GREMLIN Database
Rod-binding - Rod binding protein
PFAM: PF10135 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 51 (50)
Sequences: 17562 (11525)
Seq/√Len: 1629.9
META: 0.914

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
30_Q33_K3.2311.00
4_R28_D2.9021.00
27_L31_L2.7241.00
46_D50_R1.9661.00
2_S5_K1.9611.00
18_Q21_D1.9561.00
29_Q33_K1.8861.00
31_L34_S1.8251.00
46_D49_Y1.8021.00
34_S37_K1.7811.00
38_S41_G1.5901.00
30_Q34_S1.5671.00
45_A49_Y1.5511.00
20_E24_R1.4551.00
34_S38_S1.3741.00
47_M50_R1.3661.00
16_G20_E1.3361.00
17_G20_E1.2551.00
4_R24_R1.1771.00
33_K37_K1.1461.00
19_G22_M1.1321.00
22_M25_S1.1001.00
18_Q22_M1.0951.00
12_G15_G1.0491.00
15_G20_E1.0411.00
32_A35_M0.9891.00
32_A36_A0.9711.00
1_K5_K0.9531.00
35_M42_I0.9441.00
31_L35_M0.9011.00
23_Y26_M0.8781.00
25_S28_D0.8411.00
23_Y27_L0.8401.00
39_G42_I0.8401.00
8_P11_D0.8341.00
41_G46_D0.8151.00
24_R27_L0.7991.00
21_D25_S0.7921.00
10_E13_L0.7741.00
9_K12_G0.7741.00
24_R28_D0.7731.00
1_K4_R0.7621.00
25_S29_Q0.7281.00
7_V10_E0.7271.00
26_M30_Q0.7041.00
4_R25_S0.6721.00
36_A42_I0.6591.00
15_G21_D0.6461.00
9_K16_G0.6381.00
22_M26_M0.6381.00
23_Y29_Q0.6321.00
9_K21_D0.6281.00
36_A39_G0.6121.00
2_S6_T0.6071.00
44_L48_L0.6031.00
39_G45_A0.5951.00
19_G23_Y0.5861.00
35_M39_G0.5811.00
26_M35_M0.5751.00
43_G48_L0.5591.00
1_K25_S0.5581.00
21_D24_R0.5511.00
10_E15_G0.5391.00
1_K28_D0.5361.00
36_A41_G0.5331.00
13_L19_G0.5321.00
37_K41_G0.5261.00
11_D15_G0.5231.00
42_I47_M0.5231.00
44_L47_M0.5201.00
16_G24_R0.5131.00
42_I45_A0.5081.00
4_R7_V0.5021.00
3_M7_V0.5011.00
8_P12_G0.5001.00
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
1y8aA 1 0.3333 2.4 0.853 Contact Map
3lyrA 1 0.6667 2.3 0.855 Contact Map
1lkoA 3 0.9412 2.2 0.857 Contact Map
3v8bA 4 0.4118 2 0.86 Contact Map
4i5sA 2 0.8824 2 0.861 Contact Map
4mhcA 1 0.9412 1.9 0.862 Contact Map
4da9A 3 0.4902 1.8 0.864 Contact Map
2ebfX 1 0.7647 1.6 0.867 Contact Map
2vbkA 3 0.5686 1.5 0.87 Contact Map
2pt6A 2 0 1.4 0.871 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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