Rod-binding - PFAM28P - GREMLIN Contacts

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Rod-binding - Rod binding protein

PFAM:	PF10135	Sequences: KSMRKTVPKEDGLFGGGQGEDMYRSMLDQQLAKSMAKSGRGIGLADMLYRQ	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_Q	33_K	3.231	1.00
4_R	28_D	2.902	1.00
27_L	31_L	2.724	1.00
46_D	50_R	1.966	1.00
2_S	5_K	1.961	1.00
18_Q	21_D	1.956	1.00
29_Q	33_K	1.886	1.00
31_L	34_S	1.825	1.00
46_D	49_Y	1.802	1.00
34_S	37_K	1.781	1.00
38_S	41_G	1.590	1.00
30_Q	34_S	1.567	1.00
45_A	49_Y	1.551	1.00
20_E	24_R	1.455	1.00
34_S	38_S	1.374	1.00
47_M	50_R	1.366	1.00
16_G	20_E	1.336	1.00
17_G	20_E	1.255	1.00
4_R	24_R	1.177	1.00
33_K	37_K	1.146	1.00
19_G	22_M	1.132	1.00
22_M	25_S	1.100	1.00
18_Q	22_M	1.095	1.00
12_G	15_G	1.049	1.00
15_G	20_E	1.041	1.00
32_A	35_M	0.989	1.00
32_A	36_A	0.971	1.00
1_K	5_K	0.953	1.00
35_M	42_I	0.944	1.00
31_L	35_M	0.901	1.00
23_Y	26_M	0.878	1.00
25_S	28_D	0.841	1.00
23_Y	27_L	0.840	1.00
39_G	42_I	0.840	1.00
8_P	11_D	0.834	1.00
41_G	46_D	0.815	1.00
24_R	27_L	0.799	1.00
21_D	25_S	0.792	1.00
10_E	13_L	0.774	1.00
9_K	12_G	0.774	1.00
24_R	28_D	0.773	1.00
1_K	4_R	0.762	1.00
25_S	29_Q	0.728	1.00
7_V	10_E	0.727	1.00
26_M	30_Q	0.704	1.00
4_R	25_S	0.672	1.00
36_A	42_I	0.659	1.00
15_G	21_D	0.646	1.00
9_K	16_G	0.638	1.00
22_M	26_M	0.638	1.00
23_Y	29_Q	0.632	1.00
9_K	21_D	0.628	1.00
36_A	39_G	0.612	1.00
2_S	6_T	0.607	1.00
44_L	48_L	0.603	1.00
39_G	45_A	0.595	1.00
19_G	23_Y	0.586	1.00
35_M	39_G	0.581	1.00
26_M	35_M	0.575	1.00
43_G	48_L	0.559	1.00
1_K	25_S	0.558	1.00
21_D	24_R	0.551	1.00
10_E	15_G	0.539	1.00
1_K	28_D	0.536	1.00
36_A	41_G	0.533	1.00
13_L	19_G	0.532	1.00
37_K	41_G	0.526	1.00
11_D	15_G	0.523	1.00
42_I	47_M	0.523	1.00
44_L	47_M	0.520	1.00
16_G	24_R	0.513	1.00
42_I	45_A	0.508	1.00
4_R	7_V	0.502	1.00
3_M	7_V	0.501	1.00
8_P	12_G	0.500	1.00

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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