GERPF - BACSU - GREMLIN Contacts

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GERPF - Probable spore germination protein GerPF

UniProt:	O06716	Sequences: MPAIVGPIAINSISGGVVNFGDSFYLSPKSSSKSALGSGAGNTGDFLLLNNAVNATNYIDPDVNDQDMVGNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	72 (71)
Sequences:	193 (130)
Seq/√Len:	15.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_L	41_G	3.321	0.99
64_N	67_D	3.305	0.99
34_S	41_G	3.295	0.99
10_I	18_V	2.813	0.97
5_V	40_A	2.417	0.93
19_N	24_F	2.073	0.86
16_G	48_L	1.955	0.82
35_A	56_T	1.926	0.81
47_L	66_Q	1.860	0.79
14_S	57_N	1.850	0.79
54_N	58_Y	1.790	0.76
9_A	51_N	1.771	0.75
9_A	45_D	1.670	0.71
25_Y	66_Q	1.607	0.68
8_I	20_F	1.591	0.67
35_A	38_S	1.569	0.66
49_L	64_N	1.547	0.65
38_S	51_N	1.500	0.62
43_T	57_N	1.473	0.61
4_I	14_S	1.353	0.54
15_G	30_S	1.300	0.51
14_S	51_N	1.230	0.47
9_A	69_V	1.194	0.45
57_N	62_D	1.193	0.45
10_I	36_L	1.156	0.43
27_S	49_L	1.136	0.42
58_Y	69_V	1.120	0.41
7_P	40_A	1.113	0.41
33_K	43_T	1.100	0.40
17_V	26_L	1.091	0.39
18_V	23_S	1.086	0.39
63_V	68_M	1.069	0.38
10_I	20_F	0.997	0.34
30_S	54_N	0.959	0.33
50_N	61_P	0.958	0.32
46_F	49_L	0.953	0.32
29_K	46_F	0.952	0.32
31_S	61_P	0.927	0.31
38_S	47_L	0.917	0.30
8_I	55_A	0.899	0.30
13_I	52_A	0.890	0.29
15_G	65_D	0.888	0.29
8_I	26_L	0.884	0.29
27_S	52_A	0.873	0.28
52_A	61_P	0.849	0.27
9_A	67_D	0.845	0.27
67_D	70_G	0.840	0.27
27_S	54_N	0.832	0.26
66_Q	71_N	0.828	0.26
40_A	59_I	0.821	0.26
56_T	60_D	0.810	0.26
32_S	52_A	0.805	0.25
29_K	38_S	0.801	0.25
10_I	23_S	0.795	0.25
4_I	55_A	0.786	0.25
11_N	41_G	0.766	0.24
3_A	20_F	0.761	0.23
12_S	30_S	0.747	0.23
32_S	48_L	0.747	0.23
17_V	40_A	0.742	0.23
7_P	10_I	0.741	0.23
4_I	26_L	0.731	0.22
8_I	12_S	0.716	0.22
7_P	46_F	0.704	0.21
19_N	52_A	0.690	0.21
44_G	60_D	0.689	0.21
25_Y	50_N	0.687	0.21
5_V	12_S	0.682	0.20
34_S	55_A	0.682	0.20
3_A	68_M	0.669	0.20
47_L	61_P	0.666	0.20
45_D	62_D	0.666	0.20
45_D	67_D	0.648	0.19
23_S	26_L	0.648	0.19
13_I	36_L	0.644	0.19
18_V	24_F	0.640	0.19
7_P	71_N	0.633	0.19
14_S	32_S	0.630	0.19
35_A	41_G	0.623	0.18
15_G	50_N	0.620	0.18
15_G	59_I	0.613	0.18
54_N	59_I	0.604	0.18
26_L	53_V	0.591	0.17
46_F	50_N	0.587	0.17
35_A	58_Y	0.584	0.17
3_A	15_G	0.584	0.17
31_S	66_Q	0.579	0.17
9_A	71_N	0.572	0.17
4_I	25_Y	0.569	0.17
48_L	51_N	0.556	0.16
58_Y	64_N	0.555	0.16
20_F	46_F	0.550	0.16
38_S	48_L	0.549	0.16
20_F	32_S	0.543	0.16
49_L	59_I	0.530	0.15
27_S	51_N	0.530	0.15
29_K	53_V	0.528	0.15
19_N	25_Y	0.527	0.15
6_G	51_N	0.525	0.15
4_I	51_N	0.520	0.15
11_N	17_V	0.516	0.15
36_L	54_N	0.515	0.15
59_I	70_G	0.507	0.15
17_V	58_Y	0.507	0.15
13_I	18_V	0.505	0.15
31_S	53_V	0.500	0.14

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
1mkfA	4	0.3333	3.6	0.932	Contact Map
1xzzA	1	0.7083	3.1	0.935	Contact Map
2x3hA	3	0.6528	2.8	0.936	Contact Map
2ws94	3	0.2917	2.8	0.936	Contact Map
1qqp4	3	0.375	2.7	0.937	Contact Map
4gh4D	3	0.4306	2.6	0.937	Contact Map
4axgC	1	0	2.5	0.937	Contact Map
3uj4A	1	0.6806	1.4	0.945	Contact Map
1gksA	1	0.3333	1.4	0.946	Contact Map
2ey4C	1	0.3889	1.4	0.946	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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