RS9 - HALSA - GREMLIN Contacts

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RS9 - 30S ribosomal protein S9

UniProt:	Q9HQJ2	Sequences: MVTNTSGKKKTAVARATVSDGEGRVRINSQPVELVEPEMARLKMLEPFRISGSDLRGDVDIDIDVAGGGFAGQADAVRTAIARGLVEHYGDAELRDAFREFDRSLLVNDVRQRESKKWGGPGARARYQKSYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (123)
Sequences:	2789 (1252)
Seq/√Len:	112.9

ECOLI - RS9
BACSU - RS9
HALSA - RS9
SULSO - RS9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_G	126_R	4.528	1.00
51_S	55_L	4.287	1.00
63_I	77_V	2.922	1.00
82_A	106_L	2.793	1.00
16_A	80_A	2.646	1.00
86_V	106_L	2.428	1.00
113_R	122_G	2.413	1.00
120_G	127_Y	2.341	1.00
122_G	125_A	2.145	1.00
59_V	88_H	2.140	1.00
121_P	127_Y	2.113	1.00
4_N	17_T	2.010	1.00
46_E	105_L	1.889	1.00
96_D	100_E	1.862	1.00
38_E	41_R	1.821	1.00
46_E	78_R	1.807	1.00
23_G	60_D	1.807	1.00
11_T	112_Q	1.754	1.00
32_V	41_R	1.742	1.00
24_R	31_P	1.732	1.00
19_S	62_D	1.685	1.00
8_K	83_R	1.653	1.00
86_V	95_R	1.645	1.00
48_F	61_I	1.643	1.00
36_E	41_R	1.638	1.00
24_R	60_D	1.628	1.00
121_P	125_A	1.560	1.00
95_R	99_R	1.544	1.00
49_R	56_R	1.539	1.00
55_L	94_L	1.527	1.00
21_G	60_D	1.511	1.00
50_I	103_R	1.492	1.00
52_G	56_R	1.476	1.00
51_S	94_L	1.406	1.00
43_K	46_E	1.382	1.00
65_V	77_V	1.338	1.00
35_V	77_V	1.324	1.00
100_E	103_R	1.309	1.00
30_Q	33_E	1.288	0.99
75_D	78_R	1.267	0.99
71_A	75_D	1.223	0.99
55_L	58_D	1.217	0.99
32_V	44_M	1.205	0.99
22_E	60_D	1.189	0.99
113_R	116_K	1.129	0.99
45_L	56_R	1.107	0.98
5_T	84_G	1.101	0.98
121_P	126_R	1.079	0.98
40_A	70_F	1.072	0.98
9_K	75_D	1.068	0.98
55_L	59_V	1.046	0.98
114_E	117_K	1.044	0.98
88_H	94_L	1.035	0.97
8_K	13_V	1.030	0.97
20_D	58_D	1.028	0.97
26_R	62_D	1.024	0.97
91_D	94_L	1.018	0.97
122_G	127_Y	0.994	0.97
19_S	60_D	0.984	0.96
44_M	47_P	0.982	0.96
18_V	84_G	0.978	0.96
6_S	80_A	0.971	0.96
68_G	72_G	0.967	0.96
55_L	91_D	0.959	0.96
40_A	71_A	0.957	0.96
80_A	108_N	0.950	0.96
17_T	64_D	0.938	0.95
78_R	105_L	0.931	0.95
43_K	75_D	0.930	0.95
8_K	79_T	0.908	0.95
8_K	112_Q	0.905	0.94
42_L	46_E	0.898	0.94
37_P	70_F	0.884	0.94
44_M	74_A	0.881	0.94
122_G	126_R	0.881	0.94
12_A	72_G	0.858	0.93
29_S	64_D	0.851	0.92
45_L	48_F	0.850	0.92
97_A	103_R	0.844	0.92
72_G	75_D	0.841	0.92
82_A	86_V	0.839	0.92
15_R	64_D	0.827	0.91
118_W	129_K	0.817	0.91
43_K	74_A	0.812	0.91
79_T	108_N	0.810	0.90
50_I	97_A	0.808	0.90
50_I	105_L	0.806	0.90
18_V	61_I	0.803	0.90
39_M	42_L	0.801	0.90
14_A	65_V	0.800	0.90
45_L	49_R	0.799	0.90
5_T	16_A	0.794	0.90
107_V	110_V	0.782	0.89
37_P	40_A	0.781	0.89
99_R	107_V	0.779	0.89
125_A	129_K	0.776	0.88
51_S	98_F	0.776	0.88
22_E	42_L	0.770	0.88
26_R	31_P	0.766	0.88
18_V	59_V	0.757	0.87
99_R	106_L	0.756	0.87
86_V	94_L	0.755	0.87
32_V	36_E	0.753	0.87
52_G	55_L	0.745	0.86
4_N	64_D	0.738	0.86
48_F	57_G	0.737	0.86
113_R	125_A	0.735	0.86
38_E	42_L	0.733	0.85
116_K	121_P	0.731	0.85
42_L	45_L	0.729	0.85
5_T	87_E	0.724	0.85
30_Q	36_E	0.719	0.84
97_A	100_E	0.713	0.84
118_W	127_Y	0.711	0.84
116_K	122_G	0.707	0.83
36_E	70_F	0.704	0.83
26_R	29_S	0.701	0.83
95_R	106_L	0.700	0.83
25_V	32_V	0.692	0.82
48_F	81_I	0.691	0.82
12_A	68_G	0.687	0.82
36_E	44_M	0.687	0.82
41_R	44_M	0.684	0.81
36_E	77_V	0.683	0.81
43_K	105_L	0.657	0.79
7_G	14_A	0.656	0.78
19_S	88_H	0.651	0.78
92_A	96_D	0.649	0.78
42_L	49_R	0.641	0.77
48_F	59_V	0.637	0.76
48_F	55_L	0.621	0.75
25_V	44_M	0.620	0.75
4_N	15_R	0.616	0.74
26_R	64_D	0.609	0.73
5_T	18_V	0.608	0.73
36_E	40_A	0.607	0.73
7_G	13_V	0.605	0.73
35_V	44_M	0.603	0.72
16_A	125_A	0.603	0.72
43_K	78_R	0.602	0.72
18_V	81_I	0.600	0.72
27_I	31_P	0.598	0.72
113_R	121_P	0.590	0.71
51_S	56_R	0.583	0.70
35_V	115_S	0.583	0.70
15_R	65_V	0.579	0.69
17_T	72_G	0.577	0.69
17_T	113_R	0.577	0.69
121_P	129_K	0.577	0.69
37_P	49_R	0.576	0.69
12_A	76_A	0.576	0.69
98_F	108_N	0.565	0.68
40_A	43_K	0.562	0.67
124_R	132_R	0.560	0.67
38_E	70_F	0.560	0.67
13_V	118_W	0.560	0.67
122_G	130_S	0.555	0.66
113_R	118_W	0.555	0.66
7_G	79_T	0.553	0.66
121_P	128_Q	0.552	0.66
92_A	97_A	0.552	0.66
81_I	98_F	0.552	0.66
5_T	80_A	0.552	0.66
120_G	125_A	0.544	0.65
118_W	130_S	0.542	0.64
35_V	71_A	0.541	0.64
6_S	98_F	0.541	0.64
17_T	62_D	0.539	0.64
46_E	129_K	0.538	0.64
110_V	128_Q	0.536	0.64
30_Q	72_G	0.536	0.64
121_P	130_S	0.531	0.63
47_P	51_S	0.530	0.63
116_K	119_G	0.523	0.62
116_K	120_G	0.522	0.62
97_A	105_L	0.519	0.61
27_I	65_V	0.517	0.61
30_Q	112_Q	0.516	0.61
13_V	66_A	0.511	0.60
83_R	108_N	0.510	0.60
104_S	107_V	0.503	0.59
116_K	123_A	0.502	0.59
34_L	131_Y	0.501	0.58
37_P	41_R	0.500	0.58

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
3j20K	1	1	100	0.046	Contact Map
3j60Q	1	0.9015	100	0.064	Contact Map
4w23Q	1	1	100	0.064	Contact Map
4ujpR	1	1	100	0.064	Contact Map
3j7aM	1	0.9924	100	0.068	Contact Map
4bpeI	1	1	100	0.069	Contact Map
4tp8I	1	0.9545	100	0.073	Contact Map
4rb5I	1	0.9545	100	0.073	Contact Map
3zeyK	1	1	100	0.076	Contact Map
3bbnI	1	0.947	100	0.077	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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