DUF1699 - PFAM28P - GREMLIN Contacts

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DUF1699 - Protein of unknown function (DUF1699)

PFAM:	PF08004	Sequences: MKIRVVSSREEIPTLNPNEKIVHLAFRPSNKDIFNLVQTCPRLRAIQVPPSYKKTMSKSIEMFLEMQGIELLEGDVWGHRKDINEYYTVPDSVIEEIKELKAEGKSAEDIAEKVSRETKLSPDLIKYILK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (129)
Sequences:	552 (244)
Seq/√Len:	21.4
META:	0.889

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_E	117_E	5.107	1.00
113_K	117_E	3.901	1.00
72_L	123_D	2.694	0.99
58_K	70_E	2.539	0.98
117_E	120_L	2.272	0.96
10_E	28_P	2.220	0.96
96_E	100_L	2.073	0.94
121_S	124_L	2.015	0.93
3_I	21_I	1.962	0.92
110_I	115_S	1.945	0.91
79_H	82_D	1.923	0.91
59_S	99_E	1.868	0.89
30_N	55_T	1.778	0.87
119_K	124_L	1.743	0.86
2_K	5_V	1.713	0.85
3_I	10_E	1.674	0.83
24_L	36_L	1.674	0.83
95_E	102_A	1.632	0.82
13_P	22_V	1.628	0.82
43_L	115_S	1.626	0.81
19_E	86_Y	1.600	0.80
77_W	83_I	1.582	0.80
39_T	87_Y	1.523	0.77
78_G	82_D	1.506	0.76
21_I	44_R	1.489	0.75
40_C	44_R	1.484	0.75
54_K	66_M	1.465	0.74
93_V	107_A	1.461	0.74
25_A	52_Y	1.450	0.73
52_Y	75_D	1.433	0.72
119_K	128_I	1.390	0.70
109_D	112_E	1.381	0.69
30_N	52_Y	1.378	0.69
21_I	40_C	1.377	0.69
6_V	40_C	1.366	0.69
100_L	105_K	1.358	0.68
63_F	67_Q	1.343	0.67
58_K	65_E	1.328	0.66
4_R	86_Y	1.285	0.64
60_I	69_I	1.270	0.63
112_E	122_P	1.256	0.62
119_K	125_I	1.252	0.62
53_K	56_M	1.235	0.61
124_L	127_Y	1.185	0.57
59_S	66_M	1.183	0.57
84_N	129_L	1.177	0.57
58_K	61_E	1.174	0.57
21_I	37_V	1.173	0.57
8_S	13_P	1.167	0.56
53_K	90_P	1.163	0.56
29_S	66_M	1.160	0.56
10_E	13_P	1.158	0.56
115_S	125_I	1.156	0.55
30_N	57_S	1.146	0.55
6_V	11_E	1.105	0.52
20_K	44_R	1.099	0.52
39_T	94_I	1.099	0.52
92_S	111_A	1.092	0.51
24_L	103_E	1.081	0.50
87_Y	94_I	1.073	0.50
100_L	121_S	1.064	0.49
53_K	123_D	1.045	0.48
9_R	47_Q	1.039	0.48
2_K	60_I	1.039	0.48
79_H	86_Y	1.037	0.47
6_V	45_A	1.027	0.47
45_A	48_V	1.025	0.47
91_D	125_I	1.022	0.46
77_W	85_E	1.018	0.46
66_M	73_E	1.005	0.45
68_G	126_K	1.004	0.45
28_P	38_Q	1.002	0.45
6_V	102_A	0.994	0.45
21_I	45_A	0.990	0.44
31_K	101_K	0.984	0.44
28_P	37_V	0.978	0.43
83_I	119_K	0.970	0.43
43_L	116_R	0.968	0.43
122_P	125_I	0.966	0.43
63_F	81_K	0.959	0.42
53_K	61_E	0.958	0.42
76_V	82_D	0.951	0.42
34_F	67_Q	0.948	0.42
13_P	17_P	0.931	0.40
26_F	32_D	0.924	0.40
11_E	36_L	0.919	0.40
111_A	118_T	0.914	0.39
10_E	88_T	0.892	0.38
76_V	80_R	0.890	0.38
52_Y	81_K	0.883	0.37
38_Q	68_G	0.881	0.37
89_V	93_V	0.874	0.37
7_S	80_R	0.855	0.36
39_T	43_L	0.852	0.35
65_E	103_E	0.852	0.35
96_E	119_K	0.850	0.35
16_N	40_C	0.848	0.35
114_V	117_E	0.841	0.35
62_M	73_E	0.836	0.34
18_N	42_R	0.835	0.34
51_S	57_S	0.830	0.34
52_Y	85_E	0.828	0.34
35_N	128_I	0.824	0.34
68_G	111_A	0.823	0.34
20_K	50_P	0.822	0.34
31_K	34_F	0.815	0.33
91_D	100_L	0.811	0.33
60_I	63_F	0.805	0.33
26_F	29_S	0.805	0.33
101_K	125_I	0.794	0.32
52_Y	55_T	0.789	0.32
38_Q	42_R	0.783	0.31
90_P	107_A	0.777	0.31
15_L	40_C	0.776	0.31
90_P	106_S	0.770	0.31
112_E	128_I	0.760	0.30
62_M	110_I	0.757	0.30
9_R	20_K	0.745	0.29
93_V	129_L	0.743	0.29
91_D	114_V	0.742	0.29
61_E	70_E	0.736	0.29
91_D	121_S	0.735	0.29
102_A	112_E	0.731	0.28
2_K	95_E	0.727	0.28
36_L	124_L	0.709	0.27
38_Q	48_V	0.705	0.27
16_N	39_T	0.703	0.27
71_L	123_D	0.702	0.27
1_M	5_V	0.702	0.27
20_K	47_Q	0.695	0.26
73_E	77_W	0.695	0.26
31_K	39_T	0.693	0.26
14_T	53_K	0.693	0.26
37_V	70_E	0.683	0.26
22_V	120_L	0.678	0.26
10_E	16_N	0.673	0.25
34_F	62_M	0.672	0.25
69_I	97_I	0.665	0.25
123_D	126_K	0.664	0.25
97_I	129_L	0.660	0.25
70_E	103_E	0.658	0.25
7_S	81_K	0.656	0.24
79_H	83_I	0.656	0.24
44_R	70_E	0.654	0.24
45_A	127_Y	0.649	0.24
19_E	30_N	0.644	0.24
108_E	120_L	0.643	0.24
10_E	46_I	0.638	0.24
31_K	100_L	0.633	0.23
47_Q	87_Y	0.627	0.23
13_P	44_R	0.619	0.23
27_R	79_H	0.617	0.23
102_A	122_P	0.613	0.22
49_P	52_Y	0.609	0.22
13_P	16_N	0.609	0.22
72_L	96_E	0.608	0.22
10_E	61_E	0.603	0.22
8_S	36_L	0.590	0.21
17_P	60_I	0.587	0.21
95_E	116_R	0.586	0.21
47_Q	74_G	0.584	0.21
8_S	67_Q	0.582	0.21
9_R	13_P	0.579	0.21
92_S	96_E	0.574	0.21
52_Y	80_R	0.574	0.21
22_V	97_I	0.573	0.21
76_V	83_I	0.565	0.20
115_S	124_L	0.561	0.20
2_K	83_I	0.561	0.20
9_R	45_A	0.561	0.20
34_F	73_E	0.558	0.20
31_K	62_M	0.549	0.20
125_I	129_L	0.545	0.19
88_T	127_Y	0.542	0.19
88_T	128_I	0.542	0.19
78_G	81_K	0.539	0.19
10_E	14_T	0.539	0.19
106_S	112_E	0.538	0.19
80_R	85_E	0.535	0.19
68_G	91_D	0.533	0.19
118_T	121_S	0.526	0.19
74_G	78_G	0.523	0.18
24_L	89_V	0.522	0.18
71_L	116_R	0.522	0.18
56_M	108_E	0.521	0.18
37_V	40_C	0.518	0.18
41_P	79_H	0.513	0.18
16_N	91_D	0.510	0.18
103_E	117_E	0.509	0.18
106_S	123_D	0.509	0.18
17_P	20_K	0.506	0.18
90_P	94_I	0.505	0.18
93_V	98_K	0.501	0.18
6_V	9_R	0.500	0.18

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
4bqqA	2	0.8308	44.2	0.939	Contact Map
3eglA	1	0.8231	40.9	0.94	Contact Map
3uj3X	2	0.3308	39.3	0.94	Contact Map
4kisA	2	0.5846	38.9	0.941	Contact Map
1gdtA	2	0.7308	34.7	0.942	Contact Map
1mgpA	1	0.9077	26.4	0.946	Contact Map
4uvkA	1	0.4	21.1	0.948	Contact Map
4u7bA	2	0.3462	20.9	0.948	Contact Map
2cfuA	2	0.9	20.4	0.948	Contact Map
1u78A	1	0.3308	19.9	0.949	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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