PDDEXK_6 - PFAM28P - GREMLIN Contacts

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PDDEXK_6 - PDDEXK-like family of unknown function

PFAM:	PF04720	Sequences: SDMVQSFLEEGNESQSSSSNCFNGSDSSDDEFDFWEEQAELLKSLLSCASSAERNLLADVKKAVEKIKEAGRGCRSCLRREVMDRLRALGYDAAICKSKWEKSGSIPAGEYEYIDVVVEGSSSGKKGEERYIVDLDFRSEFEIARPTEEYKALLQSLPEVFVGKPERLKQIVRIMCEAAKQSLKEKGMHLPPWRKARYMQAKWLSPYKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	209 (204)
Sequences:	628 (435)
Seq/√Len:	30.4
META:	0.04

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_Y	134_D	4.344	1.00
93_A	115_D	3.775	1.00
28_S	31_E	3.655	1.00
115_D	130_R	3.000	1.00
13_E	16_S	2.868	1.00
53_E	167_R	2.807	1.00
146_P	186_K	2.511	0.99
79_R	113_Y	2.395	0.99
113_Y	189_H	2.273	0.99
153_L	175_M	2.242	0.99
12_N	15_Q	2.119	0.98
94_A	209_R	2.097	0.98
112_E	182_S	2.046	0.98
100_W	109_G	2.014	0.97
134_D	137_F	1.996	0.97
195_K	199_M	1.985	0.97
169_K	200_Q	1.947	0.97
92_D	95_I	1.839	0.95
111_Y	176_C	1.808	0.95
103_S	151_K	1.770	0.94
96_C	145_R	1.768	0.94
172_V	200_Q	1.765	0.94
83_M	207_Y	1.703	0.93
96_C	115_D	1.640	0.92
92_D	105_S	1.608	0.91
198_Y	201_A	1.588	0.90
153_L	163_G	1.586	0.90
27_S	30_D	1.573	0.90
27_S	175_M	1.559	0.89
161_F	168_L	1.559	0.89
119_E	128_E	1.554	0.89
13_E	17_S	1.542	0.89
42_L	180_K	1.538	0.89
99_K	207_Y	1.518	0.88
81_E	113_Y	1.505	0.88
146_P	191_P	1.501	0.87
138_R	195_K	1.490	0.87
131_Y	167_R	1.483	0.87
11_G	17_S	1.479	0.87
63_A	205_S	1.442	0.85
28_S	33_D	1.440	0.85
83_M	95_I	1.436	0.85
9_E	82_V	1.433	0.85
172_V	183_L	1.429	0.85
90_G	150_Y	1.427	0.85
98_S	197_R	1.419	0.84
82_V	195_K	1.419	0.84
134_D	140_E	1.415	0.84
97_K	197_R	1.407	0.84
176_C	187_G	1.406	0.84
142_E	198_Y	1.381	0.83
60_V	191_P	1.366	0.82
136_D	171_I	1.365	0.82
188_M	201_A	1.358	0.82
20_N	139_S	1.349	0.81
77_C	146_P	1.348	0.81
140_E	165_P	1.341	0.81
56_L	177_E	1.330	0.80
94_A	115_D	1.319	0.80
23_N	32_F	1.315	0.79
100_W	198_Y	1.314	0.79
68_K	95_I	1.292	0.78
96_C	100_W	1.280	0.78
16_S	19_S	1.254	0.76
137_F	204_L	1.251	0.76
53_E	131_Y	1.247	0.76
93_A	182_S	1.242	0.75
111_Y	184_K	1.233	0.75
100_W	157_L	1.225	0.74
4_V	7_F	1.220	0.74
58_A	114_I	1.218	0.74
4_V	9_E	1.210	0.73
42_L	171_I	1.208	0.73
20_N	23_N	1.205	0.73
98_S	113_Y	1.201	0.73
29_D	33_D	1.197	0.73
139_S	178_A	1.190	0.72
50_S	131_Y	1.182	0.72
104_G	190_L	1.180	0.71
145_R	198_Y	1.162	0.70
155_Q	161_F	1.147	0.69
95_I	167_R	1.145	0.69
197_R	200_Q	1.141	0.69
82_V	135_L	1.132	0.68
136_D	139_S	1.129	0.68
87_R	130_R	1.123	0.68
62_K	111_Y	1.122	0.68
161_F	167_R	1.110	0.67
18_S	25_S	1.109	0.67
163_G	168_L	1.107	0.66
55_N	132_I	1.100	0.66
117_V	179_A	1.096	0.66
194_R	203_W	1.094	0.66
193_W	203_W	1.094	0.66
192_P	203_W	1.094	0.66
95_I	137_F	1.092	0.65
15_Q	19_S	1.090	0.65
99_K	163_G	1.067	0.64
79_R	112_E	1.065	0.63
100_W	182_S	1.064	0.63
115_D	198_Y	1.048	0.62
111_Y	182_S	1.047	0.62
71_G	132_I	1.043	0.62
85_R	89_L	1.041	0.62
189_H	199_M	1.038	0.61
57_L	134_D	1.037	0.61
134_D	191_P	1.033	0.61
79_R	178_A	1.028	0.61
26_D	33_D	1.025	0.60
56_L	91_Y	1.023	0.60
109_G	198_Y	1.011	0.59
5_Q	8_L	1.008	0.59
5_Q	15_Q	1.004	0.59
15_Q	18_S	0.997	0.58
10_E	132_I	0.995	0.58
91_Y	134_D	0.991	0.58
173_R	196_A	0.990	0.58
17_S	23_N	0.986	0.57
130_R	145_R	0.985	0.57
96_C	130_R	0.985	0.57
98_S	107_P	0.984	0.57
83_M	87_R	0.981	0.57
95_I	133_V	0.965	0.56
84_D	170_Q	0.959	0.55
80_R	83_M	0.958	0.55
83_M	94_A	0.956	0.55
59_D	91_Y	0.952	0.55
83_M	111_Y	0.949	0.54
176_C	200_Q	0.947	0.54
106_I	138_R	0.944	0.54
79_R	115_D	0.944	0.54
113_Y	185_E	0.941	0.54
14_S	18_S	0.939	0.54
21_C	29_D	0.939	0.54
146_P	204_L	0.936	0.53
172_V	176_C	0.934	0.53
55_N	134_D	0.930	0.53
163_G	171_I	0.929	0.53
39_A	42_L	0.928	0.53
24_G	27_S	0.921	0.52
9_E	25_S	0.921	0.52
8_L	21_C	0.920	0.52
3_M	50_S	0.919	0.52
115_D	206_P	0.915	0.52
180_K	198_Y	0.915	0.52
87_R	94_A	0.909	0.51
53_E	198_Y	0.902	0.51
135_L	159_E	0.901	0.51
113_Y	145_R	0.900	0.51
102_K	166_E	0.897	0.50
130_R	198_Y	0.897	0.50
131_Y	169_K	0.895	0.50
138_R	185_E	0.894	0.50
150_Y	204_L	0.891	0.50
115_D	209_R	0.890	0.50
73_G	76_S	0.888	0.50
35_W	38_Q	0.880	0.49
104_G	161_F	0.874	0.48
3_M	8_L	0.865	0.48
139_S	142_E	0.851	0.47
11_G	14_S	0.848	0.46
156_S	188_M	0.840	0.46
77_C	135_L	0.835	0.45
96_C	198_Y	0.835	0.45
64_V	99_K	0.829	0.45
45_L	124_G	0.820	0.44
140_E	183_L	0.816	0.44
187_G	196_A	0.815	0.44
3_M	9_E	0.811	0.43
60_V	66_K	0.808	0.43
6_S	140_E	0.805	0.43
8_L	14_S	0.802	0.43
147_T	191_P	0.801	0.43
191_P	203_W	0.795	0.42
52_A	113_Y	0.790	0.42
151_K	154_L	0.790	0.42
169_K	205_S	0.785	0.41
157_L	179_A	0.782	0.41
75_R	78_L	0.780	0.41
186_K	195_K	0.771	0.40
79_R	195_K	0.764	0.40
13_E	19_S	0.763	0.40
23_N	28_S	0.763	0.40
139_S	198_Y	0.760	0.39
96_C	109_G	0.759	0.39
109_G	115_D	0.758	0.39
6_S	91_Y	0.757	0.39
25_S	30_D	0.741	0.38
161_F	171_I	0.741	0.38
44_S	120_G	0.741	0.38
172_V	196_A	0.735	0.38
133_V	205_S	0.733	0.37
91_Y	117_V	0.732	0.37
8_L	111_Y	0.727	0.37
58_A	115_D	0.726	0.37
70_A	98_S	0.725	0.37
178_A	183_L	0.720	0.36
53_E	201_A	0.716	0.36
4_V	170_Q	0.708	0.36
130_R	204_L	0.707	0.36
2_D	6_S	0.705	0.35
184_K	190_L	0.703	0.35
85_R	91_Y	0.700	0.35
97_K	111_Y	0.700	0.35
149_E	155_Q	0.694	0.35
37_E	190_L	0.694	0.35
34_F	190_L	0.693	0.34
149_E	164_K	0.691	0.34
56_L	65_E	0.691	0.34
140_E	199_M	0.690	0.34
29_D	32_F	0.689	0.34
36_E	116_V	0.682	0.34
118_V	135_L	0.671	0.33
107_P	138_R	0.669	0.33
107_P	188_M	0.667	0.33
91_Y	138_R	0.658	0.32
17_S	43_K	0.657	0.32
100_W	107_P	0.657	0.32
83_M	104_G	0.655	0.32
110_E	138_R	0.653	0.32
26_D	29_D	0.653	0.32
174_I	188_M	0.653	0.32
56_L	60_V	0.650	0.31
79_R	204_L	0.649	0.31
94_A	173_R	0.648	0.31
25_S	31_E	0.647	0.31
10_E	13_E	0.646	0.31
109_G	145_R	0.642	0.31
105_S	197_R	0.642	0.31
147_T	162_V	0.640	0.31
21_C	28_S	0.632	0.30
55_N	59_D	0.631	0.30
26_D	31_E	0.630	0.30
24_G	73_G	0.629	0.30
164_K	195_K	0.629	0.30
91_Y	132_I	0.627	0.30
114_I	170_Q	0.624	0.30
128_E	175_M	0.624	0.30
92_D	130_R	0.622	0.30
23_N	27_S	0.622	0.30
110_E	189_H	0.618	0.29
52_A	199_M	0.614	0.29
139_S	175_M	0.614	0.29
70_A	133_V	0.612	0.29
92_D	169_K	0.610	0.29
77_C	99_K	0.609	0.29
62_K	182_S	0.607	0.29
14_S	17_S	0.604	0.28
181_Q	187_G	0.603	0.28
8_L	15_Q	0.602	0.28
61_K	65_E	0.597	0.28
99_K	106_I	0.597	0.28
59_D	161_F	0.596	0.28
68_K	115_D	0.594	0.28
95_I	169_K	0.594	0.28
57_L	176_C	0.591	0.28
15_Q	27_S	0.584	0.27
93_A	113_Y	0.583	0.27
45_L	120_G	0.581	0.27
25_S	29_D	0.581	0.27
84_D	188_M	0.577	0.27
103_S	197_R	0.576	0.27
81_E	174_I	0.575	0.27
33_D	36_E	0.574	0.26
23_N	82_V	0.570	0.26
137_F	152_A	0.567	0.26
135_L	165_P	0.559	0.26
168_L	188_M	0.558	0.25
42_L	168_L	0.557	0.25
80_R	160_V	0.555	0.25
24_G	28_S	0.553	0.25
140_E	195_K	0.542	0.25
114_I	136_D	0.541	0.24
2_D	5_Q	0.539	0.24
14_S	19_S	0.538	0.24
10_E	155_Q	0.538	0.24
95_I	114_I	0.535	0.24
12_N	18_S	0.534	0.24
36_E	41_L	0.529	0.24
38_Q	191_P	0.526	0.24
194_R	202_K	0.522	0.23
192_P	202_K	0.522	0.23
193_W	202_K	0.522	0.23
127_G	149_E	0.519	0.23
75_R	171_I	0.519	0.23
40_E	43_K	0.518	0.23
35_W	134_D	0.518	0.23
34_F	37_E	0.517	0.23
13_E	29_D	0.517	0.23
136_D	186_K	0.515	0.23
42_L	151_K	0.515	0.23
81_E	118_V	0.512	0.23
42_L	156_S	0.510	0.23
189_H	200_Q	0.509	0.23
104_G	169_K	0.509	0.23
3_M	53_E	0.508	0.23
42_L	174_I	0.508	0.23
24_G	32_F	0.504	0.22
191_P	207_Y	0.503	0.22
107_P	201_A	0.503	0.22
161_F	188_M	0.502	0.22
196_A	200_Q	0.502	0.22
3_M	138_R	0.501	0.22
74_C	77_C	0.500	0.22
92_D	195_K	0.500	0.22
37_E	169_K	0.500	0.22

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
1e2tA	5	0.7703	31.8	0.955	Contact Map
4rcnA	6	0.6459	30.6	0.956	Contact Map
3hblA	4	0.6746	28	0.957	Contact Map
3i12A	2	0.7033	12.5	0.963	Contact Map
3n6rA	1	0.5885	11.8	0.963	Contact Map
4dmoA	1	0.8182	11.6	0.964	Contact Map
4qshA	4	0.622	11.3	0.964	Contact Map
4guzA	2	0.8373	11	0.964	Contact Map
4c5pA	1	0.8182	10.8	0.964	Contact Map
1w4tA	1	0.823	10.5	0.964	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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