DUF2805 - PFAM28P - GREMLIN Contacts

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DUF2805 - Protein of unknown function (DUF2805)

PFAM:	PF10985	Sequences: DRIIEMAWEDRTPFEAIEFQFGLSEKEVIKLMRRELKPSSFKLWRKRVSGRKTKHLKKRSPEVGRFKCSRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (71)
Sequences:	4067 (1584)
Seq/√Len:	188.0
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_P	42_K	4.512	1.00
61_P	64_G	2.941	1.00
29_I	41_F	2.711	1.00
36_L	43_L	2.598	1.00
24_S	27_E	2.488	1.00
9_E	12_T	2.398	1.00
39_S	43_L	2.394	1.00
25_E	48_V	2.114	1.00
59_R	63_V	1.957	1.00
18_E	24_S	1.924	1.00
40_S	43_L	1.789	1.00
19_F	56_L	1.701	1.00
37_K	40_S	1.605	1.00
33_R	41_F	1.565	1.00
26_K	29_I	1.491	1.00
11_R	53_T	1.471	1.00
23_L	31_L	1.461	1.00
39_S	42_K	1.441	1.00
2_R	5_E	1.277	1.00
2_R	9_E	1.250	1.00
13_P	56_L	1.220	1.00
16_A	20_Q	1.215	1.00
68_C	71_Q	1.210	1.00
14_F	28_V	1.206	1.00
13_P	16_A	1.196	1.00
5_E	9_E	1.184	1.00
25_E	29_I	1.180	1.00
60_S	63_V	1.168	1.00
43_L	46_K	1.131	1.00
1_D	5_E	1.098	1.00
7_A	28_V	1.044	1.00
26_K	30_K	1.044	1.00
33_R	38_P	1.003	0.99
50_G	53_T	0.996	0.99
13_P	21_F	0.990	0.99
1_D	67_K	0.977	0.99
2_R	11_R	0.973	0.99
6_M	9_E	0.947	0.99
2_R	6_M	0.940	0.99
37_K	43_L	0.937	0.99
3_I	23_L	0.926	0.99
67_K	70_R	0.902	0.99
6_M	12_T	0.885	0.99
52_K	58_K	0.879	0.99
41_F	49_S	0.878	0.99
15_E	19_F	0.863	0.98
56_L	59_R	0.858	0.98
2_R	16_A	0.843	0.98
30_K	34_R	0.839	0.98
29_I	33_R	0.834	0.98
29_I	49_S	0.799	0.97
2_R	21_F	0.794	0.97
16_A	19_F	0.793	0.97
61_P	66_F	0.765	0.97
36_L	48_V	0.756	0.96
42_K	46_K	0.734	0.96
48_V	51_R	0.730	0.96
67_K	71_Q	0.715	0.95
6_M	16_A	0.706	0.95
1_D	66_F	0.705	0.95
18_E	22_G	0.704	0.95
64_G	69_S	0.696	0.94
4_I	7_A	0.695	0.94
21_F	31_L	0.694	0.94
59_R	62_E	0.693	0.94
4_I	36_L	0.692	0.94
16_A	21_F	0.685	0.94
31_L	35_E	0.678	0.94
15_E	55_H	0.658	0.93
41_F	44_W	0.640	0.92
44_W	47_R	0.638	0.91
60_S	64_G	0.638	0.91
12_T	16_A	0.638	0.91
63_V	66_F	0.633	0.91
15_E	58_K	0.626	0.91
9_E	53_T	0.611	0.90
1_D	70_R	0.604	0.89
9_E	21_F	0.600	0.89
23_L	27_E	0.597	0.89
46_K	49_S	0.595	0.88
40_S	45_R	0.592	0.88
66_F	69_S	0.591	0.88
53_T	63_V	0.588	0.88
4_I	35_E	0.587	0.88
66_F	71_Q	0.578	0.87
8_W	12_T	0.576	0.87
23_L	35_E	0.569	0.86
6_M	21_F	0.568	0.86
66_F	70_R	0.545	0.84
19_F	30_K	0.542	0.83
24_S	28_V	0.541	0.83
64_G	67_K	0.536	0.83
22_G	57_K	0.536	0.83
15_E	57_K	0.530	0.82
29_I	48_V	0.528	0.82
2_R	20_Q	0.527	0.82
41_F	50_G	0.519	0.81
60_S	67_K	0.518	0.80
36_L	40_S	0.517	0.80
18_E	28_V	0.510	0.79
62_E	67_K	0.510	0.79
62_E	70_R	0.508	0.79
10_D	32_M	0.508	0.79
40_S	47_R	0.504	0.79
37_K	48_V	0.504	0.79
58_K	64_G	0.500	0.78

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
1l0oC	1	0	29.5	0.885	Contact Map
2q1zA	1	0.6056	23.2	0.89	Contact Map
4ch7A	1	0.9437	20.5	0.893	Contact Map
2o8xA	7	0.5775	20.3	0.893	Contact Map
2x48A	1	0.4648	20.1	0.894	Contact Map
1u78A	1	0.9155	19.3	0.895	Contact Map
3hugA	3	0.7042	19.3	0.895	Contact Map
4nqwA	1	0.6197	19.3	0.895	Contact Map
2a6hF	1	0.6901	19.1	0.895	Contact Map
4aybH	1	0.6197	18.6	0.895	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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