EX3 - ECOLI - GREMLIN Contacts

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EX3 - Exodeoxyribonuclease III

UniProt:	P09030	Sequences: MKFVSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYHGQKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCVETGIDYEIRSMEKPSDHAPVWATFRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11073
Length:	268 (249)
Sequences:	5765 (3451)
Seq/√Len:	218.7

ECOLI - EX3
BACSU - EXOA
SULSO - Q97WD6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_L	94_A	3.676	1.00
2_K	265_T	3.289	1.00
31_G	149_M	3.160	1.00
218_K	221_D	3.153	1.00
245_G	263_W	2.838	1.00
198_T	233_A	2.641	1.00
130_Q	186_W	2.464	1.00
242_V	267_R	2.351	1.00
4_V	263_W	2.334	1.00
53_N	72_T	2.309	1.00
247_D	263_W	2.268	1.00
181_P	185_E	2.118	1.00
198_T	241_C	2.087	1.00
168_R	181_P	2.037	1.00
145_P	236_P	2.009	1.00
5_S	262_V	1.995	1.00
133_Q	189_R	1.971	1.00
58_G	87_A	1.963	1.00
191_M	232_L	1.944	1.00
97_P	102_N	1.943	1.00
156_P	188_D	1.894	1.00
243_E	265_T	1.892	1.00
84_D	127_Q	1.866	1.00
211_S	262_V	1.854	1.00
31_G	105_V	1.845	1.00
196_V	235_Q	1.845	1.00
201_H	238_A	1.844	1.00
21_I	25_H	1.839	1.00
235_Q	238_A	1.828	1.00
95_E	144_N	1.819	1.00
209_R	248_Y	1.800	1.00
32_L	35_T	1.774	1.00
146_V	195_L	1.773	1.00
187_M	232_L	1.763	1.00
74_I	97_P	1.763	1.00
141_K	236_P	1.757	1.00
11_L	37_V	1.756	1.00
127_Q	131_N	1.734	1.00
202_A	241_C	1.681	1.00
231_L	264_A	1.640	1.00
199_F	209_R	1.628	1.00
242_V	265_T	1.618	1.00
116_R	180_L	1.600	1.00
206_T	209_R	1.575	1.00
163_I	166_E	1.528	1.00
203_N	206_T	1.502	1.00
233_A	241_C	1.496	1.00
165_E	168_R	1.495	1.00
115_S	216_R	1.489	1.00
185_E	189_R	1.487	1.00
38_H	41_M	1.456	1.00
196_V	201_H	1.452	1.00
196_V	238_A	1.442	1.00
27_P	30_I	1.437	1.00
75_A	95_E	1.421	1.00
95_E	104_T	1.414	1.00
80_F	91_I	1.411	1.00
218_K	222_D	1.397	1.00
8_I	32_L	1.388	1.00
241_C	264_A	1.385	1.00
188_D	192_S	1.382	1.00
149_M	231_L	1.380	1.00
156_P	230_L	1.378	1.00
115_S	118_H	1.362	1.00
20_A	23_E	1.359	1.00
38_H	60_K	1.357	1.00
187_M	230_L	1.356	1.00
145_P	240_C	1.355	1.00
158_D	168_R	1.347	1.00
136_L	148_I	1.344	1.00
12_R	41_M	1.340	1.00
19_E	23_E	1.328	1.00
23_E	50_L	1.319	1.00
29_V	105_V	1.316	1.00
22_V	30_I	1.314	1.00
139_E	142_R	1.310	1.00
37_V	42_F	1.307	1.00
133_Q	137_E	1.302	1.00
137_E	193_W	1.287	1.00
44_L	48_A	1.285	1.00
73_P	96_I	1.280	1.00
53_N	71_E	1.275	1.00
31_G	107_N	1.273	1.00
108_G	148_I	1.272	1.00
106_I	136_L	1.271	1.00
3_F	147_L	1.270	1.00
203_N	209_R	1.270	1.00
162_G	224_R	1.267	1.00
67_L	107_N	1.259	1.00
234_S	237_L	1.252	1.00
117_D	123_P	1.238	1.00
157_T	188_D	1.231	1.00
201_H	241_C	1.220	1.00
46_E	49_K	1.199	1.00
114_E	118_H	1.185	1.00
45_E	49_K	1.183	1.00
35_T	39_D	1.182	1.00
155_S	161_I	1.179	1.00
233_A	266_F	1.175	1.00
126_A	182_E	1.175	1.00
39_D	56_Y	1.173	1.00
31_G	67_L	1.170	1.00
25_H	247_D	1.169	1.00
132_L	148_I	1.164	1.00
186_W	189_R	1.155	1.00
133_Q	193_W	1.151	1.00
217_S	224_R	1.151	1.00
130_Q	189_R	1.144	1.00
26_Q	70_K	1.142	1.00
3_F	105_V	1.135	1.00
129_Y	154_I	1.133	1.00
219_G	224_R	1.130	1.00
3_F	29_V	1.117	1.00
202_A	243_E	1.113	1.00
147_L	231_L	1.108	1.00
136_L	195_L	1.096	1.00
55_F	76_V	1.083	1.00
81_P	86_E	1.083	1.00
135_Y	139_E	1.081	1.00
233_A	238_A	1.079	1.00
123_P	127_Q	1.077	1.00
85_E	131_N	1.076	1.00
21_I	247_D	1.073	1.00
28_D	70_K	1.058	1.00
148_I	152_M	1.056	1.00
137_E	141_K	1.048	1.00
155_S	179_F	1.048	1.00
37_V	41_M	1.045	1.00
104_T	144_N	1.041	1.00
158_D	179_F	1.040	1.00
202_A	244_T	1.037	1.00
244_T	264_A	1.034	1.00
223_N	248_Y	1.033	1.00
130_Q	134_N	1.032	1.00
15_P	46_E	1.027	1.00
231_L	266_F	1.027	1.00
82_G	131_N	1.021	1.00
108_G	152_M	1.015	1.00
69_T	94_A	1.006	1.00
110_F	129_Y	1.002	1.00
198_T	244_T	0.994	1.00
108_G	132_L	0.994	1.00
127_Q	130_Q	0.990	1.00
15_P	19_E	0.984	1.00
199_F	244_T	0.980	1.00
88_Q	121_K	0.978	1.00
211_S	246_I	0.977	1.00
148_I	232_L	0.976	1.00
75_A	104_T	0.976	1.00
22_V	27_P	0.971	1.00
104_T	143_D	0.969	1.00
29_V	103_V	0.969	1.00
126_A	186_W	0.967	1.00
29_V	96_I	0.960	1.00
73_P	76_V	0.958	1.00
57_H	78_R	0.957	1.00
188_D	191_M	0.952	1.00
93_M	104_T	0.948	1.00
57_H	79_G	0.947	1.00
122_F	180_L	0.942	1.00
20_A	24_K	0.939	1.00
45_E	48_A	0.931	0.99
6_F	18_L	0.930	0.99
209_R	246_I	0.927	0.99
1_M	265_T	0.914	0.99
147_L	233_A	0.902	0.99
169_K	176_K	0.896	0.99
129_Y	186_W	0.896	0.99
211_S	244_T	0.893	0.99
69_T	72_T	0.884	0.99
4_V	25_H	0.879	0.99
71_E	97_P	0.875	0.99
55_F	78_R	0.873	0.99
164_G	179_F	0.873	0.99
133_Q	190_L	0.871	0.99
102_N	145_P	0.866	0.99
55_F	73_P	0.862	0.99
59_Q	62_H	0.856	0.99
4_V	247_D	0.855	0.99
78_R	92_I	0.849	0.99
18_L	47_V	0.844	0.99
159_L	206_T	0.841	0.99
5_S	244_T	0.837	0.99
49_K	54_V	0.836	0.99
19_E	50_L	0.836	0.99
238_A	241_C	0.834	0.99
246_I	260_A	0.833	0.99
163_I	224_R	0.831	0.99
4_V	27_P	0.830	0.99
139_E	143_D	0.830	0.99
137_E	195_L	0.828	0.99
158_D	164_G	0.826	0.99
185_E	188_D	0.825	0.99
32_L	68_L	0.825	0.99
220_F	251_R	0.822	0.99
161_I	226_L	0.820	0.99
145_P	234_S	0.819	0.99
91_I	106_I	0.814	0.99
250_I	260_A	0.814	0.99
93_M	106_I	0.811	0.99
105_V	231_L	0.810	0.99
5_S	33_Q	0.808	0.99
84_D	131_N	0.804	0.99
110_F	128_F	0.802	0.98
10_G	13_A	0.799	0.98
69_T	73_P	0.798	0.98
54_V	68_L	0.798	0.98
35_T	66_A	0.798	0.98
169_K	181_P	0.796	0.98
85_E	124_A	0.789	0.98
134_N	137_E	0.788	0.98
199_F	211_S	0.788	0.98
102_N	240_C	0.787	0.98
203_N	243_E	0.786	0.98
161_I	167_N	0.785	0.98
199_F	246_I	0.785	0.98
18_L	30_I	0.785	0.98
69_T	96_I	0.774	0.98
59_Q	63_Y	0.770	0.98
83_D	87_A	0.769	0.98
213_F	260_A	0.769	0.98
178_S	226_L	0.769	0.98
180_L	183_E	0.765	0.98
209_R	245_G	0.763	0.98
199_F	206_T	0.754	0.98
2_K	25_H	0.750	0.98
113_G	122_F	0.748	0.98
233_A	237_L	0.744	0.98
29_V	71_E	0.743	0.98
24_K	249_E	0.741	0.97
73_P	94_A	0.738	0.97
91_I	135_Y	0.736	0.97
167_N	226_L	0.735	0.97
55_F	92_I	0.734	0.97
55_F	69_T	0.731	0.97
48_A	53_N	0.729	0.97
107_N	149_M	0.723	0.97
133_Q	186_W	0.723	0.97
213_F	223_N	0.722	0.97
74_I	95_E	0.714	0.97
93_M	135_Y	0.714	0.97
145_P	237_L	0.709	0.97
158_D	165_E	0.705	0.97
67_L	105_V	0.705	0.97
126_A	130_Q	0.704	0.97
203_N	245_G	0.698	0.96
33_Q	107_N	0.696	0.96
240_C	267_R	0.695	0.96
4_V	21_I	0.694	0.96
77_R	93_M	0.691	0.96
91_I	132_L	0.690	0.96
202_A	208_D	0.689	0.96
231_L	262_V	0.688	0.96
80_F	135_Y	0.688	0.96
205_Q	209_R	0.687	0.96
10_G	61_G	0.684	0.96
118_H	123_P	0.682	0.96
208_D	223_N	0.679	0.96
139_E	146_V	0.678	0.96
155_S	226_L	0.677	0.96
3_F	31_G	0.675	0.96
110_F	152_M	0.672	0.96
204_P	209_R	0.672	0.96
53_N	73_P	0.672	0.96
6_F	256_P	0.670	0.95
189_R	192_S	0.667	0.95
54_V	57_H	0.666	0.95
167_N	176_K	0.660	0.95
12_R	37_V	0.657	0.95
30_I	68_L	0.657	0.95
168_R	179_F	0.654	0.95
164_G	168_R	0.650	0.95
233_A	264_A	0.649	0.95
187_M	191_M	0.647	0.95
121_K	124_A	0.645	0.94
106_I	146_V	0.645	0.94
13_A	16_H	0.643	0.94
256_P	260_A	0.643	0.94
67_L	92_I	0.639	0.94
140_L	236_P	0.636	0.94
75_A	78_R	0.636	0.94
16_H	20_A	0.635	0.94
57_H	92_I	0.633	0.94
152_M	232_L	0.633	0.94
147_L	266_F	0.632	0.94
183_E	212_W	0.632	0.94
24_K	250_I	0.630	0.94
23_E	26_Q	0.626	0.94
44_L	56_Y	0.625	0.94
140_L	234_S	0.623	0.93
125_K	129_Y	0.622	0.93
182_E	185_E	0.621	0.93
163_I	167_N	0.621	0.93
137_E	189_R	0.620	0.93
241_C	266_F	0.617	0.93
34_E	151_D	0.617	0.93
131_N	134_N	0.616	0.93
77_R	135_Y	0.612	0.93
151_D	258_D	0.612	0.93
91_I	108_G	0.612	0.93
52_Y	70_K	0.608	0.93
53_N	69_T	0.608	0.93
44_L	54_V	0.604	0.92
16_H	19_E	0.602	0.92
114_E	176_K	0.601	0.92
220_F	260_A	0.598	0.92
11_L	18_L	0.597	0.92
217_S	222_D	0.597	0.92
15_P	42_F	0.596	0.92
115_S	176_K	0.595	0.92
243_E	263_W	0.595	0.92
51_G	71_E	0.593	0.92
203_N	244_T	0.593	0.92
10_G	62_H	0.592	0.92
162_G	167_N	0.591	0.91
162_G	166_E	0.590	0.91
109_Y	151_D	0.589	0.91
219_G	222_D	0.587	0.91
105_V	147_L	0.585	0.91
152_M	230_L	0.585	0.91
35_T	38_H	0.584	0.91
22_V	52_Y	0.582	0.91
49_K	68_L	0.581	0.91
80_F	131_N	0.581	0.91
19_E	49_K	0.578	0.91
71_E	96_I	0.578	0.91
178_S	183_E	0.577	0.91
6_F	112_Q	0.577	0.91
77_R	104_T	0.575	0.90
122_F	182_E	0.574	0.90
136_L	190_L	0.573	0.90
159_L	205_Q	0.572	0.90
35_T	56_Y	0.571	0.90
104_T	139_E	0.570	0.90
199_F	202_A	0.569	0.90
113_G	125_K	0.569	0.90
81_P	135_Y	0.568	0.90
132_L	136_L	0.567	0.90
148_I	190_L	0.566	0.90
162_G	226_L	0.562	0.89
7_N	153_N	0.558	0.89
125_K	186_W	0.552	0.88
162_G	210_F	0.550	0.88
34_E	153_N	0.548	0.88
201_H	239_E	0.547	0.88
109_Y	153_N	0.546	0.88
235_Q	239_E	0.543	0.88
29_V	69_T	0.542	0.88
65_V	92_I	0.540	0.87
220_F	248_Y	0.540	0.87
132_L	135_Y	0.539	0.87
74_I	103_V	0.537	0.87
91_I	128_F	0.537	0.87
197_D	227_R	0.536	0.87
13_A	17_Q	0.536	0.87
198_T	238_A	0.535	0.87
2_K	263_W	0.528	0.86
251_R	256_P	0.528	0.86
34_E	109_Y	0.527	0.86
126_A	129_Y	0.525	0.86
116_R	122_F	0.521	0.86
1_M	4_V	0.518	0.85
200_R	246_I	0.517	0.85
85_E	127_Q	0.515	0.85
29_V	94_A	0.513	0.85
167_N	178_S	0.509	0.84
2_K	26_Q	0.508	0.84
106_I	110_F	0.508	0.84
202_A	242_V	0.506	0.84
179_F	226_L	0.503	0.83
47_V	54_V	0.502	0.83
50_L	54_V	0.502	0.83
21_I	250_I	0.501	0.83
114_E	152_M	0.500	0.83

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
2j63A	1	0.9664	100	0.377	Contact Map
1akoA	1	0.9851	100	0.382	Contact Map
2voaA	1	0.9515	100	0.383	Contact Map
2jc4A	1	0.9552	100	0.383	Contact Map
2jc5A	1	0.9366	100	0.384	Contact Map
1hd7A	1	0.8843	100	0.386	Contact Map
3g91A	1	0.9366	100	0.386	Contact Map
4f1rA	1	0.9328	100	0.389	Contact Map
4jg3A	1	0.9366	100	0.392	Contact Map
4qheA	1	0.9366	100	0.434	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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