Table 3 Structural dependent modeling parameters for the PtNHX proteins.

From: Expression and integrated network analyses revealed functional divergence of NHX-type Na+/H+ exchanger genes in poplar

 

C-score

TM-score

RMSD (Å)

Best identified structural analogs in PDB

PDB Hit

TM-scorea

RMSDa

IDENa

Cov

PtNHX1

−1.25

0.56 ± 0.15

10.4 ± 4.6

4cz9A

0.711

1.16

0.213

0.724

PtNHX2

−1.15

0.57 ± 0.15

10.2 ± 4.6

4cz9A

0.706

1.25

0.216

0.721

PtNHX3

−0.77

0.62 ± 0.14

9.4 ± 4.6

4cz8A

0.668

1.34

0.217

0.682

PtNHX4

0.08

0.72 ± 0.11

7.3 ± 4.2

4cz8A

0.722

0.97

0.204

0.731

PtNHX5

−1.6

0.52 ± 0.15

11.2 ± 4.6

4cz8A

0.723

1.48

0.199

0.742

PtNHX6

−0.37

0.67 ± 0.13

8.3 ± 4.5

4cz9A

0.714

1.13

0.203

0.726

PtNHX7

−1.46

0.53 ± 0.15

12.9 ± 4.2

3gb8A

0.771

1.04

0.097

0.777

PtNHX8

−0.9

0.60 ± 0.14

11.4 ± 4.5

3w3tA

0.851

1.28

0.086

0.859

  1. C-score [−5, 2] is the confidence of each model, higher value signifies a model with a higher confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. TM-scorea is TM-score of the structural alignment between the query structure and known structures in the PDB library. RMSDa is the RMSD between residues that are structurally aligned by TM-align. IDENa is the percentage sequence identity in the structurally aligned region. Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.
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