RS13 - BACSU - GREMLIN Contacts

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RS13 - 30S ribosomal protein S13

UniProt:	P20282	Sequences: MARIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEELGKIRDIIDKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNSKNNARTRKGPRRTVANKKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	121 (118)
Sequences:	2396 (1006)
Seq/√Len:	92.6

ECOLI - RS13
BACSU - RS13
HALSA - RS13
SULSO - RS13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_T	52_E	5.115	1.00
80_L	87_R	4.138	1.00
101_N	104_N	3.723	1.00
37_A	59_I	2.642	1.00
15_V	45_V	2.616	1.00
29_T	63_L	2.582	1.00
68_D	71_R	2.380	1.00
89_I	93_R	2.257	1.00
16_V	31_Q	2.187	1.00
16_V	41_E	2.152	1.00
52_E	55_K	2.132	1.00
36_E	59_I	2.116	1.00
72_E	76_N	2.080	1.00
29_T	32_Q	2.053	1.00
115_T	118_N	1.982	1.00
32_Q	36_E	1.956	1.00
15_V	48_L	1.860	1.00
18_S	45_V	1.817	1.00
20_T	27_R	1.774	1.00
9_I	18_S	1.752	1.00
59_I	62_K	1.749	1.00
84_G	92_R	1.711	1.00
35_K	41_E	1.679	1.00
17_I	20_T	1.625	1.00
38_G	55_K	1.618	1.00
64_K	72_E	1.575	1.00
16_V	27_R	1.561	1.00
8_D	11_R	1.545	1.00
12_D	46_R	1.536	1.00
60_I	65_V	1.500	1.00
14_R	42_D	1.480	1.00
28_T	32_Q	1.449	1.00
15_V	39_V	1.446	1.00
31_Q	41_E	1.388	0.99
58_D	62_K	1.386	0.99
2_A	45_V	1.341	0.99
40_S	43_T	1.325	0.99
107_R	111_G	1.298	0.99
75_L	78_K	1.266	0.99
27_R	30_A	1.244	0.98
81_I	92_R	1.234	0.98
27_R	31_Q	1.231	0.98
57_R	61_D	1.201	0.98
49_T	52_E	1.190	0.98
31_Q	35_K	1.184	0.98
113_R	116_V	1.176	0.98
80_L	85_S	1.174	0.98
51_E	55_K	1.169	0.98
14_R	44_R	1.149	0.97
5_A	57_R	1.149	0.97
25_I	60_I	1.117	0.97
17_I	27_R	1.106	0.97
79_R	87_R	1.099	0.97
23_F	73_V	1.096	0.97
74_S	78_K	1.086	0.96
15_V	34_L	1.079	0.96
96_P	106_A	1.071	0.96
59_I	63_L	1.067	0.96
11_R	18_S	1.034	0.95
84_G	89_I	1.031	0.95
4_I	53_L	1.017	0.95
2_A	9_I	1.014	0.95
78_K	82_E	0.990	0.94
58_D	61_D	0.924	0.92
32_Q	35_K	0.887	0.90
97_V	109_R	0.880	0.90
30_A	34_L	0.880	0.90
16_V	30_A	0.878	0.89
43_T	47_D	0.861	0.88
32_Q	63_L	0.835	0.87
48_L	53_L	0.834	0.87
18_S	21_Y	0.819	0.86
5_A	60_I	0.809	0.85
23_F	70_R	0.808	0.85
33_V	59_I	0.801	0.85
9_I	45_V	0.798	0.84
13_K	21_Y	0.785	0.83
15_V	43_T	0.779	0.83
7_V	66_E	0.772	0.82
73_V	77_I	0.758	0.81
87_R	98_R	0.756	0.81
55_K	58_D	0.753	0.81
57_R	75_L	0.749	0.80
10_P	21_Y	0.748	0.80
2_A	53_L	0.725	0.78
54_G	58_D	0.722	0.78
36_E	62_K	0.718	0.78
11_R	46_R	0.718	0.78
16_V	42_D	0.717	0.78
34_L	56_I	0.715	0.77
50_E	54_G	0.713	0.77
113_R	117_A	0.709	0.77
39_V	43_T	0.708	0.77
20_T	29_T	0.707	0.77
66_E	70_R	0.707	0.77
93_R	101_N	0.687	0.74
5_A	65_V	0.684	0.74
11_R	53_L	0.676	0.73
6_G	84_G	0.675	0.73
41_E	56_I	0.674	0.73
8_D	115_T	0.672	0.73
24_G	69_L	0.668	0.72
48_L	71_R	0.665	0.72
10_P	13_K	0.662	0.72
50_E	53_L	0.650	0.70
15_V	44_R	0.647	0.70
3_R	107_R	0.646	0.70
14_R	40_S	0.643	0.70
81_I	94_G	0.640	0.69
6_G	66_E	0.637	0.69
85_S	89_I	0.635	0.69
112_P	116_V	0.631	0.68
48_L	68_D	0.627	0.68
8_D	40_S	0.624	0.67
96_P	105_N	0.619	0.67
88_G	91_H	0.616	0.66
5_A	61_D	0.614	0.66
7_V	47_D	0.612	0.66
78_K	81_I	0.610	0.65
2_A	93_R	0.608	0.65
94_G	97_V	0.606	0.65
14_R	21_Y	0.604	0.65
12_D	44_R	0.597	0.64
8_D	54_G	0.597	0.64
4_I	9_I	0.593	0.63
75_L	103_K	0.592	0.63
69_L	102_S	0.590	0.63
28_T	31_Q	0.589	0.63
23_F	64_K	0.588	0.63
46_R	62_K	0.588	0.63
69_L	72_E	0.581	0.62
33_V	63_L	0.581	0.62
31_Q	42_D	0.580	0.62
6_G	104_N	0.579	0.61
46_R	61_D	0.577	0.61
8_D	83_I	0.573	0.61
44_R	97_V	0.569	0.60
37_A	56_I	0.565	0.60
61_D	113_R	0.562	0.59
80_L	88_G	0.559	0.59
86_Y	96_P	0.558	0.59
11_R	15_V	0.556	0.58
85_S	97_V	0.551	0.58
3_R	111_G	0.551	0.58
61_D	118_N	0.550	0.58
8_D	94_G	0.550	0.58
9_I	16_V	0.546	0.57
11_R	56_I	0.544	0.57
104_N	114_R	0.543	0.57
46_R	58_D	0.543	0.57
56_I	98_R	0.542	0.56
94_G	112_P	0.540	0.56
16_V	34_L	0.539	0.56
14_R	34_L	0.536	0.56
22_I	86_Y	0.536	0.56
34_L	39_V	0.533	0.55
37_A	58_D	0.533	0.55
54_G	61_D	0.531	0.55
66_E	96_P	0.531	0.55
49_T	72_E	0.530	0.55
81_I	103_K	0.526	0.54
13_K	110_K	0.521	0.54
36_E	60_I	0.518	0.53
29_T	59_I	0.517	0.53
86_Y	91_H	0.516	0.53
10_P	70_R	0.515	0.53
105_N	108_T	0.510	0.52
3_R	8_D	0.510	0.52
55_K	62_K	0.510	0.52
53_L	75_L	0.509	0.52
21_Y	103_K	0.509	0.52
86_Y	93_R	0.508	0.52
69_L	96_P	0.508	0.52
36_E	55_K	0.507	0.52
2_A	75_L	0.502	0.51
4_I	51_E	0.500	0.51
43_T	49_T	0.500	0.51

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
4rb5M	1	0.9917	100	0.054	Contact Map
4bpeM	1	0.9752	100	0.072	Contact Map
3j7aS	1	0.8512	100	0.073	Contact Map
3j60S	1	0.9752	100	0.079	Contact Map
3zeyM	1	0.9752	100	0.079	Contact Map
3j20O	1	0.9835	100	0.08	Contact Map
3j38S	1	0.8926	100	0.099	Contact Map
4tp8M	1	0.9421	100	0.109	Contact Map
4ujpT	1	0.9091	100	0.116	Contact Map
3bbnM	1	0.8182	100	0.175	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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