DUF1985 - PFAM28P - GREMLIN Contacts

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DUF1985 - Domain of unknown function (DUF1985)

PFAM:	PF09331	Sequences: LCRQLVTKKKHELWFVFGGQPIRFSLREFALITGLNCGPYPDDYEYEKKKKNKFFWKKLFGKKKKVTVKDLIKMLKKKKVWSDEDRLKLALLYILDGVLLGKSKNSRIPPEYVKMVDDLEAFEKYPWGRVSFDKLIKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	138 (136)
Sequences:	743 (553)
Seq/√Len:	47.4
META:	0.122

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_S	28_E	3.742	1.00
131_S	135_L	3.345	1.00
29_F	131_S	3.022	1.00
55_F	58_K	2.826	1.00
54_F	58_K	2.764	1.00
14_W	21_P	2.576	1.00
24_F	29_F	2.457	1.00
53_K	58_K	2.168	1.00
54_F	57_K	2.161	1.00
34_G	127_W	2.143	1.00
9_K	12_E	2.129	1.00
23_R	28_E	2.104	1.00
46_Y	52_N	1.894	0.99
114_K	117_D	1.863	0.99
27_R	31_L	1.832	0.99
53_K	57_K	1.824	0.99
118_D	121_A	1.822	0.99
85_D	88_K	1.813	0.99
33_T	125_Y	1.782	0.99
74_M	78_K	1.743	0.98
81_W	92_L	1.696	0.98
95_L	99_L	1.696	0.98
60_F	66_V	1.652	0.98
51_K	99_L	1.628	0.98
29_F	33_T	1.607	0.97
38_G	94_I	1.598	0.97
66_V	71_L	1.572	0.97
14_W	23_R	1.568	0.97
125_Y	130_V	1.554	0.97
131_S	134_K	1.553	0.97
14_W	25_S	1.506	0.96
5_L	16_V	1.499	0.96
68_V	93_Y	1.418	0.95
130_V	134_K	1.408	0.94
51_K	55_F	1.363	0.93
46_Y	51_K	1.361	0.93
62_K	88_K	1.338	0.93
11_H	133_D	1.333	0.92
21_P	86_R	1.311	0.92
69_K	73_K	1.295	0.91
47_E	50_K	1.288	0.91
50_K	55_F	1.278	0.91
85_D	91_L	1.275	0.91
14_W	28_E	1.253	0.90
132_F	136_I	1.244	0.90
2_C	5_L	1.240	0.89
75_L	90_A	1.227	0.89
56_W	60_F	1.180	0.87
51_K	56_W	1.180	0.87
22_I	116_V	1.144	0.85
26_L	72_I	1.128	0.84
88_K	116_V	1.121	0.84
52_N	55_F	1.120	0.84
46_Y	49_K	1.116	0.84
11_H	118_D	1.109	0.83
42_D	125_Y	1.104	0.83
100_L	131_S	1.097	0.83
13_L	136_I	1.090	0.82
114_K	119_L	1.089	0.82
5_L	13_L	1.088	0.82
85_D	101_G	1.087	0.82
101_G	125_Y	1.084	0.82
51_K	58_K	1.068	0.81
25_S	86_R	1.057	0.80
81_W	85_D	1.050	0.80
77_K	90_A	1.045	0.79
118_D	133_D	1.032	0.79
89_L	95_L	1.030	0.78
21_P	28_E	1.021	0.78
71_L	109_P	1.000	0.76
67_T	96_D	0.997	0.76
21_P	26_L	0.985	0.75
120_E	124_K	0.975	0.75
130_V	135_L	0.973	0.74
43_D	125_Y	0.971	0.74
109_P	116_V	0.968	0.74
100_L	112_Y	0.955	0.73
12_E	69_K	0.953	0.73
15_F	25_S	0.948	0.72
131_S	137_K	0.919	0.70
5_L	11_H	0.913	0.70
89_L	97_G	0.913	0.70
15_F	133_D	0.911	0.69
109_P	117_D	0.910	0.69
92_L	95_L	0.903	0.69
32_I	106_S	0.893	0.68
60_F	85_D	0.889	0.67
50_K	54_F	0.887	0.67
100_L	134_K	0.881	0.67
34_G	89_L	0.875	0.66
115_M	122_F	0.870	0.66
25_S	131_S	0.861	0.65
20_Q	32_I	0.856	0.65
3_R	10_K	0.855	0.64
48_K	77_K	0.855	0.64
26_L	37_C	0.852	0.64
52_N	56_W	0.849	0.64
34_G	128_G	0.846	0.64
3_R	9_K	0.842	0.63
94_I	104_K	0.842	0.63
2_C	15_F	0.832	0.62
122_F	129_R	0.823	0.61
12_E	26_L	0.820	0.61
66_V	74_M	0.810	0.60
114_K	118_D	0.806	0.60
129_R	132_F	0.800	0.59
130_V	133_D	0.793	0.59
24_F	100_L	0.793	0.59
17_F	120_E	0.792	0.58
30_A	36_N	0.785	0.58
89_L	116_V	0.780	0.57
18_G	132_F	0.778	0.57
12_E	23_R	0.773	0.57
49_K	56_W	0.766	0.56
32_I	69_K	0.763	0.56
78_K	81_W	0.758	0.55
2_C	20_Q	0.755	0.55
89_L	101_G	0.753	0.55
62_K	65_K	0.753	0.55
11_H	15_F	0.734	0.53
95_L	122_F	0.733	0.53
7_T	12_E	0.728	0.52
67_T	71_L	0.725	0.52
31_L	83_D	0.719	0.51
53_K	64_K	0.713	0.51
63_K	73_K	0.699	0.49
71_L	88_K	0.699	0.49
10_K	118_D	0.697	0.49
29_F	122_F	0.697	0.49
93_Y	97_G	0.696	0.49
29_F	100_L	0.696	0.49
60_F	71_L	0.695	0.49
97_G	106_S	0.694	0.49
35_L	59_L	0.689	0.48
37_C	122_F	0.688	0.48
128_G	132_F	0.687	0.48
65_K	71_L	0.687	0.48
8_K	20_Q	0.686	0.48
101_G	114_K	0.685	0.48
13_L	16_V	0.684	0.48
90_A	96_D	0.684	0.48
13_L	71_L	0.675	0.47
2_C	8_K	0.673	0.47
29_F	96_D	0.664	0.46
37_C	129_R	0.663	0.46
18_G	29_F	0.662	0.46
48_K	55_F	0.662	0.46
5_L	36_N	0.658	0.45
133_D	137_K	0.657	0.45
16_V	21_P	0.655	0.45
121_A	130_V	0.650	0.44
12_E	76_K	0.643	0.44
40_Y	129_R	0.640	0.43
68_V	76_K	0.639	0.43
67_T	87_L	0.637	0.43
71_L	103_S	0.636	0.43
92_L	125_Y	0.634	0.43
39_P	101_G	0.628	0.42
65_K	70_D	0.623	0.42
25_S	135_L	0.623	0.42
32_I	108_I	0.623	0.42
37_C	86_R	0.622	0.42
20_Q	29_F	0.622	0.42
28_E	86_R	0.620	0.41
26_L	30_A	0.617	0.41
50_K	58_K	0.611	0.41
42_D	136_I	0.599	0.39
39_P	42_D	0.595	0.39
2_C	17_F	0.590	0.39
15_F	93_Y	0.587	0.38
8_K	18_G	0.584	0.38
8_K	19_G	0.581	0.38
65_K	124_K	0.576	0.37
66_V	117_D	0.572	0.37
22_I	31_L	0.572	0.37
58_K	85_D	0.565	0.36
94_I	109_P	0.560	0.36
108_I	118_D	0.559	0.36
121_A	124_K	0.554	0.35
55_F	60_F	0.552	0.35
78_K	136_I	0.550	0.35
47_E	77_K	0.548	0.35
32_I	123_E	0.546	0.35
102_K	113_V	0.546	0.35
88_K	122_F	0.544	0.34
63_K	70_D	0.542	0.34
26_L	104_K	0.541	0.34
94_I	136_I	0.540	0.34
15_F	98_V	0.534	0.33
119_L	132_F	0.527	0.33
89_L	94_I	0.527	0.33
6_V	38_G	0.526	0.33
36_N	129_R	0.525	0.33
8_K	82_S	0.524	0.33
122_F	135_L	0.522	0.32
43_D	47_E	0.516	0.32
30_A	37_C	0.510	0.31
45_E	50_K	0.509	0.31
22_I	130_V	0.508	0.31
57_K	79_K	0.507	0.31
9_K	87_L	0.506	0.31
109_P	112_Y	0.505	0.31
54_F	59_L	0.505	0.31
85_D	116_V	0.500	0.31

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
1dmlA	1	0.5435	5.8	0.94	Contact Map
4ok4A	2	0.2174	4.6	0.943	Contact Map
2j6bA	2	0.3406	4.2	0.944	Contact Map
2xf7A	3	0.2029	4	0.944	Contact Map
1wt6A	3	0.2174	2.8	0.948	Contact Map
4ja8A	2	0.3696	2.6	0.949	Contact Map
4tq1A	1	0.8623	2.4	0.95	Contact Map
3p0uA	2	0.2319	2.1	0.952	Contact Map
2jx3A	1	0.5	2.1	0.952	Contact Map
1zx5A	1	0.7681	2	0.952	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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