DUF4417 - PFAM28P - GREMLIN Contacts

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DUF4417 - Domain of unknown function (DUF4417)

PFAM:	PF14386	Sequences: ESDGKYEIPIIKPTDIIELPDKLIPFSKAKKKKKDKNKGVHFFLDDYRFERVWNNPEKYLEKLKKFKGVITPDFSLYRDMPLAMQIWNIYRNRWIGAYWQSNGIKVIPNVRWGDERSYDFCFDGIPKGSVVAISTVGCIKSKEDRELFLAGLEEMLERLEPSTIIVYGSPPDEMFGNIKEQIEIIQFD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (175)
Sequences:	1904 (1594)
Seq/√Len:	120.5
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
154_E	157_E	3.808	1.00
71_T	96_G	3.581	1.00
154_E	158_R	3.412	1.00
39_G	68_G	3.134	1.00
127_K	160_E	2.873	1.00
43_F	132_A	2.540	1.00
128_G	160_E	2.469	1.00
43_F	109_N	2.457	1.00
113_G	117_S	2.319	1.00
83_A	86_I	2.128	1.00
53_W	91_R	2.123	1.00
27_S	44_L	2.092	1.00
6_Y	86_I	2.035	1.00
115_E	150_A	2.010	1.00
97_A	101_S	1.989	1.00
3_D	10_I	1.973	1.00
84_M	87_W	1.946	1.00
110_V	125_I	1.937	1.00
69_V	99_W	1.929	1.00
89_I	93_R	1.834	1.00
110_V	155_M	1.820	1.00
70_I	109_N	1.718	1.00
88_N	91_R	1.716	1.00
29_A	62_K	1.638	1.00
131_V	164_I	1.605	1.00
93_R	125_I	1.604	1.00
55_N	58_K	1.589	1.00
130_V	163_T	1.571	1.00
27_S	48_R	1.569	1.00
156_L	164_I	1.561	1.00
26_F	59_Y	1.557	1.00
131_V	155_M	1.548	1.00
133_I	152_L	1.547	1.00
112_W	151_G	1.544	1.00
22_K	38_K	1.535	1.00
60_L	102_N	1.529	1.00
95_I	99_W	1.491	1.00
69_V	104_I	1.473	1.00
122_F	155_M	1.471	1.00
82_L	116_R	1.464	1.00
89_I	92_N	1.449	1.00
25_P	41_H	1.436	1.00
146_E	150_A	1.435	1.00
51_R	59_Y	1.427	1.00
4_G	123_D	1.418	1.00
82_L	120_F	1.418	1.00
14_T	105_K	1.415	1.00
155_M	159_L	1.415	1.00
57_E	98_Y	1.398	1.00
53_W	74_F	1.396	1.00
5_K	119_D	1.382	1.00
83_A	90_Y	1.373	1.00
4_G	7_E	1.370	1.00
85_Q	117_S	1.365	1.00
85_Q	120_F	1.356	1.00
25_P	44_L	1.305	1.00
89_I	120_F	1.295	1.00
42_F	49_F	1.293	1.00
80_M	84_M	1.285	1.00
25_P	28_K	1.278	1.00
63_L	69_V	1.243	0.99
93_R	124_G	1.234	0.99
13_P	100_Q	1.215	0.99
50_E	91_R	1.214	0.99
125_I	131_V	1.206	0.99
40_V	63_L	1.191	0.99
23_L	41_H	1.189	0.99
12_K	100_Q	1.179	0.99
70_I	132_A	1.157	0.99
117_S	120_F	1.151	0.99
11_I	126_P	1.151	0.99
87_W	91_R	1.146	0.99
11_I	71_T	1.143	0.99
61_E	64_K	1.139	0.99
122_F	154_E	1.129	0.99
60_L	98_Y	1.125	0.99
4_G	10_I	1.121	0.99
130_V	162_S	1.120	0.99
45_D	48_R	1.099	0.99
78_R	147_L	1.098	0.99
152_L	164_I	1.078	0.98
123_D	158_R	1.063	0.98
14_T	17_I	1.059	0.98
64_K	102_N	1.057	0.98
82_L	86_I	1.050	0.98
78_R	144_D	1.044	0.98
50_E	54_N	1.043	0.98
37_N	67_K	1.042	0.98
118_Y	122_F	1.037	0.98
112_W	122_F	1.022	0.98
36_K	65_K	1.021	0.98
62_K	65_K	1.004	0.97
52_V	99_W	0.997	0.97
21_D	37_N	0.983	0.97
152_L	178_I	0.974	0.97
94_W	97_A	0.957	0.97
49_F	52_V	0.953	0.97
99_W	104_I	0.952	0.97
110_V	131_V	0.951	0.96
7_E	82_L	0.944	0.96
53_W	87_W	0.937	0.96
118_Y	151_G	0.934	0.96
148_F	151_G	0.932	0.96
76_L	113_G	0.928	0.96
23_L	70_I	0.926	0.96
6_Y	83_A	0.924	0.96
12_K	126_P	0.916	0.96
76_L	111_R	0.912	0.96
52_V	95_I	0.912	0.96
63_L	99_W	0.908	0.95
35_D	65_K	0.907	0.95
141_S	144_D	0.903	0.95
111_R	134_S	0.902	0.95
171_P	174_M	0.896	0.95
22_K	35_D	0.893	0.95
29_A	40_V	0.891	0.95
42_F	52_V	0.883	0.95
152_L	155_M	0.880	0.95
26_F	63_L	0.879	0.95
92_N	125_I	0.878	0.95
108_P	125_I	0.878	0.95
64_K	104_I	0.870	0.94
42_F	63_L	0.869	0.94
50_E	53_W	0.868	0.94
118_Y	150_A	0.864	0.94
149_L	173_E	0.859	0.94
112_W	121_C	0.850	0.94
172_D	175_F	0.844	0.93
17_I	20_P	0.841	0.93
73_D	109_N	0.840	0.93
71_T	92_N	0.840	0.93
5_K	82_L	0.838	0.93
166_V	170_P	0.837	0.93
85_Q	113_G	0.829	0.93
12_K	97_A	0.827	0.93
56_P	95_I	0.826	0.93
128_G	162_S	0.822	0.92
26_F	42_F	0.818	0.92
22_K	37_N	0.814	0.92
107_I	132_A	0.810	0.92
43_F	70_I	0.805	0.92
128_G	159_L	0.803	0.91
56_P	99_W	0.801	0.91
11_I	96_G	0.793	0.91
90_Y	94_W	0.783	0.90
52_V	63_L	0.779	0.90
76_L	89_I	0.777	0.90
122_F	151_G	0.774	0.90
84_M	88_N	0.770	0.90
135_T	166_V	0.758	0.89
150_A	153_E	0.747	0.88
127_K	159_L	0.746	0.88
98_Y	102_N	0.743	0.88
8_I	123_D	0.735	0.87
81_P	90_Y	0.733	0.87
12_K	16_I	0.728	0.87
73_D	111_R	0.725	0.87
74_F	95_I	0.725	0.87
166_V	175_F	0.724	0.87
115_E	118_Y	0.719	0.86
131_V	159_L	0.718	0.86
85_Q	114_D	0.709	0.85
153_E	177_N	0.707	0.85
172_D	176_G	0.704	0.85
57_E	102_N	0.697	0.84
28_K	48_R	0.695	0.84
16_I	105_K	0.693	0.84
72_P	96_G	0.692	0.84
63_L	66_F	0.691	0.84
24_I	29_A	0.688	0.84
118_Y	121_C	0.688	0.84
15_D	162_S	0.688	0.84
81_P	84_M	0.687	0.84
83_A	87_W	0.686	0.84
60_L	99_W	0.684	0.83
13_P	16_I	0.682	0.83
13_P	126_P	0.679	0.83
149_L	177_N	0.674	0.82
59_Y	95_I	0.672	0.82
89_I	110_V	0.665	0.82
110_V	159_L	0.664	0.82
142_K	145_R	0.662	0.81
139_I	171_P	0.660	0.81
134_S	167_Y	0.653	0.80
58_K	62_K	0.652	0.80
7_E	116_R	0.647	0.80
23_L	39_G	0.645	0.80
56_P	94_W	0.644	0.80
152_L	175_F	0.642	0.79
145_R	149_L	0.638	0.79
117_S	121_C	0.638	0.79
26_F	51_R	0.630	0.78
174_M	177_N	0.629	0.78
83_A	91_R	0.626	0.78
114_D	117_S	0.624	0.77
74_F	91_R	0.624	0.77
24_I	40_V	0.623	0.77
94_W	98_Y	0.620	0.77
87_W	90_Y	0.620	0.77
56_P	59_Y	0.618	0.77
153_E	157_E	0.618	0.77
11_I	108_P	0.612	0.76
50_E	87_W	0.610	0.76
161_P	168_G	0.606	0.75
3_D	123_D	0.605	0.75
53_W	88_N	0.602	0.75
119_D	158_R	0.602	0.75
90_Y	124_G	0.594	0.74
111_R	138_C	0.592	0.74
148_F	155_M	0.584	0.73
153_E	178_I	0.583	0.72
63_L	104_I	0.582	0.72
157_E	160_E	0.576	0.72
6_Y	82_L	0.575	0.71
62_K	66_F	0.575	0.71
32_K	35_D	0.575	0.71
125_I	129_S	0.574	0.71
60_L	104_I	0.574	0.71
82_L	118_Y	0.573	0.71
71_T	106_V	0.572	0.71
170_P	174_M	0.569	0.71
152_L	156_L	0.568	0.71
133_I	148_F	0.567	0.70
122_F	131_V	0.558	0.69
129_S	159_L	0.556	0.69
97_A	100_Q	0.555	0.69
26_F	44_L	0.553	0.69
143_E	146_E	0.551	0.68
41_H	70_I	0.550	0.68
49_F	98_Y	0.548	0.68
33_K	36_K	0.545	0.67
117_S	147_L	0.543	0.67
82_L	85_Q	0.543	0.67
155_M	164_I	0.542	0.67
93_R	120_F	0.540	0.67
53_W	90_Y	0.538	0.66
21_D	67_K	0.538	0.66
39_G	70_I	0.535	0.66
29_A	66_F	0.535	0.66
134_S	137_G	0.535	0.66
59_Y	63_L	0.532	0.66
51_R	54_N	0.532	0.66
23_L	26_F	0.530	0.65
152_L	166_V	0.529	0.65
44_L	49_F	0.527	0.65
93_R	135_T	0.525	0.65
120_F	123_D	0.524	0.64
126_P	129_S	0.523	0.64
30_K	62_K	0.523	0.64
92_N	109_N	0.521	0.64
48_R	51_R	0.519	0.64
133_I	151_G	0.519	0.64
71_T	109_N	0.519	0.64
111_R	136_V	0.518	0.64
56_P	60_L	0.515	0.63
11_I	14_T	0.515	0.63
71_T	110_V	0.515	0.63
73_D	137_G	0.509	0.62
119_D	123_D	0.507	0.62
138_C	148_F	0.506	0.62
7_E	81_P	0.504	0.61
21_D	58_K	0.500	0.61

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
4q6tA	1	0.7713	16.9	0.944	Contact Map
4jc0A	1	0.5	15	0.945	Contact Map
2bfwA	1	0.4255	10.3	0.949	Contact Map
3pdiB	2	0.5851	9.3	0.95	Contact Map
3aekB	2	0.5585	9.3	0.95	Contact Map
2ynmD	2	0.5585	6.9	0.953	Contact Map
3qv2A	1	0.7128	6.8	0.953	Contact Map
2o6lA	2	0.3936	5.7	0.955	Contact Map
3u7qA	1	0.7819	5.3	0.955	Contact Map
2hiqA	2	0.4362	5.1	0.956	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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