DUF2373 - PFAM28P - GREMLIN Contacts

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DUF2373 - Uncharacterised conserved protein (DUF2373)

PFAM:	PF10180	Sequences: EYLRQWKTDRSNWKFNKNRQTWLLKHMFDEEKIPDEYFPALLEYLEGLQGGARERLLEKAEEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (62)
Sequences:	605 (492)
Seq/√Len:	62.5
META:	0.428

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_D	12_N	4.855	1.00
28_F	60_A	2.642	1.00
7_K	43_E	2.514	1.00
54_E	58_E	2.338	1.00
58_E	62_E	2.212	1.00
27_M	41_L	2.186	1.00
22_W	26_H	2.044	1.00
16_N	19_R	1.966	1.00
6_W	38_F	1.630	0.99
1_E	4_R	1.627	0.99
18_N	21_T	1.556	0.99
34_P	37_Y	1.510	0.98
18_N	25_K	1.508	0.98
23_L	41_L	1.409	0.98
24_L	56_L	1.406	0.97
33_I	41_L	1.404	0.97
38_F	42_L	1.367	0.97
40_A	43_E	1.353	0.97
57_L	61_E	1.342	0.97
22_W	32_K	1.339	0.97
35_D	38_F	1.308	0.96
15_F	53_R	1.180	0.93
35_D	59_K	1.172	0.93
8_T	49_Q	1.116	0.91
4_R	37_Y	1.110	0.91
55_R	58_E	1.060	0.89
14_K	17_K	1.049	0.88
33_I	42_L	1.024	0.87
7_K	40_A	1.022	0.87
41_L	45_L	1.003	0.86
20_Q	50_G	0.979	0.84
24_L	48_L	0.959	0.83
21_T	59_K	0.946	0.82
3_L	41_L	0.923	0.81
5_Q	12_N	0.921	0.81
16_N	51_G	0.896	0.79
2_Y	14_K	0.893	0.79
6_W	37_Y	0.875	0.77
29_D	32_K	0.872	0.77
4_R	8_T	0.865	0.76
21_T	25_K	0.860	0.76
30_E	35_D	0.852	0.75
32_K	46_E	0.839	0.74
5_Q	9_D	0.836	0.74
20_Q	29_D	0.813	0.72
11_S	46_E	0.809	0.71
16_N	25_K	0.803	0.71
5_Q	10_R	0.790	0.70
18_N	55_R	0.786	0.69
4_R	46_E	0.770	0.68
51_G	55_R	0.760	0.67
46_E	54_E	0.754	0.66
54_E	57_L	0.753	0.66
4_R	7_K	0.740	0.64
18_N	28_F	0.734	0.64
55_R	59_K	0.731	0.64
26_H	32_K	0.730	0.63
48_L	56_L	0.712	0.61
1_E	7_K	0.711	0.61
28_F	56_L	0.697	0.60
4_R	36_E	0.687	0.59
2_Y	17_K	0.672	0.57
1_E	5_Q	0.663	0.56
30_E	43_E	0.660	0.56
58_E	61_E	0.646	0.54
29_D	52_A	0.643	0.54
24_L	32_K	0.641	0.54
15_F	19_R	0.633	0.53
28_F	59_K	0.628	0.52
10_R	47_G	0.627	0.52
26_H	29_D	0.614	0.50
51_G	54_E	0.592	0.48
19_R	22_W	0.588	0.47
26_H	41_L	0.587	0.47
33_I	51_G	0.578	0.46
2_Y	44_Y	0.575	0.46
6_W	10_R	0.568	0.45
24_L	41_L	0.566	0.45
17_K	34_P	0.562	0.45
33_I	50_G	0.562	0.45
17_K	56_L	0.552	0.43
8_T	12_N	0.549	0.43
2_Y	13_W	0.541	0.42
22_W	31_E	0.533	0.41
5_Q	40_A	0.532	0.41
51_G	62_E	0.531	0.41
35_D	62_E	0.530	0.41
29_D	45_L	0.521	0.40
39_P	43_E	0.521	0.40
14_K	45_L	0.516	0.39
3_L	44_Y	0.516	0.39
7_K	11_S	0.506	0.38
31_E	57_L	0.500	0.38

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
4by6C	1	0.7302	54.2	0.833	Contact Map
4by6B	1	0.7302	34.5	0.852	Contact Map
4c0dB	1	1	25.6	0.861	Contact Map
4c0dC	1	0.7143	25.4	0.862	Contact Map
4c0gA	2	0.7778	20.3	0.867	Contact Map
4c0fA	2	1	9.5	0.886	Contact Map
1f75A	2	0.8095	9.3	0.886	Contact Map
4q9mA	2	1	9.2	0.886	Contact Map
2d2rA	2	0.8413	7.2	0.892	Contact Map
2vg0A	2	1	6.3	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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