RADA - SULSO - GREMLIN Contacts

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RADA - DNA repair and recombination protein RadA

UniProt:	Q55075	Sequences: MSNEVEQKKNIKTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARPDMFYGDPTVAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (249)
Sequences:	2560 (1065)
Seq/√Len:	67.5

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
104_I	127_L	5.567	1.00
168_D	171_N	5.558	1.00
285_I	297_A	4.937	1.00
127_L	206_L	4.397	1.00
259_A	275_H	4.372	1.00
110_T	250_A	3.991	1.00
104_I	250_A	3.962	1.00
124_C	254_T	3.711	1.00
91_T	104_I	3.558	1.00
100_L	283_I	3.336	1.00
285_I	299_V	3.172	1.00
195_Q	243_L	3.056	1.00
127_L	252_I	2.865	1.00
89_I	250_A	2.860	1.00
128_S	144_A	2.815	1.00
131_V	144_A	2.643	1.00
297_A	312_F	2.641	1.00
131_V	206_L	2.622	1.00
287_L	297_A	2.523	1.00
294_R	311_V	2.465	1.00
244_A	251_V	2.438	1.00
144_A	206_L	2.404	1.00
128_S	208_V	2.388	1.00
142_G	205_K	2.319	1.00
70_D	75_T	2.279	1.00
183_N	187_Q	2.161	1.00
112_F	252_I	2.134	1.00
147_I	194_L	2.121	1.00
150_E	256_Q	2.094	1.00
91_T	127_L	2.060	1.00
290_S	296_I	2.030	1.00
90_S	140_L	1.995	1.00
237_L	277_L	1.969	1.00
184_T	220_Y	1.963	1.00
315_T	320_R	1.952	1.00
164_A	317_E	1.952	1.00
273_G	277_L	1.925	1.00
244_A	250_A	1.905	1.00
121_T	125_H	1.773	1.00
112_F	123_L	1.735	1.00
60_K	63_K	1.724	1.00
317_E	320_R	1.680	0.99
128_S	146_Y	1.652	0.99
104_I	110_T	1.648	0.99
145_V	204_I	1.628	0.99
217_R	221_P	1.596	0.99
123_L	287_L	1.591	0.99
93_S	321_D	1.563	0.99
294_R	313_A	1.555	0.99
261_P	270_V	1.530	0.99
89_I	131_V	1.525	0.99
296_I	309_E	1.524	0.99
144_A	208_V	1.481	0.99
111_E	284_R	1.467	0.99
113_F	300_V	1.427	0.98
63_K	67_D	1.427	0.98
206_L	250_A	1.406	0.98
62_I	66_R	1.402	0.98
112_F	285_I	1.357	0.98
145_V	197_L	1.329	0.97
61_I	65_A	1.303	0.97
291_R	294_R	1.283	0.97
194_L	198_V	1.282	0.97
187_Q	236_H	1.263	0.96
122_Q	146_Y	1.260	0.96
99_L	308_G	1.239	0.96
56_S	59_Q	1.238	0.96
194_L	207_I	1.230	0.96
131_V	250_A	1.221	0.95
129_V	161_M	1.217	0.95
194_L	251_V	1.191	0.95
198_V	244_A	1.190	0.95
243_L	249_I	1.189	0.95
255_N	274_G	1.180	0.94
64_E	67_D	1.168	0.94
274_G	284_R	1.167	0.94
225_N	235_K	1.157	0.94
118_S	312_F	1.148	0.94
60_K	64_E	1.145	0.93
68_A	72_R	1.137	0.93
262_D	268_P	1.123	0.93
104_I	252_I	1.113	0.92
207_I	249_I	1.095	0.92
95_A	98_G	1.091	0.92
290_S	294_R	1.078	0.91
313_A	320_R	1.062	0.91
57_T	60_K	1.060	0.91
183_N	186_H	1.055	0.90
229_R	272_V	1.042	0.90
272_V	275_H	1.032	0.89
95_A	321_D	1.021	0.89
267_D	286_Q	1.021	0.89
87_K	248_D	1.007	0.88
265_Y	268_P	1.006	0.88
264_F	270_V	1.003	0.88
121_T	144_A	1.000	0.88
146_Y	179_I	0.993	0.87
296_I	311_V	0.989	0.87
213_T	272_V	0.988	0.87
150_E	219_E	0.987	0.87
95_A	310_V	0.980	0.87
286_Q	290_S	0.977	0.87
206_L	252_I	0.975	0.86
143_K	204_I	0.968	0.86
263_M	268_P	0.968	0.86
224_E	235_K	0.966	0.86
217_R	229_R	0.956	0.85
124_C	146_Y	0.952	0.85
218_A	225_N	0.946	0.85
106_T	131_V	0.942	0.85
212_V	277_L	0.940	0.84
241_T	282_G	0.938	0.84
111_E	255_N	0.933	0.84
243_L	247_Y	0.928	0.84
202_P	316_E	0.927	0.84
245_E	248_D	0.925	0.83
257_V	286_Q	0.922	0.83
151_G	180_R	0.921	0.83
77_L	81_K	0.921	0.83
241_T	245_E	0.914	0.83
287_L	295_R	0.913	0.83
289_K	298_R	0.910	0.82
91_T	97_D	0.909	0.82
150_E	213_T	0.909	0.82
287_L	312_F	0.906	0.82
277_L	295_R	0.903	0.82
226_L	229_R	0.898	0.82
87_K	106_T	0.897	0.81
148_D	154_R	0.893	0.81
58_A	62_I	0.893	0.81
212_V	236_H	0.892	0.81
212_V	253_I	0.891	0.81
132_Q	144_A	0.889	0.81
111_E	274_G	0.885	0.81
187_Q	215_H	0.881	0.80
181_A	190_I	0.881	0.80
264_F	268_P	0.877	0.80
61_I	64_E	0.874	0.80
115_E	286_Q	0.871	0.80
119_G	210_D	0.870	0.79
92_G	97_D	0.865	0.79
123_L	251_V	0.861	0.79
199_S	247_Y	0.859	0.79
126_Q	319_I	0.858	0.79
104_I	312_F	0.854	0.78
106_T	140_L	0.854	0.78
263_M	267_D	0.849	0.78
283_I	302_A	0.847	0.78
145_V	173_M	0.846	0.78
120_K	210_D	0.838	0.77
150_E	217_R	0.836	0.77
161_M	165_L	0.831	0.76
216_F	242_R	0.830	0.76
234_N	280_V	0.829	0.76
115_E	288_K	0.821	0.75
148_D	152_T	0.821	0.75
107_R	248_D	0.819	0.75
191_V	236_H	0.818	0.75
81_K	169_I	0.812	0.75
263_M	266_G	0.809	0.74
110_T	254_T	0.809	0.74
240_L	251_V	0.801	0.74
116_F	271_A	0.800	0.74
59_Q	63_K	0.798	0.73
215_H	236_H	0.796	0.73
75_T	78_E	0.792	0.73
261_P	275_H	0.786	0.72
184_T	187_Q	0.779	0.72
292_G	295_R	0.778	0.71
139_G	142_G	0.775	0.71
125_H	153_F	0.773	0.71
109_M	241_T	0.771	0.71
225_N	228_V	0.769	0.71
193_D	252_I	0.763	0.70
217_R	254_T	0.760	0.70
123_L	252_I	0.759	0.70
187_Q	192_D	0.757	0.69
93_S	319_I	0.755	0.69
148_D	153_F	0.753	0.69
80_K	171_N	0.751	0.69
209_V	236_H	0.747	0.68
273_G	276_T	0.744	0.68
146_Y	153_F	0.741	0.68
55_L	59_Q	0.740	0.68
126_Q	161_M	0.738	0.67
94_Q	98_G	0.736	0.67
206_L	244_A	0.733	0.67
286_Q	296_I	0.733	0.67
195_Q	294_R	0.730	0.67
218_A	228_V	0.726	0.66
208_V	263_M	0.725	0.66
289_K	292_G	0.724	0.66
249_I	306_P	0.723	0.66
302_A	305_L	0.722	0.66
94_Q	321_D	0.717	0.65
131_V	139_G	0.713	0.65
253_I	277_L	0.713	0.65
279_H	301_D	0.711	0.64
261_P	291_R	0.709	0.64
60_K	312_F	0.705	0.64
184_T	217_R	0.704	0.64
106_T	205_K	0.704	0.64
237_L	273_G	0.703	0.64
93_S	123_L	0.698	0.63
68_A	146_Y	0.698	0.63
186_H	190_I	0.696	0.63
145_V	194_L	0.695	0.63
161_M	316_E	0.694	0.63
194_L	209_V	0.694	0.63
124_C	252_I	0.692	0.62
220_Y	233_L	0.692	0.62
89_I	104_I	0.692	0.62
130_N	165_L	0.692	0.62
240_L	244_A	0.689	0.62
125_H	129_V	0.686	0.62
122_Q	271_A	0.685	0.62
117_G	147_I	0.684	0.61
126_Q	130_N	0.679	0.61
288_K	296_I	0.678	0.61
294_R	312_F	0.671	0.60
183_N	242_R	0.671	0.60
216_F	232_K	0.670	0.60
148_D	301_D	0.669	0.60
100_L	285_I	0.669	0.60
59_Q	143_K	0.665	0.59
217_R	256_Q	0.663	0.59
260_R	270_V	0.662	0.59
208_V	266_G	0.659	0.59
252_I	314_L	0.658	0.59
197_L	200_K	0.658	0.59
214_S	256_Q	0.655	0.58
210_D	255_N	0.655	0.58
257_V	275_H	0.654	0.58
104_I	243_L	0.654	0.58
65_A	73_F	0.652	0.58
216_F	226_L	0.651	0.58
100_L	299_V	0.648	0.57
59_Q	250_A	0.646	0.57
257_V	270_V	0.646	0.57
112_F	124_C	0.644	0.57
153_F	225_N	0.642	0.57
146_Y	190_I	0.640	0.56
116_F	301_D	0.639	0.56
59_Q	67_D	0.638	0.56
108_T	283_I	0.638	0.56
81_K	84_M	0.623	0.54
84_M	316_E	0.623	0.54
213_T	230_Q	0.621	0.54
95_A	317_E	0.621	0.54
163_K	169_I	0.620	0.54
113_F	272_V	0.620	0.54
256_Q	303_P	0.619	0.54
96_L	285_I	0.618	0.54
84_M	315_T	0.615	0.53
106_T	250_A	0.614	0.53
230_Q	276_T	0.613	0.53
108_T	304_H	0.612	0.53
312_F	320_R	0.612	0.53
220_Y	229_R	0.611	0.53
184_T	221_P	0.611	0.53
87_K	194_L	0.610	0.53
90_S	93_S	0.609	0.53
289_K	296_I	0.608	0.53
219_E	256_Q	0.607	0.53
295_R	312_F	0.604	0.52
59_Q	64_E	0.603	0.52
64_E	248_D	0.603	0.52
106_T	139_G	0.602	0.52
69_L	77_L	0.602	0.52
213_T	277_L	0.601	0.52
80_K	85_N	0.601	0.52
64_E	84_M	0.601	0.52
114_G	119_G	0.600	0.52
224_E	240_L	0.599	0.52
209_V	320_R	0.599	0.52
234_N	307_E	0.598	0.51
63_K	94_Q	0.597	0.51
58_A	61_I	0.597	0.51
163_K	316_E	0.595	0.51
99_L	299_V	0.592	0.51
268_P	286_Q	0.590	0.51
117_G	287_L	0.589	0.50
114_G	120_K	0.587	0.50
232_K	237_L	0.584	0.50
150_E	212_V	0.584	0.50
264_F	267_D	0.583	0.50
118_S	163_K	0.581	0.49
65_A	70_D	0.581	0.49
71_I	251_V	0.581	0.49
162_A	172_V	0.579	0.49
125_H	179_I	0.579	0.49
62_I	65_A	0.579	0.49
62_I	203_S	0.575	0.49
150_E	303_P	0.575	0.49
224_E	257_V	0.574	0.49
103_G	211_S	0.573	0.48
116_F	273_G	0.571	0.48
89_I	130_N	0.571	0.48
187_Q	212_V	0.570	0.48
99_L	181_A	0.570	0.48
61_I	75_T	0.569	0.48
96_L	100_L	0.569	0.48
88_K	104_I	0.569	0.48
98_G	104_I	0.568	0.48
55_L	61_I	0.567	0.48
258_M	272_V	0.567	0.48
105_E	283_I	0.565	0.48
212_V	220_Y	0.565	0.48
299_V	317_E	0.562	0.47
57_T	83_R	0.561	0.47
226_L	261_P	0.558	0.47
93_S	121_T	0.554	0.46
91_T	252_I	0.553	0.46
65_A	68_A	0.553	0.46
108_T	282_G	0.552	0.46
258_M	276_T	0.552	0.46
102_G	150_E	0.550	0.46
65_A	199_S	0.549	0.46
79_V	82_E	0.548	0.46
194_L	240_L	0.547	0.45
258_M	270_V	0.547	0.45
55_L	69_L	0.546	0.45
128_S	206_L	0.545	0.45
279_H	282_G	0.541	0.45
63_K	171_N	0.541	0.45
69_L	85_N	0.540	0.45
257_V	291_R	0.538	0.44
77_L	85_N	0.537	0.44
164_A	316_E	0.537	0.44
107_R	114_G	0.535	0.44
211_S	256_Q	0.534	0.44
163_K	209_V	0.534	0.44
145_V	199_S	0.533	0.44
163_K	315_T	0.532	0.44
122_Q	295_R	0.531	0.44
186_H	212_V	0.531	0.44
274_G	302_A	0.531	0.44
144_A	250_A	0.529	0.43
124_C	128_S	0.529	0.43
84_M	88_K	0.528	0.43
93_S	312_F	0.527	0.43
229_R	233_L	0.525	0.43
226_L	230_Q	0.524	0.43
149_T	209_V	0.523	0.43
149_T	272_V	0.523	0.43
122_Q	303_P	0.521	0.42
228_V	260_R	0.520	0.42
77_L	321_D	0.519	0.42
117_G	259_A	0.519	0.42
59_Q	290_S	0.518	0.42
92_G	214_S	0.517	0.42
226_L	259_A	0.514	0.42
72_R	84_M	0.513	0.41
216_F	229_R	0.512	0.41
91_T	100_L	0.512	0.41
127_L	140_L	0.511	0.41
246_V	260_R	0.511	0.41
202_P	247_Y	0.511	0.41
277_L	281_P	0.508	0.41
125_H	165_L	0.508	0.41
99_L	305_L	0.508	0.41
144_A	207_I	0.507	0.41
59_Q	66_R	0.506	0.41
216_F	275_H	0.505	0.40
181_A	186_H	0.504	0.40
197_L	204_I	0.504	0.40
292_G	309_E	0.504	0.40
251_V	259_A	0.504	0.40
118_S	289_K	0.504	0.40
230_Q	234_N	0.502	0.40
117_G	145_V	0.501	0.40
298_R	309_E	0.501	0.40
153_F	179_I	0.500	0.40
63_K	208_V	0.500	0.40

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	0.8951	100	0.324	Contact Map
2i1qA	1	0.929	100	0.357	Contact Map
1v5wA	5	0.7346	100	0.362	Contact Map
3ldaA	1	0.9043	100	0.386	Contact Map
1pznA	5	0.9105	100	0.386	Contact Map
1n0wA	1	0.6481	100	0.526	Contact Map
4hyyA	4	0.7407	100	0.55	Contact Map
4b3bA	1	0.679	100	0.583	Contact Map
2cvhA	1	0.6728	100	0.592	Contact Map
3cmuA	1	0.6821	100	0.613	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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