DUF4330 - PFAM28P - GREMLIN Contacts

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DUF4330 - Domain of unknown function (DUF4330)

PFAM:	PF14221	Sequences: MKIIDEKGRLFGKINIIDLLVILVILAVAAGVFYKPGGSGSVAQVGGAATKPVEVTVTVRGLGVPEELADIKVGDKVYDSIRNQPYGEVTITDVEVEPATVAVPDPDGTVVAAPDEPGRYDVLITLEGKATITDDGIVVGGQEIKVGTPIELKTKNYEFNGTVIDVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	167 (160)
Sequences:	1799 (1532)
Seq/√Len:	121.1
META:	0.839

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_D	109_T	4.291	1.00
90_T	127_E	4.070	1.00
54_E	127_E	3.353	1.00
92_T	127_E	3.204	1.00
76_K	90_T	3.111	1.00
66_E	70_D	2.897	1.00
99_A	121_D	2.849	1.00
60_R	121_D	2.706	1.00
32_V	36_P	2.558	1.00
15_N	19_L	2.426	1.00
33_F	37_G	2.333	1.00
128_G	139_V	2.264	1.00
56_T	127_E	2.225	1.00
5_D	9_R	2.196	1.00
100_T	114_P	2.168	1.00
93_D	125_T	2.109	1.00
98_P	114_P	2.028	1.00
153_K	158_E	1.971	1.00
73_V	93_D	1.964	1.00
136_G	145_K	1.921	1.00
65_P	68_L	1.907	1.00
100_T	112_A	1.856	1.00
146_V	166_V	1.818	1.00
30_A	34_Y	1.814	1.00
154_T	157_Y	1.802	1.00
94_V	124_I	1.782	1.00
54_E	129_K	1.748	1.00
20_L	27_A	1.685	1.00
52_P	129_K	1.684	1.00
71_I	91_I	1.662	1.00
105_D	111_V	1.660	1.00
55_V	130_A	1.651	1.00
97_E	123_L	1.629	1.00
96_V	120_Y	1.618	1.00
132_I	137_I	1.606	1.00
86_Y	89_V	1.599	1.00
8_G	12_G	1.584	1.00
72_K	75_D	1.561	1.00
71_I	75_D	1.475	1.00
8_G	14_I	1.439	1.00
13_K	19_L	1.418	1.00
146_V	165_D	1.403	1.00
3_I	6_E	1.388	1.00
31_G	35_K	1.380	1.00
29_A	33_F	1.353	1.00
35_K	38_G	1.335	1.00
76_K	88_E	1.327	1.00
61_G	159_F	1.302	1.00
4_I	8_G	1.296	1.00
58_T	123_L	1.275	1.00
73_V	94_V	1.275	1.00
8_G	11_F	1.219	0.99
163_V	166_V	1.216	0.99
95_E	123_L	1.209	0.99
56_T	125_T	1.204	0.99
92_T	125_T	1.181	0.99
151_E	158_E	1.169	0.99
23_L	27_A	1.161	0.99
115_D	118_G	1.148	0.99
95_E	125_T	1.139	0.99
31_G	34_Y	1.135	0.99
149_P	160_N	1.134	0.99
54_E	58_T	1.131	0.99
143_E	148_T	1.127	0.99
115_D	120_Y	1.125	0.99
69_A	120_Y	1.123	0.99
97_E	121_D	1.121	0.99
28_V	31_G	1.119	0.99
62_L	121_D	1.104	0.99
14_I	22_I	1.099	0.99
59_V	161_G	1.080	0.98
77_V	126_L	1.075	0.98
142_Q	150_I	1.052	0.98
75_D	156_N	1.042	0.98
32_V	35_K	1.029	0.98
147_G	152_L	1.015	0.98
15_N	18_D	1.012	0.98
34_Y	37_G	0.970	0.97
123_L	164_I	0.960	0.97
71_I	157_Y	0.954	0.97
10_L	14_I	0.944	0.96
75_D	157_Y	0.940	0.96
145_K	153_K	0.928	0.96
9_R	12_G	0.921	0.96
149_P	162_T	0.916	0.96
135_D	143_E	0.909	0.96
61_G	64_V	0.894	0.95
130_A	136_G	0.890	0.95
144_I	148_T	0.890	0.95
53_V	56_T	0.881	0.95
9_R	13_K	0.877	0.95
66_E	120_Y	0.877	0.95
24_V	28_V	0.875	0.94
63_G	119_R	0.874	0.94
15_N	139_V	0.874	0.94
11_F	14_I	0.873	0.94
66_E	118_G	0.863	0.94
99_A	119_R	0.858	0.94
14_I	19_L	0.852	0.94
101_V	115_D	0.847	0.93
16_I	37_G	0.844	0.93
4_I	7_K	0.842	0.93
128_G	142_Q	0.838	0.93
79_D	150_I	0.834	0.93
61_G	65_P	0.827	0.93
34_Y	38_G	0.826	0.93
99_A	115_D	0.824	0.93
102_A	110_V	0.823	0.92
105_D	108_G	0.821	0.92
5_D	25_I	0.821	0.92
33_F	36_P	0.817	0.92
35_K	143_E	0.809	0.92
60_R	123_L	0.802	0.91
13_K	35_K	0.795	0.91
97_E	100_T	0.787	0.91
3_I	66_E	0.786	0.91
140_G	153_K	0.786	0.91
146_V	153_K	0.778	0.90
56_T	60_R	0.776	0.90
27_A	34_Y	0.774	0.90
104_P	110_V	0.767	0.90
28_V	34_Y	0.766	0.90
104_P	107_D	0.754	0.89
83_N	145_K	0.751	0.89
25_I	29_A	0.743	0.88
28_V	32_V	0.738	0.88
157_Y	160_N	0.735	0.88
17_I	38_G	0.733	0.87
8_G	16_I	0.732	0.87
74_G	79_D	0.732	0.87
57_V	61_G	0.723	0.87
17_I	154_T	0.720	0.86
140_G	152_L	0.711	0.86
5_D	14_I	0.703	0.85
79_D	142_Q	0.703	0.85
142_Q	145_K	0.695	0.84
6_E	66_E	0.693	0.84
63_G	102_A	0.692	0.84
92_T	96_V	0.689	0.84
152_L	159_F	0.686	0.84
69_A	96_V	0.685	0.84
22_I	133_T	0.677	0.83
49_A	111_V	0.674	0.83
138_V	141_G	0.673	0.83
108_G	111_V	0.667	0.82
136_G	143_E	0.666	0.82
130_A	153_K	0.665	0.82
23_L	144_I	0.658	0.81
7_K	10_L	0.657	0.81
138_V	143_E	0.657	0.81
32_V	73_V	0.655	0.81
74_G	90_T	0.654	0.81
105_D	113_A	0.652	0.81
55_V	128_G	0.650	0.80
59_V	62_L	0.648	0.80
56_T	63_G	0.646	0.80
26_L	29_A	0.646	0.80
8_G	15_N	0.641	0.79
143_E	151_E	0.639	0.79
143_E	153_K	0.638	0.79
62_L	99_A	0.637	0.79
133_T	138_V	0.633	0.79
74_G	80_S	0.633	0.79
145_K	157_Y	0.630	0.78
130_A	139_V	0.629	0.78
156_N	160_N	0.625	0.78
57_V	128_G	0.623	0.77
71_I	124_I	0.622	0.77
152_L	161_G	0.622	0.77
31_G	154_T	0.618	0.77
102_A	112_A	0.615	0.77
74_G	77_V	0.613	0.76
96_V	122_V	0.612	0.76
78_Y	81_I	0.611	0.76
5_D	8_G	0.610	0.76
3_I	10_L	0.607	0.76
73_V	92_T	0.605	0.75
99_A	117_P	0.604	0.75
58_T	61_G	0.604	0.75
58_T	165_D	0.604	0.75
16_I	95_E	0.602	0.75
93_D	96_V	0.599	0.75
55_V	137_I	0.597	0.74
17_I	21_V	0.597	0.74
5_D	15_N	0.596	0.74
69_A	91_I	0.592	0.74
42_V	45_V	0.591	0.74
46_G	50_T	0.589	0.73
121_D	137_I	0.587	0.73
108_G	115_D	0.587	0.73
81_I	154_T	0.586	0.73
101_V	135_D	0.585	0.73
154_T	158_E	0.585	0.73
33_F	38_G	0.585	0.73
23_L	30_A	0.582	0.73
13_K	16_I	0.581	0.72
20_L	28_V	0.579	0.72
104_P	112_A	0.579	0.72
151_E	160_N	0.572	0.71
67_E	70_D	0.572	0.71
89_V	131_T	0.571	0.71
80_S	83_N	0.568	0.71
57_V	157_Y	0.565	0.70
108_G	113_A	0.564	0.70
77_V	130_A	0.563	0.70
148_T	162_T	0.562	0.70
74_G	124_I	0.562	0.70
15_N	63_G	0.562	0.70
100_T	111_V	0.560	0.70
62_L	122_V	0.558	0.69
109_T	113_A	0.552	0.69
32_V	123_L	0.549	0.68
8_G	17_I	0.547	0.68
72_K	94_V	0.540	0.67
70_D	94_V	0.540	0.67
25_I	50_T	0.537	0.66
143_E	154_T	0.533	0.66
75_D	79_D	0.532	0.66
128_G	140_G	0.530	0.65
3_I	125_T	0.527	0.65
64_V	68_L	0.527	0.65
141_G	148_T	0.526	0.65
6_E	21_V	0.522	0.64
114_P	124_I	0.521	0.64
83_N	88_E	0.520	0.64
80_S	158_E	0.519	0.64
83_N	154_T	0.514	0.63
7_K	92_T	0.513	0.63
98_P	120_Y	0.511	0.63
78_Y	152_L	0.511	0.63
57_V	144_I	0.511	0.63
9_R	117_P	0.510	0.63
31_G	36_P	0.510	0.63
58_T	124_I	0.509	0.62
35_K	141_G	0.508	0.62
60_R	63_G	0.506	0.62
147_G	159_F	0.506	0.62
123_L	136_G	0.504	0.62
74_G	86_Y	0.500	0.61
145_K	154_T	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
3kxrA	3	0.1677	19.3	0.918	Contact Map
2m7gA	1	0.3593	5.4	0.936	Contact Map
3j1rA	5	0.1557	5.4	0.936	Contact Map
2y6tE	2	0.3593	5	0.937	Contact Map
3umnA	1	0.4731	4.6	0.938	Contact Map
4pliA	1	0.1497	4.2	0.939	Contact Map
2wwbC	1	0.2156	3.6	0.941	Contact Map
2m8rA	1	0.2275	3.5	0.942	Contact Map
2ww9C	1	0.1257	3.4	0.942	Contact Map
3j3wP	1	0.2455	3.2	0.942	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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