DUF4446 - PFAM28P - GREMLIN Contacts

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DUF4446 - Protein of unknown function (DUF4446)

PFAM:	PF14584	Sequences: YIAIALAALALVLLILAIVLAVRLRRLRRRYRRLLGGKGGKDLEEVLVSLLERVDDLEEAVDELEARLARLERRLDGAIQKVGLVRYNAFEDTGGDQSFSLALLDENGDGVVLSSIHGRDGTRVYAKPIKNGKSEYELSPEEKEAIERAM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	150 (147)
Sequences:	7028 (5236)
Seq/√Len:	431.9
META:	0.907

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_L	21_A	3.300	1.00
67_R	72_E	2.829	1.00
53_R	58_E	2.724	1.00
144_E	148_R	2.611	1.00
100_S	114_S	2.508	1.00
81_K	108_G	2.499	1.00
88_N	96_D	2.465	1.00
102_A	145_A	2.362	1.00
17_A	20_L	2.304	1.00
6_L	10_A	2.259	1.00
75_L	78_A	2.240	1.00
128_P	136_Y	2.158	1.00
60_A	65_E	2.150	1.00
85_V	145_A	2.010	1.00
13_L	17_A	1.963	1.00
105_D	109_D	1.899	1.00
143_K	147_E	1.882	1.00
84_L	101_L	1.862	1.00
23_R	28_R	1.801	1.00
83_G	145_A	1.799	1.00
76_D	106_E	1.783	1.00
10_A	13_L	1.781	1.00
109_D	131_N	1.777	1.00
20_L	24_L	1.725	1.00
57_L	61_V	1.713	1.00
99_F	124_V	1.697	1.00
63_E	67_R	1.650	1.00
50_L	54_V	1.631	1.00
74_R	106_E	1.616	1.00
112_V	146_I	1.573	1.00
79_I	82_V	1.542	1.00
130_K	135_E	1.532	1.00
108_G	132_G	1.532	1.00
18_I	22_V	1.525	1.00
3_A	6_L	1.444	1.00
74_R	80_Q	1.436	1.00
64_L	68_L	1.425	1.00
42_D	45_E	1.424	1.00
71_L	75_L	1.390	1.00
31_Y	35_L	1.377	1.00
87_Y	100_S	1.364	1.00
104_L	129_I	1.359	1.00
76_D	107_N	1.355	1.00
16_L	20_L	1.321	1.00
128_P	135_E	1.312	1.00
79_I	103_L	1.290	1.00
140_P	143_K	1.280	1.00
22_V	26_R	1.261	1.00
80_Q	106_E	1.257	1.00
87_Y	114_S	1.235	1.00
129_I	146_I	1.223	1.00
4_I	8_A	1.202	1.00
60_A	63_E	1.183	1.00
129_I	134_S	1.180	1.00
51_L	54_V	1.177	1.00
137_E	143_K	1.166	1.00
109_D	130_K	1.156	1.00
77_G	107_N	1.146	1.00
96_D	135_E	1.140	1.00
101_L	113_L	1.138	1.00
107_N	131_N	1.126	1.00
15_I	19_V	1.124	1.00
102_A	112_V	1.109	1.00
68_L	71_L	1.091	1.00
28_R	32_R	1.089	1.00
92_D	120_D	1.081	1.00
96_D	136_Y	1.073	1.00
54_V	57_L	1.068	1.00
21_A	25_R	1.066	1.00
44_E	48_V	1.064	1.00
117_H	122_T	1.055	1.00
140_P	144_E	1.044	1.00
67_R	70_R	1.039	1.00
84_L	126_A	1.036	1.00
133_K	143_K	1.017	1.00
56_D	60_A	1.010	1.00
48_V	52_E	1.007	1.00
103_L	111_V	1.004	1.00
10_A	17_A	0.999	1.00
49_S	53_R	0.981	1.00
58_E	62_D	0.975	1.00
144_E	147_E	0.969	1.00
79_I	111_V	0.969	1.00
92_D	119_R	0.964	1.00
45_E	49_S	0.956	1.00
25_R	29_R	0.945	1.00
118_G	121_G	0.935	1.00
49_S	52_E	0.933	1.00
83_G	148_R	0.909	1.00
81_K	106_E	0.892	1.00
19_V	23_R	0.886	1.00
104_L	132_G	0.884	1.00
13_L	20_L	0.878	1.00
74_R	78_A	0.870	1.00
85_V	144_E	0.867	1.00
118_G	122_T	0.867	1.00
22_V	25_R	0.863	1.00
99_F	126_A	0.861	1.00
77_G	80_Q	0.853	1.00
89_A	116_I	0.848	1.00
101_L	111_V	0.847	1.00
61_V	64_L	0.845	1.00
59_E	63_E	0.843	1.00
48_V	51_L	0.839	1.00
70_R	74_R	0.838	1.00
63_E	66_A	0.837	1.00
104_L	146_I	0.837	1.00
47_L	51_L	0.826	1.00
24_L	27_L	0.820	1.00
62_D	65_E	0.816	1.00
52_E	55_D	0.814	1.00
145_A	149_A	0.811	1.00
134_S	138_L	0.810	1.00
89_A	121_G	0.808	1.00
62_D	66_A	0.807	1.00
39_G	42_D	0.804	1.00
40_G	43_L	0.804	1.00
17_A	21_A	0.799	1.00
55_D	59_E	0.796	1.00
86_R	136_Y	0.794	1.00
55_D	58_E	0.793	1.00
83_G	149_A	0.791	1.00
72_E	76_D	0.790	1.00
89_A	97_Q	0.786	1.00
88_N	95_G	0.783	1.00
51_L	55_D	0.783	1.00
3_A	10_A	0.780	1.00
65_E	69_A	0.770	1.00
66_A	70_R	0.769	1.00
59_E	62_D	0.766	1.00
11_L	15_I	0.751	1.00
89_A	96_D	0.748	1.00
37_G	44_E	0.745	1.00
73_R	76_D	0.733	1.00
9_L	13_L	0.731	1.00
6_L	13_L	0.728	1.00
31_Y	34_L	0.726	1.00
56_D	59_E	0.725	1.00
12_V	15_I	0.720	1.00
129_I	138_L	0.713	1.00
104_L	108_G	0.712	1.00
38_K	45_E	0.709	1.00
27_L	31_Y	0.707	1.00
66_A	69_A	0.701	1.00
42_D	46_V	0.701	1.00
113_L	126_A	0.697	1.00
46_V	50_L	0.690	1.00
138_L	146_I	0.685	1.00
19_V	22_V	0.682	1.00
134_S	146_I	0.680	1.00
130_K	133_K	0.678	1.00
21_A	24_L	0.668	1.00
53_R	56_D	0.668	1.00
58_E	61_V	0.654	0.99
46_V	51_L	0.643	0.99
43_L	47_L	0.637	0.99
41_K	45_E	0.635	0.99
93_T	117_H	0.633	0.99
47_L	50_L	0.633	0.99
24_L	28_R	0.633	0.99
7_A	11_L	0.632	0.99
114_S	139_S	0.631	0.99
50_L	53_R	0.626	0.99
38_K	42_D	0.621	0.99
89_A	98_S	0.614	0.99
45_E	48_V	0.612	0.99
115_S	126_A	0.612	0.99
37_G	42_D	0.612	0.99
82_V	109_D	0.612	0.99
120_D	124_V	0.608	0.99
52_E	56_D	0.607	0.99
36_G	55_D	0.604	0.99
105_D	132_G	0.601	0.99
49_S	55_D	0.599	0.99
26_R	30_R	0.598	0.99
27_L	30_R	0.598	0.99
5_A	8_A	0.596	0.99
9_L	14_L	0.592	0.99
99_F	117_H	0.590	0.99
35_L	46_V	0.589	0.99
8_A	12_V	0.589	0.99
115_S	122_T	0.588	0.99
7_A	10_A	0.583	0.99
57_L	60_A	0.582	0.99
35_L	38_K	0.582	0.99
24_L	31_Y	0.581	0.99
18_I	25_R	0.580	0.99
128_P	134_S	0.574	0.99
117_H	124_V	0.573	0.99
129_I	132_G	0.570	0.99
85_V	100_S	0.568	0.99
40_G	44_E	0.566	0.98
6_L	9_L	0.563	0.98
10_A	14_L	0.562	0.98
91_E	94_G	0.562	0.98
14_L	17_A	0.555	0.98
79_I	105_D	0.555	0.98
92_D	118_G	0.545	0.98
34_L	46_V	0.544	0.98
102_A	149_A	0.542	0.98
90_F	118_G	0.538	0.98
53_R	57_L	0.538	0.98
8_A	11_L	0.533	0.98
30_R	48_V	0.531	0.98
11_L	14_L	0.531	0.98
126_A	136_Y	0.530	0.98
86_R	96_D	0.527	0.98
90_F	99_F	0.519	0.97
75_L	79_I	0.519	0.97
97_Q	121_G	0.516	0.97
37_G	43_L	0.515	0.97
35_L	97_Q	0.512	0.97
43_L	46_V	0.511	0.97
34_L	40_G	0.510	0.97
51_L	57_L	0.510	0.97
70_R	73_R	0.508	0.97
84_L	111_V	0.506	0.97
112_V	127_K	0.506	0.97
85_V	148_R	0.503	0.97
35_L	89_A	0.500	0.97

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
4cq4A	4	0.5333	68.5	0.907	Contact Map
4i5sA	2	0.7467	57.7	0.913	Contact Map
3pjsK	4	0.46	56.5	0.914	Contact Map
3effK	4	0.4333	52.7	0.916	Contact Map
4cbcA	3	0.1667	48	0.918	Contact Map
3rvyA	3	0.1667	44.8	0.92	Contact Map
4gycB	2	0.14	44.3	0.92	Contact Map
2wujA	2	0.3333	37	0.923	Contact Map
4ltoA	3	0.46	35.4	0.924	Contact Map
3c9iA	5	0.9467	33.6	0.925	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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