DUF4253 - PFAM28P - GREMLIN Contacts

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DUF4253 - Domain of unknown function (DUF4253)

PFAM:	PF14062	Sequences: RLALVPTADPWDVPAALGWGGAWNYCPDPEEHIAVLRSWEERYGAELVGIGFDTLELRVARPPTDREEALALAAEHYAFCPDIVDQGTGTLEALAAELLGSRVWYFWWD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (107)
Sequences:	3148 (2455)
Seq/√Len:	237.4
META:	0.859

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_H	79_F	4.063	1.00
36_L	57_L	3.098	1.00
77_Y	85_D	2.821	1.00
9_D	12_D	2.701	1.00
15_A	33_I	2.588	1.00
65_D	68_E	2.566	1.00
38_S	42_R	2.562	1.00
44_G	60_A	2.185	1.00
76_H	83_I	2.035	1.00
20_G	23_W	2.012	1.00
14_P	36_L	1.959	1.00
90_T	93_A	1.902	1.00
11_W	40_E	1.802	1.00
76_H	106_F	1.776	1.00
39_W	75_E	1.758	1.00
42_R	75_E	1.732	1.00
69_A	99_L	1.637	1.00
70_L	95_A	1.627	1.00
38_S	75_E	1.588	1.00
10_P	40_E	1.584	1.00
51_G	54_T	1.575	1.00
49_G	56_E	1.515	1.00
10_P	47_L	1.515	1.00
28_D	31_E	1.479	1.00
5_V	13_V	1.473	1.00
46_E	60_A	1.399	1.00
37_R	41_E	1.392	1.00
21_G	27_P	1.334	1.00
21_G	24_N	1.332	1.00
14_P	50_I	1.302	1.00
82_D	86_Q	1.297	1.00
76_H	98_L	1.292	1.00
72_L	76_H	1.284	1.00
81_P	85_D	1.255	1.00
49_G	54_T	1.238	1.00
76_H	94_L	1.193	1.00
72_L	98_L	1.183	1.00
39_W	76_H	1.176	1.00
36_L	55_L	1.134	1.00
11_W	37_R	1.112	1.00
35_V	75_E	1.099	1.00
77_Y	84_V	1.069	1.00
89_G	93_A	1.057	1.00
56_E	105_Y	1.053	1.00
23_W	27_P	1.046	1.00
45_A	57_L	1.041	1.00
7_T	13_V	1.039	1.00
7_T	16_A	1.026	1.00
82_D	107_W	1.025	1.00
8_A	12_D	1.015	1.00
56_E	103_V	0.999	1.00
59_V	104_W	0.992	1.00
62_P	102_R	0.991	1.00
66_R	70_L	0.988	1.00
38_S	41_E	0.977	1.00
23_W	26_C	0.974	1.00
3_A	17_L	0.955	1.00
25_Y	81_P	0.946	1.00
35_V	39_W	0.946	1.00
39_W	43_Y	0.943	1.00
20_G	27_P	0.938	1.00
66_R	99_L	0.938	1.00
46_E	58_R	0.937	1.00
79_F	106_F	0.915	1.00
88_T	97_E	0.913	1.00
45_A	104_W	0.879	0.99
38_S	43_Y	0.868	0.99
27_P	31_E	0.866	0.99
84_V	94_L	0.865	0.99
29_P	33_I	0.852	0.99
40_E	46_E	0.850	0.99
53_D	107_W	0.849	0.99
97_E	100_G	0.847	0.99
19_W	50_I	0.844	0.99
40_E	45_A	0.837	0.99
59_V	62_P	0.835	0.99
29_P	32_H	0.834	0.99
10_P	46_E	0.834	0.99
24_N	82_D	0.833	0.99
92_E	96_A	0.827	0.99
15_A	30_E	0.821	0.99
37_R	40_E	0.820	0.99
69_A	73_A	0.818	0.99
20_G	26_C	0.815	0.99
84_V	88_T	0.813	0.99
44_G	61_R	0.807	0.99
83_I	87_G	0.804	0.99
42_R	68_E	0.801	0.99
43_Y	72_L	0.792	0.99
54_T	105_Y	0.790	0.99
24_N	109_D	0.786	0.99
33_I	40_E	0.785	0.99
35_V	38_S	0.782	0.99
40_E	44_G	0.781	0.99
35_V	79_F	0.775	0.99
9_D	40_E	0.760	0.98
91_L	95_A	0.757	0.98
3_A	6_P	0.751	0.98
70_L	92_E	0.751	0.98
74_A	91_L	0.732	0.98
83_I	88_T	0.730	0.98
84_V	87_G	0.726	0.98
50_I	55_L	0.712	0.98
73_A	95_A	0.705	0.97
33_I	47_L	0.701	0.97
68_E	71_A	0.699	0.97
97_E	101_S	0.684	0.97
59_V	63_P	0.684	0.97
36_L	45_A	0.676	0.97
63_P	72_L	0.674	0.97
86_Q	107_W	0.671	0.96
6_P	16_A	0.671	0.96
27_P	32_H	0.669	0.96
43_Y	63_P	0.662	0.96
39_W	57_L	0.661	0.96
48_V	58_R	0.649	0.96
30_E	33_I	0.649	0.96
12_D	15_A	0.645	0.96
31_E	35_V	0.643	0.96
64_T	100_G	0.639	0.95
77_Y	86_Q	0.638	0.95
34_A	37_R	0.632	0.95
65_D	69_A	0.631	0.95
62_P	69_A	0.629	0.95
47_L	50_I	0.627	0.95
83_I	94_L	0.626	0.95
36_L	47_L	0.624	0.95
93_A	97_E	0.619	0.94
33_I	37_R	0.617	0.94
42_R	71_A	0.604	0.94
26_C	31_E	0.604	0.94
7_T	12_D	0.600	0.94
84_V	93_A	0.599	0.93
63_P	66_R	0.597	0.93
57_L	104_W	0.597	0.93
45_A	59_V	0.592	0.93
24_N	52_F	0.581	0.92
10_P	13_V	0.578	0.92
39_W	72_L	0.576	0.92
19_W	26_C	0.575	0.92
35_V	106_F	0.571	0.92
66_R	72_L	0.564	0.91
64_T	68_E	0.558	0.91
102_R	105_Y	0.556	0.91
12_D	38_S	0.551	0.90
87_G	94_L	0.547	0.90
10_P	106_F	0.544	0.90
73_A	94_L	0.542	0.90
43_Y	75_E	0.524	0.88
70_L	74_A	0.522	0.88
43_Y	60_A	0.516	0.87
84_V	91_L	0.510	0.87
5_V	17_L	0.509	0.87
96_A	99_L	0.509	0.87
99_L	102_R	0.508	0.86
47_L	55_L	0.505	0.86
100_G	103_V	0.505	0.86
14_P	33_I	0.505	0.86
39_W	44_G	0.503	0.86
67_E	70_L	0.500	0.86

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
3vz9B	1	0.7798	23.4	0.893	Contact Map
1gqiA	2	0.945	9	0.911	Contact Map
1l8nA	2	0.9358	8.3	0.912	Contact Map
4qclA	1	0.9817	7.8	0.914	Contact Map
1dgsA	1	0.9633	7.3	0.915	Contact Map
1w7pD	1	0.8807	7.1	0.915	Contact Map
3iayA	1	0.9725	6.9	0.916	Contact Map
3a4uB	1	0.5688	6.9	0.916	Contact Map
3sgiA	1	0.1284	5.7	0.919	Contact Map
2d1pA	2	0.9083	5.6	0.919	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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