Spore_II_R - PFAM28P - GREMLIN Contacts

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Spore_II_R - Stage II sporulation protein R (spore_II_R)

PFAM:	PF09551	Sequences: DEVIRLHVIANSDSEEDQALKLKVRDAVLEYLTPLLAGAKSIEEAREIIKENLPEIEEIAEEVLKENGYDYPVKVELGNEYFPTKTYGDITLPAGEYEALRITIGEGEGQNWWCVLFPPLCFVDAT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (125)
Sequences:	3331 (2810)
Seq/√Len:	251.3
META:	0.804

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_T	107_G	4.196	1.00
46_R	98_E	2.809	1.00
13_D	110_Q	2.778	1.00
27_A	63_V	2.620	1.00
23_K	67_N	2.593	1.00
52_N	55_E	2.373	1.00
61_E	73_V	2.070	1.00
42_I	46_R	1.925	1.00
64_L	69_Y	1.858	1.00
42_I	98_E	1.842	1.00
12_S	17_D	1.803	1.00
79_N	96_E	1.799	1.00
57_E	75_V	1.794	1.00
4_I	77_L	1.792	1.00
76_E	103_T	1.775	1.00
11_N	17_D	1.757	1.00
63_V	66_E	1.745	1.00
3_V	92_L	1.743	1.00
61_E	65_K	1.737	1.00
35_L	52_N	1.703	1.00
82_F	99_A	1.691	1.00
57_E	61_E	1.672	1.00
41_S	44_E	1.636	1.00
63_V	67_N	1.621	1.00
4_I	49_I	1.614	1.00
79_N	98_E	1.608	1.00
80_E	101_R	1.594	1.00
28_V	102_I	1.593	1.00
60_A	73_V	1.558	1.00
9_I	103_T	1.555	1.00
15_E	19_A	1.536	1.00
20_L	64_L	1.527	1.00
53_L	75_V	1.520	1.00
11_N	106_E	1.516	1.00
81_Y	96_E	1.508	1.00
39_A	48_I	1.485	1.00
86_T	91_T	1.466	1.00
31_Y	59_I	1.457	1.00
31_Y	55_E	1.456	1.00
35_L	48_I	1.445	1.00
27_A	30_E	1.435	1.00
62_E	66_E	1.429	1.00
20_L	69_Y	1.421	1.00
39_A	45_A	1.380	1.00
53_L	100_L	1.364	1.00
61_E	72_P	1.308	1.00
84_T	91_T	1.305	1.00
27_A	59_I	1.301	1.00
25_R	29_L	1.250	1.00
74_K	103_T	1.230	1.00
3_V	7_H	1.204	1.00
57_E	74_K	1.194	1.00
84_T	94_A	1.190	1.00
59_I	63_V	1.180	1.00
48_I	52_N	1.172	1.00
71_Y	104_I	1.160	1.00
16_E	69_Y	1.128	1.00
4_I	46_R	1.121	1.00
9_I	101_R	1.109	1.00
64_L	73_V	1.107	1.00
73_V	104_I	1.104	1.00
64_L	71_Y	1.096	1.00
53_L	57_E	1.063	1.00
64_L	104_I	1.058	1.00
22_L	26_D	1.032	1.00
54_P	57_E	1.023	1.00
47_E	51_E	1.010	1.00
22_L	25_R	0.996	1.00
20_L	104_I	0.982	1.00
49_I	77_L	0.963	1.00
40_K	44_E	0.963	1.00
32_L	36_L	0.960	1.00
36_L	45_A	0.957	1.00
114_C	121_C	0.943	1.00
58_E	62_E	0.935	1.00
32_L	35_L	0.923	1.00
23_K	63_V	0.919	1.00
28_V	56_I	0.912	1.00
11_N	71_Y	0.910	1.00
27_A	62_E	0.891	1.00
17_D	71_Y	0.888	1.00
27_A	31_Y	0.882	1.00
11_N	14_S	0.882	1.00
81_Y	94_A	0.880	1.00
55_E	58_E	0.877	1.00
19_A	23_K	0.859	0.99
24_V	63_V	0.850	0.99
22_L	110_Q	0.826	0.99
31_Y	35_L	0.819	0.99
27_A	66_E	0.818	0.99
80_E	99_A	0.811	0.99
36_L	49_I	0.810	0.99
76_E	80_E	0.807	0.99
9_I	80_E	0.806	0.99
32_L	56_I	0.796	0.99
83_P	92_L	0.788	0.99
77_L	100_L	0.788	0.99
75_V	100_L	0.786	0.99
44_E	47_E	0.761	0.99
28_V	59_I	0.759	0.99
50_K	53_L	0.759	0.99
16_E	19_A	0.750	0.99
46_R	50_K	0.735	0.98
7_H	85_K	0.735	0.98
9_I	85_K	0.727	0.98
32_L	116_L	0.727	0.98
8_V	102_I	0.721	0.98
60_A	63_V	0.717	0.98
56_I	75_V	0.715	0.98
34_P	37_A	0.715	0.98
6_L	87_Y	0.712	0.98
32_L	49_I	0.712	0.98
75_V	102_I	0.711	0.98
51_E	54_P	0.707	0.98
4_I	42_I	0.704	0.98
43_E	47_E	0.691	0.98
24_V	64_L	0.688	0.97
29_L	125_A	0.682	0.97
86_T	92_L	0.682	0.97
24_V	27_A	0.679	0.97
46_R	77_L	0.677	0.97
72_P	104_I	0.667	0.97
7_H	101_R	0.663	0.97
43_E	46_R	0.661	0.97
50_K	54_P	0.660	0.97
115_V	119_P	0.660	0.97
60_A	75_V	0.648	0.96
55_E	59_I	0.647	0.96
76_E	101_R	0.647	0.96
82_F	116_L	0.644	0.96
28_V	31_Y	0.640	0.96
34_P	48_I	0.637	0.96
60_A	64_L	0.637	0.96
57_E	73_V	0.631	0.96
31_Y	36_L	0.622	0.95
55_E	62_E	0.619	0.95
36_L	116_L	0.616	0.95
7_H	73_V	0.611	0.95
40_K	50_K	0.605	0.95
86_T	89_D	0.604	0.95
47_E	50_K	0.601	0.94
20_L	71_Y	0.595	0.94
7_H	80_E	0.592	0.94
39_A	44_E	0.591	0.94
78_G	101_R	0.589	0.94
6_L	45_A	0.586	0.94
9_I	78_G	0.585	0.94
35_L	55_E	0.585	0.94
116_L	124_D	0.583	0.94
84_T	92_L	0.576	0.93
54_P	58_E	0.571	0.93
15_E	110_Q	0.568	0.93
80_E	85_K	0.568	0.93
66_E	106_E	0.567	0.93
69_Y	104_I	0.557	0.92
58_E	61_E	0.555	0.92
6_L	116_L	0.552	0.92
10_A	110_Q	0.547	0.91
18_Q	22_L	0.547	0.91
6_L	29_L	0.544	0.91
80_E	103_T	0.544	0.91
85_K	99_A	0.544	0.91
92_L	115_V	0.543	0.91
28_V	32_L	0.540	0.91
14_S	17_D	0.537	0.91
8_V	25_R	0.537	0.91
31_Y	100_L	0.537	0.91
87_Y	114_C	0.535	0.90
100_L	103_T	0.533	0.90
33_T	125_A	0.532	0.90
2_E	116_L	0.531	0.90
18_Q	112_W	0.526	0.90
4_I	98_E	0.518	0.89
50_K	77_L	0.517	0.89
37_A	40_K	0.517	0.89
3_V	80_E	0.515	0.89
86_T	90_I	0.514	0.89
52_N	56_I	0.511	0.88
29_L	101_R	0.511	0.88
59_I	62_E	0.508	0.88
64_L	67_N	0.508	0.88
49_I	83_P	0.508	0.88
5_R	82_F	0.507	0.88
33_T	37_A	0.505	0.88
58_E	65_K	0.503	0.87
60_A	102_I	0.502	0.87
4_I	100_L	0.501	0.87
31_Y	34_P	0.500	0.87

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
3somA	5	0.5714	26	0.934	Contact Map
1usuB	1	0.3968	24.5	0.935	Contact Map
3sc0A	2	0.5635	12.7	0.943	Contact Map
2b5dX	3	0.7222	9.9	0.946	Contact Map
3n72A	2	0.4603	9.7	0.946	Contact Map
4lkbF	4	0.4921	9.5	0.946	Contact Map
1x05A	1	0.381	9	0.947	Contact Map
3pe0A	1	0.9444	8.5	0.947	Contact Map
4qn1A	1	0.7302	7.9	0.948	Contact Map
2yjeM	1	0	7.5	0.949	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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