DUF1676 - PFAM28P - GREMLIN Contacts

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DUF1676 - Protein of unknown function (DUF1676)

PFAM:	PF07898	Sequences: KALSFLDRALRKDEIELTDGVSLVRTPDADERSARSGKEPLSESEIEASLPRDLESREEELDNLLLDKVARFLKSHSLQVKLPDFSGEEIARSLLELDVGVVEGRGKKKKLKKMLLMPLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (117)
Sequences:	635 (466)
Seq/√Len:	43.1
META:	0.076

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_R	95_L	3.858	1.00
116_L	120_L	2.725	1.00
37_G	40_P	2.673	1.00
7_D	68_K	2.266	1.00
106_G	109_K	2.182	1.00
85_F	88_E	2.122	0.99
72_F	83_P	2.057	0.99
41_L	46_I	1.992	0.99
15_I	23_L	1.853	0.99
35_R	38_K	1.845	0.99
70_A	91_A	1.838	0.98
113_K	118_P	1.831	0.98
34_A	38_K	1.806	0.98
97_L	100_G	1.791	0.98
25_R	49_S	1.740	0.98
32_R	35_R	1.628	0.97
2_A	80_V	1.615	0.97
30_D	34_A	1.609	0.96
90_I	119_L	1.585	0.96
65_L	119_L	1.565	0.96
26_T	81_K	1.565	0.96
20_G	76_H	1.535	0.95
12_K	78_L	1.528	0.95
89_E	93_S	1.516	0.95
2_A	9_A	1.452	0.94
57_R	71_R	1.445	0.94
76_H	94_L	1.441	0.93
30_D	33_S	1.417	0.93
111_L	114_M	1.393	0.92
101_V	105_R	1.364	0.91
112_K	118_P	1.347	0.91
31_E	34_A	1.339	0.91
24_V	79_Q	1.336	0.91
14_E	24_V	1.333	0.90
23_L	72_F	1.332	0.90
42_S	46_I	1.330	0.90
36_S	39_E	1.328	0.90
9_A	83_P	1.321	0.90
107_K	111_L	1.306	0.89
34_A	37_G	1.292	0.89
2_A	6_L	1.277	0.88
89_E	92_R	1.247	0.87
109_K	112_K	1.237	0.87
106_G	111_L	1.232	0.87
33_S	36_S	1.228	0.86
72_F	115_L	1.197	0.85
73_L	76_H	1.195	0.85
72_F	76_H	1.190	0.85
112_K	116_L	1.188	0.84
86_S	89_E	1.187	0.84
97_L	103_E	1.163	0.83
115_L	118_P	1.162	0.83
40_P	43_E	1.140	0.82
38_K	41_L	1.137	0.82
111_L	116_L	1.099	0.79
88_E	95_L	1.096	0.79
10_L	68_K	1.080	0.78
64_L	91_A	1.070	0.78
56_S	59_E	1.044	0.76
27_P	30_D	1.030	0.75
31_E	35_R	1.025	0.74
19_D	80_V	1.013	0.74
1_K	19_D	0.998	0.72
47_E	51_P	0.984	0.71
108_K	111_L	0.981	0.71
74_K	82_L	0.972	0.70
45_E	48_A	0.959	0.69
17_L	71_R	0.949	0.69
11_R	83_P	0.945	0.68
21_V	49_S	0.926	0.67
109_K	119_L	0.926	0.67
100_G	105_R	0.923	0.66
34_A	40_P	0.919	0.66
69_V	73_L	0.919	0.66
72_F	79_Q	0.906	0.65
14_E	17_L	0.902	0.65
111_L	115_L	0.902	0.65
14_E	72_F	0.888	0.63
57_R	82_L	0.872	0.62
11_R	64_L	0.872	0.62
24_V	28_D	0.871	0.62
69_V	92_R	0.863	0.61
74_K	84_D	0.859	0.61
58_E	62_D	0.855	0.60
31_E	40_P	0.855	0.60
9_A	18_T	0.853	0.60
6_L	60_E	0.852	0.60
86_S	94_L	0.851	0.60
91_A	94_L	0.850	0.60
97_L	101_V	0.846	0.60
68_K	120_L	0.841	0.59
70_A	104_G	0.839	0.59
10_L	76_H	0.835	0.59
19_D	36_S	0.829	0.58
45_E	50_L	0.825	0.58
106_G	110_K	0.819	0.57
43_E	51_P	0.815	0.57
50_L	53_D	0.812	0.56
36_S	40_P	0.811	0.56
5_F	8_R	0.807	0.56
93_S	96_E	0.805	0.56
33_S	38_K	0.796	0.55
111_L	118_P	0.792	0.55
57_R	64_L	0.791	0.55
61_L	109_K	0.782	0.54
30_D	36_S	0.779	0.53
102_V	105_R	0.777	0.53
2_A	82_L	0.771	0.53
112_K	120_L	0.770	0.53
3_L	62_D	0.767	0.52
100_G	103_E	0.764	0.52
73_L	82_L	0.762	0.52
108_K	112_K	0.752	0.51
77_S	82_L	0.748	0.50
7_D	11_R	0.745	0.50
73_L	78_L	0.745	0.50
108_K	116_L	0.741	0.50
109_K	113_K	0.739	0.50
21_V	59_E	0.718	0.48
68_K	114_M	0.718	0.48
8_R	50_L	0.714	0.47
44_S	48_A	0.710	0.47
90_I	95_L	0.707	0.47
17_L	90_I	0.706	0.46
39_E	42_S	0.696	0.46
62_D	72_F	0.678	0.44
115_L	120_L	0.677	0.44
106_G	112_K	0.676	0.44
6_L	10_L	0.674	0.43
70_A	83_P	0.663	0.42
82_L	92_R	0.659	0.42
55_E	67_D	0.658	0.42
108_K	113_K	0.657	0.42
48_A	51_P	0.657	0.42
21_V	102_V	0.649	0.41
58_E	68_K	0.641	0.40
69_V	78_L	0.637	0.40
102_V	106_G	0.630	0.39
83_P	96_E	0.628	0.39
24_V	76_H	0.628	0.39
16_E	76_H	0.623	0.39
22_S	73_L	0.617	0.38
22_S	64_L	0.616	0.38
63_N	90_I	0.614	0.38
5_F	20_G	0.611	0.38
3_L	60_E	0.608	0.37
25_R	73_L	0.601	0.37
41_L	44_S	0.600	0.37
7_D	71_R	0.599	0.37
114_M	118_P	0.595	0.36
14_E	61_L	0.583	0.35
25_R	48_A	0.578	0.35
29_A	88_E	0.577	0.35
92_R	96_E	0.576	0.35
8_R	83_P	0.571	0.34
66_L	76_H	0.568	0.34
34_A	54_L	0.564	0.34
47_E	78_L	0.563	0.33
55_E	86_S	0.559	0.33
12_K	81_K	0.552	0.33
59_E	87_G	0.547	0.32
66_L	80_V	0.539	0.31
31_E	38_K	0.530	0.31
20_G	73_L	0.529	0.31
6_L	86_S	0.528	0.31
87_G	91_A	0.526	0.30
87_G	93_S	0.525	0.30
18_T	55_E	0.523	0.30
4_S	40_P	0.522	0.30
96_E	107_K	0.521	0.30
51_P	54_L	0.519	0.30
44_S	47_E	0.518	0.30
31_E	41_L	0.511	0.29
17_L	27_P	0.506	0.29
6_L	87_G	0.504	0.29
88_E	94_L	0.500	0.28

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
2f6mA	1	0.3833	4.2	0.921	Contact Map
2p22A	1	0.3833	4.2	0.921	Contact Map
1vr7A	2	0.2583	3	0.927	Contact Map
4l3uA	1	0.3	2.5	0.93	Contact Map
1tdpA	1	0.7417	2.4	0.93	Contact Map
3bonA	1	0.4417	1.5	0.938	Contact Map
2kxeA	1	0.4583	1.4	0.939	Contact Map
3kv0A	2	0.575	1.3	0.941	Contact Map
2qsfA	1	0.2917	1.3	0.941	Contact Map
2jz1A	2	0.2583	1.2	0.941	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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