RL35 - BACSU - GREMLIN Contacts

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RL35 - 50S ribosomal protein L35

UniProt:	P55874	Sequences: MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQMLANIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	66 (63)
Sequences:	1209 (575)
Seq/√Len:	72.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_R	11_A	3.764	1.00
32_L	35_N	3.187	1.00
10_S	14_F	2.380	1.00
54_D	57_R	2.239	1.00
29_T	45_R	2.137	1.00
16_K	22_L	1.836	1.00
26_H	48_A	1.756	1.00
51_S	54_D	1.717	1.00
39_K	43_K	1.625	0.99
4_M	63_A	1.581	0.99
7_H	61_M	1.518	0.99
22_L	58_I	1.513	0.99
50_V	58_I	1.398	0.98
23_K	49_V	1.375	0.98
21_K	49_V	1.370	0.98
15_K	23_K	1.306	0.97
37_S	41_K	1.218	0.96
16_K	59_K	1.217	0.96
58_I	61_M	1.185	0.96
27_A	54_D	1.183	0.95
25_S	45_R	1.158	0.95
55_F	59_K	1.149	0.95
10_S	61_M	1.133	0.94
17_T	49_V	1.126	0.94
26_H	29_T	1.109	0.94
6_T	11_A	1.107	0.94
52_A	55_F	1.107	0.94
23_K	47_S	1.085	0.93
38_Q	41_K	1.067	0.92
17_T	21_K	1.063	0.92
22_L	59_K	1.062	0.92
40_Q	44_L	1.061	0.92
25_S	29_T	1.050	0.92
25_S	30_S	1.039	0.91
9_G	34_A	1.019	0.90
28_Y	40_Q	1.010	0.90
22_L	62_L	0.988	0.89
32_L	40_Q	0.966	0.88
35_N	40_Q	0.950	0.87
17_T	23_K	0.949	0.87
37_S	40_Q	0.945	0.87
18_G	49_V	0.942	0.87
24_R	50_V	0.942	0.87
42_R	45_R	0.928	0.86
57_R	60_Q	0.874	0.82
34_A	38_Q	0.866	0.82
24_R	27_A	0.858	0.81
57_R	61_M	0.849	0.80
24_R	48_A	0.830	0.79
4_M	41_K	0.809	0.77
53_G	56_K	0.795	0.76
10_S	33_F	0.793	0.76
29_T	33_F	0.780	0.74
30_S	40_Q	0.769	0.73
19_S	49_V	0.768	0.73
33_F	41_K	0.766	0.73
7_H	34_A	0.766	0.73
7_H	10_S	0.764	0.73
22_L	50_V	0.749	0.71
34_A	40_Q	0.747	0.71
30_S	43_K	0.747	0.71
6_T	62_L	0.742	0.71
42_R	46_K	0.737	0.70
26_H	46_K	0.735	0.70
22_L	55_F	0.714	0.68
18_G	21_K	0.703	0.66
37_S	43_K	0.702	0.66
4_M	8_R	0.664	0.62
43_K	46_K	0.663	0.62
32_L	39_K	0.648	0.60
56_K	60_Q	0.640	0.59
38_Q	45_R	0.637	0.59
21_K	57_R	0.633	0.58
26_H	43_K	0.628	0.58
24_R	46_K	0.624	0.57
51_S	60_Q	0.621	0.57
22_L	63_A	0.616	0.56
51_S	55_F	0.613	0.56
18_G	22_L	0.586	0.53
52_A	56_K	0.573	0.51
52_A	63_A	0.557	0.49
35_N	38_Q	0.556	0.49
26_H	44_L	0.555	0.49
33_F	40_Q	0.554	0.49
36_K	63_A	0.551	0.48
45_R	63_A	0.551	0.48
33_F	63_A	0.549	0.48
38_Q	44_L	0.544	0.48
2_P	33_F	0.536	0.47
6_T	13_R	0.525	0.45
15_K	41_K	0.522	0.45
8_R	38_Q	0.516	0.44
44_L	61_M	0.513	0.44
11_A	16_K	0.500	0.42

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
3bbo5	1	0.9394	99.9	0.102	Contact Map
2zjr3	1	0.9545	99.9	0.104	Contact Map
4rb68	1	0.9697	99.9	0.109	Contact Map
1vw4Z	1	0.9394	99.9	0.137	Contact Map
4tp93	1	0.9697	99.9	0.145	Contact Map
3j7y3	1	1	99.9	0.174	Contact Map
3ivrA	2	0	4.6	0.92	Contact Map
4xbaA	2	0.3182	4	0.923	Contact Map
3rixA	1	0	3.4	0.925	Contact Map
4o30A	1	0.1364	3.4	0.925	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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