YmaF - PFAM28P - GREMLIN Contacts

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YmaF - YmaF family

PFAM:	PF12788	Sequences: QTHVHEFLGSTSLAEEGEDGHNHRFAGVTGPAIPTGGSHVHEIEGNTDFFDGHFHEIRGTTGPAIPVGNGKHVHFVEGVTTVNDGHRHEFRFATLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (92)
Sequences:	824 (569)
Seq/√Len:	59.3
META:	0.686

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_I	59_G	3.960	1.00
45_G	57_I	3.474	1.00
29_T	61_T	3.216	1.00
40_V	60_T	3.190	1.00
9_G	25_F	2.817	1.00
7_F	45_G	2.672	1.00
7_F	27_G	2.644	1.00
38_S	64_A	2.450	1.00
78_G	90_F	2.247	1.00
59_G	90_F	2.208	1.00
42_E	58_R	2.098	1.00
19_D	84_D	2.065	1.00
35_T	38_S	2.064	1.00
13_L	20_G	2.056	1.00
67_V	70_G	1.972	1.00
35_T	63_P	1.828	1.00
67_V	73_V	1.771	0.99
67_V	75_F	1.770	0.99
79_V	87_R	1.689	0.99
2_T	32_A	1.570	0.99
44_E	56_E	1.543	0.98
44_E	58_R	1.497	0.98
61_T	94_T	1.416	0.97
17_G	20_G	1.365	0.96
43_I	76_V	1.361	0.96
46_N	54_F	1.302	0.95
82_V	87_R	1.282	0.95
6_E	48_D	1.261	0.94
34_P	38_S	1.171	0.92
38_S	63_P	1.156	0.91
14_A	19_D	1.141	0.91
36_G	64_A	1.129	0.90
6_E	10_S	1.125	0.90
43_I	90_F	1.124	0.90
34_P	37_G	1.112	0.90
30_G	42_E	1.091	0.89
69_N	91_R	1.055	0.87
42_E	54_F	1.012	0.85
76_V	92_F	1.010	0.85
59_G	78_G	1.008	0.85
7_F	57_I	0.995	0.84
17_G	51_D	0.993	0.84
10_S	24_R	0.982	0.83
54_F	83_N	0.977	0.83
23_H	53_H	0.962	0.82
35_T	40_V	0.940	0.80
62_G	65_I	0.933	0.80
51_D	84_D	0.932	0.80
22_N	48_D	0.919	0.79
6_E	26_A	0.910	0.78
29_T	94_T	0.901	0.77
19_D	51_D	0.899	0.77
27_G	43_I	0.897	0.77
35_T	58_R	0.880	0.76
10_S	22_N	0.863	0.74
73_V	93_A	0.852	0.73
6_E	24_R	0.846	0.73
71_K	91_R	0.842	0.72
85_G	90_F	0.825	0.71
30_G	33_I	0.816	0.70
40_V	44_E	0.811	0.69
20_G	71_K	0.811	0.69
7_F	11_T	0.806	0.69
8_L	48_D	0.781	0.66
24_R	73_V	0.781	0.66
12_S	91_R	0.775	0.66
1_Q	49_F	0.772	0.66
5_H	39_H	0.766	0.65
42_E	59_G	0.756	0.64
20_G	51_D	0.740	0.62
56_E	65_I	0.735	0.62
68_G	71_K	0.731	0.61
42_E	60_T	0.727	0.61
27_G	61_T	0.719	0.60
52_G	84_D	0.718	0.60
27_G	57_I	0.712	0.59
2_T	83_N	0.711	0.59
66_P	70_G	0.701	0.58
54_F	58_R	0.700	0.58
24_R	48_D	0.695	0.57
31_P	49_F	0.693	0.57
67_V	93_A	0.684	0.56
2_T	34_P	0.679	0.56
46_N	49_F	0.679	0.56
30_G	58_R	0.665	0.54
7_F	43_I	0.663	0.54
27_G	45_G	0.659	0.54
87_R	90_F	0.656	0.53
59_G	76_V	0.644	0.52
79_V	89_E	0.638	0.51
6_E	28_V	0.634	0.51
41_H	55_H	0.630	0.50
48_D	54_F	0.629	0.50
27_G	59_G	0.622	0.49
25_F	57_I	0.617	0.49
49_F	52_G	0.612	0.48
90_F	94_T	0.605	0.47
50_F	84_D	0.598	0.47
39_H	80_T	0.597	0.47
75_F	93_A	0.591	0.46
45_G	59_G	0.588	0.46
10_S	48_D	0.586	0.45
35_T	64_A	0.586	0.45
61_T	78_G	0.578	0.45
19_D	69_N	0.566	0.43
20_G	49_F	0.564	0.43
35_T	79_V	0.563	0.43
32_A	76_V	0.560	0.43
28_V	75_F	0.550	0.41
6_E	22_N	0.548	0.41
34_P	64_A	0.548	0.41
51_D	69_N	0.545	0.41
11_T	52_G	0.536	0.40
20_G	50_F	0.534	0.40
12_S	89_E	0.532	0.40
81_T	92_F	0.528	0.39
39_H	74_H	0.525	0.39
30_G	44_E	0.525	0.39
65_I	70_G	0.524	0.39
14_A	89_E	0.521	0.38
40_V	54_F	0.520	0.38
28_V	49_F	0.518	0.38
49_F	75_F	0.518	0.38
11_T	20_G	0.517	0.38
21_H	55_H	0.517	0.38
22_N	54_F	0.513	0.37
5_H	11_T	0.512	0.37
7_F	92_F	0.512	0.37
13_L	22_N	0.509	0.37
44_E	66_P	0.507	0.37
6_E	75_F	0.507	0.37
24_R	50_F	0.506	0.37
35_T	60_T	0.504	0.37
46_N	56_E	0.502	0.36
41_H	53_H	0.501	0.36
31_P	46_N	0.500	0.36
4_V	46_N	0.500	0.36
7_F	78_G	0.500	0.36

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
2xgfA	3	0.9583	78.4	0.853	Contact Map
3i2tA	2	0.3646	0.4	0.963	Contact Map
2eocA	1	0.3958	0.4	0.963	Contact Map
2pebA	2	0.3229	0.3	0.965	Contact Map
3r2gA	3	0.1771	0.3	0.967	Contact Map
2mhrA	1	0.3646	0.3	0.968	Contact Map
1ef5A	1	0.2188	0.3	0.968	Contact Map
3l5aA	1	0.1562	0.3	0.968	Contact Map
2hmqA	5	0.3646	0.3	0.969	Contact Map
1ymmC	1	0.1458	0.2	0.969	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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