RS4E - SULSO - GREMLIN Contacts

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RS4E - 30S ribosomal protein S4e

UniProt:	Q9UX94	Sequences: MAHITRFEAPWFLMISKKQYKWTVRPNAGPHSIEKSIPLAVVIRDYLKLAGTIREAKHIIFDGKVLVDGKVRKDYKYPVGLMDIVSIPSADLYFRVLPDNVRFMRFSKISADEARYKYVRIINKTTIKEGRIQLNLEDGRNILVDKETAKNFKTLMTLKIELPSQQILDSFTISERSYAIFVGGRNVGIHGIVKNINLSKFKSRKYSVITLESRDGNTYQTNIMNVMSIGREKSDLRVD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	239 (226)
Sequences:	454 (300)
Seq/√Len:	19.9

HALSA - RS4E
SULSO - RS4E

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_R	33_I	5.977	1.00
179_A	211_L	4.345	1.00
68_D	117_K	3.997	1.00
86_S	93_Y	3.889	1.00
60_I	65_V	3.798	1.00
42_V	106_F	3.723	1.00
134_L	167_I	3.408	1.00
66_L	88_P	3.168	1.00
65_V	87_I	3.153	0.99
119_V	160_I	2.931	0.99
155_L	223_I	2.878	0.99
116_Y	159_K	2.753	0.99
96_V	106_F	2.708	0.98
27_N	74_D	2.677	0.98
63_G	73_K	2.672	0.98
121_I	152_F	2.610	0.98
92_L	108_K	2.543	0.98
123_N	135_N	2.339	0.96
91_D	178_Y	2.321	0.96
64_K	89_S	2.295	0.95
205_K	216_G	2.164	0.94
54_R	58_H	2.076	0.92
169_D	231_R	2.011	0.91
179_A	193_V	2.000	0.91
140_R	165_Q	1.909	0.89
8_E	25_R	1.828	0.86
57_K	75_Y	1.708	0.82
161_E	164_S	1.695	0.82
117_K	140_R	1.658	0.80
177_S	228_S	1.654	0.80
97_L	107_S	1.647	0.80
49_L	92_L	1.575	0.77
52_T	60_I	1.565	0.76
171_F	228_S	1.553	0.76
162_L	208_V	1.540	0.75
28_A	139_G	1.539	0.75
115_R	163_P	1.536	0.75
4_I	26_P	1.518	0.74
50_A	59_I	1.516	0.74
189_I	213_S	1.484	0.72
156_M	170_S	1.464	0.71
30_P	78_P	1.460	0.71
183_G	227_M	1.430	0.69
4_I	22_W	1.415	0.68
82_M	140_R	1.407	0.68
22_W	58_H	1.399	0.67
68_D	140_R	1.362	0.65
68_D	138_D	1.358	0.65
4_I	13_L	1.349	0.65
43_I	65_V	1.344	0.64
25_R	28_A	1.333	0.64
44_R	68_D	1.332	0.64
179_A	203_S	1.331	0.63
68_D	163_P	1.326	0.63
222_N	225_N	1.318	0.63
95_R	143_L	1.305	0.62
68_D	82_M	1.278	0.60
22_W	126_T	1.247	0.58
190_H	229_I	1.246	0.58
56_A	60_I	1.233	0.57
117_K	138_D	1.222	0.57
58_H	126_T	1.221	0.57
167_I	170_S	1.218	0.56
130_G	133_Q	1.169	0.53
52_T	185_R	1.167	0.53
66_L	71_V	1.166	0.53
85_V	97_L	1.164	0.53
161_E	168_L	1.153	0.52
82_M	137_E	1.145	0.52
55_E	80_G	1.144	0.52
179_A	187_V	1.141	0.52
53_I	128_K	1.140	0.51
79_V	87_I	1.136	0.51
172_T	176_R	1.135	0.51
4_I	8_E	1.134	0.51
120_R	190_H	1.132	0.51
198_L	207_S	1.130	0.51
14_M	46_Y	1.129	0.51
221_T	225_N	1.125	0.50
4_I	9_A	1.125	0.50
177_S	193_V	1.119	0.50
161_E	166_Q	1.117	0.50
7_F	129_E	1.113	0.50
19_Q	57_K	1.112	0.50
79_V	96_V	1.106	0.49
125_T	135_N	1.103	0.49
6_R	29_G	1.096	0.49
112_D	128_K	1.086	0.48
132_I	181_F	1.085	0.48
184_G	188_G	1.083	0.48
99_D	102_R	1.074	0.47
60_I	75_Y	1.070	0.47
54_R	125_T	1.064	0.47
128_K	192_I	1.052	0.46
41_V	56_A	1.045	0.45
85_V	123_N	1.040	0.45
135_N	141_N	1.039	0.45
197_N	210_T	1.036	0.45
132_I	145_D	1.027	0.44
24_V	40_A	1.024	0.44
125_T	133_Q	1.017	0.44
93_Y	114_A	1.008	0.43
85_V	115_R	0.999	0.42
6_R	95_R	0.992	0.42
133_Q	139_G	0.991	0.42
49_L	90_A	0.976	0.41
41_V	209_I	0.976	0.41
7_F	181_F	0.972	0.41
72_R	78_P	0.960	0.40
29_G	80_G	0.958	0.40
21_K	28_A	0.955	0.40
81_L	157_T	0.955	0.40
197_N	208_V	0.946	0.39
57_K	119_V	0.946	0.39
69_G	162_L	0.945	0.39
109_I	113_E	0.944	0.39
22_W	120_R	0.939	0.39
31_H	68_D	0.935	0.38
82_M	117_K	0.933	0.38
94_F	142_I	0.931	0.38
40_A	53_I	0.928	0.38
14_M	34_E	0.926	0.38
91_D	198_L	0.924	0.38
10_P	13_L	0.922	0.38
22_W	231_R	0.920	0.37
39_L	79_V	0.916	0.37
117_K	163_P	0.915	0.37
177_S	232_E	0.913	0.37
83_D	95_R	0.912	0.37
177_S	187_V	0.904	0.37
89_S	115_R	0.901	0.36
102_R	219_Y	0.901	0.36
31_H	138_D	0.896	0.36
9_A	158_L	0.894	0.36
49_L	145_D	0.892	0.36
86_S	162_L	0.889	0.36
126_T	203_S	0.884	0.35
174_S	211_L	0.878	0.35
71_V	211_L	0.873	0.35
124_K	133_Q	0.865	0.34
32_S	35_K	0.863	0.34
22_W	42_V	0.862	0.34
91_D	111_A	0.860	0.34
121_I	161_E	0.858	0.34
114_A	181_F	0.857	0.34
58_H	216_G	0.856	0.34
39_L	78_P	0.855	0.34
49_L	94_F	0.853	0.34
114_A	159_K	0.850	0.33
43_I	76_K	0.849	0.33
125_T	128_K	0.848	0.33
133_Q	152_F	0.848	0.33
58_H	87_I	0.844	0.33
202_K	206_Y	0.838	0.33
23_T	78_P	0.834	0.32
189_I	204_R	0.834	0.32
139_G	179_A	0.832	0.32
22_W	187_V	0.826	0.32
53_I	76_K	0.825	0.32
159_K	187_V	0.824	0.32
4_I	15_I	0.821	0.32
187_V	216_G	0.818	0.32
25_R	181_F	0.816	0.31
121_I	143_L	0.816	0.31
139_G	160_I	0.815	0.31
57_K	154_T	0.814	0.31
134_L	158_L	0.812	0.31
15_I	50_A	0.811	0.31
215_D	226_V	0.810	0.31
22_W	207_S	0.803	0.31
211_L	226_V	0.794	0.30
63_G	95_R	0.794	0.30
77_Y	87_I	0.792	0.30
186_N	207_S	0.787	0.30
168_L	171_F	0.785	0.30
26_P	36_S	0.784	0.30
167_I	233_K	0.783	0.30
99_D	219_Y	0.782	0.30
60_I	129_E	0.781	0.29
92_L	107_S	0.776	0.29
66_L	226_V	0.775	0.29
52_T	148_T	0.775	0.29
206_Y	222_N	0.772	0.29
19_Q	128_K	0.771	0.29
204_R	207_S	0.769	0.29
5_T	156_M	0.765	0.29
177_S	210_T	0.763	0.29
28_A	187_V	0.763	0.29
19_Q	36_S	0.762	0.28
129_E	233_K	0.756	0.28
209_I	226_V	0.755	0.28
212_E	220_Q	0.751	0.28
186_N	204_R	0.750	0.28
126_T	209_I	0.748	0.28
85_V	92_L	0.747	0.28
67_V	121_I	0.747	0.28
45_D	68_D	0.746	0.28
12_F	82_M	0.737	0.27
97_L	106_F	0.737	0.27
17_K	137_E	0.737	0.27
95_R	140_R	0.736	0.27
119_V	158_L	0.736	0.27
43_I	60_I	0.735	0.27
128_K	163_P	0.732	0.27
22_W	193_V	0.730	0.27
168_L	196_I	0.725	0.27
179_A	192_I	0.725	0.27
3_H	8_E	0.721	0.26
160_I	165_Q	0.719	0.26
117_K	176_R	0.719	0.26
14_M	25_R	0.715	0.26
60_I	133_Q	0.715	0.26
6_R	13_L	0.712	0.26
80_G	230_G	0.709	0.26
124_K	163_P	0.709	0.26
48_K	65_V	0.706	0.26
177_S	231_R	0.702	0.25
29_G	121_I	0.701	0.25
61_F	163_P	0.699	0.25
20_Y	23_T	0.689	0.25
61_F	76_K	0.689	0.25
85_V	179_A	0.686	0.25
29_G	95_R	0.685	0.25
159_K	225_N	0.684	0.25
37_I	103_F	0.683	0.24
109_I	186_N	0.683	0.24
115_R	177_S	0.683	0.24
5_T	13_L	0.682	0.24
11_W	155_L	0.675	0.24
159_K	182_V	0.675	0.24
123_N	141_N	0.664	0.24
209_I	221_T	0.662	0.24
162_L	168_L	0.660	0.23
53_I	175_E	0.659	0.23
10_P	30_P	0.653	0.23
23_T	81_L	0.653	0.23
5_T	102_R	0.652	0.23
194_K	212_E	0.652	0.23
194_K	218_T	0.651	0.23
178_Y	190_H	0.650	0.23
37_I	51_G	0.650	0.23
16_S	34_E	0.650	0.23
160_I	192_I	0.647	0.23
120_R	185_R	0.647	0.23
160_I	175_E	0.646	0.23
202_K	205_K	0.632	0.22
159_K	168_L	0.632	0.22
84_I	116_Y	0.630	0.22
118_Y	157_T	0.628	0.22
36_S	96_V	0.628	0.22
39_L	152_F	0.627	0.22
69_G	142_I	0.626	0.22
3_H	7_F	0.626	0.22
108_K	146_K	0.625	0.22
135_N	154_T	0.623	0.22
93_Y	171_F	0.620	0.22
28_A	41_V	0.618	0.22
158_L	162_L	0.617	0.21
42_V	61_F	0.615	0.21
85_V	216_G	0.614	0.21
119_V	179_A	0.610	0.21
24_V	76_K	0.609	0.21
103_F	143_L	0.606	0.21
106_F	187_V	0.605	0.21
38_P	47_L	0.602	0.21
132_I	152_F	0.601	0.21
132_I	144_V	0.601	0.21
65_V	89_S	0.598	0.21
80_G	95_R	0.598	0.21
42_V	174_S	0.597	0.21
28_A	77_Y	0.597	0.21
191_G	211_L	0.596	0.21
190_H	226_V	0.596	0.21
17_K	46_Y	0.594	0.20
85_V	105_R	0.593	0.20
54_R	68_D	0.590	0.20
59_I	173_I	0.589	0.20
90_A	128_K	0.584	0.20
67_V	226_V	0.582	0.20
74_D	163_P	0.577	0.20
157_T	178_Y	0.576	0.20
99_D	118_Y	0.573	0.20
122_I	210_T	0.567	0.19
57_K	125_T	0.563	0.19
77_Y	169_D	0.562	0.19
72_R	143_L	0.562	0.19
103_F	118_Y	0.558	0.19
136_L	144_V	0.557	0.19
5_T	219_Y	0.556	0.19
60_I	165_Q	0.556	0.19
19_Q	41_V	0.555	0.19
178_Y	182_V	0.553	0.19
129_E	134_L	0.553	0.19
181_F	219_Y	0.553	0.19
56_A	140_R	0.552	0.19
5_T	12_F	0.552	0.19
102_R	207_S	0.552	0.19
97_L	105_R	0.551	0.19
44_R	82_M	0.550	0.19
102_R	221_T	0.549	0.19
120_R	229_I	0.547	0.19
57_K	76_K	0.545	0.18
46_Y	87_I	0.543	0.18
162_L	209_I	0.542	0.18
74_D	211_L	0.541	0.18
128_K	185_R	0.541	0.18
15_I	147_E	0.539	0.18
39_L	221_T	0.539	0.18
22_W	159_K	0.538	0.18
186_N	189_I	0.533	0.18
30_P	84_I	0.532	0.18
174_S	231_R	0.531	0.18
65_V	182_V	0.529	0.18
153_K	156_M	0.529	0.18
84_I	118_Y	0.526	0.18
193_V	228_S	0.525	0.18
12_F	173_I	0.524	0.18
131_R	216_G	0.523	0.18
74_D	221_T	0.523	0.18
186_N	198_L	0.521	0.18
27_N	223_I	0.521	0.18
8_E	130_G	0.519	0.17
48_K	121_I	0.517	0.17
50_A	68_D	0.517	0.17
44_R	221_T	0.517	0.17
85_V	91_D	0.513	0.17
219_Y	227_M	0.513	0.17
78_P	191_G	0.513	0.17
35_K	164_S	0.511	0.17
8_E	12_F	0.509	0.17
34_E	74_D	0.507	0.17
187_V	194_K	0.507	0.17
197_N	220_Q	0.507	0.17
67_V	108_K	0.506	0.17
108_K	158_L	0.502	0.17
176_R	209_I	0.502	0.17
68_D	72_R	0.501	0.17
3_H	10_P	0.501	0.17
37_I	41_V	0.500	0.17

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
4ujpF	1	0.9749	100	0.023	Contact Map
3j60E	1	0.8201	100	0.024	Contact Map
3j7aF	1	0.9749	100	0.025	Contact Map
3zey1	1	0.9498	100	0.026	Contact Map
4bpeW	1	0.9749	100	0.028	Contact Map
3j20E	1	0.9916	100	0.161	Contact Map
3kbgA	2	0.8033	100	0.365	Contact Map
1p9kA	1	0.3222	95.8	0.931	Contact Map
2cqjA	1	0.2887	95.8	0.932	Contact Map
4rb5D	1	0.5565	90.8	0.944	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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