CHO - ECOLI - GREMLIN Contacts

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CHO - Excinuclease cho

UniProt:	P76213	Sequences: MVRRLTSPRLEFEAAAIYEYPEHLRSFLNDLPTRPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLRTPDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQQPLFNKRLRRNRQLCALQLNEKRVDVVYAKEVDFSRAPNLFGLFANRRAALQALQTIADEQKLCYGLLGLEPLSRGRACFRSALKRCAGACCGKESHEEHALRLRQSLERLRVVCWPWQGAVALKEQHPEMTQYHIIQNWLWLGAVNSLEEATTLIRTPAGFDHDGYKILCKPLLSGNYEITELDPANDQRAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13993
Length:	295 (235)
Sequences:	3931 (2452)
Seq/√Len:	160.0

ECOLI - CHO UVRC
BACSU - UVRC
HALSA - UVRC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_T	56_N	5.445	1.00
31_L	61_V	4.537	1.00
125_R	199_H	3.995	1.00
198_S	201_E	3.507	1.00
42_G	46_T	3.359	1.00
141_N	210_L	2.961	1.00
27_F	79_R	2.851	1.00
45_D	79_R	2.800	1.00
74_L	77_S	2.647	1.00
227_K	238_I	2.636	1.00
34_R	84_C	2.356	1.00
41_H	81_S	2.354	1.00
47_M	102_Q	2.347	1.00
225_A	246_G	2.320	1.00
43_E	78_R	2.301	1.00
120_Q	140_P	2.285	1.00
33_T	58_R	2.233	1.00
211_E	216_V	2.141	1.00
40_F	77_S	2.098	1.00
70_E	73_M	2.087	1.00
131_A	153_L	2.024	1.00
225_A	229_Q	2.021	1.00
221_Q	242_W	1.989	1.00
86_A	253_E	1.968	1.00
224_V	242_W	1.952	1.00
49_L	105_L	1.950	1.00
221_Q	246_G	1.930	1.00
88_E	92_L	1.901	1.00
190_A	197_E	1.886	1.00
199_H	203_A	1.879	1.00
121_L	210_L	1.858	1.00
231_P	238_I	1.823	1.00
180_A	194_C	1.809	1.00
33_T	59_S	1.733	1.00
229_Q	232_E	1.729	1.00
56_N	59_S	1.701	1.00
41_H	79_R	1.700	1.00
227_K	234_T	1.662	1.00
234_T	237_H	1.659	1.00
236_Y	240_Q	1.652	1.00
164_K	190_A	1.644	1.00
121_L	129_V	1.638	1.00
184_S	191_G	1.626	1.00
208_Q	223_A	1.605	1.00
141_N	214_R	1.595	1.00
181_C	189_C	1.590	1.00
41_H	47_M	1.587	1.00
42_G	76_Q	1.573	1.00
31_L	57_I	1.567	1.00
227_K	230_H	1.565	1.00
181_C	193_C	1.550	1.00
226_L	230_H	1.534	1.00
165_L	209_S	1.521	1.00
203_A	207_R	1.505	1.00
39_L	83_I	1.466	1.00
164_K	205_R	1.462	1.00
236_Y	239_I	1.449	1.00
126_V	173_E	1.447	1.00
59_S	62_L	1.441	1.00
167_Y	183_R	1.411	1.00
49_L	69_D	1.409	1.00
42_G	49_L	1.406	1.00
197_E	201_E	1.405	1.00
160_A	167_Y	1.399	1.00
27_F	30_D	1.378	1.00
218_W	222_G	1.368	1.00
47_M	51_I	1.366	1.00
197_E	205_R	1.356	1.00
161_D	188_R	1.350	1.00
73_M	77_S	1.348	1.00
76_Q	106_F	1.347	1.00
201_E	204_L	1.341	1.00
223_A	227_K	1.336	1.00
234_T	238_I	1.333	1.00
190_A	205_R	1.314	1.00
39_L	98_L	1.276	1.00
183_R	188_R	1.273	1.00
120_Q	138_R	1.270	1.00
59_S	67_T	1.266	1.00
49_L	70_E	1.258	1.00
189_C	193_C	1.252	1.00
69_D	73_M	1.251	1.00
143_F	210_L	1.246	1.00
124_K	128_V	1.243	1.00
191_G	196_K	1.222	1.00
123_E	140_P	1.214	1.00
122_N	130_Y	1.208	1.00
96_A	110_L	1.208	1.00
138_R	142_L	1.201	1.00
243_L	246_G	1.196	1.00
40_F	80_I	1.195	1.00
72_A	76_Q	1.195	1.00
221_Q	225_A	1.194	1.00
31_L	80_I	1.171	1.00
63_S	66_R	1.170	1.00
124_K	170_L	1.160	1.00
64_H	70_E	1.151	1.00
207_R	211_E	1.143	1.00
32_P	82_W	1.137	1.00
26_S	29_N	1.137	1.00
164_K	209_S	1.134	1.00
39_L	81_S	1.115	1.00
222_G	226_L	1.110	1.00
126_V	199_H	1.109	1.00
207_R	210_L	1.106	1.00
28_L	31_L	1.104	1.00
58_R	62_L	1.085	0.99
164_K	187_K	1.084	0.99
231_P	234_T	1.083	0.99
120_Q	142_L	1.082	0.99
170_L	173_E	1.074	0.99
132_K	135_D	1.063	0.99
41_H	45_D	1.051	0.99
222_G	225_A	1.044	0.99
119_L	152_A	1.037	0.99
158_T	162_E	1.037	0.99
211_E	219_P	1.031	0.99
96_A	115_Q	1.025	0.99
205_R	208_Q	1.020	0.99
120_Q	130_Y	1.006	0.99
154_Q	244_W	1.004	0.99
204_L	207_R	1.000	0.99
149_R	153_L	0.996	0.99
184_S	187_K	0.995	0.99
114_R	133_E	0.989	0.99
224_V	238_I	0.987	0.99
129_V	209_S	0.975	0.99
223_A	226_L	0.954	0.99
226_L	229_Q	0.947	0.99
97_R	255_T	0.936	0.98
24_L	28_L	0.934	0.98
131_A	152_A	0.927	0.98
165_L	206_L	0.917	0.98
228_E	239_I	0.914	0.98
156_L	160_A	0.909	0.98
132_K	140_P	0.907	0.98
53_K	99_I	0.886	0.98
70_E	108_K	0.881	0.98
39_L	102_Q	0.881	0.98
160_A	183_R	0.879	0.98
90_G	252_E	0.876	0.98
42_G	78_R	0.874	0.98
136_F	140_P	0.872	0.98
53_K	92_L	0.871	0.98
69_D	108_K	0.862	0.97
228_E	242_W	0.860	0.97
159_I	209_S	0.859	0.97
39_L	47_M	0.857	0.97
123_E	139_A	0.856	0.97
28_L	62_L	0.856	0.97
152_A	156_L	0.854	0.97
119_L	156_L	0.852	0.97
100_K	113_N	0.852	0.97
96_A	100_K	0.852	0.97
121_L	206_L	0.848	0.97
127_D	133_E	0.845	0.97
137_S	140_P	0.844	0.97
62_L	65_L	0.840	0.97
32_P	56_N	0.839	0.97
51_I	102_Q	0.837	0.97
211_E	223_A	0.836	0.97
208_Q	219_P	0.833	0.97
124_K	130_Y	0.829	0.97
25_R	29_N	0.824	0.97
39_L	51_I	0.822	0.96
26_S	30_D	0.819	0.96
165_L	205_R	0.819	0.96
130_Y	169_L	0.811	0.96
112_R	133_E	0.811	0.96
152_A	248_V	0.806	0.96
159_I	212_R	0.798	0.96
173_E	176_S	0.792	0.96
238_I	242_W	0.788	0.96
135_D	138_R	0.788	0.96
23_H	28_L	0.783	0.95
31_L	58_R	0.781	0.95
38_Y	52_G	0.778	0.95
85_T	94_L	0.767	0.95
25_R	28_L	0.760	0.95
100_K	110_L	0.757	0.94
27_F	80_I	0.751	0.94
70_E	77_S	0.751	0.94
166_C	192_A	0.750	0.94
85_T	155_A	0.749	0.94
247_A	250_S	0.749	0.94
72_A	105_L	0.742	0.94
168_G	189_C	0.741	0.94
97_R	101_E	0.738	0.94
129_V	156_L	0.735	0.94
33_T	62_L	0.731	0.93
182_F	185_A	0.730	0.93
42_G	45_D	0.726	0.93
89_I	96_A	0.723	0.93
95_E	107_N	0.715	0.93
54_S	59_S	0.713	0.92
173_E	177_R	0.713	0.92
96_A	105_L	0.712	0.92
46_T	105_L	0.712	0.92
32_P	36_G	0.703	0.92
49_L	76_Q	0.698	0.92
98_L	102_Q	0.697	0.92
131_A	149_R	0.697	0.92
97_R	252_E	0.696	0.92
181_C	191_G	0.696	0.92
100_K	114_R	0.695	0.92
128_V	133_E	0.694	0.91
164_K	167_Y	0.688	0.91
211_E	220_W	0.687	0.91
52_G	99_I	0.687	0.91
160_A	165_L	0.687	0.91
184_S	196_K	0.686	0.91
146_F	213_L	0.683	0.91
239_I	243_L	0.682	0.91
45_D	78_R	0.681	0.91
38_Y	50_Y	0.680	0.91
171_G	174_P	0.679	0.91
151_A	247_A	0.675	0.90
126_V	190_A	0.675	0.90
206_L	209_S	0.671	0.90
68_P	71_A	0.670	0.90
23_H	27_F	0.655	0.89
135_D	142_L	0.653	0.89
212_R	215_V	0.652	0.89
242_W	246_G	0.650	0.89
131_A	156_L	0.648	0.88
32_P	84_C	0.644	0.88
104_P	107_N	0.644	0.88
155_A	248_V	0.641	0.88
28_L	65_L	0.639	0.88
72_A	75_R	0.639	0.88
52_G	107_N	0.638	0.88
145_L	215_V	0.636	0.88
126_V	133_E	0.636	0.88
125_R	203_A	0.635	0.87
27_F	31_L	0.632	0.87
210_L	214_R	0.629	0.87
40_F	63_S	0.629	0.87
99_I	107_N	0.628	0.87
182_F	186_L	0.626	0.87
35_P	85_T	0.625	0.87
90_G	253_E	0.621	0.86
35_P	57_I	0.620	0.86
126_V	195_G	0.616	0.86
40_F	61_V	0.616	0.86
69_D	72_A	0.616	0.86
87_G	90_G	0.611	0.85
206_L	210_L	0.609	0.85
170_L	178_G	0.609	0.85
204_L	208_Q	0.607	0.85
111_R	147_A	0.605	0.85
62_L	66_R	0.605	0.85
70_E	74_L	0.604	0.85
132_K	136_F	0.603	0.85
170_L	177_R	0.597	0.84
32_P	61_V	0.595	0.84
38_Y	99_I	0.595	0.84
237_H	241_N	0.595	0.84
163_Q	212_R	0.595	0.84
53_K	100_K	0.593	0.84
185_A	214_R	0.592	0.84
166_C	193_C	0.592	0.84
219_P	223_A	0.592	0.84
89_I	250_S	0.590	0.83
23_H	78_R	0.589	0.83
205_R	209_S	0.589	0.83
167_Y	173_E	0.588	0.83
183_R	190_A	0.588	0.83
72_A	106_F	0.588	0.83
61_V	80_I	0.585	0.83
60_R	107_N	0.582	0.82
40_F	85_T	0.582	0.82
83_I	94_L	0.579	0.82
208_Q	227_K	0.577	0.82
177_R	194_C	0.576	0.82
172_L	176_S	0.576	0.82
43_E	46_T	0.574	0.82
124_K	174_P	0.571	0.81
163_Q	209_S	0.571	0.81
246_G	249_N	0.570	0.81
120_Q	139_A	0.568	0.81
61_V	82_W	0.567	0.81
65_L	74_L	0.567	0.81
37_V	98_L	0.566	0.81
89_I	152_A	0.564	0.81
34_R	56_N	0.562	0.80
95_E	104_P	0.561	0.80
122_N	138_R	0.558	0.80
124_K	166_C	0.558	0.80
212_R	217_C	0.557	0.80
208_Q	241_N	0.557	0.80
103_Q	111_R	0.555	0.79
168_G	193_C	0.553	0.79
136_F	139_A	0.552	0.79
216_V	219_P	0.552	0.79
51_I	99_I	0.551	0.79
225_A	242_W	0.546	0.78
24_L	27_F	0.545	0.78
218_W	223_A	0.544	0.78
157_Q	160_A	0.544	0.78
180_A	191_G	0.544	0.78
218_W	246_G	0.543	0.78
85_T	91_A	0.543	0.78
109_R	150_R	0.543	0.78
154_Q	157_Q	0.541	0.78
166_C	191_G	0.541	0.78
50_Y	53_K	0.540	0.78
117_C	133_E	0.540	0.78
61_V	65_L	0.539	0.77
54_S	105_L	0.539	0.77
251_L	254_A	0.536	0.77
63_S	68_P	0.535	0.77
83_I	98_L	0.533	0.77
134_V	138_R	0.533	0.77
73_M	106_F	0.533	0.77
159_I	163_Q	0.533	0.77
158_T	241_N	0.532	0.77
169_L	172_L	0.532	0.77
27_F	82_W	0.532	0.77
217_C	249_N	0.532	0.77
200_E	203_A	0.530	0.76
145_L	235_Q	0.529	0.76
160_A	164_K	0.528	0.76
184_S	194_C	0.527	0.76
168_G	181_C	0.527	0.76
172_L	183_R	0.527	0.76
77_S	80_I	0.526	0.76
39_L	73_M	0.526	0.76
250_S	255_T	0.526	0.76
157_Q	186_L	0.524	0.75
166_C	181_C	0.522	0.75
90_G	254_A	0.521	0.75
224_V	245_L	0.520	0.75
66_R	72_A	0.518	0.75
227_K	241_N	0.518	0.75
150_R	153_L	0.518	0.75
222_G	259_R	0.517	0.75
38_Y	64_H	0.516	0.74
123_E	138_R	0.515	0.74
155_A	159_I	0.513	0.74
161_D	245_L	0.512	0.74
93_L	101_E	0.510	0.74
82_W	119_L	0.509	0.73
145_L	239_I	0.509	0.73
55_V	217_C	0.508	0.73
166_C	189_C	0.506	0.73
111_R	115_Q	0.506	0.73
167_Y	188_R	0.505	0.73
125_R	130_Y	0.504	0.73
122_N	128_V	0.503	0.73
211_E	214_R	0.502	0.72
53_K	88_E	0.502	0.72
56_N	254_A	0.500	0.72

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
1yd6A	5	0.3186	100	0.634	Contact Map
1yd0A	1	0.2949	100	0.646	Contact Map
2wshA	4	0.3492	100	0.67	Contact Map
1mk0A	1	0.2847	99.4	0.826	Contact Map
3mx1A	2	0.5254	97	0.914	Contact Map
2lwfA	1	0.3763	94.6	0.93	Contact Map
1zg2A	1	0.3119	88.9	0.941	Contact Map
1ywlA	1	0.3085	78.4	0.948	Contact Map
1e52A	2	0.1695	28.7	0.963	Contact Map
4csoA	1	0.3424	8.6	0.971	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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