RRP42 - SULSO - GREMLIN Contacts

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RRP42 - Exosome complex component Rrp42

UniProt:	Q9UXC0	Sequences: MSSTPSNQNIIPIIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLEELKKHLGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	275 (220)
Sequences:	5295 (2550)
Seq/√Len:	171.9

ECOLI - RNPH
BACSU - RNPH
SULSO - RRP42 RRP41

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_L	167_N	3.852	1.00
33_K	36_D	3.811	1.00
48_K	60_T	3.560	1.00
268_E	271_K	3.205	1.00
57_K	62_M	3.175	1.00
67_T	164_A	3.100	1.00
41_S	57_K	3.071	1.00
195_Y	232_D	2.969	1.00
30_D	214_D	2.949	1.00
211_V	261_T	2.932	1.00
35_T	260_S	2.832	1.00
195_Y	231_P	2.809	1.00
65_A	160_A	2.793	1.00
51_D	93_L	2.718	1.00
45_D	167_N	2.681	1.00
64_L	147_L	2.589	1.00
159_L	265_L	2.513	1.00
162_V	196_P	2.511	1.00
203_A	213_P	2.467	1.00
227_F	258_A	2.464	1.00
63_V	146_V	2.386	1.00
43_T	57_K	2.381	1.00
73_K	76_E	2.306	1.00
196_P	270_K	2.212	1.00
260_S	264_K	2.145	1.00
248_L	259_R	2.116	1.00
248_L	252_D	2.102	1.00
72_D	75_Y	1.999	1.00
82_G	115_D	1.976	1.00
42_I	56_V	1.951	1.00
72_D	76_E	1.867	1.00
47_A	66_G	1.820	1.00
267_E	271_K	1.793	1.00
198_V	262_A	1.793	1.00
40_L	265_L	1.749	1.00
196_P	266_L	1.714	1.00
247_S	250_D	1.692	1.00
42_I	163_A	1.688	1.00
81_Q	127_T	1.649	1.00
231_P	270_K	1.635	1.00
204_K	250_D	1.632	1.00
34_L	208_Y	1.618	1.00
67_T	142_L	1.612	1.00
37_Y	211_V	1.582	1.00
29_Q	216_D	1.580	1.00
117_S	237_G	1.546	1.00
29_Q	214_D	1.530	1.00
104_D	108_I	1.429	1.00
118_L	161_S	1.427	1.00
264_K	268_E	1.408	1.00
256_N	260_S	1.406	1.00
35_T	257_T	1.405	1.00
55_L	62_M	1.399	1.00
166_Y	193_L	1.398	1.00
259_R	263_V	1.372	1.00
42_I	272_H	1.368	1.00
42_I	268_E	1.361	1.00
262_A	266_L	1.357	1.00
71_I	136_S	1.341	1.00
209_L	257_T	1.336	1.00
252_D	256_N	1.330	1.00
40_L	268_E	1.323	1.00
248_L	256_N	1.306	1.00
124_L	165_L	1.293	1.00
89_E	103_P	1.287	1.00
231_P	267_E	1.283	1.00
67_T	168_T	1.276	1.00
47_A	50_A	1.259	1.00
195_Y	230_T	1.258	1.00
229_Y	262_A	1.257	1.00
230_T	234_K	1.257	1.00
162_V	270_K	1.225	1.00
227_F	255_E	1.217	1.00
266_L	270_K	1.211	1.00
162_V	166_Y	1.206	1.00
230_T	236_V	1.195	1.00
81_Q	126_L	1.188	1.00
264_K	267_E	1.183	1.00
229_Y	259_R	1.164	1.00
104_D	107_A	1.143	1.00
142_L	161_S	1.117	1.00
203_A	221_M	1.111	1.00
144_V	157_C	1.107	1.00
103_P	108_I	1.083	1.00
211_V	257_T	1.077	1.00
65_A	144_V	1.073	1.00
70_E	141_W	1.066	1.00
256_N	259_R	1.062	1.00
123_A	197_V	1.055	1.00
115_D	119_R	1.039	0.99
200_I	211_V	1.038	0.99
159_L	269_L	1.030	0.99
37_Y	264_K	1.026	0.99
50_A	66_G	1.021	0.99
123_A	195_Y	1.019	0.99
129_L	169_K	1.014	0.99
30_D	205_V	1.010	0.99
40_L	58_L	1.006	0.99
65_A	142_L	1.004	0.99
206_D	220_I	0.995	0.99
199_T	228_S	0.986	0.99
68_K	141_W	0.979	0.99
263_V	267_E	0.978	0.99
58_L	156_A	0.975	0.99
205_V	220_I	0.973	0.99
202_V	225_I	0.971	0.99
45_D	52_G	0.963	0.99
167_N	171_Y	0.962	0.99
69_L	140_V	0.962	0.99
89_E	99_E	0.961	0.99
209_L	253_Q	0.960	0.99
209_L	254_A	0.956	0.99
249_Q	253_Q	0.954	0.99
123_A	230_T	0.953	0.99
28_R	217_E	0.951	0.99
123_A	162_V	0.949	0.99
38_R	212_D	0.945	0.99
56_V	156_A	0.929	0.99
140_V	169_K	0.926	0.99
167_N	170_V	0.921	0.99
268_E	272_H	0.918	0.99
252_D	259_R	0.914	0.99
205_V	210_V	0.914	0.99
63_V	157_C	0.908	0.99
169_K	193_L	0.904	0.98
204_K	209_L	0.900	0.98
89_E	101_G	0.895	0.98
47_A	54_A	0.895	0.98
202_V	209_L	0.887	0.98
162_V	193_L	0.880	0.98
267_E	270_K	0.871	0.98
58_L	155_D	0.870	0.98
44_L	272_H	0.870	0.98
202_V	258_A	0.869	0.98
43_T	55_L	0.856	0.98
58_L	200_I	0.855	0.98
52_G	168_T	0.848	0.98
78_T	81_Q	0.845	0.98
166_Y	170_V	0.844	0.98
144_V	161_S	0.837	0.97
142_L	165_L	0.837	0.97
163_A	269_L	0.836	0.97
209_L	250_D	0.829	0.97
60_T	150_G	0.822	0.97
123_A	194_N	0.819	0.97
208_Y	253_Q	0.816	0.97
228_S	237_G	0.815	0.97
43_T	46_Y	0.815	0.97
155_D	199_T	0.808	0.97
36_D	39_P	0.805	0.97
69_L	168_T	0.804	0.97
202_V	227_F	0.798	0.97
253_Q	256_N	0.796	0.97
99_E	103_P	0.793	0.96
207_K	222_D	0.792	0.96
70_E	136_S	0.789	0.96
126_L	135_K	0.787	0.96
90_L	149_Y	0.786	0.96
41_S	55_L	0.782	0.96
218_E	224_K	0.778	0.96
84_L	124_L	0.775	0.96
27_I	33_K	0.769	0.96
124_L	140_V	0.767	0.96
86_V	161_S	0.764	0.96
261_T	264_K	0.762	0.96
198_V	265_L	0.761	0.96
214_D	220_I	0.761	0.96
253_Q	257_T	0.759	0.96
63_V	160_A	0.758	0.95
114_V	144_V	0.757	0.95
75_Y	81_Q	0.755	0.95
75_Y	78_T	0.755	0.95
196_P	231_P	0.753	0.95
89_E	143_D	0.748	0.95
223_A	242_G	0.737	0.95
80_N	135_K	0.733	0.95
242_G	245_S	0.730	0.94
140_V	165_L	0.729	0.94
42_I	159_L	0.727	0.94
251_I	255_E	0.727	0.94
144_V	160_A	0.727	0.94
129_L	171_Y	0.726	0.94
155_D	158_T	0.720	0.94
66_G	145_Y	0.717	0.94
26_G	208_Y	0.715	0.94
56_V	159_L	0.711	0.94
162_V	273_L	0.710	0.94
69_L	170_V	0.709	0.94
136_S	171_Y	0.708	0.94
60_T	148_D	0.707	0.93
65_A	86_V	0.704	0.93
30_D	210_V	0.702	0.93
250_D	253_Q	0.702	0.93
94_A	153_V	0.700	0.93
216_D	220_I	0.700	0.93
210_V	214_D	0.697	0.93
235_I	255_E	0.694	0.93
65_A	161_S	0.693	0.93
100_P	103_P	0.692	0.93
206_D	243_K	0.691	0.93
112_R	119_R	0.689	0.93
82_G	112_R	0.677	0.92
67_T	140_V	0.669	0.91
249_Q	259_R	0.669	0.91
54_A	163_A	0.657	0.91
67_T	160_A	0.657	0.91
119_R	122_K	0.655	0.91
166_Y	169_K	0.654	0.91
87_N	143_D	0.653	0.90
37_Y	200_I	0.653	0.90
260_S	263_V	0.652	0.90
84_L	142_L	0.648	0.90
26_G	34_L	0.647	0.90
112_R	115_D	0.647	0.90
125_D	128_K	0.646	0.90
158_T	199_T	0.642	0.90
82_G	126_L	0.641	0.90
166_Y	270_K	0.639	0.90
166_Y	196_P	0.637	0.89
200_I	261_T	0.636	0.89
63_V	156_A	0.635	0.89
88_V	218_E	0.634	0.89
79_P	124_L	0.632	0.89
249_Q	252_D	0.632	0.89
193_L	196_P	0.632	0.89
88_V	153_V	0.631	0.89
69_L	136_S	0.630	0.89
74_P	82_G	0.628	0.89
99_E	104_D	0.628	0.89
225_I	240_K	0.627	0.89
109_E	116_R	0.623	0.88
52_G	167_N	0.616	0.88
231_P	266_L	0.615	0.88
117_S	228_S	0.613	0.88
98_F	101_G	0.613	0.88
61_T	151_G	0.612	0.87
95_Y	149_Y	0.610	0.87
149_Y	215_L	0.609	0.87
98_F	149_Y	0.609	0.87
44_L	171_Y	0.608	0.87
89_E	94_A	0.607	0.87
194_N	230_T	0.607	0.87
28_R	31_G	0.607	0.87
166_Y	273_L	0.603	0.87
113_V	239_Q	0.602	0.87
244_G	247_S	0.601	0.86
32_R	217_E	0.601	0.86
201_S	226_S	0.600	0.86
258_A	261_T	0.597	0.86
113_V	154_L	0.596	0.86
144_V	153_V	0.596	0.86
44_L	163_A	0.595	0.86
248_L	255_E	0.595	0.86
110_L	153_V	0.593	0.86
114_V	158_T	0.591	0.86
77_D	232_D	0.590	0.85
29_Q	210_V	0.590	0.85
206_D	222_D	0.588	0.85
253_Q	267_E	0.588	0.85
84_L	161_S	0.587	0.85
46_Y	62_M	0.584	0.85
41_S	268_E	0.584	0.85
153_V	218_E	0.583	0.85
233_L	263_V	0.582	0.85
154_L	224_K	0.582	0.85
49_K	96_E	0.580	0.85
76_E	79_P	0.578	0.84
63_V	144_V	0.577	0.84
200_I	262_A	0.575	0.84
224_K	241_S	0.570	0.83
222_D	243_K	0.569	0.83
122_K	236_V	0.566	0.83
155_D	201_S	0.565	0.83
229_Y	235_I	0.564	0.83
149_Y	152_N	0.564	0.83
157_C	161_S	0.562	0.83
110_L	154_L	0.561	0.83
68_K	143_D	0.560	0.82
76_E	81_Q	0.555	0.82
65_A	162_V	0.555	0.82
205_V	222_D	0.554	0.82
230_T	266_L	0.554	0.82
86_V	157_C	0.554	0.82
255_E	259_R	0.553	0.82
112_R	116_R	0.547	0.81
46_Y	66_G	0.547	0.81
117_S	122_K	0.545	0.81
66_G	142_L	0.543	0.80
50_A	53_S	0.540	0.80
256_N	263_V	0.539	0.80
72_D	81_Q	0.539	0.80
70_E	74_P	0.539	0.80
28_R	32_R	0.537	0.80
240_K	243_K	0.537	0.80
146_V	157_C	0.536	0.80
37_Y	40_L	0.535	0.79
37_Y	58_L	0.535	0.79
58_L	159_L	0.535	0.79
160_A	206_D	0.533	0.79
154_L	218_E	0.533	0.79
235_I	238_I	0.532	0.79
257_T	261_T	0.528	0.79
61_T	156_A	0.528	0.79
128_K	171_Y	0.527	0.78
238_I	259_R	0.524	0.78
212_D	217_E	0.522	0.78
154_L	226_S	0.521	0.78
34_L	210_V	0.521	0.78
45_D	171_Y	0.520	0.78
36_D	264_K	0.519	0.77
215_L	219_S	0.519	0.77
83_N	86_V	0.519	0.77
88_V	157_C	0.519	0.77
195_Y	270_K	0.517	0.77
112_R	228_S	0.516	0.77
28_R	38_R	0.514	0.77
72_D	139_T	0.512	0.76
85_I	141_W	0.511	0.76
153_V	224_K	0.510	0.76
149_Y	154_L	0.507	0.76
225_I	235_I	0.507	0.76
209_L	216_D	0.506	0.76
46_Y	55_L	0.505	0.76
83_N	119_R	0.505	0.76
199_T	226_S	0.503	0.75
49_K	60_T	0.503	0.75
99_E	141_W	0.502	0.75
81_Q	128_K	0.502	0.75
79_P	82_G	0.501	0.75
106_N	154_L	0.500	0.75

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
2po1B	1	0.96	100	0.126	Contact Map
2je6A	3	0.9891	100	0.126	Contact Map
2wnrA	1	0.9491	100	0.14	Contact Map
4ifdA	1	0.9709	100	0.161	Contact Map
2nn6C	1	0.96	100	0.164	Contact Map
2nn6E	1	0.9564	100	0.165	Contact Map
3m7nG	1	0.9236	100	0.167	Contact Map
2nn6A	1	0.9673	100	0.193	Contact Map
4ifdC	1	0.9491	100	0.232	Contact Map
4ifdE	1	0.9127	100	0.258	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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