RS7 - HALSA - GREMLIN Contacts

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RS7 - 30S ribosomal protein S7

UniProt:	P0CX01	Sequences: MSDEQPAEDETEEAAAESEDTQEVAANAKLFGKWDVAEIHYEDPSTRRYLAVTPVAHTMGRHAQKQFKKSEISIVERLANRLMKTGANAGKKQQALKIVRDAFDIVHERTDENPIQVLVSAVENAAPREETVRLKYGGISVPQAVDTAPQRRVDQALKFLADGAHSASFKTPTDAAEALANQLAGAADYNVQTYAIGQKKEKERVAAAAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	210 (185)
Sequences:	413 (185)
Seq/√Len:	13.6

ECOLI - RS7
BACSU - RS7
HALSA - RS7
SULSO - RS7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_L	141_V	4.266	1.00
198_Q	201_E	3.937	1.00
79_A	96_L	3.551	0.99
36_V	115_I	3.191	0.98
35_D	38_E	2.941	0.97
78_L	179_L	2.817	0.96
78_L	99_V	2.742	0.95
27_N	35_D	2.625	0.94
164_A	183_L	2.431	0.91
70_S	150_Q	2.246	0.87
74_I	117_V	2.103	0.83
131_T	142_P	2.073	0.82
30_L	36_V	2.069	0.82
112_E	120_S	2.063	0.82
98_I	175_A	2.002	0.80
56_A	67_F	1.991	0.79
155_Q	159_F	1.957	0.78
142_P	209_A	1.907	0.76
105_I	184_A	1.887	0.75
98_I	176_A	1.832	0.73
182_Q	193_T	1.802	0.72
134_L	143_Q	1.780	0.71
103_F	118_L	1.775	0.70
122_V	153_V	1.754	0.70
50_L	148_A	1.716	0.68
33_K	104_D	1.712	0.68
173_T	198_Q	1.708	0.67
135_K	209_A	1.668	0.66
120_S	123_E	1.649	0.65
196_I	199_K	1.623	0.63
44_P	79_A	1.606	0.62
141_V	170_K	1.599	0.62
105_I	180_A	1.577	0.61
200_K	207_A	1.550	0.60
160_L	195_A	1.535	0.59
104_D	107_H	1.528	0.58
135_K	141_V	1.523	0.58
183_L	195_A	1.521	0.58
121_A	124_N	1.510	0.58
144_A	191_V	1.508	0.57
68_K	208_A	1.503	0.57
140_S	144_A	1.469	0.55
86_G	165_H	1.450	0.54
81_R	84_K	1.443	0.54
126_A	207_A	1.441	0.54
86_G	89_A	1.421	0.53
125_A	183_L	1.421	0.53
123_E	126_A	1.418	0.53
134_L	139_I	1.392	0.51
87_A	165_H	1.385	0.51
79_A	99_V	1.382	0.51
131_T	159_F	1.378	0.51
58_T	61_R	1.376	0.50
81_R	159_F	1.366	0.50
187_A	204_R	1.355	0.49
135_K	142_P	1.351	0.49
185_G	190_N	1.351	0.49
46_T	199_K	1.313	0.47
107_H	208_A	1.263	0.44
152_R	206_A	1.251	0.44
32_G	144_A	1.246	0.43
162_D	194_Y	1.227	0.43
46_T	56_A	1.224	0.42
87_A	169_F	1.206	0.41
135_K	207_A	1.198	0.41
166_S	197_G	1.182	0.40
81_R	157_L	1.174	0.40
98_I	179_L	1.172	0.40
53_T	131_T	1.170	0.40
73_S	140_S	1.166	0.39
62_H	72_I	1.163	0.39
93_Q	97_K	1.159	0.39
116_Q	120_S	1.159	0.39
85_T	207_A	1.149	0.38
141_V	209_A	1.144	0.38
27_N	37_A	1.136	0.38
116_Q	163_G	1.122	0.37
93_Q	202_K	1.119	0.37
132_V	141_V	1.112	0.37
32_G	168_S	1.089	0.35
42_E	120_S	1.078	0.35
95_A	187_A	1.069	0.35
63_A	99_V	1.061	0.34
68_K	122_V	1.059	0.34
156_A	210_R	1.052	0.34
160_L	186_A	1.049	0.34
88_N	126_A	1.046	0.33
99_V	103_F	1.045	0.33
40_H	47_R	1.044	0.33
73_S	147_T	1.027	0.33
166_S	192_Q	1.024	0.32
100_R	122_V	1.021	0.32
139_I	190_N	1.021	0.32
167_A	178_A	1.021	0.32
133_R	140_S	1.014	0.32
28_A	53_T	1.013	0.32
72_I	188_D	1.010	0.32
68_K	205_V	1.006	0.32
85_T	162_D	0.997	0.31
143_Q	155_Q	0.994	0.31
47_R	54_P	0.986	0.31
112_E	198_Q	0.985	0.31
200_K	205_V	0.982	0.30
58_T	81_R	0.977	0.30
89_A	209_A	0.974	0.30
157_L	204_R	0.961	0.29
100_R	104_D	0.958	0.29
88_N	98_I	0.957	0.29
162_D	167_A	0.954	0.29
34_W	63_A	0.945	0.29
45_S	176_A	0.937	0.28
175_A	178_A	0.931	0.28
26_A	36_V	0.915	0.27
59_M	143_Q	0.913	0.27
115_I	174_D	0.910	0.27
120_S	196_I	0.910	0.27
43_D	152_R	0.909	0.27
48_R	155_Q	0.908	0.27
130_E	197_G	0.904	0.27
45_S	109_R	0.896	0.27
37_A	155_Q	0.895	0.27
174_D	197_G	0.895	0.27
110_T	184_A	0.892	0.27
46_T	148_A	0.879	0.26
115_I	202_K	0.878	0.26
97_K	100_R	0.871	0.26
106_V	117_V	0.870	0.26
50_L	65_K	0.869	0.26
49_Y	69_K	0.867	0.25
119_V	124_N	0.861	0.25
173_T	197_G	0.857	0.25
49_Y	139_I	0.857	0.25
60_G	179_L	0.857	0.25
129_E	145_V	0.856	0.25
159_F	162_D	0.856	0.25
61_R	96_L	0.849	0.25
54_P	208_A	0.848	0.25
83_M	92_K	0.848	0.25
63_A	144_A	0.845	0.25
111_D	181_N	0.842	0.24
86_G	155_Q	0.840	0.24
183_L	202_K	0.838	0.24
30_L	183_L	0.835	0.24
82_L	201_E	0.830	0.24
123_E	207_A	0.828	0.24
40_H	117_V	0.817	0.24
29_K	35_D	0.815	0.23
178_A	194_Y	0.812	0.23
36_V	169_F	0.809	0.23
101_D	176_A	0.808	0.23
34_W	166_S	0.805	0.23
32_G	111_D	0.803	0.23
151_R	179_L	0.793	0.23
72_I	96_L	0.791	0.23
201_E	205_V	0.784	0.22
41_Y	198_Q	0.781	0.22
47_R	71_E	0.774	0.22
72_I	81_R	0.771	0.22
126_A	185_G	0.759	0.21
173_T	181_N	0.741	0.21
103_F	115_I	0.739	0.21
68_K	147_T	0.738	0.21
73_S	177_E	0.737	0.21
57_H	133_R	0.733	0.20
94_Q	97_K	0.729	0.20
52_V	155_Q	0.726	0.20
44_P	54_P	0.724	0.20
37_A	101_D	0.722	0.20
153_V	159_F	0.722	0.20
159_F	207_A	0.714	0.20
46_T	201_E	0.713	0.20
81_R	162_D	0.708	0.20
37_A	115_I	0.707	0.20
39_I	192_Q	0.706	0.20
154_D	190_N	0.685	0.19
118_L	200_K	0.683	0.19
29_K	47_R	0.672	0.18
67_F	74_I	0.666	0.18
59_M	96_L	0.664	0.18
39_I	53_T	0.663	0.18
162_D	183_L	0.663	0.18
120_S	187_A	0.663	0.18
81_R	198_Q	0.659	0.18
87_A	192_Q	0.656	0.18
102_A	111_D	0.655	0.18
185_G	192_Q	0.652	0.18
62_H	144_A	0.648	0.18
37_A	160_L	0.647	0.18
126_A	143_Q	0.645	0.18
86_G	134_L	0.643	0.17
34_W	107_H	0.639	0.17
128_R	146_D	0.638	0.17
32_G	73_S	0.634	0.17
60_G	132_V	0.634	0.17
74_I	177_E	0.633	0.17
123_E	136_Y	0.633	0.17
95_A	176_A	0.632	0.17
54_P	158_K	0.631	0.17
40_H	161_A	0.628	0.17
30_L	72_I	0.628	0.17
99_V	181_N	0.625	0.17
51_A	82_L	0.622	0.17
173_T	188_D	0.621	0.17
86_G	141_V	0.616	0.17
118_L	157_L	0.615	0.17
49_Y	58_T	0.614	0.17
102_A	153_V	0.613	0.17
125_A	166_S	0.610	0.16
55_V	82_L	0.609	0.16
35_D	89_A	0.609	0.16
130_E	170_K	0.609	0.16
164_A	167_A	0.609	0.16
189_Y	196_I	0.608	0.16
129_E	148_A	0.607	0.16
45_S	49_Y	0.607	0.16
81_R	103_F	0.606	0.16
98_I	199_K	0.601	0.16
192_Q	197_G	0.601	0.16
101_D	187_A	0.597	0.16
97_K	199_K	0.597	0.16
72_I	173_T	0.596	0.16
160_L	174_D	0.593	0.16
115_I	162_D	0.590	0.16
132_V	143_Q	0.589	0.16
116_Q	119_V	0.589	0.16
64_Q	207_A	0.586	0.16
53_T	166_S	0.585	0.16
105_I	196_I	0.584	0.16
125_A	160_L	0.582	0.16
146_D	203_E	0.581	0.16
148_A	192_Q	0.581	0.16
128_R	163_G	0.577	0.16
36_V	160_L	0.576	0.16
85_T	209_A	0.576	0.16
49_Y	67_F	0.575	0.15
80_N	139_I	0.574	0.15
33_K	178_A	0.571	0.15
40_H	150_Q	0.570	0.15
90_G	138_G	0.569	0.15
118_L	160_L	0.569	0.15
37_A	85_T	0.568	0.15
86_G	160_L	0.568	0.15
46_T	52_V	0.568	0.15
29_K	183_L	0.564	0.15
121_A	138_G	0.555	0.15
112_E	123_E	0.553	0.15
179_L	196_I	0.552	0.15
30_L	82_L	0.551	0.15
165_H	197_G	0.550	0.15
167_A	175_A	0.548	0.15
177_E	184_A	0.544	0.15
72_I	144_A	0.541	0.15
155_Q	202_K	0.540	0.15
164_A	179_L	0.537	0.14
57_H	116_Q	0.532	0.14
96_L	202_K	0.529	0.14
77_R	154_D	0.526	0.14
50_L	192_Q	0.525	0.14
129_E	203_E	0.525	0.14
29_K	176_A	0.524	0.14
34_W	60_G	0.523	0.14
167_A	173_T	0.518	0.14
64_Q	189_Y	0.517	0.14
88_N	94_Q	0.515	0.14
100_R	175_A	0.513	0.14
41_Y	112_E	0.513	0.14
141_V	155_Q	0.511	0.14
96_L	176_A	0.511	0.14
161_A	164_A	0.510	0.14
41_Y	191_V	0.508	0.14
126_A	200_K	0.508	0.14
84_K	139_I	0.508	0.14
180_A	184_A	0.506	0.14
144_A	150_Q	0.505	0.14
154_D	209_A	0.505	0.14
28_A	144_A	0.501	0.14
67_F	76_E	0.500	0.13
62_H	73_S	0.500	0.13

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
1iqvA	1	0.7857	100	0.197	Contact Map
3j7aI	1	0.8333	100	0.2	Contact Map
3zey2	1	0.881	100	0.2	Contact Map
4ujpG	1	0.9095	100	0.201	Contact Map
4bpeG	1	0.881	100	0.201	Contact Map
3j38F	1	0.8762	100	0.214	Contact Map
5aj3G	1	0.8048	100	0.428	Contact Map
4tp8G	1	0.7048	100	0.441	Contact Map
1rssA	1	0.6476	100	0.442	Contact Map
4kiyG	1	0.7048	100	0.442	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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