NFI - SULSO - GREMLIN Contacts

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NFI - Endonuclease V

UniProt:	Q97VZ6	Sequences: MVEKHLLEFLEKLQFLISKNVKISHYGIENVKKICGVDIAYKGNLGFSVGVSMDINSGDYNYKSYVGEVNFPYIPGFLFMREAPLMIKAIEGLDCHLLLVDGHGIAHPRKSGIAAVIGVLLDFPTIGVAKSRLTGDLVNESEITYVYLNGEKVGVKFGRYFYSPGNKVDLQDCIELGKRGYPKVLKIADMLTKKIKKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	198 (186)
Sequences:	1034 (705)
Seq/√Len:	51.7

ECOLI - NFI
BACSU - NFI
HALSA - NFI
SULSO - NFI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_D	57_S	3.939	1.00
110_K	151_E	3.594	1.00
23_I	164_P	3.080	1.00
189_D	193_K	3.025	1.00
37_V	86_M	2.832	1.00
111_S	115_A	2.793	1.00
169_D	172_D	2.765	1.00
155_V	174_I	2.570	1.00
33_K	60_Y	2.445	1.00
122_D	167_K	2.419	1.00
137_L	161_F	2.368	1.00
62_Y	191_L	2.352	1.00
90_I	121_L	2.298	1.00
103_H	106_A	2.192	1.00
105_I	115_A	2.133	1.00
99_L	185_L	2.122	1.00
164_P	170_L	2.108	1.00
97_L	176_L	2.073	1.00
105_I	164_P	2.073	1.00
46_G	69_V	2.025	1.00
21_V	119_V	2.019	1.00
17_I	111_S	2.014	1.00
26_Y	169_D	1.997	1.00
126_I	177_G	1.912	0.99
15_F	18_S	1.911	0.99
11_E	77_F	1.877	0.99
99_L	177_G	1.872	0.99
141_S	145_Y	1.864	0.99
67_G	85_L	1.852	0.99
41_Y	69_V	1.828	0.99
46_G	85_L	1.780	0.99
40_A	192_T	1.735	0.99
98_L	125_T	1.709	0.99
61_N	94_D	1.702	0.99
90_I	98_L	1.689	0.99
35_C	52_S	1.681	0.99
189_D	192_T	1.652	0.98
83_A	117_I	1.640	0.98
152_K	155_V	1.622	0.98
132_R	156_K	1.576	0.98
141_S	146_V	1.560	0.98
53_M	58_G	1.537	0.97
35_C	50_G	1.508	0.97
40_A	47_F	1.493	0.97
141_S	144_T	1.477	0.97
26_Y	167_K	1.446	0.96
157_F	178_K	1.438	0.96
49_V	192_T	1.403	0.95
50_G	90_I	1.382	0.95
156_K	161_F	1.375	0.95
159_R	180_G	1.364	0.95
67_G	88_K	1.355	0.94
100_V	117_I	1.345	0.94
39_I	86_M	1.337	0.94
99_L	128_V	1.316	0.94
11_E	15_F	1.313	0.93
148_L	153_V	1.308	0.93
146_V	156_K	1.296	0.93
155_V	170_L	1.294	0.93
40_A	193_K	1.289	0.93
88_K	91_E	1.270	0.92
117_I	121_L	1.266	0.92
100_V	184_V	1.234	0.91
159_R	186_K	1.217	0.91
52_S	94_D	1.204	0.90
183_K	186_K	1.195	0.90
16_L	20_N	1.178	0.89
31_V	176_L	1.176	0.89
129_A	187_I	1.172	0.89
184_V	187_I	1.157	0.88
103_H	129_A	1.156	0.88
139_N	142_E	1.144	0.88
71_F	189_D	1.142	0.88
37_V	117_I	1.141	0.88
110_K	148_L	1.140	0.87
141_S	147_Y	1.133	0.87
21_V	115_A	1.132	0.87
137_L	144_T	1.111	0.86
54_D	59_D	1.107	0.86
103_H	133_L	1.099	0.85
55_I	179_R	1.083	0.85
174_I	178_K	1.081	0.84
164_P	173_C	1.068	0.84
89_A	93_L	1.052	0.83
31_V	96_H	1.041	0.82
10_L	71_F	1.034	0.82
51_V	187_I	1.034	0.82
126_I	176_L	1.031	0.82
180_G	186_K	1.028	0.81
47_F	193_K	1.024	0.81
45_L	66_V	1.010	0.80
33_K	52_S	1.000	0.80
53_M	185_L	0.996	0.79
106_A	154_G	0.992	0.79
13_L	77_F	0.990	0.79
176_L	184_V	0.989	0.79
143_I	155_V	0.980	0.78
103_H	131_S	0.977	0.78
28_I	31_V	0.975	0.78
35_C	96_H	0.974	0.78
134_T	153_V	0.967	0.77
79_F	116_V	0.955	0.76
39_I	46_G	0.953	0.76
42_K	47_F	0.952	0.76
18_S	21_V	0.951	0.76
22_K	27_G	0.948	0.76
52_S	93_L	0.938	0.75
176_L	179_R	0.934	0.75
39_I	85_L	0.919	0.73
34_I	37_V	0.914	0.73
90_I	117_I	0.907	0.73
36_G	185_L	0.887	0.71
119_V	166_N	0.886	0.71
21_V	105_I	0.883	0.70
132_R	146_V	0.878	0.70
157_F	174_I	0.875	0.70
98_L	123_F	0.868	0.69
141_S	148_L	0.868	0.69
143_I	174_I	0.865	0.69
65_Y	92_G	0.865	0.69
145_Y	152_K	0.861	0.69
41_Y	78_L	0.860	0.68
13_L	16_L	0.848	0.67
48_S	89_A	0.848	0.67
26_Y	122_D	0.835	0.66
98_L	117_I	0.835	0.66
27_G	169_D	0.834	0.66
143_I	157_F	0.828	0.65
22_K	167_K	0.828	0.65
49_V	64_S	0.824	0.65
113_I	133_L	0.823	0.65
175_E	179_R	0.823	0.65
115_A	125_T	0.804	0.63
10_L	77_F	0.798	0.63
80_M	116_V	0.797	0.63
64_S	191_L	0.797	0.63
50_G	89_A	0.792	0.62
40_A	189_D	0.787	0.62
46_G	113_I	0.786	0.61
180_G	183_K	0.782	0.61
106_A	153_V	0.781	0.61
63_K	92_G	0.781	0.61
26_Y	172_D	0.780	0.61
86_M	100_V	0.778	0.61
39_I	78_L	0.765	0.59
17_I	20_N	0.761	0.59
12_K	15_F	0.756	0.58
37_V	78_L	0.753	0.58
61_N	92_G	0.747	0.58
187_I	190_M	0.740	0.57
33_K	96_H	0.733	0.56
21_V	111_S	0.733	0.56
103_H	135_G	0.731	0.56
71_F	77_F	0.728	0.56
69_V	85_L	0.727	0.55
177_G	180_G	0.722	0.55
77_F	119_V	0.719	0.55
87_I	121_L	0.718	0.55
9_F	12_K	0.715	0.54
8_E	12_K	0.712	0.54
166_N	172_D	0.705	0.53
37_V	100_V	0.703	0.53
9_F	13_L	0.698	0.52
99_L	126_I	0.697	0.52
132_R	161_F	0.697	0.52
159_R	183_K	0.696	0.52
65_Y	89_A	0.682	0.51
99_L	121_L	0.681	0.51
128_V	192_T	0.681	0.51
132_R	148_L	0.681	0.51
47_F	66_V	0.679	0.50
152_K	170_L	0.677	0.50
34_I	59_D	0.676	0.50
53_M	187_I	0.675	0.50
38_D	130_K	0.673	0.50
23_I	105_I	0.672	0.50
79_F	103_H	0.671	0.50
87_I	91_E	0.671	0.50
155_V	164_P	0.670	0.50
106_A	163_S	0.667	0.49
34_I	43_G	0.661	0.49
118_G	166_N	0.661	0.49
106_A	132_R	0.661	0.49
128_V	177_G	0.658	0.48
46_G	51_V	0.658	0.48
78_L	103_H	0.657	0.48
148_L	151_E	0.654	0.48
101_D	130_K	0.654	0.48
73_Y	81_R	0.653	0.48
34_I	126_I	0.647	0.47
18_S	111_S	0.647	0.47
26_Y	29_E	0.646	0.47
48_S	180_G	0.644	0.47
115_A	164_P	0.636	0.46
16_L	19_K	0.631	0.45
168_V	172_D	0.631	0.45
129_A	153_V	0.631	0.45
132_R	135_G	0.629	0.45
83_A	100_V	0.625	0.45
73_Y	78_L	0.624	0.45
105_I	111_S	0.623	0.45
40_A	190_M	0.618	0.44
117_I	123_F	0.613	0.44
77_F	174_I	0.611	0.43
32_K	54_D	0.609	0.43
123_F	167_K	0.605	0.43
190_M	194_K	0.605	0.43
47_F	192_T	0.604	0.43
145_Y	155_V	0.601	0.42
39_I	113_I	0.595	0.42
80_M	101_D	0.594	0.42
36_G	53_M	0.594	0.42
118_G	167_K	0.593	0.42
31_V	98_L	0.593	0.42
136_D	150_G	0.592	0.41
37_V	90_I	0.591	0.41
128_V	180_G	0.591	0.41
84_P	87_I	0.589	0.41
63_K	94_D	0.589	0.41
20_N	24_S	0.587	0.41
71_F	113_I	0.586	0.41
77_F	106_A	0.586	0.41
73_Y	82_E	0.584	0.41
44_N	158_G	0.582	0.40
65_Y	88_K	0.582	0.40
13_L	194_K	0.582	0.40
95_C	116_V	0.580	0.40
164_P	167_K	0.579	0.40
103_H	132_R	0.577	0.40
171_Q	175_E	0.577	0.40
13_L	20_N	0.576	0.40
45_L	49_V	0.574	0.40
47_F	189_D	0.573	0.40
39_I	90_I	0.573	0.40
181_Y	184_V	0.570	0.39
43_G	175_E	0.569	0.39
124_P	173_C	0.568	0.39
114_A	127_G	0.568	0.39
79_F	193_K	0.565	0.39
90_I	123_F	0.564	0.39
27_G	30_N	0.562	0.38
138_V	142_E	0.560	0.38
39_I	181_Y	0.560	0.38
145_Y	148_L	0.559	0.38
187_I	191_L	0.555	0.38
31_V	131_S	0.554	0.38
132_R	155_V	0.552	0.38
36_G	52_S	0.550	0.37
147_Y	153_V	0.549	0.37
70_N	143_I	0.549	0.37
56_N	179_R	0.549	0.37
45_L	68_E	0.548	0.37
140_E	178_K	0.547	0.37
11_E	39_I	0.543	0.37
152_K	162_Y	0.542	0.37
124_P	189_D	0.540	0.36
97_L	126_I	0.538	0.36
147_Y	152_K	0.534	0.36
34_I	125_T	0.534	0.36
78_L	131_S	0.532	0.36
160_Y	177_G	0.532	0.36
39_I	83_A	0.530	0.35
41_Y	64_S	0.528	0.35
157_F	162_Y	0.527	0.35
143_I	170_L	0.523	0.35
41_Y	47_F	0.519	0.34
34_I	99_L	0.519	0.34
54_D	58_G	0.518	0.34
68_E	78_L	0.517	0.34
62_Y	187_I	0.516	0.34
35_C	131_S	0.512	0.34
12_K	152_K	0.511	0.34
119_V	124_P	0.510	0.33
136_D	147_Y	0.510	0.33
130_K	163_S	0.506	0.33
31_V	168_V	0.504	0.33
138_V	147_Y	0.504	0.33
78_L	81_R	0.503	0.33
37_V	41_Y	0.500	0.33

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
3ga2A	1	1	100	0.214	Contact Map
4nspA	1	0.9697	100	0.239	Contact Map
2w36A	1	0.9949	100	0.334	Contact Map
3gocA	2	0.9949	100	0.365	Contact Map
2qh9A	2	0.803	100	0.516	Contact Map
2ygkA	2	0.9444	96.7	0.906	Contact Map
2nrrA	1	0.6717	96.1	0.911	Contact Map
3c65A	1	0.7121	94.5	0.92	Contact Map
2nrtA	1	0.7475	94	0.922	Contact Map
2w42A	1	0.8485	54.3	0.949	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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