RS2 - HALSA - GREMLIN Contacts

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RS2 - 30S ribosomal protein S2

UniProt:	P57713	Sequences: MSENESDTEAELEENAPDEAAADAESTAQTDEQTPDTEADEPAPESTATEDVMSDEEADLLIPVEDYLGAGVHIGTQQKTNDMDRFIHRVRTDGLYVLDVSRTDDRVRTAADFLANYDPEQILVTSSRQYGRFPAEKFAEAVGARARTGRFIPGTLTNPDYDGYIEPDVLVVTDPIGDSQAVKEAITVGIPVIAMCDSNNQTGNVDLVVPTNNKGRRALSVVYWLLANETLDRRGAEPTYGLDDFEDGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	249 (189)
Sequences:	630 (351)
Seq/√Len:	25.5

ECOLI - RS2
BACSU - RS2
HALSA - RS2
SULSO - RS2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_L	198_S	5.780	1.00
211_T	222_V	4.972	1.00
195_M	211_T	4.422	1.00
72_V	218_A	4.063	1.00
170_L	185_A	4.049	1.00
229_E	233_R	2.973	1.00
79_K	96_Y	2.937	1.00
113_F	193_I	2.821	1.00
113_F	207_L	2.802	1.00
79_K	87_I	2.750	0.99
195_M	222_V	2.621	0.99
126_S	131_G	2.593	0.99
67_Y	72_V	2.355	0.98
120_E	168_D	2.355	0.98
171_V	226_L	2.330	0.98
86_F	134_P	2.256	0.98
114_L	169_V	2.155	0.97
86_F	106_R	2.145	0.97
174_D	178_D	2.100	0.96
107_V	225_L	2.096	0.96
123_L	156_L	2.059	0.96
72_V	211_T	1.972	0.95
197_D	214_K	1.913	0.94
115_A	232_D	1.907	0.94
131_G	173_T	1.897	0.94
100_V	169_V	1.811	0.92
196_C	205_V	1.800	0.92
87_I	198_S	1.756	0.91
135_A	186_I	1.721	0.90
114_L	193_I	1.714	0.90
77_Q	197_D	1.569	0.85
117_Y	169_V	1.550	0.84
113_F	169_V	1.549	0.84
151_F	156_L	1.532	0.83
139_A	144_A	1.520	0.83
91_R	190_I	1.505	0.82
137_K	140_E	1.461	0.80
154_G	158_N	1.445	0.80
65_E	104_D	1.441	0.79
154_G	184_E	1.419	0.78
82_D	203_G	1.404	0.78
173_T	178_D	1.399	0.77
99_D	102_R	1.383	0.76
128_R	173_T	1.361	0.75
76_T	197_D	1.340	0.74
158_N	184_E	1.331	0.74
136_E	140_E	1.315	0.73
186_I	204_N	1.313	0.73
169_V	193_I	1.309	0.72
114_L	209_V	1.301	0.72
154_G	157_T	1.289	0.71
134_P	219_L	1.255	0.69
114_L	230_T	1.245	0.68
70_A	232_D	1.233	0.68
173_T	219_L	1.197	0.65
81_N	84_D	1.193	0.65
80_T	201_Q	1.191	0.65
152_I	166_E	1.185	0.65
149_G	180_Q	1.185	0.65
106_R	109_T	1.180	0.64
73_H	139_A	1.180	0.64
97_V	132_R	1.169	0.63
169_V	194_A	1.169	0.63
181_A	185_A	1.167	0.63
111_A	226_L	1.156	0.63
140_E	211_T	1.156	0.63
229_E	239_T	1.152	0.62
193_I	198_S	1.149	0.62
122_I	234_R	1.140	0.61
86_F	117_Y	1.122	0.60
233_R	237_E	1.112	0.59
112_D	115_A	1.112	0.59
127_S	150_R	1.112	0.59
194_A	205_V	1.104	0.59
128_R	199_N	1.094	0.58
135_A	139_A	1.082	0.57
169_V	191_P	1.067	0.56
222_V	226_L	1.059	0.56
128_R	131_G	1.056	0.55
228_N	231_L	1.056	0.55
159_P	188_V	1.053	0.55
155_T	184_E	1.050	0.55
122_I	142_V	1.031	0.54
173_T	223_Y	1.020	0.53
127_S	177_G	1.019	0.53
76_T	130_Y	1.002	0.52
147_R	188_V	0.995	0.51
75_G	167_P	0.995	0.51
167_P	190_I	0.995	0.51
127_S	146_A	0.995	0.51
147_R	150_R	0.991	0.51
123_L	157_T	0.986	0.50
129_Q	153_P	0.963	0.49
71_G	155_T	0.960	0.48
179_S	183_K	0.959	0.48
185_A	192_V	0.952	0.48
80_T	161_Y	0.952	0.48
66_D	197_D	0.938	0.47
54_S	57_E	0.930	0.46
142_V	218_A	0.925	0.46
55_D	86_F	0.923	0.46
231_L	237_E	0.922	0.46
76_T	213_N	0.918	0.45
125_T	170_L	0.915	0.45
79_K	135_A	0.915	0.45
88_H	180_Q	0.912	0.45
131_G	174_D	0.909	0.45
70_A	91_R	0.900	0.44
70_A	218_A	0.896	0.44
76_T	214_K	0.886	0.43
79_K	83_M	0.883	0.43
125_T	181_A	0.877	0.42
69_G	111_A	0.864	0.42
85_R	203_G	0.861	0.41
58_A	70_A	0.859	0.41
130_Y	213_N	0.847	0.40
135_A	211_T	0.844	0.40
86_F	96_Y	0.842	0.40
178_D	206_D	0.837	0.40
117_Y	191_P	0.833	0.39
91_R	197_D	0.833	0.39
73_H	122_I	0.832	0.39
174_D	177_G	0.832	0.39
182_V	192_V	0.827	0.39
54_S	58_A	0.823	0.39
88_H	205_V	0.822	0.39
165_I	193_I	0.821	0.39
127_S	141_A	0.818	0.38
86_F	160_D	0.809	0.38
232_D	239_T	0.809	0.38
117_Y	193_I	0.805	0.37
99_D	143_G	0.805	0.37
147_R	179_S	0.802	0.37
107_V	222_V	0.800	0.37
183_K	197_D	0.786	0.36
199_N	218_A	0.785	0.36
156_L	231_L	0.778	0.36
125_T	151_F	0.764	0.35
143_G	235_G	0.759	0.34
68_L	150_R	0.759	0.34
89_R	101_S	0.749	0.34
106_R	206_D	0.748	0.34
151_F	229_E	0.747	0.34
78_Q	94_G	0.747	0.34
99_D	130_Y	0.746	0.33
87_I	199_N	0.744	0.33
179_S	199_N	0.734	0.33
171_V	215_G	0.733	0.33
125_T	195_M	0.732	0.33
186_I	195_M	0.722	0.32
182_V	196_C	0.719	0.32
82_D	151_F	0.717	0.32
221_V	229_E	0.717	0.32
122_I	191_P	0.716	0.32
105_D	232_D	0.715	0.31
120_E	145_R	0.715	0.31
94_G	216_R	0.712	0.31
123_L	170_L	0.710	0.31
170_L	181_A	0.707	0.31
83_M	182_V	0.707	0.31
86_F	208_V	0.705	0.31
176_I	199_N	0.699	0.30
174_D	206_D	0.698	0.30
66_D	200_N	0.696	0.30
121_Q	169_V	0.695	0.30
145_R	175_P	0.688	0.30
141_A	195_M	0.686	0.30
122_I	168_D	0.685	0.30
63_P	104_D	0.684	0.30
96_Y	198_S	0.682	0.29
86_F	105_D	0.679	0.29
139_A	142_V	0.675	0.29
114_L	184_E	0.674	0.29
66_D	148_T	0.671	0.29
182_V	190_I	0.671	0.29
63_P	98_L	0.670	0.29
166_E	188_V	0.669	0.29
71_G	189_G	0.668	0.29
130_Y	219_L	0.667	0.29
69_G	236_A	0.663	0.28
131_G	206_D	0.663	0.28
100_V	207_L	0.662	0.28
129_Q	219_L	0.661	0.28
77_Q	87_I	0.659	0.28
150_R	184_E	0.656	0.28
72_V	145_R	0.655	0.28
117_Y	120_E	0.652	0.28
70_A	225_L	0.652	0.28
138_F	193_I	0.652	0.28
90_V	235_G	0.650	0.28
111_A	227_A	0.649	0.27
161_Y	181_A	0.648	0.27
138_F	177_G	0.648	0.27
150_R	153_P	0.646	0.27
172_V	186_I	0.642	0.27
146_A	155_T	0.640	0.27
64_V	77_Q	0.637	0.27
141_A	228_N	0.631	0.26
153_P	184_E	0.629	0.26
200_N	218_A	0.629	0.26
97_V	133_F	0.628	0.26
97_V	242_L	0.624	0.26
94_G	142_V	0.624	0.26
77_Q	208_V	0.623	0.26
128_R	174_D	0.621	0.26
80_T	215_G	0.620	0.26
76_T	87_I	0.616	0.26
155_T	161_Y	0.616	0.26
97_V	117_Y	0.616	0.26
66_D	123_L	0.611	0.25
95_L	147_R	0.607	0.25
136_E	187_T	0.606	0.25
127_S	147_R	0.605	0.25
117_Y	153_P	0.603	0.25
148_T	179_S	0.603	0.25
146_A	163_G	0.601	0.25
182_V	186_I	0.599	0.25
86_F	140_E	0.597	0.25
124_V	214_K	0.595	0.24
84_D	193_I	0.595	0.24
80_T	97_V	0.595	0.24
79_K	192_V	0.592	0.24
99_D	142_V	0.591	0.24
236_A	239_T	0.590	0.24
202_T	213_N	0.589	0.24
73_H	191_P	0.587	0.24
152_I	181_A	0.585	0.24
60_L	239_T	0.584	0.24
181_A	196_C	0.582	0.24
85_R	201_Q	0.581	0.24
107_V	208_V	0.581	0.24
190_I	205_V	0.579	0.24
151_F	188_V	0.578	0.24
135_A	177_G	0.576	0.23
171_V	209_V	0.574	0.23
161_Y	188_V	0.572	0.23
195_M	203_G	0.572	0.23
123_L	198_S	0.569	0.23
138_F	141_A	0.568	0.23
116_N	134_P	0.565	0.23
156_L	217_R	0.564	0.23
117_Y	189_G	0.563	0.23
123_L	197_D	0.562	0.23
66_D	69_G	0.562	0.23
183_K	223_Y	0.560	0.23
238_P	243_D	0.560	0.23
117_Y	216_R	0.559	0.23
116_N	133_F	0.558	0.22
117_Y	205_V	0.556	0.22
70_A	156_L	0.554	0.22
137_K	231_L	0.550	0.22
197_D	213_N	0.549	0.22
111_A	170_L	0.547	0.22
189_G	218_A	0.547	0.22
98_L	211_T	0.544	0.22
120_E	207_L	0.544	0.22
99_D	112_D	0.542	0.22
74_I	192_V	0.539	0.22
71_G	95_L	0.539	0.22
99_D	136_E	0.538	0.21
132_R	143_G	0.538	0.21
232_D	236_A	0.534	0.21
198_S	238_P	0.534	0.21
86_F	100_V	0.530	0.21
63_P	221_V	0.530	0.21
68_L	95_L	0.529	0.21
106_R	196_C	0.528	0.21
64_V	161_Y	0.527	0.21
123_L	208_V	0.526	0.21
193_I	207_L	0.523	0.21
90_V	119_P	0.523	0.21
187_T	208_V	0.519	0.21
99_D	187_T	0.518	0.20
70_A	214_K	0.516	0.20
104_D	221_V	0.515	0.20
63_P	230_T	0.513	0.20
132_R	149_G	0.511	0.20
91_R	95_L	0.510	0.20
199_N	219_L	0.510	0.20
63_P	217_R	0.509	0.20
133_F	166_E	0.509	0.20
78_Q	195_M	0.508	0.20
89_R	167_P	0.502	0.20
131_G	172_V	0.500	0.20

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
3j7aC	1	0.7631	100	0.171	Contact Map
4ujpB	1	0.7952	100	0.173	Contact Map
3j60A	1	0.7871	100	0.176	Contact Map
3zeyC	1	0.7871	100	0.177	Contact Map
4bpeB	1	0.7791	100	0.18	Contact Map
3bchA	1	0.7711	100	0.184	Contact Map
3j38A	1	0.7831	100	0.184	Contact Map
3j20B	1	0.7791	100	0.184	Contact Map
4w23A	1	0.7952	100	0.198	Contact Map
1vi6A	2	0.755	100	0.202	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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