NEP1 - SULSO - GREMLIN Contacts

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NEP1 - Ribosomal RNA small subunit methyltransferase Nep1

UniProt:	Q97WJ0	Sequences: MHLNIILLEASLELVPKEIVNHPAVIKNAKRRNKKPEDTLLDISLHYHAMKYLENSHKRGRPDILHQALLVILTDPVIKGDIFIHTIQSKIIKVNPNMRPPKNYLRFIGLMEQLLKYGKIPINGDETLMEVTNLTLDNIVNRYDLILLSEKGEKINPEEICKLDEKWLLGIGAFPHGDFSDKILNLAKKIYSISGFPLETQQVLCRIFSACNSILGWP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (189)
Sequences:	374 (248)
Seq/√Len:	18.1

SULSO - NEP1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_R	109_G	5.033	1.00
68_A	204_L	4.526	1.00
45_L	105_L	4.212	1.00
77_V	212_N	3.536	1.00
69_L	82_I	3.189	0.99
75_D	78_I	3.163	0.99
74_T	102_K	3.038	0.99
136_L	139_I	3.015	0.99
40_L	108_I	2.991	0.99
174_F	179_F	2.971	0.99
84_I	94_V	2.648	0.97
119_K	127_T	2.528	0.97
105_L	108_I	2.279	0.94
38_D	116_K	2.221	0.93
73_L	78_I	2.196	0.92
173_A	176_H	2.193	0.92
172_G	177_G	2.034	0.89
104_Y	108_I	1.972	0.88
83_F	142_R	1.965	0.87
144_D	189_K	1.874	0.85
32_R	49_A	1.808	0.83
84_I	92_I	1.777	0.81
74_T	199_E	1.761	0.81
194_S	198_L	1.717	0.79
159_E	165_E	1.707	0.79
68_A	72_I	1.683	0.78
94_V	129_M	1.680	0.78
65_L	82_I	1.669	0.77
84_I	100_P	1.627	0.75
49_A	60_G	1.622	0.75
178_D	190_I	1.582	0.73
96_P	200_T	1.526	0.70
194_S	206_R	1.512	0.69
160_I	188_K	1.506	0.69
204_L	208_F	1.476	0.68
129_M	217_W	1.444	0.66
37_E	40_L	1.429	0.65
134_L	145_L	1.424	0.65
58_K	120_I	1.422	0.65
193_I	198_L	1.413	0.64
104_Y	127_T	1.399	0.63
29_A	34_K	1.395	0.63
102_K	106_R	1.383	0.62
206_R	213_S	1.373	0.62
89_S	143_Y	1.350	0.60
41_L	62_P	1.346	0.60
42_D	45_L	1.335	0.60
67_Q	201_Q	1.326	0.59
70_L	74_T	1.317	0.58
146_I	156_N	1.314	0.58
29_A	32_R	1.310	0.58
52_Y	111_M	1.296	0.57
52_Y	116_K	1.292	0.57
30_K	33_N	1.290	0.57
73_L	94_V	1.274	0.56
29_A	33_N	1.270	0.56
144_D	165_E	1.268	0.56
63_D	66_H	1.238	0.54
93_K	132_T	1.233	0.53
78_I	201_Q	1.215	0.52
68_A	200_T	1.207	0.52
83_F	91_I	1.198	0.51
76_P	206_R	1.194	0.51
202_Q	205_C	1.174	0.50
171_I	204_L	1.174	0.50
153_E	189_K	1.164	0.49
114_L	129_M	1.150	0.48
140_V	182_K	1.149	0.48
106_R	110_L	1.144	0.48
75_D	102_K	1.136	0.47
91_I	134_L	1.135	0.47
45_L	108_I	1.134	0.47
43_I	47_Y	1.134	0.47
157_P	165_E	1.125	0.47
53_L	59_R	1.093	0.45
91_I	140_V	1.091	0.45
47_Y	58_K	1.084	0.44
93_K	134_L	1.077	0.44
102_K	109_G	1.076	0.44
61_R	64_I	1.074	0.44
72_I	204_L	1.067	0.43
163_L	203_V	1.065	0.43
114_L	120_I	1.057	0.43
93_K	130_E	1.056	0.43
27_K	30_K	1.051	0.42
75_D	199_E	1.046	0.42
106_R	114_L	1.041	0.42
154_K	195_G	1.038	0.41
192_S	195_G	1.037	0.41
34_K	112_E	1.023	0.41
49_A	59_R	1.023	0.41
50_M	53_L	1.023	0.41
66_H	70_L	1.007	0.40
50_M	55_N	0.997	0.39
36_P	171_I	0.994	0.39
146_I	169_L	0.993	0.39
83_F	92_I	0.986	0.38
147_L	169_L	0.983	0.38
46_H	63_D	0.974	0.38
88_Q	136_L	0.968	0.37
135_T	138_N	0.965	0.37
158_E	181_D	0.959	0.37
81_D	93_K	0.955	0.37
75_D	96_P	0.951	0.36
153_E	163_L	0.947	0.36
160_I	191_Y	0.944	0.36
73_L	106_R	0.941	0.36
149_S	178_D	0.937	0.36
206_R	212_N	0.937	0.36
69_L	94_V	0.935	0.35
135_T	141_N	0.935	0.35
53_L	216_G	0.930	0.35
27_K	170_G	0.923	0.35
94_V	119_K	0.922	0.35
147_L	207_I	0.920	0.35
92_I	129_M	0.913	0.34
28_N	45_L	0.908	0.34
73_L	79_K	0.889	0.33
171_I	200_T	0.883	0.33
72_I	134_L	0.873	0.32
154_K	176_H	0.872	0.32
109_G	120_I	0.871	0.32
64_I	84_I	0.865	0.32
89_S	98_M	0.864	0.32
59_R	65_L	0.861	0.31
124_G	180_S	0.859	0.31
94_V	98_M	0.858	0.31
30_K	35_K	0.853	0.31
65_L	157_P	0.852	0.31
118_G	133_N	0.851	0.31
61_R	66_H	0.842	0.30
114_L	176_H	0.826	0.30
40_L	65_L	0.823	0.29
44_S	106_R	0.813	0.29
82_I	196_F	0.811	0.29
94_V	198_L	0.808	0.29
98_M	109_G	0.807	0.29
98_M	106_R	0.802	0.28
126_E	146_I	0.801	0.28
54_E	120_I	0.798	0.28
35_K	171_I	0.795	0.28
85_H	125_D	0.790	0.28
92_I	114_L	0.787	0.28
60_G	179_F	0.770	0.27
150_E	172_G	0.768	0.27
90_K	140_V	0.763	0.26
120_I	164_D	0.761	0.26
111_M	131_V	0.759	0.26
163_L	189_K	0.758	0.26
73_L	76_P	0.753	0.26
34_K	49_A	0.753	0.26
78_I	96_P	0.752	0.26
111_M	159_E	0.750	0.26
79_K	209_S	0.747	0.26
129_M	207_I	0.746	0.26
49_A	57_H	0.741	0.25
203_V	216_G	0.738	0.25
155_I	159_E	0.737	0.25
75_D	201_Q	0.736	0.25
29_A	36_P	0.735	0.25
106_R	120_I	0.733	0.25
71_V	157_P	0.733	0.25
158_E	165_E	0.729	0.25
164_D	216_G	0.729	0.25
85_H	142_R	0.728	0.25
52_Y	142_R	0.727	0.25
46_H	172_G	0.725	0.25
50_M	59_R	0.721	0.24
79_K	82_I	0.720	0.24
42_D	60_G	0.719	0.24
71_V	205_C	0.715	0.24
47_Y	60_G	0.715	0.24
90_K	131_V	0.713	0.24
65_L	98_M	0.711	0.24
101_P	128_L	0.709	0.24
193_I	209_S	0.704	0.24
75_D	212_N	0.701	0.24
170_G	183_I	0.697	0.23
154_K	207_I	0.696	0.23
65_L	163_L	0.690	0.23
57_H	175_P	0.684	0.23
109_G	177_G	0.680	0.23
81_D	146_I	0.677	0.23
172_G	175_P	0.675	0.22
94_V	196_F	0.671	0.22
146_I	192_S	0.669	0.22
60_G	174_F	0.668	0.22
62_P	172_G	0.667	0.22
58_K	136_L	0.665	0.22
97_N	160_I	0.658	0.22
57_H	60_G	0.656	0.22
142_R	165_E	0.656	0.22
68_A	206_R	0.653	0.22
80_G	194_S	0.651	0.21
134_L	142_R	0.650	0.21
151_K	154_K	0.649	0.21
50_M	54_E	0.647	0.21
113_Q	168_L	0.647	0.21
93_K	217_W	0.643	0.21
103_N	121_P	0.641	0.21
86_T	89_S	0.641	0.21
161_C	192_S	0.633	0.21
94_V	130_E	0.633	0.21
121_P	127_T	0.629	0.21
169_L	214_I	0.628	0.20
115_L	196_F	0.628	0.20
139_I	142_R	0.626	0.20
113_Q	122_I	0.625	0.20
146_I	159_E	0.619	0.20
54_E	59_R	0.618	0.20
78_I	100_P	0.617	0.20
36_P	136_L	0.617	0.20
35_K	122_I	0.616	0.20
133_N	137_D	0.611	0.20
145_L	204_L	0.607	0.20
87_I	216_G	0.606	0.20
208_F	211_C	0.606	0.20
194_S	201_Q	0.605	0.20
147_L	190_I	0.603	0.20
44_S	103_N	0.603	0.20
41_L	46_H	0.602	0.19
73_L	82_I	0.601	0.19
121_P	125_D	0.593	0.19
32_R	35_K	0.593	0.19
36_P	108_I	0.590	0.19
147_L	187_A	0.582	0.19
160_I	195_G	0.580	0.19
175_P	216_G	0.579	0.19
145_L	188_K	0.577	0.19
166_K	182_K	0.576	0.18
46_H	175_P	0.576	0.18
97_N	111_M	0.576	0.18
72_I	206_R	0.575	0.18
188_K	193_I	0.573	0.18
97_N	123_N	0.569	0.18
90_K	115_L	0.568	0.18
94_V	159_E	0.566	0.18
77_V	211_C	0.563	0.18
50_M	176_H	0.559	0.18
72_I	81_D	0.558	0.18
108_I	139_I	0.557	0.18
160_I	189_K	0.555	0.18
76_P	106_R	0.554	0.18
69_L	75_D	0.553	0.18
94_V	134_L	0.553	0.18
91_I	132_T	0.552	0.18
108_I	112_E	0.552	0.18
134_L	139_I	0.552	0.18
98_M	148_L	0.552	0.18
45_L	103_N	0.552	0.18
49_A	112_E	0.548	0.17
146_I	164_D	0.545	0.17
119_K	153_E	0.542	0.17
27_K	147_L	0.541	0.17
122_I	127_T	0.540	0.17
89_S	95_N	0.539	0.17
149_S	161_C	0.539	0.17
55_N	87_I	0.536	0.17
78_I	102_K	0.536	0.17
110_L	113_Q	0.535	0.17
129_M	157_P	0.535	0.17
48_H	84_I	0.534	0.17
135_T	199_E	0.532	0.17
44_S	199_E	0.532	0.17
173_A	208_F	0.531	0.17
154_K	159_E	0.530	0.17
205_C	208_F	0.529	0.17
41_L	140_V	0.526	0.17
92_I	112_E	0.522	0.17
54_E	58_K	0.521	0.17
137_D	159_E	0.520	0.16
79_K	120_I	0.517	0.16
60_G	203_V	0.516	0.16
160_I	202_Q	0.514	0.16
104_Y	205_C	0.513	0.16
39_T	194_S	0.512	0.16
55_N	59_R	0.509	0.16
143_Y	160_I	0.509	0.16
64_I	69_L	0.508	0.16
105_L	149_S	0.508	0.16
126_E	167_W	0.508	0.16
73_L	102_K	0.507	0.16
91_I	206_R	0.506	0.16
35_K	38_D	0.500	0.16

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
3o7bA	2	0.9817	100	0.09	Contact Map
3bbdA	2	0.9037	100	0.184	Contact Map
3oiiA	2	0.8945	100	0.205	Contact Map
3aiaA	2	0.7248	100	0.568	Contact Map
2qmmA	2	0.8073	100	0.649	Contact Map
2qwvA	2	0.789	99.9	0.734	Contact Map
1ns5A	2	0.578	95.8	0.921	Contact Map
1o6dA	2	0.5734	95.5	0.923	Contact Map
1to0A	2	0.5596	94.8	0.926	Contact Map
4fakA	2	0.5963	92.5	0.933	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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