD3G_PIG; CD3G_RAT;CD3G_MOUSE; CD3G_BOVIN;CD3G_SHEEP

  

CD3-ζ

CD3Z_HUMAN

2.04

2.10

-2.04

CD3Z_PIG;CD3Z_SHEEP; CD3Z_RABIT;CD3Z_MOUSE

  

Fc-γ

FCERG_HUMAN

2.03

3.09

-2.60

FCERG_MACFA;FCERG_RAT; FCERG_MOUSE;FCERG_PIG; FCERG_CAVPO;FCERG_BOVIN

  

CD3-ε

CD3E_HUMAN

1.90

1.95

-3.38

CD3E_MACFA;CD3E_CANFA; CD3E_RABIT;CD3E_BOVIN; CD3E_PIG;CD3E_FELCA; CD3E_MOUSE;CD3E_SHEEP; CD3E_CHICK

  

mlgM

MUCM_RABIT

2.05

4.30

-3.40

MUCM_MOUSE;MUCM_ICTPU

  

CD3-δ

CD3D_HUMAN

1.89

1.61

-3.43

CD3D_MACFA;CD3D_PIG; CD3D_RAT;CD3D_MOUSE; CD3D_SHEEP;CD3D_BOVIN

  

IREM-2

CLM2_HUMAN

2.04

4.37

-3.56

CLM2_MOUSE

  

G-CSFR

CSF3R_HUMAN

1.90

2.60

-3.73

CSF3R_MOUSE

  

DAP12

TYOBP_HUMAN

1.79

2.02

-4.93

TYOBP_MACMU;TYOBP_PANTR; TYOBP_BOVIN;TYOBP_MOUSE; TYOBP_RAT;TYOBP_PIG

  

NKG2C

NKG2E_HUMAN

1.95

5.50

-5.62

NKG2E_PANTR

  

FXYD2

ATNG_HUMAN

1.72

2.94

-6.40

ATNG_RAT;ATNG_MOUSE; ATNG_SHEEP;ATNG_BOVIN; ATNG_XENLA

  

CD200RLa

MO2R2_HUMAN

1.68

4.48

-8.39

MO2R2_MOUSE

  

GPIX

GPIX_HUMAN

1.53

0.10

-9.18

GPIX_MOUSE

B

Cases of 8 sole hits between full length and TM-only sequence

TREM-2a

TREM2_HUMAN

1.91

2.47

-3.52

TREM2_MOUSE

  

mlgA

IGHG3_MOUSE

2.04

4.45

-3.65

IGHG3_HUMAN

  

Oscar

OSCAR_MOUSE

1.88

2.66

-3.95

OSCAR_HUMAN

  

MPL

TPOR_HUMAN

1.80

2.28

-4.86

TPOR_MOUSE

  

TREM-2b

TREM2_HUMAN

1.87

4.18

-5.25

TREM2_MOUSE

  

GPVI

GPVI_HUMAN

1.57

3.84

-9.75

GPVI_MOUSE

  

SILR-β

PILRB_HUMAN

1.57

4.16

-10.13

PILRB_MOUSE

  

Ig-β

CD79B_HUMAN

1.29

11.26

-28.63

CD79B_MOUSE

  1. There are in total 27 valid cases of functionally-related single-spanning membrane proteins from [34], out of which 19 cases are complete matches (section A) and 8 cases are sole hits (section B). The gene name and the UniProt ID of the seed sequences are given in column 3 and 4 respectively. The sequence complexity x c , hydrophobicity xΦ and z-score of the seed sequences are given in column 5, 6 and 7 respectively. The last column gives the orthologues of the seed sequences. For the 19 cases of complete matches, the TM-only sequences are able to retrieve their orthologous helices where their z-scores range from -9.18 to -0.10. For the other 8 cases of sole hits, they have failed to retrieve their orthologues. Their z-scores are between -28.63 to -3.52. The conflict zone between the 19 exact matches and 8 sole hits spans from -9.18 to -3.52. Note that TREM-2a (Table one of [34]) and TREM-2b (Table one of [34]) denote the same full length sequence but with a slight variation in the borders of the TM segment. Regardless of the variant, the conclusions remain unchanged.
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