RS13 - ECOLI - GREMLIN Contacts

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RS13 - 30S ribosomal protein S13

UniProt:	P0A7S9	Sequences: MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10912
Length:	118 (114)
Sequences:	2425 (1001)
Seq/√Len:	93.8

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_V	52_Q	4.774	1.00
80_L	87_R	4.182	1.00
101_R	104_T	3.713	1.00
37_A	59_E	2.637	1.00
15_A	45_I	2.606	1.00
29_R	63_F	2.555	1.00
68_D	71_R	2.412	1.00
89_L	93_R	2.305	1.00
52_Q	55_T	2.159	1.00
16_V	31_K	2.138	1.00
72_E	76_S	2.115	1.00
16_V	41_E	2.098	1.00
36_A	59_E	2.059	1.00
29_R	32_A	2.052	1.00
32_A	36_A	2.046	1.00
15_A	48_L	1.950	1.00
18_A	45_I	1.845	1.00
59_E	62_K	1.832	1.00
20_T	27_K	1.818	1.00
84_G	92_R	1.737	1.00
9_I	18_A	1.723	1.00
35_A	41_E	1.669	1.00
17_I	20_T	1.650	1.00
38_G	55_T	1.633	1.00
8_N	11_D	1.615	1.00
64_V	72_E	1.582	1.00
16_V	27_K	1.560	1.00
12_H	46_S	1.544	1.00
60_V	65_V	1.477	1.00
28_T	32_A	1.476	1.00
58_D	62_K	1.462	1.00
15_A	39_I	1.443	1.00
14_H	42_D	1.402	0.99
75_M	78_K	1.350	0.99
31_K	41_E	1.338	0.99
49_S	52_Q	1.327	0.99
2_A	45_I	1.323	0.99
27_K	31_K	1.261	0.99
57_R	61_A	1.255	0.99
40_A	43_V	1.234	0.98
107_R	111_G	1.211	0.98
14_H	44_K	1.168	0.98
51_G	55_T	1.164	0.98
80_L	85_C	1.145	0.98
31_K	35_A	1.144	0.97
81_M	92_R	1.138	0.97
27_K	30_S	1.118	0.97
5_A	57_R	1.100	0.97
79_R	87_R	1.094	0.97
25_V	60_V	1.092	0.97
4_I	53_I	1.083	0.97
96_P	106_A	1.068	0.96
15_A	34_L	1.052	0.96
17_I	27_K	1.024	0.95
59_E	63_F	0.992	0.94
74_S	78_K	0.983	0.94
23_Y	73_I	0.962	0.93
58_D	61_A	0.962	0.93
11_D	18_A	0.959	0.93
2_A	9_I	0.953	0.93
84_G	89_L	0.952	0.93
78_K	82_D	0.922	0.92
18_A	21_S	0.897	0.91
32_A	63_F	0.872	0.89
5_A	60_V	0.853	0.88
9_I	45_I	0.852	0.88
16_V	30_S	0.838	0.87
97_V	109_R	0.834	0.87
32_A	35_A	0.831	0.87
33_I	59_E	0.817	0.86
30_S	34_L	0.807	0.85
48_L	71_R	0.804	0.85
23_Y	70_R	0.776	0.83
43_V	47_E	0.776	0.83
67_G	111_G	0.772	0.83
48_L	53_I	0.767	0.82
36_A	62_K	0.759	0.82
54_D	58_D	0.753	0.81
13_K	21_S	0.748	0.81
55_T	58_D	0.747	0.81
7_I	66_E	0.746	0.81
73_I	77_I	0.741	0.80
8_N	54_D	0.729	0.79
57_R	75_M	0.719	0.78
78_K	81_M	0.716	0.78
11_D	46_S	0.716	0.78
109_R	112_P	0.715	0.78
10_P	21_S	0.714	0.78
20_T	29_R	0.710	0.77
61_A	113_R	0.704	0.77
46_S	58_D	0.698	0.76
87_R	98_R	0.693	0.76
41_E	56_L	0.689	0.75
75_M	103_K	0.689	0.75
34_L	56_L	0.684	0.75
66_E	70_R	0.683	0.75
8_N	40_A	0.681	0.74
5_A	65_V	0.673	0.73
11_D	15_A	0.668	0.73
2_A	53_I	0.662	0.72
39_I	43_V	0.656	0.72
50_E	53_I	0.656	0.72
5_A	61_A	0.653	0.71
15_A	43_V	0.651	0.71
11_D	53_I	0.647	0.70
93_R	101_R	0.646	0.70
24_G	69_L	0.645	0.70
14_H	21_S	0.645	0.70
4_I	9_I	0.639	0.70
16_V	42_D	0.637	0.69
10_P	13_K	0.634	0.69
14_H	40_A	0.631	0.69
6_G	84_G	0.627	0.68
96_P	105_N	0.625	0.68
56_L	98_R	0.624	0.68
50_E	54_D	0.624	0.68
3_R	107_R	0.624	0.68
8_N	94_G	0.624	0.68
94_G	114_K	0.617	0.67
48_L	68_D	0.615	0.67
85_C	89_L	0.615	0.67
34_L	39_I	0.614	0.66
14_H	34_L	0.612	0.66
94_G	112_P	0.612	0.66
69_L	102_T	0.611	0.66
46_S	61_A	0.608	0.66
81_M	94_G	0.603	0.65
15_A	44_K	0.600	0.65
7_I	47_E	0.592	0.64
88_G	91_H	0.591	0.64
104_T	114_K	0.589	0.63
54_D	114_K	0.587	0.63
6_G	66_E	0.576	0.62
9_I	16_V	0.574	0.61
2_A	93_R	0.573	0.61
81_M	103_K	0.563	0.60
69_L	72_E	0.562	0.60
94_G	97_V	0.562	0.60
22_I	86_Y	0.559	0.59
85_C	97_V	0.558	0.59
54_D	61_A	0.548	0.58
46_S	62_K	0.547	0.58
8_N	83_L	0.546	0.58
49_S	72_E	0.542	0.57
37_A	56_L	0.542	0.57
92_R	109_R	0.542	0.57
28_T	31_K	0.541	0.57
86_Y	91_H	0.539	0.57
46_S	114_K	0.537	0.56
3_R	8_N	0.537	0.56
11_D	56_L	0.537	0.56
86_Y	96_P	0.535	0.56
43_V	46_S	0.535	0.56
86_Y	93_R	0.534	0.56
8_N	12_H	0.533	0.56
33_I	63_F	0.531	0.55
106_A	109_R	0.529	0.55
12_H	44_K	0.528	0.55
29_R	59_E	0.526	0.55
33_I	56_L	0.525	0.55
89_L	110_K	0.517	0.53
6_G	104_T	0.516	0.53
64_V	97_V	0.516	0.53
53_I	68_D	0.514	0.53
66_E	96_P	0.512	0.53
63_F	72_E	0.509	0.52
36_A	60_V	0.508	0.52
15_A	50_E	0.508	0.52
105_N	110_K	0.506	0.52
13_K	17_I	0.506	0.52
54_D	103_K	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	0.9915	100	0.059	Contact Map
3j7aS	1	0.8729	100	0.089	Contact Map
4bpeM	1	1	100	0.089	Contact Map
3zeyM	1	1	100	0.09	Contact Map
3j60S	1	1	100	0.09	Contact Map
4tp8M	1	0.9661	100	0.092	Contact Map
3j20O	1	1	100	0.093	Contact Map
4ujpT	1	0.9322	100	0.098	Contact Map
3j38S	1	0.9153	100	0.104	Contact Map
3bbnM	1	0.839	100	0.168	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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