DUF3892 - PFAM28P - GREMLIN Contacts

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DUF3892 - Protein of unknown function (DUF3892)

PFAM:	PF13031	Sequences: QITCIRKDDRGDPHERITHVGGPDGGTRWKLTREEAIAGIESGTWTFYVSGGKRADVIVVVSRNGRKYLRTEADGTWPDNLLSLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (85)
Sequences:	5995 (4780)
Seq/√Len:	518.4
META:	0.901

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_E	67_K	5.064	1.00
39_G	45_W	2.724	1.00
4_C	21_G	2.562	1.00
19_H	30_K	2.500	1.00
20_V	69_L	2.491	1.00
60_V	70_R	2.287	1.00
58_I	72_E	2.236	1.00
31_L	39_G	2.073	1.00
20_V	36_A	2.054	1.00
39_G	47_F	2.044	1.00
50_S	54_R	2.034	1.00
74_D	79_D	1.994	1.00
46_T	56_D	1.932	1.00
32_T	35_E	1.914	1.00
31_L	36_A	1.772	1.00
38_A	42_S	1.718	1.00
22_G	25_G	1.707	1.00
2_I	20_V	1.653	1.00
6_R	30_K	1.600	1.00
56_D	72_E	1.598	1.00
41_E	59_V	1.515	1.00
61_V	67_K	1.470	1.00
31_L	47_F	1.459	1.00
8_D	18_T	1.409	1.00
6_R	19_H	1.386	1.00
34_E	38_A	1.349	1.00
37_I	59_V	1.335	1.00
36_A	69_L	1.314	1.00
35_E	38_A	1.298	1.00
62_S	65_G	1.231	1.00
39_G	44_T	1.222	1.00
1_Q	50_S	1.191	1.00
33_R	66_R	1.143	1.00
77_W	83_S	1.104	1.00
35_E	39_G	1.100	1.00
8_D	12_D	1.095	1.00
19_H	32_T	1.074	1.00
58_I	70_R	1.054	1.00
71_T	80_N	0.996	1.00
74_D	80_N	0.991	1.00
53_K	76_T	0.988	1.00
31_L	35_E	0.935	1.00
7_K	82_L	0.932	1.00
9_D	12_D	0.919	1.00
12_D	15_E	0.917	1.00
57_V	69_L	0.907	1.00
70_R	73_A	0.890	1.00
61_V	64_N	0.877	1.00
37_I	41_E	0.875	1.00
75_G	78_P	0.872	1.00
62_S	66_R	0.860	1.00
48_Y	54_R	0.855	1.00
52_G	55_A	0.850	1.00
31_L	45_W	0.833	1.00
21_G	30_K	0.812	1.00
40_I	47_F	0.802	1.00
36_A	39_G	0.799	1.00
72_E	77_W	0.795	1.00
20_V	33_R	0.793	1.00
50_S	53_K	0.792	1.00
1_Q	48_Y	0.774	1.00
16_R	33_R	0.772	1.00
22_G	28_R	0.765	1.00
48_Y	56_D	0.757	1.00
45_W	48_Y	0.747	1.00
36_A	40_I	0.744	1.00
8_D	11_G	0.740	1.00
49_V	55_A	0.736	1.00
7_K	11_G	0.733	1.00
60_V	68_Y	0.731	1.00
8_D	15_E	0.715	1.00
25_G	29_W	0.709	1.00
62_S	67_K	0.702	1.00
73_A	80_N	0.698	1.00
25_G	28_R	0.695	1.00
80_N	83_S	0.695	1.00
22_G	27_T	0.693	1.00
33_R	68_Y	0.692	1.00
37_I	67_K	0.689	1.00
36_A	47_F	0.689	1.00
20_V	40_I	0.689	1.00
59_V	67_K	0.681	1.00
1_Q	23_P	0.673	1.00
17_I	20_V	0.668	1.00
41_E	61_V	0.665	1.00
33_R	69_L	0.665	1.00
23_P	28_R	0.659	1.00
28_R	39_G	0.653	1.00
27_T	31_L	0.627	1.00
37_I	40_I	0.627	1.00
10_R	13_P	0.622	1.00
72_E	78_P	0.604	1.00
11_G	16_R	0.603	1.00
23_P	27_T	0.600	1.00
73_A	77_W	0.594	0.99
81_L	84_L	0.581	0.99
58_I	77_W	0.578	0.99
55_A	58_I	0.576	0.99
72_E	75_G	0.573	0.99
20_V	57_V	0.572	0.99
70_R	79_D	0.568	0.99
29_W	47_F	0.566	0.99
38_A	41_E	0.564	0.99
53_K	56_D	0.560	0.99
5_I	17_I	0.558	0.99
70_R	77_W	0.556	0.99
43_G	46_T	0.555	0.99
24_D	27_T	0.552	0.99
57_V	60_V	0.552	0.99
3_T	22_G	0.551	0.99
51_G	76_T	0.544	0.99
49_V	80_N	0.541	0.99
37_I	69_L	0.539	0.99
29_W	39_G	0.535	0.99
34_E	37_I	0.533	0.99
23_P	26_G	0.533	0.99
53_K	79_D	0.529	0.99
4_C	7_K	0.527	0.99
46_T	49_V	0.526	0.99
78_P	82_L	0.525	0.99
38_A	44_T	0.525	0.99
6_R	10_R	0.520	0.99
70_R	74_D	0.518	0.99
70_R	78_P	0.516	0.99
63_R	76_T	0.516	0.99
40_I	43_G	0.507	0.98
75_G	80_N	0.504	0.98
61_V	66_R	0.500	0.98

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
2r4fA	4	0.8588	5.4	0.884	Contact Map
2hhzA	2	0.6471	5	0.886	Contact Map
1efvA	1	0.4353	3.4	0.895	Contact Map
3j60K	1	0.7412	3.2	0.896	Contact Map
3k2tA	1	0.6118	3.2	0.897	Contact Map
4ekxC	2	0.2941	3.1	0.897	Contact Map
1o97D	1	0.4235	3.1	0.898	Contact Map
3a98B	1	0.8588	3	0.898	Contact Map
4lo6A	1	0.4235	2.8	0.899	Contact Map
2fiyA	1	0.9059	2.7	0.901	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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