RADA - HALSA - GREMLIN Contacts

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RADA - DNA repair and recombination protein RadA

UniProt:	Q9HMM4	Sequences: MPESDLEELPGVGPATAEKLRDNGFDAFQSLAVANSAELSNTADIGESTAADVIQAAREAADVGGFETGATVLERREQIGKLTWNIPEVDDLLGGGVETQSITEVYGEFGAGKSQVTHQLAVNVQLPTEYGGLHGRAVFIDSEDTFRPERIDDMVRGLSDETLQAAMEAHEIEGSTDDEDTLTELVDAFLDKIHVAKGFNSNHQMLLAEKAKEIASEHEDGDWPVRMLTVDSLTAHFRAEYVGRGELADRQQKLNKHLHDLEKVGNLYNAAVLVTNQVQSNPDAFFGDPTKPIGGNILGHKSTFRMYLRKSKNDKRIVKLVDAPNLADGEAVMRVQDEGLKPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	343 (300)
Sequences:	1236 (782)
Seq/√Len:	45.2

HALSA - RADA RADB
SULSO - RADA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
151_I	193_I	6.133	1.00
124_V	137_A	4.567	1.00
120_L	273_L	4.225	1.00
121_A	137_A	4.003	1.00
105_V	273_L	3.835	1.00
127_P	132_G	3.776	1.00
306_M	318_V	3.672	1.00
117_T	275_T	3.639	1.00
308_L	318_V	3.434	1.00
258_L	298_L	3.408	1.00
143_E	277_Q	3.084	1.00
45_I	50_A	3.082	1.00
97_V	271_A	2.923	1.00
120_L	227_M	2.887	1.00
103_T	271_A	2.875	1.00
82_L	271_A	2.810	1.00
137_A	229_T	2.791	1.00
84_W	97_V	2.768	1.00
105_V	306_M	2.686	1.00
204_Q	257_H	2.535	1.00
294_G	298_L	2.491	1.00
97_V	103_T	2.488	1.00
276_N	295_G	2.468	1.00
135_G	226_R	2.455	1.00
114_S	118_H	2.413	1.00
264_V	270_A	2.398	1.00
115_Q	150_R	2.223	1.00
117_T	273_L	2.213	1.00
106_Y	321_V	2.203	1.00
128_T	134_H	2.197	1.00
336_Q	341_K	2.096	1.00
115_Q	139_F	2.030	0.99
238_R	250_R	2.003	0.99
338_E	341_K	1.991	0.99
265_G	271_A	1.975	0.99
105_V	116_V	1.973	0.99
136_R	192_K	1.944	0.99
228_L	270_A	1.933	0.99
143_E	238_R	1.893	0.99
97_V	273_L	1.870	0.99
125_Q	192_K	1.860	0.99
153_D	337_D	1.814	0.99
14_P	18_E	1.802	0.99
25_F	30_S	1.783	0.98
121_A	229_T	1.762	0.98
261_L	272_V	1.759	0.98
247_L	250_R	1.752	0.98
138_V	225_V	1.751	0.98
315_K	332_V	1.748	0.98
126_L	132_G	1.735	0.98
204_Q	236_H	1.722	0.98
234_T	293_I	1.712	0.98
104_E	305_R	1.687	0.98
127_P	131_G	1.681	0.98
141_D	146_F	1.658	0.97
138_V	211_A	1.616	0.97
122_V	154_M	1.612	0.97
68_T	71_T	1.609	0.97
141_D	147_R	1.605	0.97
144_D	197_K	1.568	0.96
211_A	228_L	1.495	0.95
88_E	91_D	1.495	0.95
84_W	90_D	1.484	0.95
97_V	120_L	1.471	0.95
233_L	298_L	1.452	0.94
304_F	323_A	1.434	0.94
99_T	271_A	1.409	0.94
200_N	263_K	1.392	0.93
216_S	268_Y	1.379	0.93
119_Q	154_M	1.366	0.92
306_M	320_L	1.365	0.92
308_L	333_M	1.363	0.92
227_M	271_A	1.333	0.91
238_R	277_Q	1.331	0.91
274_V	298_L	1.331	0.91
318_V	333_M	1.327	0.91
111_A	333_M	1.325	0.91
116_V	306_M	1.310	0.91
18_E	21_R	1.310	0.91
127_P	130_Y	1.305	0.91
12_V	18_E	1.298	0.90
298_L	316_R	1.284	0.90
92_L	329_G	1.283	0.90
13_G	16_T	1.269	0.89
114_S	137_A	1.268	0.89
31_L	56_A	1.255	0.89
140_I	229_T	1.230	0.88
39_L	44_D	1.228	0.88
37_A	47_E	1.225	0.88
143_E	234_T	1.224	0.87
86_I	340_L	1.207	0.87
277_Q	324_P	1.206	0.87
121_A	139_F	1.200	0.86
45_I	53_V	1.193	0.86
143_E	240_E	1.184	0.86
118_H	151_I	1.174	0.85
101_S	304_F	1.164	0.85
19_K	24_G	1.162	0.85
255_N	301_K	1.156	0.84
139_F	278_V	1.153	0.84
136_R	194_H	1.151	0.84
200_N	203_H	1.143	0.84
138_V	196_A	1.139	0.83
127_P	133_L	1.138	0.83
54_I	57_A	1.132	0.83
143_E	324_P	1.120	0.82
124_V	227_M	1.113	0.82
198_G	207_L	1.110	0.82
237_F	247_L	1.109	0.82
46_G	49_T	1.097	0.81
214_I	218_H	1.089	0.81
136_R	230_V	1.088	0.80
77_E	337_D	1.081	0.80
310_K	319_K	1.080	0.80
115_Q	232_S	1.079	0.80
150_R	193_I	1.076	0.80
100_Q	269_N	1.073	0.80
54_I	58_R	1.068	0.79
67_E	75_R	1.060	0.79
193_I	228_L	1.058	0.79
101_S	325_N	1.042	0.77
116_V	208_A	1.033	0.77
31_L	54_I	1.029	0.77
240_E	277_Q	1.028	0.77
12_V	19_K	1.025	0.76
241_Y	254_L	1.020	0.76
285_F	335_V	1.020	0.76
74_E	77_E	1.016	0.76
262_E	303_T	1.014	0.76
125_Q	137_A	1.005	0.75
230_V	338_E	0.999	0.74
47_E	51_A	0.998	0.74
108_E	322_D	0.996	0.74
126_L	130_Y	0.996	0.74
84_W	93_L	0.993	0.74
70_A	320_L	0.988	0.74
210_K	273_L	0.987	0.74
17_A	21_R	0.986	0.73
15_A	19_K	0.981	0.73
29_Q	216_S	0.973	0.72
119_Q	340_L	0.970	0.72
47_E	53_V	0.964	0.72
35_N	38_E	0.963	0.72
149_E	154_M	0.961	0.72
124_V	132_G	0.958	0.71
234_T	298_L	0.954	0.71
233_L	274_V	0.951	0.71
141_D	145_T	0.950	0.71
25_F	31_L	0.945	0.70
156_R	337_D	0.940	0.70
237_F	253_K	0.924	0.68
294_G	297_I	0.923	0.68
90_D	93_L	0.919	0.68
233_L	257_H	0.918	0.68
257_H	262_E	0.917	0.68
123_N	158_L	0.916	0.68
37_A	335_V	0.905	0.67
117_T	229_T	0.903	0.67
141_D	197_K	0.901	0.67
309_R	331_A	0.901	0.67
84_W	273_L	0.892	0.66
89_V	327_A	0.889	0.65
103_T	124_V	0.887	0.65
95_G	143_E	0.887	0.65
232_S	275_T	0.887	0.65
16_T	24_G	0.877	0.64
148_P	195_V	0.876	0.64
109_F	292_P	0.874	0.64
249_D	281_N	0.874	0.64
247_L	251_Q	0.873	0.64
288_D	307_Y	0.869	0.64
115_Q	316_R	0.868	0.64
111_A	310_K	0.858	0.63
141_D	322_D	0.851	0.62
295_G	305_R	0.849	0.62
102_I	218_H	0.847	0.62
154_M	158_L	0.844	0.61
203_H	207_L	0.836	0.61
131_G	135_G	0.836	0.61
300_H	322_D	0.834	0.60
90_D	231_D	0.831	0.60
201_S	241_Y	0.828	0.60
143_E	278_V	0.828	0.60
39_L	272_V	0.826	0.60
281_N	291_K	0.823	0.59
33_V	36_S	0.821	0.59
136_R	224_P	0.821	0.59
98_E	304_F	0.814	0.59
230_V	257_H	0.811	0.58
102_I	198_G	0.810	0.58
250_R	254_L	0.809	0.58
136_R	218_H	0.806	0.58
265_G	272_V	0.806	0.58
18_E	22_D	0.805	0.58
68_T	229_T	0.802	0.57
91_D	229_T	0.801	0.57
143_E	232_S	0.801	0.57
227_M	273_L	0.801	0.57
124_V	133_L	0.800	0.57
71_T	74_E	0.799	0.57
150_R	316_R	0.798	0.57
119_Q	254_L	0.795	0.57
86_I	114_S	0.792	0.57
15_A	30_S	0.788	0.56
251_Q	297_I	0.783	0.56
215_A	325_N	0.783	0.56
129_E	134_H	0.783	0.56
56_A	59_E	0.782	0.56
23_N	31_L	0.775	0.55
235_A	278_V	0.775	0.55
335_V	339_G	0.774	0.55
279_Q	293_I	0.768	0.54
298_L	302_S	0.767	0.54
332_V	340_L	0.764	0.54
101_S	303_T	0.763	0.54
53_V	61_A	0.757	0.53
210_K	213_E	0.757	0.53
85_N	123_N	0.756	0.53
201_S	205_M	0.755	0.53
51_A	54_I	0.753	0.53
315_K	334_R	0.750	0.52
43_A	51_A	0.749	0.52
25_F	54_I	0.745	0.52
93_L	306_M	0.744	0.52
215_A	225_V	0.743	0.52
117_T	264_V	0.740	0.51
276_N	323_A	0.739	0.51
38_E	116_V	0.739	0.51
102_I	336_Q	0.735	0.51
81_K	97_V	0.734	0.51
13_G	17_A	0.732	0.51
13_G	21_R	0.730	0.51
215_A	268_Y	0.728	0.50
104_E	276_N	0.727	0.50
115_Q	193_I	0.726	0.50
139_F	318_V	0.726	0.50
255_N	292_P	0.725	0.50
241_Y	250_R	0.724	0.50
41_N	49_T	0.724	0.50
127_P	134_H	0.724	0.50
274_V	320_L	0.723	0.50
97_V	264_V	0.723	0.50
106_Y	299_G	0.723	0.50
50_A	54_I	0.722	0.50
141_D	296_N	0.719	0.49
127_P	146_F	0.719	0.49
107_G	113_K	0.718	0.49
296_N	300_H	0.713	0.49
155_V	189_F	0.713	0.49
214_I	229_T	0.713	0.49
250_R	300_H	0.710	0.49
138_V	194_H	0.710	0.49
12_V	21_R	0.709	0.48
187_D	191_D	0.708	0.48
36_S	42_T	0.708	0.48
92_L	292_P	0.707	0.48
232_S	277_Q	0.706	0.48
51_A	59_E	0.705	0.48
25_F	53_V	0.704	0.48
37_A	48_S	0.703	0.48
25_F	42_T	0.700	0.48
88_E	130_Y	0.699	0.47
85_N	90_D	0.698	0.47
25_F	50_A	0.690	0.47
200_N	239_A	0.690	0.47
143_E	233_L	0.689	0.47
236_H	257_H	0.688	0.46
258_L	302_S	0.686	0.46
215_A	226_R	0.684	0.46
99_T	200_N	0.681	0.46
76_R	79_I	0.679	0.46
47_E	61_A	0.679	0.46
299_G	302_S	0.678	0.45
250_R	277_Q	0.676	0.45
25_F	129_E	0.671	0.45
53_V	56_A	0.669	0.45
190_L	297_I	0.669	0.45
29_Q	121_A	0.668	0.44
320_L	327_A	0.667	0.44
192_K	333_M	0.666	0.44
46_G	246_E	0.666	0.44
251_Q	300_H	0.665	0.44
92_L	326_L	0.664	0.44
258_L	294_G	0.663	0.44
141_D	148_P	0.662	0.44
49_T	53_V	0.661	0.44
49_T	52_D	0.660	0.44
16_T	49_T	0.659	0.44
77_E	306_M	0.659	0.44
269_N	283_D	0.656	0.43
191_D	320_L	0.656	0.43
70_A	191_D	0.654	0.43
144_D	211_A	0.653	0.43
86_I	116_V	0.651	0.43
286_F	289_P	0.649	0.43
335_V	341_K	0.647	0.42
249_D	253_K	0.647	0.42
119_Q	270_A	0.646	0.42
44_D	50_A	0.643	0.42
151_I	154_M	0.642	0.42
189_F	280_S	0.641	0.42
15_A	18_E	0.641	0.42
71_T	130_Y	0.640	0.42
102_I	246_E	0.639	0.42
264_V	335_V	0.639	0.42
200_N	212_K	0.639	0.42
52_D	55_Q	0.636	0.41
127_P	135_G	0.636	0.41
17_A	22_D	0.636	0.41
88_E	338_E	0.635	0.41
284_A	315_K	0.634	0.41
32_A	35_N	0.634	0.41
76_R	99_T	0.634	0.41
43_A	48_S	0.632	0.41
105_V	153_D	0.630	0.41
307_Y	321_V	0.630	0.41
115_Q	125_Q	0.629	0.41
106_Y	203_H	0.629	0.41
16_T	19_K	0.629	0.41
309_R	317_I	0.628	0.41
38_E	41_N	0.626	0.40
116_V	308_L	0.625	0.40
115_Q	278_V	0.624	0.40
26_D	82_L	0.624	0.40
116_V	340_L	0.623	0.40
148_P	275_T	0.621	0.40
108_E	280_S	0.621	0.40
75_R	78_Q	0.620	0.40
150_R	298_L	0.620	0.40
208_A	257_H	0.619	0.40
75_R	146_F	0.618	0.40
120_L	193_I	0.617	0.40
317_I	332_V	0.617	0.40
285_F	289_P	0.616	0.40
131_G	134_H	0.616	0.40
299_G	335_V	0.615	0.39
12_V	27_A	0.615	0.39
70_A	74_E	0.614	0.39
113_K	232_S	0.614	0.39
234_T	251_Q	0.614	0.39
205_M	253_K	0.613	0.39
145_T	251_Q	0.613	0.39
155_V	200_N	0.612	0.39
50_A	212_K	0.610	0.39
195_V	262_E	0.610	0.39
48_S	51_A	0.609	0.39
122_V	296_N	0.607	0.39
244_R	251_Q	0.605	0.39
57_A	62_D	0.603	0.38
48_S	242_V	0.603	0.38
27_A	55_Q	0.601	0.38
85_N	310_K	0.599	0.38
81_K	326_L	0.596	0.38
217_E	265_G	0.596	0.38
273_L	335_V	0.596	0.38
252_Q	282_P	0.594	0.38
25_F	45_I	0.593	0.37
279_Q	291_K	0.592	0.37
39_L	59_E	0.592	0.37
251_Q	254_L	0.592	0.37
125_Q	193_I	0.592	0.37
258_L	261_L	0.591	0.37
84_W	265_G	0.590	0.37
125_Q	238_R	0.589	0.37
29_Q	33_V	0.587	0.37
233_L	242_V	0.584	0.37
38_E	91_D	0.584	0.37
327_A	340_L	0.578	0.36
72_V	87_P	0.575	0.36
58_R	62_D	0.572	0.36
14_P	226_R	0.572	0.36
114_S	130_Y	0.572	0.36
264_V	333_M	0.570	0.35
194_H	225_V	0.569	0.35
208_A	260_D	0.568	0.35
211_A	297_I	0.566	0.35
100_Q	265_G	0.565	0.35
284_A	314_D	0.565	0.35
324_P	333_M	0.564	0.35
25_F	34_A	0.564	0.35
211_A	335_V	0.563	0.35
111_A	315_K	0.563	0.35
132_G	144_D	0.563	0.35
112_G	231_D	0.562	0.35
84_W	120_L	0.562	0.35
257_H	319_K	0.561	0.35
83_T	86_I	0.560	0.34
196_A	202_N	0.560	0.34
50_A	57_A	0.559	0.34
132_G	238_R	0.559	0.34
117_T	265_G	0.559	0.34
122_V	300_H	0.559	0.34
42_T	45_I	0.556	0.34
324_P	327_A	0.556	0.34
240_E	278_V	0.550	0.34
52_D	59_E	0.549	0.34
12_V	111_A	0.548	0.33
311_S	317_I	0.548	0.33
82_L	227_M	0.548	0.33
49_T	56_A	0.547	0.33
105_V	256_K	0.545	0.33
254_L	297_I	0.545	0.33
311_S	314_D	0.544	0.33
53_V	217_E	0.543	0.33
39_L	43_A	0.542	0.33
59_E	62_D	0.537	0.32
138_V	212_K	0.537	0.32
18_E	31_L	0.536	0.32
31_L	39_L	0.535	0.32
279_Q	297_I	0.534	0.32
153_D	335_V	0.534	0.32
105_V	117_T	0.533	0.32
83_T	123_N	0.533	0.32
120_L	131_G	0.532	0.32
89_V	274_V	0.532	0.32
22_D	333_M	0.531	0.32
55_Q	59_E	0.529	0.32
129_E	205_M	0.528	0.32
111_A	234_T	0.528	0.32
262_E	266_N	0.527	0.32
46_G	268_Y	0.527	0.32
13_G	18_E	0.525	0.31
290_T	335_V	0.524	0.31
51_A	55_Q	0.524	0.31
97_V	208_A	0.521	0.31
203_H	267_L	0.521	0.31
144_D	323_A	0.520	0.31
84_W	100_Q	0.519	0.31
277_Q	299_G	0.518	0.31
70_A	73_L	0.518	0.31
32_A	50_A	0.518	0.31
237_F	250_R	0.515	0.31
258_L	316_R	0.514	0.31
18_E	35_N	0.514	0.31
84_W	141_D	0.513	0.30
141_D	280_S	0.512	0.30
145_T	296_N	0.510	0.30
265_G	307_Y	0.510	0.30
136_R	225_V	0.508	0.30
13_G	34_A	0.507	0.30
235_A	277_Q	0.506	0.30
36_S	43_A	0.505	0.30
87_P	205_M	0.504	0.30
73_L	114_S	0.503	0.30
116_V	260_D	0.502	0.30
35_N	117_T	0.502	0.30
141_D	300_H	0.502	0.30
83_T	90_D	0.502	0.30
249_D	259_H	0.501	0.29
198_G	235_A	0.500	0.29

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
2z43A	1	0.8397	100	0.363	Contact Map
2i1qA	1	0.8776	100	0.373	Contact Map
1v5wA	5	0.691	100	0.397	Contact Map
1pznA	5	0.8746	100	0.399	Contact Map
3ldaA	1	0.8426	100	0.409	Contact Map
1n0wA	1	0.6064	100	0.551	Contact Map
4hyyA	4	0.7026	100	0.564	Contact Map
4b3bA	1	0.6531	100	0.598	Contact Map
2cvhA	1	0.6327	100	0.616	Contact Map
3cmuA	1	0.6385	100	0.618	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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