DUF2946 - PFAM28P - GREMLIN Contacts

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DUF2946 - Protein of unknown function (DUF2946)

PFAM:	PF11162	Sequences: AWLALLALLLQALAPLVSQAAAAAAAAPLLWAEICSADGAAAAAAAAAAGSDPSPAHAAHGEHCPYCSLLAHAPALPPPAAALLLPAAAAARAPPLFLAAPPPLPAWPPAAPRAPP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (115)
Sequences:	5030 (4023)
Seq/√Len:	375.1
META:	0.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_W	112_P	3.591	1.00
15_P	19_Q	3.091	1.00
16_L	19_Q	2.833	1.00
107_W	111_A	2.367	1.00
108_P	112_P	2.355	1.00
11_Q	18_S	2.233	1.00
108_P	111_A	2.217	1.00
107_W	110_A	2.156	1.00
41_A	44_A	2.071	1.00
36_S	40_A	2.037	1.00
15_P	18_S	1.969	1.00
43_A	46_A	1.890	1.00
11_Q	19_Q	1.868	1.00
15_P	66_Y	1.832	1.00
36_S	39_G	1.810	1.00
109_P	112_P	1.771	1.00
14_A	18_S	1.770	1.00
24_A	27_A	1.681	1.00
10_L	14_A	1.643	1.00
75_A	78_P	1.558	1.00
21_A	25_A	1.533	1.00
63_H	66_Y	1.530	1.00
34_I	37_A	1.527	1.00
46_A	49_A	1.468	1.00
42_A	45_A	1.452	1.00
113_R	116_P	1.442	1.00
29_L	32_A	1.396	1.00
102_P	107_W	1.396	1.00
33_E	39_G	1.361	1.00
102_P	105_P	1.343	1.00
3_L	8_L	1.332	1.00
105_P	108_P	1.322	1.00
102_P	108_P	1.301	1.00
4_A	7_A	1.257	1.00
73_A	76_L	1.257	1.00
37_A	40_A	1.233	1.00
41_A	45_A	1.229	1.00
20_A	24_A	1.206	1.00
14_A	17_V	1.193	1.00
51_S	54_S	1.170	1.00
83_L	86_P	1.164	1.00
105_P	109_P	1.151	1.00
14_A	63_H	1.142	1.00
10_L	18_S	1.140	1.00
104_L	107_W	1.092	1.00
44_A	47_A	1.086	1.00
47_A	50_G	1.085	1.00
85_L	88_A	1.085	1.00
68_S	72_H	1.084	1.00
96_L	104_L	1.073	1.00
77_P	80_A	1.064	1.00
32_A	35_C	1.037	1.00
63_H	68_S	1.035	1.00
76_L	79_P	1.018	1.00
103_P	112_P	0.997	1.00
23_A	26_A	0.990	1.00
98_L	101_P	0.978	1.00
28_P	31_W	0.976	1.00
89_A	93_A	0.970	1.00
98_L	104_L	0.969	1.00
54_S	57_H	0.958	1.00
26_A	31_W	0.956	1.00
33_E	36_S	0.956	1.00
94_P	98_L	0.948	1.00
104_L	108_P	0.940	1.00
106_A	112_P	0.935	1.00
103_P	107_W	0.933	1.00
98_L	102_P	0.928	1.00
65_P	68_S	0.920	1.00
5_L	8_L	0.913	1.00
13_L	18_S	0.903	1.00
22_A	25_A	0.899	1.00
20_A	23_A	0.898	1.00
57_H	62_E	0.896	1.00
18_S	63_H	0.876	1.00
73_A	78_P	0.873	1.00
19_Q	63_H	0.871	1.00
56_A	59_A	0.869	1.00
55_P	58_A	0.864	1.00
50_G	53_P	0.861	1.00
101_P	104_L	0.858	1.00
8_L	12_A	0.855	1.00
93_A	96_L	0.855	1.00
97_F	102_P	0.853	1.00
17_V	66_Y	0.848	1.00
65_P	69_L	0.848	1.00
25_A	28_P	0.840	1.00
100_A	108_P	0.838	1.00
58_A	62_E	0.834	1.00
103_P	108_P	0.831	1.00
91_A	95_P	0.830	1.00
35_C	40_A	0.829	1.00
34_I	40_A	0.829	1.00
42_A	46_A	0.826	1.00
86_P	90_A	0.817	1.00
11_Q	16_L	0.813	1.00
105_P	112_P	0.813	1.00
12_A	18_S	0.810	1.00
41_A	46_A	0.810	1.00
2_W	6_L	0.800	1.00
106_A	109_P	0.790	1.00
104_L	111_A	0.789	1.00
41_A	48_A	0.786	1.00
62_E	68_S	0.778	1.00
29_L	33_E	0.769	1.00
5_L	11_Q	0.769	1.00
46_A	51_S	0.766	1.00
84_L	87_A	0.765	1.00
4_A	66_Y	0.762	1.00
56_A	60_H	0.757	1.00
86_P	94_P	0.756	1.00
57_H	60_H	0.751	1.00
104_L	109_P	0.749	1.00
86_P	89_A	0.743	1.00
92_R	95_P	0.742	1.00
6_L	23_A	0.724	1.00
7_A	15_P	0.724	1.00
75_A	79_P	0.724	1.00
27_A	34_I	0.716	1.00
104_L	112_P	0.715	1.00
31_W	40_A	0.715	1.00
12_A	16_L	0.707	0.99
10_L	66_Y	0.705	0.99
97_F	106_A	0.699	0.99
91_A	96_L	0.690	0.99
100_A	103_P	0.662	0.99
103_P	106_A	0.661	0.99
11_Q	17_V	0.660	0.99
27_A	30_L	0.658	0.99
85_L	89_A	0.654	0.99
4_A	10_L	0.650	0.99
8_L	11_Q	0.647	0.99
78_P	82_A	0.645	0.99
18_S	67_C	0.640	0.99
45_A	54_S	0.635	0.99
83_L	87_A	0.633	0.99
13_L	16_L	0.633	0.99
30_L	34_I	0.630	0.99
91_A	94_P	0.628	0.99
94_P	97_F	0.625	0.99
92_R	100_A	0.624	0.99
14_A	19_Q	0.624	0.99
35_C	39_G	0.622	0.99
23_A	27_A	0.620	0.99
4_A	11_Q	0.609	0.99
95_P	99_A	0.606	0.98
83_L	88_A	0.605	0.98
29_L	34_I	0.602	0.98
82_A	85_L	0.602	0.98
11_Q	15_P	0.591	0.98
89_A	94_P	0.582	0.98
93_A	97_F	0.579	0.98
9_L	12_A	0.578	0.98
30_L	40_A	0.571	0.98
2_W	5_L	0.566	0.98
81_A	89_A	0.565	0.98
32_A	37_A	0.562	0.97
106_A	110_A	0.559	0.97
70_L	74_P	0.554	0.97
82_A	88_A	0.554	0.97
19_Q	62_E	0.551	0.97
30_L	33_E	0.551	0.97
91_A	97_F	0.543	0.97
26_A	29_L	0.542	0.97
80_A	86_P	0.538	0.97
97_F	100_A	0.522	0.96
31_W	35_C	0.515	0.96
66_Y	70_L	0.515	0.96
97_F	105_P	0.514	0.96
31_W	34_I	0.513	0.96
18_S	65_P	0.500	0.95
103_P	110_A	0.500	0.95

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
2qjyB	1	0.2241	2.8	0.893	Contact Map
3cx5D	2	0.3362	2.6	0.894	Contact Map
2m1jA	1	0.1983	2.4	0.897	Contact Map
1z65A	1	0.1983	2.4	0.897	Contact Map
3dl8E	1	0.1724	2.1	0.9	Contact Map
3wwqC	1	0.3362	2	0.9	Contact Map
3qxfA	1	0.2328	1.7	0.904	Contact Map
2xq2A	2	0.2069	1.6	0.906	Contact Map
2jlnA	1	0.2759	1.6	0.906	Contact Map
2i68A	2	0.1552	1.5	0.908	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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