SpoVAB - PFAM28P - GREMLIN Contacts

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SpoVAB - Stage V sporulation protein AB

PFAM:	PF13782	Sequences: LTVLGIIPRLAQLTKTAKHIRLYEWAIILGGILGTLLSLFDISLPLGPILLIIFGLFAGIFVGCLAAALAEVLNVIPILARRIGLKRGLGYLILAIALGKVAGSLFYWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (109)
Sequences:	1010 (765)
Seq/√Len:	73.3
META:	0.665

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_T	23_Y	7.979	1.00
14_T	23_Y	4.205	1.00
54_F	58_A	4.044	1.00
7_I	27_I	3.210	1.00
102_A	106_F	2.591	1.00
46_L	50_L	2.376	1.00
1_L	31_G	2.313	1.00
36_L	42_I	2.043	1.00
105_L	109_L	1.948	1.00
101_V	104_S	1.831	1.00
31_G	67_A	1.764	1.00
47_G	50_L	1.722	1.00
34_G	38_S	1.722	1.00
5_G	38_S	1.719	1.00
13_L	68_A	1.635	1.00
67_A	70_A	1.575	0.99
101_V	105_L	1.572	0.99
3_V	65_L	1.559	0.99
4_L	68_A	1.513	0.99
10_L	64_C	1.446	0.99
4_L	75_V	1.442	0.99
5_G	34_G	1.437	0.99
98_L	102_A	1.431	0.99
66_A	96_I	1.416	0.99
33_L	37_L	1.389	0.98
9_R	12_Q	1.375	0.98
48_P	57_F	1.349	0.98
98_L	101_V	1.306	0.98
55_G	83_I	1.275	0.97
67_A	93_I	1.261	0.97
49_I	53_I	1.233	0.97
7_I	11_A	1.232	0.97
36_L	40_F	1.228	0.96
79_L	83_I	1.211	0.96
72_V	75_V	1.176	0.96
44_L	47_G	1.173	0.95
50_L	73_L	1.156	0.95
96_I	100_K	1.136	0.95
33_L	52_I	1.133	0.94
24_E	82_R	1.115	0.94
27_I	66_A	1.087	0.93
25_W	28_I	1.071	0.93
11_A	24_E	1.066	0.92
10_L	67_A	1.064	0.92
26_A	37_L	1.044	0.92
35_T	38_S	1.038	0.91
94_L	98_L	1.026	0.91
43_S	55_G	1.009	0.90
37_L	98_L	0.975	0.89
24_E	34_G	0.968	0.88
17_A	107_Y	0.968	0.88
33_L	98_L	0.966	0.88
64_C	108_W	0.962	0.88
76_I	93_I	0.943	0.87
49_I	52_I	0.942	0.87
3_V	76_I	0.940	0.87
21_R	25_W	0.937	0.87
34_G	82_R	0.932	0.86
24_E	31_G	0.931	0.86
13_L	67_A	0.923	0.86
104_S	108_W	0.918	0.86
34_G	58_A	0.917	0.85
6_I	23_Y	0.915	0.85
35_T	40_F	0.914	0.85
90_G	94_L	0.905	0.85
32_I	35_T	0.904	0.85
61_F	104_S	0.892	0.84
26_A	78_I	0.888	0.84
55_G	62_V	0.883	0.83
26_A	30_G	0.856	0.81
25_W	29_L	0.849	0.81
37_L	41_D	0.848	0.81
36_L	49_I	0.843	0.80
2_T	108_W	0.834	0.80
8_P	65_L	0.833	0.79
64_C	70_A	0.827	0.79
13_L	64_C	0.815	0.78
50_L	89_L	0.813	0.78
84_G	101_V	0.811	0.78
61_F	66_A	0.810	0.78
61_F	96_I	0.805	0.77
55_G	106_F	0.793	0.76
24_E	62_V	0.789	0.76
34_G	103_G	0.788	0.76
95_A	104_S	0.786	0.75
32_I	37_L	0.781	0.75
47_G	53_I	0.771	0.74
38_S	62_V	0.759	0.73
33_L	41_D	0.752	0.72
58_A	86_K	0.751	0.72
49_I	84_G	0.742	0.71
15_K	26_A	0.737	0.71
90_G	93_I	0.733	0.70
2_T	96_I	0.725	0.69
45_P	50_L	0.716	0.68
3_V	96_I	0.711	0.68
96_I	106_F	0.710	0.68
83_I	86_K	0.706	0.67
87_R	90_G	0.704	0.67
4_L	65_L	0.703	0.67
76_I	97_A	0.700	0.67
47_G	54_F	0.696	0.66
48_P	102_A	0.693	0.66
5_G	96_I	0.691	0.66
15_K	29_L	0.688	0.65
1_L	84_G	0.677	0.64
73_L	85_L	0.673	0.64
28_I	95_A	0.673	0.64
10_L	66_A	0.672	0.63
13_L	66_A	0.672	0.63
10_L	65_L	0.670	0.63
16_T	20_I	0.669	0.63
78_I	97_A	0.667	0.63
43_S	102_A	0.665	0.63
87_R	108_W	0.660	0.62
77_P	103_G	0.654	0.61
32_I	45_P	0.654	0.61
1_L	75_V	0.648	0.61
72_V	77_P	0.643	0.60
30_G	34_G	0.635	0.59
10_L	85_L	0.630	0.59
17_A	109_L	0.620	0.57
6_I	65_L	0.615	0.57
105_L	108_W	0.613	0.56
8_P	12_Q	0.610	0.56
70_A	77_P	0.601	0.55
48_P	53_I	0.600	0.55
71_E	100_K	0.596	0.54
31_G	91_Y	0.592	0.54
8_P	13_L	0.584	0.53
49_I	54_F	0.575	0.52
13_L	97_A	0.572	0.51
51_L	55_G	0.561	0.50
46_L	73_L	0.561	0.50
99_G	103_G	0.560	0.50
33_L	87_R	0.559	0.50
5_G	64_C	0.558	0.50
22_L	26_A	0.557	0.50
47_G	88_G	0.551	0.49
26_A	61_F	0.546	0.48
78_I	82_R	0.545	0.48
27_I	78_I	0.545	0.48
8_P	81_R	0.544	0.48
22_L	25_W	0.541	0.48
68_A	75_V	0.540	0.47
58_A	62_V	0.539	0.47
25_W	51_L	0.539	0.47
45_P	53_I	0.537	0.47
26_A	36_L	0.536	0.47
11_A	17_A	0.534	0.47
64_C	109_L	0.534	0.47
68_A	72_V	0.533	0.47
1_L	38_S	0.532	0.46
67_A	72_V	0.530	0.46
84_G	87_R	0.528	0.46
33_L	42_I	0.524	0.45
35_T	39_L	0.521	0.45
19_H	51_L	0.520	0.45
65_L	73_L	0.514	0.44
33_L	43_S	0.513	0.44
66_A	72_V	0.511	0.44
52_I	55_G	0.509	0.44
46_L	109_L	0.504	0.43
84_G	91_Y	0.500	0.43

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
2cfqA	1	0.945	21.9	0.917	Contact Map
3l1lA	2	0.7706	13.7	0.924	Contact Map
2zy9A	2	0.945	13	0.925	Contact Map
2nwlA	3	0.7615	11.9	0.926	Contact Map
3orgA	2	0.5963	6.8	0.934	Contact Map
4u9nA	2	0.9541	6.7	0.934	Contact Map
4djkA	2	0.7248	6.2	0.935	Contact Map
4m64A	1	0.945	5.7	0.936	Contact Map
4j05A	3	0.9541	5.6	0.937	Contact Map
4ikvA	1	0.9083	5.4	0.937	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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