RNC - ECOLI - GREMLIN Contacts

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RNC - Ribonuclease 3

UniProt:	P0A7Y0	Sequences: MNPIVINRLQRKLGYTFNHQELLQQALTHRSASSKHNERLEFLGDSILSYVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFELGECLRLGPGELKSGGFRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLDEISPGDKQKDPKTRLQEYLQGRHLPLPTYLVVQVRGEAHDQEFTIHCQVSGLSEPVVGTGSSRRKAEQAAAEQALKKLELE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10857
Length:	226 (216)
Sequences:	4777 (3382)
Seq/√Len:	230.1

ECOLI - RNC
BACSU - RNC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_N	133_E	3.992	1.00
89_E	92_E	3.061	1.00
15_Y	127_S	2.915	1.00
10_Q	20_Q	2.897	1.00
101_L	106_F	2.868	1.00
37_N	115_T	2.620	1.00
54_N	58_H	2.619	1.00
177_V	191_H	2.355	1.00
86_R	109_E	2.345	1.00
175_L	193_Q	2.277	1.00
190_I	211_A	2.218	1.00
187_E	204_T	2.196	1.00
176_V	190_I	2.180	1.00
49_S	53_A	2.161	1.00
17_F	23_L	2.084	1.00
51_V	136_I	2.066	1.00
46_S	49_S	2.041	1.00
47_I	50_Y	2.039	1.00
123_V	135_L	2.017	1.00
191_H	198_S	2.016	1.00
131_T	134_K	1.962	1.00
55_A	59_R	1.937	1.00
175_L	191_H	1.931	1.00
191_H	202_V	1.901	1.00
86_R	107_R	1.869	1.00
30_R	38_E	1.861	1.00
189_T	204_T	1.855	1.00
157_K	212_E	1.848	1.00
214_A	217_E	1.845	1.00
178_Q	189_T	1.833	1.00
193_Q	198_S	1.815	1.00
155_D	158_T	1.802	1.00
189_T	202_V	1.799	1.00
181_G	184_H	1.785	1.00
94_L	115_T	1.784	1.00
24_Q	95_R	1.782	1.00
78_G	113_A	1.749	1.00
87_E	143_R	1.741	1.00
84_L	116_V	1.737	1.00
156_P	217_E	1.717	1.00
85_A	112_L	1.701	1.00
130_Q	133_E	1.619	1.00
127_S	131_T	1.616	1.00
201_V	218_Q	1.600	1.00
194_V	200_P	1.521	1.00
120_I	135_L	1.520	1.00
217_E	221_K	1.510	1.00
83_E	143_R	1.508	1.00
90_L	119_L	1.506	1.00
53_A	72_R	1.499	1.00
180_R	189_T	1.487	1.00
116_V	120_I	1.484	1.00
32_A	95_R	1.460	1.00
201_V	219_A	1.445	1.00
55_A	137_L	1.432	1.00
33_S	36_H	1.419	1.00
63_V	67_D	1.403	1.00
203_G	215_A	1.403	1.00
160_L	192_C	1.401	1.00
180_R	187_E	1.401	1.00
128_D	131_T	1.399	1.00
17_F	126_D	1.388	1.00
210_K	214_A	1.385	1.00
179_V	186_Q	1.368	1.00
163_Y	220_L	1.361	1.00
135_L	139_W	1.353	1.00
12_K	89_E	1.348	1.00
134_K	138_N	1.332	1.00
41_E	45_D	1.320	1.00
218_Q	222_K	1.295	1.00
185_D	206_S	1.293	1.00
27_L	90_L	1.293	1.00
59_R	145_D	1.292	1.00
183_A	186_Q	1.281	1.00
206_S	210_K	1.277	1.00
205_G	214_A	1.266	1.00
28_T	95_R	1.263	1.00
10_Q	17_F	1.253	1.00
201_V	222_K	1.243	1.00
214_A	218_Q	1.241	1.00
77_R	80_T	1.236	1.00
50_Y	129_I	1.230	1.00
7_N	11_R	1.224	1.00
41_E	117_E	1.222	1.00
51_V	129_I	1.217	1.00
86_R	112_L	1.201	1.00
27_L	119_L	1.201	1.00
27_L	115_T	1.197	1.00
9_L	13_L	1.186	1.00
137_L	141_Q	1.185	1.00
85_A	116_V	1.184	1.00
200_P	219_A	1.181	1.00
10_Q	16_T	1.179	1.00
12_K	93_C	1.166	1.00
45_D	117_E	1.163	1.00
8_R	12_K	1.158	1.00
20_Q	24_Q	1.154	1.00
156_P	213_Q	1.147	1.00
46_S	72_R	1.139	1.00
91_G	112_L	1.138	1.00
133_E	137_L	1.119	1.00
100_E	108_R	1.115	1.00
10_Q	15_Y	1.111	1.00
54_N	124_F	1.085	1.00
30_R	37_N	1.071	1.00
161_Q	174_Y	1.068	1.00
82_A	113_A	1.064	1.00
78_G	110_S	1.061	1.00
7_N	16_T	1.060	1.00
87_E	142_T	1.057	1.00
39_R	57_Y	1.047	1.00
170_P	195_S	1.044	1.00
192_C	201_V	1.033	1.00
48_L	120_I	1.026	1.00
119_L	123_V	1.026	1.00
218_Q	221_K	1.018	1.00
47_I	121_G	1.013	1.00
14_G	138_N	1.013	1.00
198_S	202_V	0.997	1.00
173_T	193_Q	0.993	1.00
15_Y	18_N	0.965	1.00
120_I	136_I	0.963	1.00
86_R	91_G	0.962	1.00
52_I	140_Y	0.957	1.00
80_T	143_R	0.955	1.00
164_L	172_P	0.954	1.00
79_N	109_E	0.950	1.00
63_V	71_M	0.949	1.00
82_A	86_R	0.936	1.00
37_N	118_A	0.935	1.00
17_F	127_S	0.934	1.00
132_V	136_I	0.934	1.00
16_T	20_Q	0.931	1.00
193_Q	200_P	0.926	1.00
100_E	105_G	0.926	1.00
105_G	108_R	0.907	0.99
17_F	122_G	0.903	0.99
9_L	93_C	0.902	0.99
88_F	139_W	0.901	0.99
21_E	24_Q	0.886	0.99
122_G	126_D	0.881	0.99
163_Y	167_R	0.881	0.99
110_S	114_D	0.877	0.99
19_H	25_Q	0.872	0.99
141_Q	145_D	0.863	0.99
51_V	132_V	0.861	0.99
51_V	133_E	0.860	0.99
75_L	144_L	0.857	0.99
32_A	35_K	0.854	0.99
159_R	220_L	0.852	0.99
162_E	165_Q	0.844	0.99
173_T	196_G	0.842	0.99
64_D	67_D	0.838	0.99
11_R	16_T	0.833	0.99
9_L	12_K	0.832	0.99
10_Q	23_L	0.831	0.99
9_L	119_L	0.830	0.99
207_S	210_K	0.830	0.99
84_L	140_Y	0.829	0.99
15_Y	126_D	0.828	0.99
164_L	194_V	0.825	0.99
159_R	163_Y	0.820	0.99
58_H	137_L	0.808	0.99
75_L	80_T	0.804	0.99
161_Q	165_Q	0.804	0.99
23_L	119_L	0.794	0.99
158_T	162_E	0.785	0.99
172_P	192_C	0.782	0.99
131_T	135_L	0.775	0.98
23_L	126_D	0.775	0.98
176_V	179_V	0.775	0.98
50_Y	54_N	0.766	0.98
8_R	92_E	0.758	0.98
115_T	118_A	0.756	0.98
200_P	222_K	0.754	0.98
75_L	140_Y	0.751	0.98
39_R	68_M	0.751	0.98
15_Y	123_V	0.743	0.98
82_A	109_E	0.742	0.98
78_G	114_D	0.740	0.98
46_S	50_Y	0.740	0.98
15_Y	23_L	0.738	0.98
48_L	81_L	0.733	0.98
18_N	126_D	0.733	0.98
155_D	213_Q	0.733	0.98
181_G	186_Q	0.729	0.98
7_N	20_Q	0.723	0.98
56_L	68_M	0.723	0.98
8_R	11_R	0.722	0.97
22_L	126_D	0.712	0.97
197_L	200_P	0.712	0.97
49_S	72_R	0.712	0.97
154_K	159_R	0.712	0.97
94_L	111_I	0.710	0.97
47_I	124_F	0.710	0.97
38_E	41_E	0.704	0.97
69_S	72_R	0.702	0.97
123_V	139_W	0.701	0.97
27_L	88_F	0.696	0.97
45_D	76_V	0.686	0.97
30_R	36_H	0.686	0.97
7_N	10_Q	0.684	0.97
168_H	172_P	0.681	0.96
191_H	200_P	0.679	0.96
139_W	142_T	0.676	0.96
88_F	116_V	0.671	0.96
13_L	139_W	0.671	0.96
163_Y	223_L	0.666	0.96
41_E	114_D	0.666	0.96
82_A	112_L	0.664	0.96
176_V	212_E	0.663	0.96
108_R	111_I	0.663	0.96
23_L	27_L	0.658	0.96
147_I	150_G	0.658	0.96
66_G	69_S	0.657	0.96
59_R	141_Q	0.656	0.96
157_K	161_Q	0.655	0.96
123_V	132_V	0.654	0.96
40_L	121_G	0.648	0.95
129_I	133_E	0.648	0.95
23_L	127_S	0.647	0.95
42_F	45_D	0.646	0.95
132_V	135_L	0.644	0.95
180_R	204_T	0.644	0.95
63_V	68_M	0.643	0.95
15_Y	135_L	0.643	0.95
73_A	113_A	0.643	0.95
35_K	98_P	0.642	0.95
51_V	137_L	0.640	0.95
79_N	210_K	0.635	0.95
76_V	117_E	0.634	0.95
91_G	107_R	0.625	0.94
42_F	68_M	0.625	0.94
78_G	109_E	0.625	0.94
157_K	174_Y	0.625	0.94
205_G	210_K	0.624	0.94
193_Q	196_G	0.621	0.94
208_R	212_E	0.620	0.94
96_L	99_G	0.611	0.94
46_S	69_S	0.609	0.94
72_R	81_L	0.609	0.94
69_S	76_V	0.605	0.93
23_L	93_C	0.603	0.93
203_G	214_A	0.603	0.93
157_K	216_A	0.600	0.93
81_L	120_I	0.594	0.93
9_L	90_L	0.589	0.92
203_G	218_Q	0.586	0.92
41_E	76_V	0.585	0.92
134_K	137_L	0.583	0.92
8_R	93_C	0.582	0.92
90_L	116_V	0.582	0.92
83_E	86_R	0.580	0.92
182_E	186_Q	0.579	0.92
69_S	117_E	0.579	0.92
202_V	218_Q	0.579	0.92
116_V	139_W	0.579	0.92
96_L	104_G	0.577	0.92
38_E	114_D	0.576	0.92
121_G	125_L	0.574	0.91
39_R	43_L	0.571	0.91
19_H	22_L	0.570	0.91
145_D	149_P	0.564	0.91
66_G	94_L	0.563	0.91
10_Q	13_L	0.562	0.91
52_I	76_V	0.562	0.91
60_F	148_S	0.561	0.90
176_V	208_R	0.560	0.90
164_L	171_L	0.559	0.90
198_S	219_A	0.559	0.90
156_P	220_L	0.559	0.90
18_N	127_S	0.559	0.90
130_Q	134_K	0.558	0.90
183_A	207_S	0.557	0.90
188_F	212_E	0.557	0.90
104_G	107_R	0.556	0.90
49_S	52_I	0.555	0.90
22_L	125_L	0.551	0.90
25_Q	36_H	0.551	0.90
56_L	75_L	0.550	0.90
43_L	57_Y	0.548	0.89
91_G	105_G	0.548	0.89
85_A	115_T	0.548	0.89
26_A	122_G	0.547	0.89
98_P	101_L	0.547	0.89
60_F	124_F	0.546	0.89
37_N	94_L	0.544	0.89
45_D	69_S	0.542	0.89
84_L	136_I	0.542	0.89
160_L	220_L	0.541	0.89
11_R	58_H	0.540	0.89
127_S	132_V	0.539	0.89
46_S	53_A	0.538	0.89
35_K	97_G	0.536	0.88
67_D	70_R	0.536	0.88
100_E	103_S	0.536	0.88
69_S	97_G	0.535	0.88
56_L	71_M	0.535	0.88
90_L	93_C	0.530	0.88
144_L	147_I	0.530	0.88
30_R	111_I	0.527	0.88
45_D	66_G	0.527	0.88
66_G	117_E	0.527	0.88
69_S	73_A	0.526	0.87
72_R	77_R	0.525	0.87
17_F	20_Q	0.525	0.87
138_N	141_Q	0.522	0.87
46_S	71_M	0.521	0.87
42_F	117_E	0.520	0.87
13_L	119_L	0.519	0.87
9_L	85_A	0.517	0.87
219_A	222_K	0.516	0.86
80_T	140_Y	0.515	0.86
45_D	72_R	0.514	0.86
158_T	209_R	0.512	0.86
67_D	71_M	0.510	0.86
194_V	197_L	0.510	0.86
195_S	200_P	0.509	0.86
71_M	186_Q	0.508	0.86
63_V	194_V	0.508	0.86
161_Q	216_A	0.505	0.85
181_G	185_D	0.505	0.85
80_T	84_L	0.501	0.85
22_L	40_L	0.500	0.85

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
1o0wA	2	0.9912	100	0.128	Contact Map
3n3wA	2	0.6416	100	0.14	Contact Map
2a11A	2	0.646	100	0.156	Contact Map
1vw45	1	0.9912	100	0.16	Contact Map
2nugA	2	0.9469	100	0.162	Contact Map
3j7yc	1	0.9646	100	0.17	Contact Map
4ce4h	1	0.9602	100	0.172	Contact Map
3rv0A	2	0.9602	100	0.199	Contact Map
3c4bA	2	0.9469	100	0.205	Contact Map
4oogC	2	0.9513	100	0.224	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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