Gemini_coat - PFAM28P - GREMLIN Contacts

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Gemini_coat - Geminivirus coat protein/nuclear export factor BR1 family

PFAM:	PF00844	Sequences: RRRLNFDSRRSRARAPFKRSTNKKRAWGKRPMRRKPRMYRMYRSPPCKVQSFEINQYGPRFDVSNTGKVTCISDPTRGKGETNRVGKRIKLKSLYFKGTVWMDENIKDKNHTGVVMFVLVRDRRPHGATPGTFDELFGMRDNSPSTLTVKNDLRDRFQVLRKFKRTVTGGKDTLMVDYAGKEQLSVRRFNKWVNFKVVYNDSEAGKYENITKNALLLYYAWTSASNPVYATLKIRVYFYDSYVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	244 (239)
Sequences:	635 (345)
Seq/√Len:	22.3
META:	0.271

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_R	213_N	5.958	1.00
71_C	74_D	4.983	1.00
116_M	162_K	4.946	1.00
94_L	119_L	4.858	1.00
50_Q	53_E	3.940	1.00
48_K	53_E	3.638	1.00
125_P	214_A	3.521	1.00
48_K	51_S	3.197	1.00
129_T	207_Y	2.759	0.99
207_Y	213_N	2.709	0.99
203_E	209_N	2.632	0.99
40_R	43_R	2.630	0.99
118_V	137_F	2.355	0.97
17_F	21_T	2.243	0.96
5_N	8_S	2.204	0.96
195_F	213_N	2.107	0.95
16_P	21_T	2.042	0.94
8_S	11_S	1.942	0.92
71_C	216_L	1.906	0.91
16_P	20_S	1.895	0.91
151_N	154_R	1.882	0.91
22_N	26_A	1.873	0.90
8_S	15_A	1.828	0.89
11_S	15_A	1.826	0.89
24_K	28_G	1.796	0.88
122_D	157_F	1.744	0.87
8_S	13_A	1.726	0.86
127_G	130_P	1.717	0.86
9_R	12_R	1.702	0.86
122_D	156_R	1.696	0.85
6_F	15_A	1.673	0.85
208_E	238_F	1.659	0.84
117_F	217_L	1.653	0.84
229_Y	232_L	1.651	0.84
76_T	204_A	1.635	0.83
7_D	11_S	1.623	0.83
6_F	13_A	1.618	0.82
137_F	159_V	1.618	0.82
235_R	240_D	1.580	0.81
11_S	14_R	1.555	0.80
80_G	87_K	1.539	0.79
13_A	16_P	1.496	0.77
8_S	12_R	1.485	0.77
161_R	190_N	1.485	0.77
200_N	203_E	1.479	0.76
92_K	208_E	1.478	0.76
98_G	125_P	1.455	0.75
194_N	197_V	1.437	0.74
91_L	94_L	1.432	0.74
7_D	17_F	1.415	0.73
5_N	18_K	1.410	0.73
5_N	12_R	1.403	0.72
17_F	119_L	1.400	0.72
6_F	21_T	1.399	0.72
7_D	15_A	1.392	0.72
71_C	210_I	1.380	0.71
123_R	158_Q	1.369	0.70
7_D	12_R	1.362	0.70
6_F	12_R	1.357	0.70
7_D	13_A	1.354	0.69
207_Y	216_L	1.353	0.69
75_P	89_I	1.339	0.69
12_R	17_F	1.328	0.68
93_S	208_E	1.313	0.67
26_A	119_L	1.309	0.67
136_L	147_L	1.308	0.67
10_R	15_A	1.301	0.66
120_V	218_Y	1.299	0.66
7_D	21_T	1.297	0.66
235_R	238_F	1.291	0.66
133_F	137_F	1.282	0.65
143_S	147_L	1.274	0.65
77_R	87_K	1.265	0.64
23_K	26_A	1.263	0.64
127_G	132_T	1.254	0.63
228_V	231_T	1.251	0.63
209_N	216_L	1.243	0.63
37_R	130_P	1.224	0.61
200_N	204_A	1.217	0.61
11_S	16_P	1.215	0.61
5_N	13_A	1.212	0.61
7_D	16_P	1.206	0.60
126_H	212_K	1.196	0.60
137_F	216_L	1.192	0.59
136_L	157_F	1.181	0.59
9_R	13_A	1.158	0.57
118_V	159_V	1.155	0.57
75_P	205_G	1.144	0.56
127_G	199_Y	1.139	0.56
118_V	162_K	1.139	0.56
76_T	200_N	1.125	0.55
14_R	18_K	1.117	0.54
207_Y	214_A	1.115	0.54
121_R	195_F	1.113	0.54
25_R	30_R	1.101	0.53
35_K	41_M	1.099	0.53
77_R	81_E	1.096	0.53
217_L	236_V	1.090	0.52
49_V	52_F	1.085	0.52
147_L	150_K	1.085	0.52
20_S	23_K	1.085	0.52
20_S	28_G	1.084	0.52
69_V	136_L	1.081	0.52
5_N	9_R	1.076	0.52
18_K	21_T	1.072	0.51
20_S	42_Y	1.061	0.51
10_R	13_A	1.056	0.50
37_R	42_Y	1.051	0.50
10_R	24_K	1.023	0.48
12_R	16_P	1.021	0.48
8_S	16_P	1.015	0.47
94_L	236_V	1.008	0.47
211_T	214_A	1.005	0.47
28_G	217_L	1.003	0.47
29_K	167_V	0.999	0.46
92_K	123_R	0.986	0.45
123_R	151_N	0.985	0.45
95_Y	159_V	0.983	0.45
199_Y	208_E	0.983	0.45
162_K	168_T	0.975	0.45
103_D	167_V	0.975	0.45
21_T	26_A	0.974	0.45
118_V	218_Y	0.972	0.44
16_P	35_K	0.972	0.44
153_L	157_F	0.966	0.44
87_K	194_N	0.965	0.44
127_G	135_E	0.964	0.44
125_P	207_Y	0.955	0.43
111_H	114_V	0.953	0.43
27_W	32_M	0.941	0.42
12_R	15_A	0.936	0.42
182_E	185_S	0.934	0.42
76_T	205_G	0.925	0.41
209_N	218_Y	0.918	0.41
204_A	208_E	0.915	0.41
25_R	29_K	0.912	0.40
11_S	20_S	0.908	0.40
30_R	34_R	0.905	0.40
97_K	148_T	0.901	0.40
88_R	155_D	0.899	0.40
7_D	10_R	0.896	0.39
59_P	62_D	0.894	0.39
221_W	226_N	0.894	0.39
36_P	40_R	0.894	0.39
192_W	197_V	0.894	0.39
136_L	216_L	0.892	0.39
78_G	238_F	0.884	0.39
230_A	233_K	0.883	0.39
9_R	15_A	0.877	0.38
5_N	16_P	0.875	0.38
110_N	167_V	0.873	0.38
13_A	21_T	0.870	0.38
59_P	94_L	0.869	0.38
131_G	134_D	0.868	0.38
6_F	11_S	0.864	0.37
144_P	147_L	0.861	0.37
186_V	190_N	0.858	0.37
87_K	162_K	0.853	0.37
88_R	196_K	0.843	0.36
125_P	133_F	0.836	0.36
10_R	14_R	0.836	0.36
21_T	37_R	0.829	0.35
148_T	189_F	0.824	0.35
11_S	21_T	0.824	0.35
55_N	100_V	0.823	0.35
95_Y	187_R	0.823	0.35
142_N	147_L	0.820	0.35
118_V	144_P	0.818	0.34
107_K	243_V	0.816	0.34
119_L	217_L	0.815	0.34
221_W	224_A	0.813	0.34
120_V	129_T	0.805	0.34
169_G	182_E	0.804	0.34
12_R	22_N	0.801	0.33
149_V	214_A	0.800	0.33
69_V	218_Y	0.798	0.33
86_G	240_D	0.790	0.33
15_A	22_N	0.783	0.32
134_D	213_N	0.782	0.32
65_N	70_T	0.780	0.32
15_A	23_K	0.777	0.32
47_C	50_Q	0.772	0.32
6_F	23_K	0.771	0.32
163_F	198_V	0.766	0.31
7_D	157_F	0.766	0.31
96_F	119_L	0.765	0.31
93_S	168_T	0.764	0.31
9_R	21_T	0.759	0.31
237_Y	240_D	0.758	0.31
73_S	91_L	0.756	0.31
5_N	21_T	0.755	0.31
88_R	126_H	0.755	0.31
93_S	98_G	0.754	0.31
12_R	21_T	0.751	0.30
203_E	206_K	0.750	0.30
84_R	122_D	0.749	0.30
79_K	207_Y	0.749	0.30
159_V	171_K	0.749	0.30
81_E	187_R	0.744	0.30
10_R	27_W	0.743	0.30
17_F	20_S	0.739	0.30
5_N	10_R	0.738	0.30
134_D	139_M	0.732	0.29
26_A	167_V	0.730	0.29
8_S	17_F	0.726	0.29
33_R	37_R	0.725	0.29
19_R	28_G	0.720	0.29
27_W	42_Y	0.717	0.28
19_R	26_A	0.715	0.28
17_F	23_K	0.713	0.28
228_V	238_F	0.713	0.28
218_Y	222_T	0.711	0.28
162_K	212_K	0.707	0.28
6_F	16_P	0.704	0.28
26_A	32_M	0.704	0.28
11_S	17_F	0.703	0.28
27_W	30_R	0.703	0.28
173_T	180_G	0.703	0.28
33_R	40_R	0.697	0.27
224_A	227_P	0.696	0.27
100_V	231_T	0.696	0.27
97_K	187_R	0.696	0.27
105_N	127_G	0.696	0.27
38_M	43_R	0.692	0.27
29_K	32_M	0.691	0.27
9_R	16_P	0.686	0.27
128_A	138_G	0.685	0.27
16_P	45_P	0.684	0.27
130_P	136_L	0.684	0.27
89_I	195_F	0.683	0.27
89_I	206_K	0.676	0.26
132_T	137_F	0.675	0.26
97_K	234_I	0.674	0.26
239_Y	242_Y	0.673	0.26
8_S	14_R	0.673	0.26
55_N	128_A	0.668	0.26
115_V	213_N	0.667	0.26
14_R	17_F	0.666	0.26
15_A	19_R	0.663	0.26
209_N	213_N	0.660	0.25
92_K	237_Y	0.660	0.25
8_S	23_K	0.659	0.25
96_F	100_V	0.658	0.25
28_G	37_R	0.657	0.25
35_K	106_I	0.656	0.25
34_R	40_R	0.655	0.25
61_F	69_V	0.654	0.25
23_K	37_R	0.653	0.25
9_R	14_R	0.651	0.25
136_L	168_T	0.651	0.25
187_R	190_N	0.650	0.25
146_T	215_L	0.648	0.25
93_S	160_L	0.648	0.25
205_G	213_N	0.647	0.25
91_L	160_L	0.647	0.25
60_R	225_S	0.640	0.24
6_F	10_R	0.634	0.24
17_F	22_N	0.629	0.24
5_N	11_S	0.628	0.24
97_K	164_K	0.628	0.24
16_P	26_A	0.628	0.24
203_E	219_Y	0.627	0.24
5_N	17_F	0.626	0.24
116_M	137_F	0.623	0.24
144_P	150_K	0.622	0.23
25_R	72_I	0.622	0.23
41_M	45_P	0.619	0.23
37_R	73_S	0.619	0.23
32_M	35_K	0.618	0.23
18_K	26_A	0.618	0.23
18_K	23_K	0.617	0.23
227_P	231_T	0.616	0.23
124_R	212_K	0.616	0.23
187_R	192_W	0.616	0.23
38_M	45_P	0.615	0.23
73_S	78_G	0.614	0.23
36_P	42_Y	0.613	0.23
27_W	35_K	0.613	0.23
23_K	28_G	0.611	0.23
7_D	23_K	0.611	0.23
58_G	214_A	0.609	0.23
124_R	150_K	0.605	0.23
11_S	157_F	0.604	0.23
9_R	23_K	0.604	0.23
84_R	156_R	0.603	0.23
127_G	232_L	0.603	0.23
11_S	23_K	0.602	0.23
46_P	158_Q	0.602	0.23
33_R	43_R	0.601	0.22
164_K	205_G	0.599	0.22
61_F	103_D	0.593	0.22
79_K	197_V	0.592	0.22
154_R	200_N	0.592	0.22
71_C	111_H	0.585	0.22
46_P	51_S	0.585	0.22
207_Y	219_Y	0.582	0.22
223_S	230_A	0.582	0.22
39_Y	43_R	0.581	0.22
15_A	18_K	0.580	0.21
134_D	153_L	0.580	0.21
26_A	42_Y	0.579	0.21
194_N	199_Y	0.574	0.21
223_S	228_V	0.573	0.21
70_T	142_N	0.573	0.21
102_M	113_G	0.571	0.21
173_T	176_V	0.569	0.21
88_R	98_G	0.567	0.21
33_R	36_P	0.566	0.21
73_S	76_T	0.564	0.21
106_I	148_T	0.563	0.21
70_T	114_V	0.563	0.21
82_T	213_N	0.563	0.21
64_S	73_S	0.562	0.21
20_S	31_P	0.561	0.21
225_S	228_V	0.558	0.20
38_M	41_M	0.558	0.20
7_D	159_V	0.557	0.20
110_N	189_F	0.555	0.20
21_T	43_R	0.555	0.20
165_R	189_F	0.553	0.20
214_A	238_F	0.553	0.20
134_D	138_G	0.552	0.20
9_R	20_S	0.549	0.20
110_N	113_G	0.549	0.20
51_S	64_S	0.548	0.20
20_S	215_L	0.545	0.20
7_D	22_N	0.543	0.20
26_A	41_M	0.543	0.20
64_S	107_K	0.542	0.20
65_N	134_D	0.542	0.20
28_G	35_K	0.542	0.20
10_R	18_K	0.541	0.20
64_S	113_G	0.540	0.20
125_P	137_F	0.537	0.20
74_D	202_S	0.535	0.19
7_D	20_S	0.533	0.19
13_A	36_P	0.529	0.19
140_R	144_P	0.529	0.19
81_E	154_R	0.527	0.19
223_S	226_N	0.526	0.19
233_K	236_V	0.526	0.19
33_R	41_M	0.525	0.19
83_N	196_K	0.522	0.19
159_V	165_R	0.521	0.19
181_K	189_F	0.521	0.19
115_V	165_R	0.519	0.19
36_P	98_G	0.518	0.19
195_F	198_V	0.515	0.19
113_G	116_M	0.514	0.19
184_L	197_V	0.514	0.19
229_Y	239_Y	0.509	0.18
204_A	209_N	0.509	0.18
76_T	83_N	0.509	0.18
133_F	175_M	0.508	0.18
45_P	59_P	0.508	0.18
196_K	213_N	0.503	0.18
21_T	25_R	0.502	0.18
188_R	192_W	0.500	0.18

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
1vtze	8	0.75	99.4	0.757	Contact Map
1f2nA	12	0.7008	4.6	0.962	Contact Map
3zqxA	1	0.2049	4.6	0.962	Contact Map
1c8nA	8	0.7746	4.2	0.963	Contact Map
4htvB	1	0.0287	4.2	0.963	Contact Map
1opoA	7	0.7213	3.8	0.963	Contact Map
4llfA	8	0.7828	3.3	0.965	Contact Map
2tbvA	9	0.7992	3.3	0.965	Contact Map
4fp5D	3	0.209	2.1	0.968	Contact Map
4b97A	1	0.209	2.1	0.968	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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