RS4 - HALSA - GREMLIN Contacts

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RS4 - 30S ribosomal protein S4

UniProt:	Q9HQJ6	Sequences: MALPGENTKFYETPNHPYQGERIAEESDLLSRYGLKNKEELWRAQSELRDYRREARRLLGQTGTVSGEEFVARLQRIGILSEEERLDDVLSLEVTDVLERRLQTVVYREGLANTMGQARQFVSHGHVTVDGSRVTEPSYTVPVSEENTLAFDETSDLTDELHPARAGAQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	170 (162)
Sequences:	600 (352)
Seq/√Len:	27.6

HALSA - RS4
SULSO - RS4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_V	127_V	5.017	1.00
139_Y	145_E	3.446	1.00
126_H	155_S	3.110	1.00
79_I	97_V	2.893	1.00
56_R	90_L	2.709	1.00
14_P	17_P	2.534	0.99
36_K	40_E	2.450	0.99
32_R	95_T	2.376	0.99
30_L	41_L	2.269	0.98
103_Q	122_V	2.265	0.98
31_S	116_G	2.178	0.98
105_V	149_L	2.071	0.97
52_R	56_R	2.041	0.97
109_E	112_A	2.014	0.96
129_V	139_Y	2.005	0.96
75_Q	143_V	1.905	0.95
99_E	108_R	1.887	0.95
86_L	102_L	1.865	0.94
117_Q	120_Q	1.833	0.94
93_E	96_D	1.793	0.93
80_L	89_V	1.776	0.93
105_V	108_R	1.761	0.92
52_R	55_A	1.740	0.92
103_Q	119_R	1.736	0.92
20_G	24_A	1.726	0.92
85_R	120_Q	1.704	0.91
84_E	88_D	1.685	0.91
3_L	9_K	1.681	0.91
114_T	117_Q	1.670	0.90
85_R	88_D	1.638	0.89
34_G	119_R	1.588	0.88
14_P	34_G	1.583	0.88
23_I	27_S	1.581	0.88
129_V	149_L	1.577	0.87
74_L	79_I	1.555	0.87
33_Y	92_L	1.539	0.86
33_Y	80_L	1.432	0.82
35_L	94_V	1.414	0.81
115_M	122_V	1.363	0.78
84_E	134_V	1.318	0.76
4_P	7_N	1.305	0.75
67_G	85_R	1.304	0.75
26_E	118_A	1.294	0.75
117_Q	121_F	1.277	0.74
94_V	146_E	1.256	0.72
103_Q	106_V	1.254	0.72
33_Y	99_E	1.244	0.72
2_A	8_T	1.227	0.71
7_N	10_F	1.219	0.70
16_H	19_Q	1.196	0.69
138_S	143_V	1.194	0.68
61_Q	108_R	1.189	0.68
34_G	40_E	1.188	0.68
129_V	138_S	1.182	0.68
35_L	42_W	1.177	0.67
17_P	59_L	1.139	0.65
55_A	84_E	1.134	0.64
48_L	90_L	1.110	0.63
89_V	92_L	1.109	0.63
159_D	163_P	1.109	0.63
128_T	136_E	1.107	0.62
3_L	95_T	1.104	0.62
97_V	146_E	1.098	0.62
7_N	44_A	1.082	0.61
32_R	93_E	1.082	0.61
22_R	35_L	1.072	0.60
41_L	45_Q	1.068	0.60
104_T	115_M	1.066	0.59
144_S	157_L	1.063	0.59
87_D	90_L	1.055	0.59
88_D	120_Q	1.042	0.58
109_E	163_P	1.041	0.58
7_N	123_S	1.039	0.57
12_E	15_N	1.027	0.57
19_Q	56_R	1.026	0.57
27_S	116_G	1.022	0.56
82_E	149_L	1.018	0.56
23_I	36_K	1.016	0.56
128_T	152_D	1.014	0.56
151_F	158_T	1.004	0.55
36_K	39_E	1.001	0.55
108_R	127_V	0.997	0.54
5_G	18_Y	0.997	0.54
123_S	128_T	0.996	0.54
35_L	40_E	0.996	0.54
53_R	79_I	0.994	0.54
69_E	110_G	0.983	0.53
105_V	147_N	0.978	0.53
36_K	119_R	0.975	0.53
49_R	53_R	0.973	0.53
34_G	120_Q	0.971	0.52
55_A	88_D	0.971	0.52
9_K	149_L	0.957	0.51
151_F	155_S	0.956	0.51
111_L	127_V	0.951	0.51
55_A	68_E	0.947	0.51
64_T	69_E	0.946	0.50
56_R	59_L	0.938	0.50
143_V	147_N	0.936	0.50
115_M	121_F	0.935	0.50
160_E	163_P	0.927	0.49
35_L	104_T	0.923	0.49
41_L	93_E	0.914	0.48
106_V	111_L	0.913	0.48
58_L	66_S	0.906	0.47
151_F	161_L	0.903	0.47
20_G	127_V	0.890	0.46
13_T	134_V	0.887	0.46
130_D	150_A	0.882	0.46
5_G	10_F	0.878	0.45
47_E	140_T	0.877	0.45
14_P	55_A	0.874	0.45
132_S	138_S	0.872	0.45
96_D	147_N	0.867	0.44
28_D	139_Y	0.866	0.44
40_E	119_R	0.863	0.44
142_P	145_E	0.861	0.44
21_E	30_L	0.857	0.44
134_V	149_L	0.856	0.44
30_L	80_L	0.853	0.43
86_L	89_V	0.847	0.43
8_T	11_Y	0.843	0.43
44_A	97_V	0.841	0.43
93_E	129_V	0.835	0.42
128_T	131_G	0.828	0.42
42_W	58_L	0.824	0.41
87_D	120_Q	0.817	0.41
83_E	88_D	0.816	0.41
109_E	147_N	0.810	0.40
20_G	70_F	0.810	0.40
59_L	67_G	0.809	0.40
7_N	19_Q	0.800	0.39
25_E	45_Q	0.799	0.39
77_I	140_T	0.787	0.39
29_L	36_K	0.786	0.38
41_L	132_S	0.784	0.38
14_P	24_A	0.770	0.37
16_H	22_R	0.762	0.37
53_R	57_R	0.759	0.37
58_L	86_L	0.758	0.36
61_Q	78_G	0.755	0.36
10_F	147_N	0.752	0.36
51_Y	70_F	0.751	0.36
14_P	119_R	0.751	0.36
114_T	124_H	0.750	0.36
17_P	26_E	0.741	0.35
73_R	77_I	0.737	0.35
32_R	105_V	0.735	0.35
116_G	120_Q	0.734	0.35
89_V	106_V	0.727	0.34
51_Y	89_V	0.725	0.34
128_T	148_T	0.725	0.34
98_L	107_Y	0.723	0.34
55_A	117_Q	0.721	0.34
2_A	7_N	0.721	0.34
42_W	49_R	0.715	0.33
121_F	145_E	0.715	0.33
62_T	116_G	0.715	0.33
51_Y	80_L	0.714	0.33
51_Y	97_V	0.713	0.33
17_P	42_W	0.713	0.33
147_N	150_A	0.709	0.33
130_D	151_F	0.701	0.33
41_L	98_L	0.699	0.32
49_R	52_R	0.699	0.32
16_H	37_N	0.694	0.32
27_S	87_D	0.693	0.32
37_N	92_L	0.693	0.32
64_T	86_L	0.692	0.32
130_D	147_N	0.692	0.32
72_A	88_D	0.684	0.31
91_S	158_T	0.684	0.31
24_A	28_D	0.681	0.31
67_G	120_Q	0.675	0.31
19_Q	53_R	0.664	0.30
104_T	141_V	0.663	0.30
27_S	31_S	0.662	0.30
47_E	97_V	0.661	0.30
115_M	120_Q	0.661	0.30
111_L	129_V	0.659	0.30
81_S	157_L	0.657	0.30
34_G	38_K	0.650	0.29
104_T	114_T	0.632	0.28
72_A	76_R	0.627	0.28
81_S	113_N	0.627	0.28
25_E	30_L	0.622	0.27
73_R	99_E	0.620	0.27
76_R	148_T	0.619	0.27
8_T	12_E	0.619	0.27
51_Y	140_T	0.618	0.27
112_A	127_V	0.618	0.27
56_R	112_A	0.615	0.27
102_L	149_L	0.612	0.27
52_R	92_L	0.611	0.27
8_T	18_Y	0.606	0.27
67_G	83_E	0.605	0.26
89_V	152_D	0.604	0.26
48_L	94_V	0.597	0.26
101_R	130_D	0.596	0.26
76_R	81_S	0.595	0.26
30_L	91_S	0.595	0.26
129_V	153_E	0.595	0.26
9_K	122_V	0.593	0.26
31_S	70_F	0.587	0.25
39_E	92_L	0.587	0.25
50_D	122_V	0.584	0.25
60_G	84_E	0.583	0.25
29_L	76_R	0.581	0.25
151_F	156_D	0.578	0.25
35_L	106_V	0.577	0.25
80_L	122_V	0.575	0.25
26_E	89_V	0.573	0.25
20_G	121_F	0.571	0.25
41_L	157_L	0.570	0.24
128_T	151_F	0.559	0.24
121_F	157_L	0.558	0.24
19_Q	25_E	0.551	0.23
4_P	11_Y	0.542	0.23
15_N	19_Q	0.542	0.23
11_Y	53_R	0.537	0.23
52_R	101_R	0.536	0.23
47_E	115_M	0.535	0.23
53_R	92_L	0.533	0.22
70_F	74_L	0.530	0.22
85_R	109_E	0.528	0.22
20_G	77_I	0.528	0.22
9_K	154_T	0.522	0.22
7_N	12_E	0.522	0.22
44_A	143_V	0.519	0.22
113_N	127_V	0.518	0.22
64_T	154_T	0.516	0.22
106_V	110_G	0.516	0.22
136_E	150_A	0.514	0.21
28_D	89_V	0.512	0.21
50_D	64_T	0.509	0.21
124_H	159_D	0.509	0.21
2_A	11_Y	0.507	0.21
77_I	144_S	0.507	0.21
34_G	117_Q	0.507	0.21
22_R	119_R	0.505	0.21
29_L	95_T	0.504	0.21
13_T	48_L	0.501	0.21
133_R	152_D	0.500	0.21

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
3zey6	1	0.9882	100	0.347	Contact Map
4bpeD	2	0.9941	100	0.378	Contact Map
3j80J	1	0.9941	100	0.382	Contact Map
4ujpK	1	1	100	0.389	Contact Map
3j38J	1	1	100	0.42	Contact Map
3j20D	1	0.9529	100	0.421	Contact Map
3j7aE	1	1	100	0.423	Contact Map
3bbnD	1	0.7706	98.9	0.817	Contact Map
2cqjA	1	0.4176	98.8	0.825	Contact Map
1c05A	1	0.7	98.7	0.83	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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