RADB - HALSA - GREMLIN Contacts

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RADB - DNA repair and recombination protein RadB

UniProt:	Q9HPF2	Sequences: MREDDTHLPTGCGALDELLGGGVERGTVTQLYGPPAAGKTNVALTTAVTTAAAGGLAVYVDTEGLSLARFQQLLEARATDPEAASANVIVSDAHDFDEQAQAVRDTADFADRADLIVVDSVTGFYRLARGGDDTTGDALRQVADQITHLLSLARKHDLAVVVTNQVFTDVDNDSDRARPLGGHTLAHWTGTVLRLDRFRGGTRRATLEKHRAKPDGEHAQFQITDGGIDAASADDY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	236 (208)
Sequences:	6958 (3650)
Seq/√Len:	253.1

ECOLI - RECA
BACSU - RECA
HALSA - RADB RADA Q9HP98 Q9HNX8 GVPD2
SULSO - RADA Y1861 Q97VZ8 Q97WB6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_A	163_T	3.935	1.00
55_G	114_D	3.769	1.00
47_A	57_A	3.514	1.00
9_P	16_D	2.945	1.00
47_A	117_V	2.915	1.00
28_V	150_L	2.882	1.00
224_T	229_D	2.755	1.00
50_T	115_L	2.706	1.00
6_T	25_R	2.593	1.00
56_L	114_D	2.579	1.00
103_V	116_I	2.557	1.00
10_T	23_V	2.546	1.00
23_V	46_T	2.527	1.00
11_G	16_D	2.442	1.00
153_A	160_V	2.397	1.00
23_V	159_A	2.244	1.00
199_R	202_T	2.210	1.00
226_G	229_D	2.193	1.00
43_A	117_V	2.169	1.00
202_T	220_Q	2.095	1.00
29_T	159_A	2.067	1.00
49_T	52_A	2.055	1.00
116_I	160_V	2.028	1.00
102_A	106_T	2.006	1.00
95_D	127_L	2.002	1.00
58_V	113_A	1.986	1.00
12_C	230_A	1.884	1.00
71_Q	75_E	1.848	1.00
168_T	183_H	1.794	1.00
18_L	219_A	1.785	1.00
56_L	87_N	1.745	1.00
49_T	53_A	1.730	1.00
25_R	114_D	1.713	1.00
152_L	158_L	1.684	1.00
23_V	161_V	1.676	1.00
10_T	16_D	1.671	1.00
69_R	73_L	1.654	1.00
44_L	74_L	1.627	1.00
222_Q	229_D	1.587	1.00
193_L	205_A	1.557	1.00
102_A	105_D	1.557	1.00
187_H	190_G	1.547	1.00
152_L	156_H	1.533	1.00
115_L	159_A	1.510	1.00
50_T	55_G	1.503	1.00
55_G	115_L	1.500	1.00
29_T	191_T	1.469	1.00
50_T	57_A	1.450	1.00
189_T	192_V	1.437	1.00
48_V	79_T	1.425	1.00
9_P	53_A	1.417	1.00
46_T	115_L	1.404	1.00
80_D	87_N	1.400	1.00
43_A	161_V	1.390	1.00
30_Q	192_V	1.388	1.00
194_R	208_E	1.372	1.00
210_H	213_K	1.362	1.00
15_L	42_V	1.355	1.00
108_D	113_A	1.346	1.00
47_A	59_Y	1.340	1.00
95_D	98_E	1.330	1.00
151_S	155_K	1.328	1.00
25_R	55_G	1.317	1.00
14_A	17_E	1.312	1.00
46_T	161_V	1.308	1.00
186_A	192_V	1.297	1.00
13_G	230_A	1.289	1.00
63_E	165_Q	1.282	1.00
190_G	193_L	1.257	1.00
15_L	19_L	1.246	1.00
56_L	112_R	1.236	1.00
65_L	68_A	1.230	1.00
116_I	158_L	1.215	1.00
44_L	70_F	1.200	1.00
100_A	104_R	1.199	1.00
149_L	160_V	1.198	1.00
104_R	156_H	1.181	1.00
23_V	29_T	1.169	1.00
47_A	115_L	1.155	1.00
61_D	70_F	1.146	1.00
56_L	111_D	1.139	1.00
8_L	159_A	1.131	1.00
115_L	161_V	1.127	1.00
98_E	101_Q	1.114	1.00
101_Q	104_R	1.109	1.00
31_L	193_L	1.107	1.00
182_G	187_H	1.092	1.00
56_L	89_I	1.085	1.00
100_A	103_V	1.083	1.00
41_N	223_I	1.080	1.00
73_L	77_R	1.077	1.00
203_R	217_E	1.072	1.00
34_P	37_A	1.065	1.00
51_A	57_A	1.062	1.00
93_A	98_E	1.054	1.00
181_G	185_L	1.054	1.00
7_H	213_K	1.041	1.00
104_R	108_D	1.037	1.00
126_R	129_R	1.023	1.00
195_L	205_A	1.016	1.00
31_L	42_V	1.014	1.00
66_S	71_Q	1.008	1.00
99_Q	102_A	1.002	1.00
204_R	218_H	1.001	1.00
148_H	151_S	1.000	1.00
98_E	102_A	1.000	1.00
118_V	124_F	0.989	1.00
89_I	93_A	0.986	1.00
14_A	219_A	0.986	1.00
187_H	192_V	0.985	1.00
146_I	185_L	0.983	1.00
48_V	52_A	0.982	1.00
131_G	135_T	0.981	1.00
89_I	106_T	0.976	1.00
99_Q	124_F	0.975	1.00
184_T	187_H	0.960	1.00
28_V	160_V	0.952	1.00
104_R	152_L	0.946	1.00
91_S	102_A	0.945	1.00
32_Y	194_R	0.940	1.00
19_L	191_T	0.939	1.00
72_Q	75_E	0.936	1.00
182_G	192_V	0.927	1.00
198_F	204_R	0.922	1.00
103_V	152_L	0.913	1.00
118_V	121_V	0.913	1.00
179_P	182_G	0.904	1.00
126_R	130_G	0.896	1.00
205_A	221_F	0.894	1.00
69_R	72_Q	0.889	1.00
100_A	148_H	0.887	1.00
216_G	219_A	0.882	1.00
96_F	100_A	0.876	1.00
45_T	49_T	0.873	1.00
12_C	16_D	0.871	1.00
59_Y	117_V	0.870	1.00
34_P	194_R	0.868	1.00
180_L	183_H	0.867	1.00
183_H	187_H	0.867	1.00
181_G	186_A	0.852	0.99
182_G	186_A	0.847	0.99
182_G	185_L	0.844	0.99
94_H	98_E	0.843	0.99
8_L	115_L	0.841	0.99
100_A	152_L	0.835	0.99
28_V	146_I	0.834	0.99
186_A	190_G	0.822	0.99
190_G	195_L	0.820	0.99
146_I	162_V	0.818	0.99
190_G	196_D	0.811	0.99
61_D	92_D	0.800	0.99
179_P	192_V	0.798	0.99
42_V	228_I	0.795	0.99
195_L	228_I	0.794	0.99
99_Q	103_V	0.793	0.99
193_L	196_D	0.792	0.99
153_A	159_A	0.789	0.99
61_D	65_L	0.786	0.99
164_N	182_G	0.786	0.99
188_W	192_V	0.784	0.99
105_D	108_D	0.780	0.99
171_D	179_P	0.780	0.99
103_V	106_T	0.774	0.99
25_R	157_D	0.773	0.99
34_P	183_H	0.757	0.99
130_G	140_R	0.756	0.99
100_A	106_T	0.752	0.99
70_F	73_L	0.751	0.99
135_T	139_L	0.751	0.99
57_A	115_L	0.750	0.99
12_C	49_T	0.749	0.99
101_Q	108_D	0.748	0.99
120_S	163_T	0.746	0.99
107_A	156_H	0.743	0.98
24_E	210_H	0.739	0.98
189_T	193_L	0.738	0.98
41_N	77_R	0.731	0.98
73_L	76_A	0.730	0.98
51_A	88_V	0.727	0.98
73_L	212_A	0.719	0.98
89_I	95_D	0.719	0.98
104_R	107_A	0.709	0.98
59_Y	123_G	0.700	0.98
85_S	88_V	0.697	0.98
183_H	186_A	0.694	0.98
46_T	50_T	0.693	0.98
181_G	192_V	0.690	0.98
191_T	210_H	0.686	0.97
20_G	214_P	0.684	0.97
103_V	107_A	0.684	0.97
105_D	226_G	0.683	0.97
196_D	206_T	0.681	0.97
40_T	44_L	0.678	0.97
122_T	180_L	0.676	0.97
78_A	226_G	0.673	0.97
26_G	157_D	0.672	0.97
13_G	17_E	0.672	0.97
48_V	80_D	0.670	0.97
96_F	99_Q	0.668	0.97
26_G	33_G	0.668	0.97
181_G	184_T	0.666	0.97
24_E	191_T	0.665	0.97
167_F	180_L	0.665	0.97
118_V	162_V	0.664	0.97
97_D	100_A	0.664	0.97
186_A	191_T	0.660	0.97
129_R	140_R	0.658	0.97
14_A	230_A	0.648	0.96
12_C	221_F	0.645	0.96
184_T	192_V	0.645	0.96
125_Y	128_A	0.640	0.96
73_L	78_A	0.640	0.96
222_Q	225_D	0.637	0.96
61_D	66_S	0.635	0.96
205_A	209_K	0.631	0.96
89_I	92_D	0.631	0.96
94_H	97_D	0.630	0.96
62_T	123_G	0.628	0.96
99_Q	107_A	0.626	0.96
97_D	106_T	0.625	0.96
90_V	93_A	0.624	0.96
201_G	206_T	0.624	0.96
31_L	161_V	0.621	0.95
202_T	222_Q	0.620	0.95
70_F	88_V	0.620	0.95
63_E	123_G	0.617	0.95
18_L	205_A	0.616	0.95
25_R	159_A	0.615	0.95
122_T	164_N	0.614	0.95
97_D	107_A	0.613	0.95
75_E	79_T	0.613	0.95
18_L	216_G	0.613	0.95
88_V	92_D	0.612	0.95
121_V	145_Q	0.608	0.95
7_H	21_G	0.606	0.95
181_G	187_H	0.606	0.95
150_L	188_W	0.597	0.94
80_D	86_A	0.590	0.94
46_T	207_L	0.590	0.94
97_D	101_Q	0.587	0.94
54_G	114_D	0.587	0.94
88_V	95_D	0.587	0.94
37_A	204_R	0.586	0.94
13_G	49_T	0.583	0.94
61_D	69_R	0.583	0.94
115_L	225_D	0.582	0.94
80_D	85_S	0.580	0.94
6_T	53_A	0.574	0.93
146_I	188_W	0.573	0.93
204_R	220_Q	0.573	0.93
15_L	193_L	0.572	0.93
101_Q	105_D	0.572	0.93
18_L	207_L	0.571	0.93
100_A	107_A	0.571	0.93
97_D	126_R	0.567	0.93
191_T	194_R	0.566	0.93
117_V	163_T	0.566	0.93
68_A	72_Q	0.566	0.93
101_Q	107_A	0.564	0.93
64_G	211_R	0.560	0.92
57_A	117_V	0.559	0.92
93_A	102_A	0.558	0.92
8_L	25_R	0.558	0.92
7_H	24_E	0.558	0.92
10_T	15_L	0.556	0.92
96_F	145_Q	0.555	0.92
150_L	162_V	0.555	0.92
188_W	193_L	0.555	0.92
72_Q	225_D	0.553	0.92
194_R	198_F	0.552	0.92
197_R	206_T	0.552	0.92
131_G	138_A	0.550	0.92
30_Q	164_N	0.549	0.92
16_D	49_T	0.548	0.91
103_V	108_D	0.548	0.91
90_V	94_H	0.548	0.91
193_L	207_L	0.547	0.91
88_V	93_A	0.547	0.91
201_G	216_G	0.545	0.91
147_T	151_S	0.545	0.91
99_Q	104_R	0.544	0.91
188_W	191_T	0.542	0.91
63_E	128_A	0.542	0.91
144_D	148_H	0.541	0.91
60_V	103_V	0.540	0.91
46_T	55_G	0.539	0.91
62_T	124_F	0.539	0.91
61_D	64_G	0.538	0.91
115_L	148_H	0.537	0.91
34_P	196_D	0.533	0.90
165_Q	168_T	0.529	0.90
190_G	197_R	0.529	0.90
75_E	80_D	0.528	0.90
36_A	203_R	0.527	0.90
214_P	217_E	0.526	0.90
63_E	121_V	0.526	0.90
118_V	149_L	0.524	0.90
8_L	29_T	0.523	0.90
135_T	138_A	0.518	0.89
31_L	228_I	0.517	0.89
93_A	99_Q	0.515	0.89
43_A	46_T	0.514	0.89
43_A	47_A	0.514	0.89
64_G	73_L	0.513	0.89
65_L	90_V	0.512	0.89
54_G	75_E	0.511	0.88
195_L	207_L	0.508	0.88
18_L	215_D	0.505	0.88
144_D	147_T	0.503	0.88
166_V	194_R	0.503	0.88
44_L	73_L	0.501	0.87
12_C	46_T	0.500	0.87

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	0.8898	100	0.332	Contact Map
2i1qA	1	0.9449	100	0.359	Contact Map
3ldaA	1	0.8856	100	0.361	Contact Map
1v5wA	5	0.9195	100	0.361	Contact Map
1n0wA	1	0.8517	100	0.363	Contact Map
1pznA	5	0.911	100	0.377	Contact Map
2cvhA	1	0.9195	100	0.4	Contact Map
4hyyA	4	0.9322	100	0.408	Contact Map
2dr3A	3	0.9025	100	0.445	Contact Map
4b3bA	1	0.8898	100	0.447	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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