DUF2280 - PFAM28P - GREMLIN Contacts

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DUF2280 - Uncharacterized conserved protein (DUF2280)

PFAM:	PF10045	Sequences: MAALTDEVKAFIVQALACFDTPSQVAEAVKEEFGIEVSRQQVEAYDPTKRAGRNLAKKWRDLFEATRKAFLEDTADIPIANKAVRLRALQRMAEKAEEMGNMA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	103 (101)
Sequences:	976 (647)
Seq/√Len:	64.4
META:	0.746

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_K	72_E	3.817	1.00
57_K	61_D	3.749	1.00
90_Q	94_E	3.224	1.00
30_K	36_E	2.956	1.00
8_V	29_V	2.594	1.00
5_T	8_V	2.215	1.00
31_E	54_N	2.143	1.00
10_A	62_L	2.018	1.00
88_A	93_A	1.871	1.00
95_K	99_M	1.858	1.00
50_R	53_R	1.776	1.00
29_V	33_F	1.771	1.00
11_F	28_A	1.762	1.00
6_D	9_K	1.745	1.00
73_D	76_D	1.682	0.99
15_A	20_D	1.672	0.99
12_I	25_V	1.635	0.99
56_A	59_W	1.630	0.99
84_V	88_A	1.574	0.99
30_K	44_A	1.554	0.99
88_A	97_E	1.544	0.99
61_D	65_A	1.507	0.99
25_V	42_V	1.502	0.99
43_E	49_K	1.478	0.98
93_A	97_E	1.471	0.98
79_I	86_L	1.452	0.98
74_T	83_A	1.415	0.98
2_A	41_Q	1.377	0.97
8_V	35_I	1.343	0.97
55_L	60_R	1.313	0.96
69_A	76_D	1.291	0.96
62_L	66_T	1.284	0.96
91_R	97_E	1.280	0.96
38_S	41_Q	1.253	0.95
40_Q	43_E	1.229	0.95
20_D	28_A	1.228	0.95
1_M	41_Q	1.219	0.95
21_T	24_Q	1.205	0.94
45_Y	56_A	1.203	0.94
37_V	42_V	1.195	0.94
78_P	81_N	1.190	0.94
26_A	42_V	1.185	0.94
37_V	41_Q	1.178	0.94
29_V	35_I	1.175	0.94
19_F	81_N	1.167	0.93
11_F	33_F	1.161	0.93
6_D	58_K	1.158	0.93
19_F	71_L	1.153	0.93
60_R	64_E	1.131	0.92
26_A	39_R	1.066	0.90
69_A	73_D	1.027	0.88
65_A	69_A	1.019	0.88
48_T	63_F	1.014	0.87
27_E	31_E	1.013	0.87
70_F	83_A	1.003	0.87
12_I	41_Q	0.991	0.86
79_I	84_V	0.990	0.86
78_P	90_Q	0.982	0.86
29_V	39_R	0.978	0.85
47_P	55_L	0.966	0.85
73_D	83_A	0.960	0.84
65_A	75_A	0.953	0.84
14_Q	66_T	0.943	0.83
18_C	66_T	0.933	0.82
11_F	29_V	0.911	0.81
52_G	55_L	0.911	0.81
19_F	60_R	0.892	0.80
49_K	52_G	0.886	0.79
43_E	52_G	0.866	0.77
20_D	24_Q	0.863	0.77
12_I	29_V	0.848	0.76
92_M	96_A	0.817	0.73
20_D	87_R	0.813	0.73
23_S	27_E	0.804	0.72
65_A	71_L	0.794	0.71
8_V	12_I	0.781	0.70
16_L	46_D	0.779	0.70
29_V	37_V	0.762	0.68
88_A	91_R	0.760	0.68
19_F	61_D	0.754	0.67
61_D	64_E	0.752	0.67
95_K	98_E	0.746	0.66
10_A	59_W	0.745	0.66
27_E	98_E	0.742	0.66
96_A	99_M	0.735	0.65
69_A	84_V	0.732	0.65
46_D	49_K	0.728	0.64
74_T	78_P	0.718	0.63
83_A	87_R	0.714	0.63
18_C	70_F	0.702	0.62
44_A	54_N	0.689	0.60
62_L	65_A	0.689	0.60
43_E	53_R	0.679	0.59
84_V	90_Q	0.679	0.59
44_A	56_A	0.676	0.59
79_I	90_Q	0.674	0.58
41_Q	44_A	0.674	0.58
79_I	93_A	0.661	0.57
25_V	28_A	0.659	0.57
43_E	51_A	0.653	0.56
55_L	63_F	0.647	0.55
92_M	97_E	0.646	0.55
52_G	63_F	0.644	0.55
12_I	42_V	0.638	0.54
30_K	35_I	0.616	0.52
57_K	60_R	0.610	0.51
3_A	41_Q	0.610	0.51
32_E	57_K	0.610	0.51
16_L	42_V	0.608	0.51
78_P	83_A	0.604	0.50
74_T	82_K	0.601	0.50
71_L	90_Q	0.598	0.50
3_A	44_A	0.598	0.50
55_L	59_W	0.598	0.50
47_P	63_F	0.592	0.49
25_V	46_D	0.588	0.49
9_K	41_Q	0.588	0.49
92_M	95_K	0.584	0.48
96_A	101_N	0.582	0.48
39_R	42_V	0.581	0.48
46_D	63_F	0.580	0.48
41_Q	45_Y	0.580	0.48
22_P	46_D	0.579	0.47
48_T	52_G	0.578	0.47
7_E	53_R	0.569	0.46
95_K	100_G	0.566	0.46
59_W	75_A	0.560	0.45
71_L	75_A	0.560	0.45
7_E	78_P	0.559	0.45
66_T	70_F	0.558	0.45
34_G	38_S	0.556	0.45
13_V	59_W	0.546	0.44
26_A	37_V	0.544	0.43
26_A	40_Q	0.544	0.43
47_P	52_G	0.536	0.43
6_D	10_A	0.536	0.43
94_E	97_E	0.534	0.42
20_D	82_K	0.531	0.42
77_I	80_A	0.527	0.42
44_A	53_R	0.525	0.41
33_F	39_R	0.525	0.41
89_L	93_A	0.522	0.41
79_I	97_E	0.520	0.41
12_I	16_L	0.516	0.40
56_A	98_E	0.510	0.40
74_T	77_I	0.508	0.39
28_A	33_F	0.506	0.39
65_A	94_E	0.506	0.39
58_K	64_E	0.506	0.39
52_G	59_W	0.503	0.39
11_F	15_A	0.502	0.39
2_A	48_T	0.500	0.39

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
2ao9A	7	0.8544	51.7	0.894	Contact Map
2jn6A	1	0.7864	47.9	0.896	Contact Map
1iufA	1	0.7864	43.9	0.899	Contact Map
1pdnC	1	0.4369	41.2	0.901	Contact Map
2hl7A	1	0.4078	39.7	0.901	Contact Map
1u78A	1	0.8447	38.1	0.902	Contact Map
2kw0A	1	0.4369	35.7	0.904	Contact Map
4yfkF	1	0.5922	33.5	0.905	Contact Map
1s7oA	3	0.7767	32.5	0.906	Contact Map
1k78A	1	0.4757	31.2	0.907	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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