DUF3425 - PFAM28P - GREMLIN Contacts

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DUF3425 - Domain of unknown function (DUF3425)

PFAM:	PF11905	Sequences: YHLMRWQISPTQENYERLPPSLRPTPLQLTVPHHPWIDLLPWPRLRDNLIRAFHQGEYDEDELCRDLVGGLIVWGDPWDPRNWEVGEGFLRKWPWLLDGCDGELM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (91)
Sequences:	1356 (1039)
Seq/√Len:	108.9
META:	0.173

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_T	47_D	4.624	1.00
66_D	92_K	3.823	1.00
27_L	47_D	3.436	1.00
48_N	99_G	2.440	1.00
21_S	80_P	2.420	1.00
44_R	48_N	2.385	1.00
26_P	30_T	2.385	1.00
11_T	14_N	2.275	1.00
87_E	91_R	2.188	1.00
70_G	74_W	2.169	1.00
65_R	69_G	2.101	1.00
37_I	49_L	1.819	1.00
28_Q	38_D	1.810	1.00
10_P	14_N	1.747	1.00
62_E	92_K	1.743	1.00
20_P	23_R	1.701	1.00
36_W	45_L	1.700	1.00
70_G	73_V	1.620	1.00
61_D	64_C	1.609	1.00
64_C	68_V	1.503	1.00
18_L	69_G	1.412	1.00
23_R	85_V	1.359	1.00
21_S	42_W	1.334	1.00
37_I	68_V	1.326	0.99
12_Q	16_E	1.319	0.99
73_V	84_E	1.292	0.99
25_T	50_I	1.279	0.99
75_G	82_N	1.213	0.99
36_W	82_N	1.188	0.99
49_L	57_E	1.158	0.99
24_P	41_P	1.134	0.98
85_V	90_L	1.131	0.98
88_G	92_K	1.122	0.98
22_L	92_K	1.117	0.98
22_L	84_E	1.095	0.98
84_E	90_L	1.090	0.98
24_P	33_H	1.072	0.98
27_L	50_I	1.068	0.98
19_P	40_L	1.065	0.98
49_L	96_L	1.035	0.97
19_P	22_L	1.035	0.97
12_Q	15_Y	1.023	0.97
77_P	84_E	1.013	0.97
27_L	51_R	1.006	0.97
61_D	65_R	0.995	0.96
73_V	76_D	0.936	0.95
24_P	29_L	0.929	0.95
48_N	98_D	0.921	0.94
10_P	15_Y	0.915	0.94
78_W	82_N	0.878	0.93
23_R	43_P	0.850	0.92
71_L	85_V	0.850	0.92
52_A	95_W	0.848	0.92
60_E	64_C	0.843	0.91
60_E	79_D	0.842	0.91
19_P	83_W	0.840	0.91
58_Y	96_L	0.832	0.91
18_L	91_R	0.822	0.90
22_L	59_D	0.820	0.90
63_L	67_L	0.818	0.90
42_W	45_L	0.802	0.89
87_E	90_L	0.802	0.89
13_E	16_E	0.792	0.89
18_L	50_I	0.773	0.87
90_L	97_L	0.769	0.87
65_R	72_I	0.767	0.87
71_L	74_W	0.765	0.87
84_E	97_L	0.756	0.86
45_L	80_P	0.756	0.86
26_P	47_D	0.755	0.86
27_L	31_V	0.754	0.86
30_T	47_D	0.751	0.86
15_Y	23_R	0.737	0.85
44_R	98_D	0.737	0.85
39_L	63_L	0.734	0.84
55_Q	58_Y	0.730	0.84
37_I	50_I	0.723	0.84
14_N	17_R	0.719	0.83
23_R	39_L	0.717	0.83
27_L	37_I	0.716	0.83
69_G	88_G	0.716	0.83
63_L	69_G	0.712	0.83
21_S	29_L	0.710	0.82
39_L	72_I	0.708	0.82
85_V	99_G	0.701	0.82
28_Q	46_R	0.692	0.81
55_Q	60_E	0.689	0.81
27_L	88_G	0.687	0.80
31_V	47_D	0.683	0.80
40_L	68_V	0.681	0.80
34_H	64_C	0.669	0.79
27_L	48_N	0.662	0.78
10_P	13_E	0.660	0.78
58_Y	79_D	0.660	0.78
53_F	58_Y	0.658	0.77
86_G	90_L	0.649	0.76
45_L	49_L	0.643	0.76
44_R	47_D	0.640	0.75
60_E	65_R	0.639	0.75
9_S	12_Q	0.633	0.75
20_P	29_L	0.632	0.75
60_E	63_L	0.628	0.74
30_T	51_R	0.627	0.74
51_R	98_D	0.624	0.74
90_L	98_D	0.607	0.72
32_P	56_G	0.603	0.71
61_D	68_V	0.596	0.70
70_G	84_E	0.593	0.70
25_T	32_P	0.592	0.70
9_S	13_E	0.588	0.69
36_W	76_D	0.586	0.69
74_W	84_E	0.580	0.68
18_L	80_P	0.572	0.67
16_E	45_L	0.571	0.67
29_L	34_H	0.568	0.67
59_D	92_K	0.565	0.66
43_P	54_H	0.553	0.64
88_G	91_R	0.553	0.64
35_P	60_E	0.553	0.64
60_E	66_D	0.550	0.64
82_N	93_W	0.548	0.64
35_P	75_G	0.546	0.63
54_H	58_Y	0.542	0.63
30_T	97_L	0.542	0.63
49_L	88_G	0.539	0.63
34_H	37_I	0.536	0.62
12_Q	85_V	0.534	0.62
64_C	67_L	0.532	0.62
26_P	81_R	0.527	0.61
35_P	41_P	0.520	0.60
66_D	77_P	0.511	0.58
20_P	92_K	0.509	0.58
44_R	99_G	0.505	0.58
69_G	86_G	0.502	0.57
14_N	19_P	0.500	0.57
23_R	44_R	0.500	0.57

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
1m3wA	3	0.2667	8.2	0.921	Contact Map
4dx8H	1	0.381	3.4	0.934	Contact Map
2o62A	1	0.6667	2.3	0.94	Contact Map
2om2B	1	0.2095	1.7	0.944	Contact Map
4lnsA	2	0.9429	1.6	0.945	Contact Map
1sesA	2	0.3238	1.4	0.946	Contact Map
2o61A	1	0.7048	1.4	0.947	Contact Map
2qyuA	1	0.9429	1.2	0.948	Contact Map
2yijA	2	0.3429	1.1	0.949	Contact Map
1d02A	2	0.3905	1.1	0.95	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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