GERPB - BACSU - GREMLIN Contacts

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GERPB - Probable spore germination protein GerPB

UniProt:	O06720	Sequences: MNFYINQTIQINYLRLESISNSSILQIGSAGSIKSLSNLYNTGSYVEPAPEVSGSGQPLQLQEPDTGSLVPLQPPGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	77 (68)
Sequences:	105 (76)
Seq/√Len:	9.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_I	30_A	3.524	0.96
30_A	33_I	2.616	0.84
16_L	25_L	2.401	0.78
14_L	25_L	2.116	0.68
6_N	27_I	1.979	0.63
42_T	50_P	1.846	0.57
4_Y	10_Q	1.778	0.54
25_L	73_Q	1.773	0.54
3_F	29_S	1.726	0.52
18_S	38_N	1.678	0.50
16_L	73_Q	1.603	0.46
32_S	35_S	1.561	0.45
4_Y	50_P	1.508	0.42
3_F	6_N	1.428	0.39
12_N	38_N	1.424	0.39
6_N	38_N	1.385	0.37
15_R	24_I	1.384	0.37
16_L	50_P	1.349	0.36
34_K	38_N	1.346	0.35
17_E	20_S	1.311	0.34
68_S	72_L	1.290	0.33
17_E	52_V	1.248	0.32
14_L	17_E	1.214	0.30
6_N	16_L	1.210	0.30
55_S	68_S	1.182	0.29
63_E	68_S	1.173	0.29
13_Y	19_I	1.168	0.29
8_T	27_I	1.128	0.27
47_E	53_S	1.088	0.26
5_I	12_N	1.086	0.26
29_S	33_I	1.085	0.26
3_F	12_N	1.074	0.25
4_Y	54_G	1.067	0.25
29_S	34_K	1.058	0.25
51_E	55_S	1.049	0.25
39_L	49_A	1.037	0.24
16_L	46_V	1.013	0.23
37_S	44_S	1.008	0.23
3_F	73_Q	0.989	0.23
6_N	36_L	0.988	0.23
46_V	67_G	0.974	0.22
45_Y	55_S	0.968	0.22
39_L	70_V	0.965	0.22
4_Y	73_Q	0.921	0.21
5_I	8_T	0.895	0.20
14_L	36_L	0.890	0.20
12_N	19_I	0.889	0.20
46_V	64_P	0.888	0.20
8_T	56_G	0.884	0.20
30_A	36_L	0.877	0.19
12_N	29_S	0.869	0.19
19_I	34_K	0.855	0.19
8_T	51_E	0.839	0.18
6_N	56_G	0.831	0.18
21_N	39_L	0.826	0.18
47_E	51_E	0.824	0.18
20_S	44_S	0.814	0.18
5_I	29_S	0.808	0.18
20_S	66_T	0.795	0.17
13_Y	36_L	0.795	0.17
35_S	54_G	0.790	0.17
17_E	32_S	0.779	0.17
45_Y	66_T	0.765	0.17
17_E	63_E	0.755	0.16
17_E	30_A	0.751	0.16
32_S	54_G	0.750	0.16
20_S	68_S	0.741	0.16
20_S	40_Y	0.735	0.16
25_L	69_L	0.734	0.16
48_P	64_P	0.721	0.15
56_G	65_D	0.715	0.15
42_T	66_T	0.685	0.15
13_Y	48_P	0.683	0.15
14_L	64_P	0.681	0.15
10_Q	19_I	0.677	0.15
25_L	51_E	0.677	0.15
55_S	67_G	0.676	0.14
53_S	56_G	0.668	0.14
2_N	6_N	0.657	0.14
33_I	44_S	0.637	0.14
52_V	68_S	0.633	0.14
2_N	47_E	0.627	0.13
67_G	73_Q	0.620	0.13
17_E	36_L	0.618	0.13
19_I	74_P	0.609	0.13
14_L	19_I	0.599	0.13
51_E	67_G	0.597	0.13
21_N	49_A	0.591	0.13
39_L	69_L	0.590	0.13
32_S	55_S	0.583	0.13
18_S	36_L	0.567	0.12
46_V	69_L	0.563	0.12
32_S	36_L	0.561	0.12
37_S	66_T	0.541	0.12
20_S	46_V	0.535	0.12
51_E	56_G	0.528	0.12
29_S	63_E	0.525	0.12
12_N	30_A	0.516	0.11
53_S	67_G	0.510	0.11
47_E	74_P	0.508	0.11
65_D	73_Q	0.502	0.11
37_S	55_S	0.500	0.11

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
2gqbA	1	0.3377	4.6	0.938	Contact Map
1gl4A	1	0.4805	2.9	0.944	Contact Map
4mtlA	4	0.1558	2.5	0.946	Contact Map
3riqA	3	0.6494	2.2	0.947	Contact Map
1mhyB	2	0.3377	2.2	0.948	Contact Map
2yi9A	1	0.2727	2.2	0.948	Contact Map
2yibD	1	0.4286	2.2	0.948	Contact Map
3ub0B	2	0.3377	1.9	0.949	Contact Map
2ahmA	2	0.2078	1.9	0.949	Contact Map
1nnxA	1	0.2597	1.9	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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