DUF2585 - PFAM28P - GREMLIN Contacts

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DUF2585 - Protein of unknown function (DUF2585)

PFAM:	PF10755	Sequences: LLAMGRPPICTCGYVKLWHGVVWSSENSQHLADWYSFSHIIHGFLFYGLLWLVARRLPVGWRLLLAVLIEAAWEILENTPFVINRYRAATISLGYYGDSVLNSVSDILAMALGFLLARRLPVWASVALAVALELVLLLWIRDNLTLNILMLIHPIEAIKAWQAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	164 (162)
Sequences:	3829 (2348)
Seq/√Len:	184.4
META:	0.946

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_S	109_A	3.735	1.00
116_L	120_L	3.256	1.00
132_L	136_L	2.455	1.00
149_L	158_I	2.455	1.00
38_S	136_L	2.350	1.00
135_V	139_W	2.349	1.00
2_L	100_V	2.264	1.00
26_E	30_H	2.171	1.00
80_P	84_N	2.168	1.00
71_A	107_I	2.164	1.00
76_L	81_F	2.128	1.00
72_A	76_L	2.070	1.00
63_L	111_A	2.028	1.00
19_H	26_E	1.979	1.00
7_P	11_T	1.973	1.00
32_A	109_A	1.925	1.00
54_A	57_L	1.897	1.00
122_V	126_V	1.895	1.00
22_V	27_N	1.867	1.00
41_I	132_L	1.829	1.00
2_L	8_P	1.829	1.00
105_S	109_A	1.821	1.00
137_L	143_N	1.814	1.00
9_I	15_V	1.790	1.00
125_S	129_A	1.790	1.00
84_N	88_A	1.779	1.00
44_F	128_L	1.773	1.00
67_V	111_A	1.767	1.00
121_P	124_A	1.722	1.00
41_I	129_A	1.692	1.00
50_L	65_L	1.680	1.00
131_A	135_V	1.626	1.00
50_L	54_A	1.622	1.00
44_F	129_A	1.573	1.00
51_W	55_R	1.568	1.00
37_F	136_L	1.491	1.00
19_H	24_S	1.490	1.00
156_E	159_K	1.483	1.00
156_E	160_A	1.481	1.00
85_R	151_L	1.480	1.00
105_S	108_L	1.476	1.00
45_L	49_L	1.470	1.00
57_L	61_W	1.465	1.00
16_K	26_E	1.452	1.00
16_K	30_H	1.423	1.00
48_G	51_W	1.421	1.00
44_F	125_S	1.399	1.00
45_L	129_A	1.372	1.00
134_L	138_L	1.368	1.00
31_L	105_S	1.346	1.00
57_L	65_L	1.342	1.00
58_P	61_W	1.330	1.00
120_L	124_A	1.322	1.00
136_L	139_W	1.285	1.00
63_L	67_V	1.279	1.00
90_T	150_M	1.268	1.00
128_L	132_L	1.266	1.00
48_G	52_L	1.251	1.00
101_L	105_S	1.239	1.00
61_W	64_L	1.232	1.00
150_M	159_K	1.208	1.00
50_L	62_R	1.205	1.00
89_A	92_S	1.200	1.00
41_I	44_F	1.199	1.00
14_Y	26_E	1.141	1.00
59_V	114_F	1.139	1.00
32_A	36_S	1.133	1.00
67_V	71_A	1.125	1.00
145_T	149_L	1.107	1.00
45_L	48_G	1.096	1.00
159_K	163_A	1.090	1.00
51_W	62_R	1.087	1.00
108_L	111_A	1.080	1.00
79_T	82_V	1.066	1.00
84_N	96_Y	1.058	1.00
155_I	158_I	1.056	1.00
50_L	69_I	1.050	1.00
132_L	135_V	1.049	1.00
41_I	136_L	1.049	1.00
45_L	148_I	1.042	1.00
67_V	107_I	1.042	1.00
118_R	121_P	1.031	1.00
104_V	108_L	1.030	1.00
10_C	16_K	1.030	1.00
20_G	32_A	1.029	1.00
111_A	115_L	1.023	1.00
130_V	134_L	1.022	1.00
16_K	19_H	1.022	1.00
59_V	118_R	1.017	1.00
19_H	27_N	1.015	0.99
90_T	159_K	1.008	0.99
21_V	24_S	0.991	0.99
49_L	69_I	0.987	0.99
68_L	75_I	0.977	0.99
52_L	55_R	0.974	0.99
34_W	139_W	0.971	0.99
9_I	30_H	0.968	0.99
40_I	116_L	0.964	0.99
82_V	85_R	0.954	0.99
10_C	30_H	0.952	0.99
68_L	72_A	0.949	0.99
46_F	70_E	0.948	0.99
85_R	89_A	0.930	0.99
112_L	116_L	0.923	0.99
76_L	82_V	0.903	0.99
9_I	26_E	0.897	0.99
50_L	66_A	0.895	0.99
22_V	91_I	0.893	0.99
19_H	30_H	0.883	0.99
11_T	94_G	0.882	0.99
9_I	101_L	0.881	0.99
80_P	96_Y	0.874	0.98
7_P	99_S	0.869	0.98
64_L	68_L	0.860	0.98
2_L	6_R	0.859	0.98
15_V	30_H	0.832	0.98
31_L	101_L	0.831	0.98
155_I	159_K	0.831	0.98
88_A	91_I	0.827	0.98
19_H	25_S	0.827	0.98
120_L	125_S	0.825	0.98
64_L	67_V	0.823	0.98
10_C	14_Y	0.820	0.98
50_L	57_L	0.812	0.98
12_C	15_V	0.805	0.97
155_I	160_A	0.785	0.97
15_V	26_E	0.784	0.97
86_Y	147_N	0.775	0.97
19_H	22_V	0.773	0.97
123_W	127_A	0.773	0.97
17_L	20_G	0.769	0.97
63_L	114_F	0.768	0.97
42_H	70_E	0.752	0.96
93_L	96_Y	0.751	0.96
37_F	132_L	0.751	0.96
4_M	8_P	0.751	0.96
38_S	70_E	0.749	0.96
134_L	137_L	0.749	0.96
58_P	62_R	0.749	0.96
47_Y	121_P	0.744	0.96
116_L	128_L	0.740	0.96
137_L	146_L	0.735	0.96
11_T	14_Y	0.729	0.95
15_V	101_L	0.727	0.95
14_Y	19_H	0.718	0.95
12_C	25_S	0.711	0.95
54_A	60_G	0.711	0.95
21_V	27_N	0.709	0.95
12_C	16_K	0.707	0.95
108_L	112_L	0.707	0.95
137_L	145_T	0.706	0.95
66_A	110_M	0.704	0.94
30_H	101_L	0.700	0.94
9_I	12_C	0.699	0.94
4_M	79_T	0.698	0.94
14_Y	30_H	0.698	0.94
112_L	115_L	0.696	0.94
134_L	145_T	0.694	0.94
60_G	64_L	0.692	0.94
40_I	44_F	0.692	0.94
52_L	56_R	0.688	0.94
135_V	138_L	0.685	0.94
75_I	79_T	0.680	0.93
160_A	163_A	0.679	0.93
25_S	30_H	0.678	0.93
27_N	30_H	0.673	0.93
65_L	68_L	0.672	0.93
124_A	127_A	0.671	0.93
55_R	62_R	0.668	0.93
89_A	150_M	0.664	0.93
49_L	53_V	0.662	0.92
40_I	109_A	0.659	0.92
129_A	145_T	0.657	0.92
129_A	148_I	0.655	0.92
54_A	65_L	0.652	0.92
121_P	125_S	0.650	0.92
104_V	107_I	0.647	0.92
24_S	27_N	0.647	0.92
115_L	118_R	0.640	0.91
59_V	63_L	0.639	0.91
36_S	40_I	0.638	0.91
6_R	23_W	0.629	0.90
4_M	80_P	0.625	0.90
70_E	147_N	0.619	0.90
89_A	93_L	0.616	0.90
81_F	85_R	0.614	0.89
59_V	115_L	0.614	0.89
37_F	135_V	0.604	0.89
76_L	79_T	0.603	0.89
131_A	138_L	0.600	0.88
47_Y	62_R	0.597	0.88
154_P	159_K	0.591	0.88
157_A	160_A	0.590	0.87
131_A	136_L	0.588	0.87
152_I	155_I	0.588	0.87
88_A	92_S	0.586	0.87
123_W	126_V	0.585	0.87
6_R	11_T	0.585	0.87
42_H	87_R	0.585	0.87
72_A	75_I	0.583	0.87
80_P	88_A	0.582	0.87
27_N	91_I	0.581	0.87
49_L	127_A	0.577	0.86
109_A	112_L	0.570	0.86
60_G	68_L	0.566	0.85
90_T	93_L	0.565	0.85
37_F	40_I	0.561	0.85
91_I	150_M	0.560	0.85
136_L	153_H	0.560	0.85
23_W	89_A	0.558	0.84
101_L	104_V	0.554	0.84
129_A	132_L	0.550	0.84
19_H	34_W	0.548	0.83
38_S	45_L	0.545	0.83
70_E	87_R	0.545	0.83
118_R	125_S	0.545	0.83
69_I	72_A	0.542	0.83
149_L	155_I	0.541	0.83
37_F	139_W	0.540	0.82
70_E	86_Y	0.540	0.82
64_L	115_L	0.538	0.82
124_A	128_L	0.530	0.81
91_I	96_Y	0.530	0.81
92_S	150_M	0.528	0.81
85_R	154_P	0.524	0.81
4_M	75_I	0.523	0.80
31_L	34_W	0.521	0.80
38_S	42_H	0.521	0.80
76_L	80_P	0.518	0.80
137_L	158_I	0.517	0.80
54_A	61_W	0.515	0.79
9_I	16_K	0.514	0.79
16_K	20_G	0.514	0.79
20_G	27_N	0.513	0.79
115_L	119_R	0.512	0.79
130_V	160_A	0.512	0.79
47_Y	59_V	0.510	0.79
89_A	159_K	0.510	0.79
38_S	41_I	0.510	0.79
25_S	75_I	0.505	0.78
48_G	110_M	0.504	0.78
41_I	143_N	0.502	0.78
59_V	62_R	0.500	0.77

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
3t6qA	1	0.3354	4.6	0.97	Contact Map
4p8sA	1	0.3354	3.2	0.972	Contact Map
3vq2A	2	0.2256	2.9	0.973	Contact Map
2dw3A	1	0.2866	2.4	0.974	Contact Map
2mdlA	1	0.061	2.4	0.974	Contact Map
3qryB	1	0.5	1.7	0.976	Contact Map
3hdxA	1	0.3354	1.6	0.976	Contact Map
2ksfA	1	0.2927	1.6	0.976	Contact Map
3ks7A	3	0.3598	1.4	0.977	Contact Map
2epbA	1	0.3293	1.3	0.978	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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