GERPA - BACSU - GREMLIN Contacts

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GERPA - Probable spore germination protein GerPA

UniProt:	O06721	Sequences: MPAIVGAFKINAIGTSGVVHIGDCITISPQAQVRTFAGAGSFNTGDSLKVMNYQNATNVYDNDAVDQPIVANA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	73 (71)
Sequences:	191 (126)
Seq/√Len:	14.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_V	68_P	3.276	0.99
37_A	42_F	3.140	0.98
35_T	42_F	3.107	0.98
5_V	41_S	2.260	0.90
14_G	58_N	2.073	0.85
20_H	25_I	1.984	0.82
10_I	19_V	1.870	0.78
44_T	58_N	1.776	0.74
48_L	67_Q	1.676	0.70
9_K	52_N	1.635	0.68
8_F	21_I	1.612	0.67
17_G	49_K	1.610	0.67
39_A	52_N	1.583	0.65
36_F	39_A	1.432	0.57
36_F	57_T	1.408	0.56
19_V	24_C	1.398	0.55
4_I	14_G	1.313	0.51
16_S	41_S	1.304	0.50
50_V	65_V	1.294	0.50
34_R	44_T	1.234	0.46
18_V	41_S	1.201	0.44
14_G	52_N	1.195	0.44
10_I	37_A	1.183	0.43
10_I	21_I	1.180	0.43
47_S	50_V	1.129	0.40
9_K	46_D	1.129	0.40
24_C	27_I	1.114	0.40
46_D	63_D	1.107	0.39
55_N	59_V	1.096	0.39
7_A	10_I	1.053	0.36
26_T	67_Q	1.052	0.36
8_F	19_V	1.037	0.36
51_M	62_N	1.025	0.35
3_A	21_I	1.010	0.34
13_I	53_Y	1.006	0.34
9_K	70_V	0.993	0.33
32_Q	62_N	0.992	0.33
14_G	39_A	0.991	0.33
64_A	69_I	0.980	0.33
28_S	50_V	0.976	0.32
4_I	27_I	0.971	0.32
21_I	47_S	0.968	0.32
31_A	55_N	0.964	0.32
45_G	61_D	0.959	0.32
12_A	49_K	0.935	0.30
7_A	16_S	0.935	0.30
36_F	63_D	0.930	0.30
18_V	27_I	0.928	0.30
8_F	56_A	0.915	0.30
30_Q	47_S	0.915	0.30
67_Q	72_N	0.894	0.29
7_A	41_S	0.894	0.29
26_T	51_M	0.873	0.28
59_V	70_V	0.850	0.27
43_N	58_N	0.847	0.26
12_A	24_C	0.838	0.26
7_A	35_T	0.827	0.26
7_A	47_S	0.827	0.26
9_K	68_P	0.800	0.24
30_Q	39_A	0.791	0.24
8_F	27_I	0.786	0.24
58_N	63_D	0.776	0.24
33_V	49_K	0.772	0.23
10_I	55_N	0.768	0.23
27_I	54_Q	0.759	0.23
13_I	19_V	0.744	0.22
12_A	31_A	0.732	0.22
3_A	24_C	0.731	0.22
25_I	67_Q	0.729	0.22
4_I	56_A	0.724	0.21
63_D	71_A	0.723	0.21
8_F	28_S	0.711	0.21
39_A	48_L	0.711	0.21
33_V	53_Y	0.710	0.21
53_Y	62_N	0.710	0.21
28_S	55_N	0.705	0.21
49_K	52_N	0.687	0.20
59_V	65_V	0.685	0.20
68_P	71_A	0.678	0.20
4_I	26_T	0.675	0.20
14_G	65_V	0.669	0.19
47_S	51_M	0.666	0.19
19_V	64_A	0.665	0.19
60_Y	70_V	0.662	0.19
36_F	42_F	0.631	0.18
20_H	26_T	0.631	0.18
20_H	24_C	0.629	0.18
7_A	26_T	0.625	0.18
32_Q	67_Q	0.624	0.18
18_V	59_V	0.606	0.17
20_H	51_M	0.580	0.17
30_Q	64_A	0.578	0.16
19_V	25_I	0.574	0.16
7_A	72_N	0.573	0.16
11_N	71_A	0.567	0.16
12_A	33_V	0.560	0.16
7_A	21_I	0.558	0.16
33_V	47_S	0.558	0.16
9_K	72_N	0.555	0.16
32_Q	55_N	0.548	0.16
32_Q	37_A	0.543	0.15
48_L	58_N	0.533	0.15
30_Q	51_M	0.533	0.15
4_I	9_K	0.519	0.15
33_V	64_A	0.502	0.14
20_H	53_Y	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
2ws94	3	0.2877	2.9	0.936	Contact Map
1poiB	1	0.9041	2.5	0.939	Contact Map
4gh4D	3	0.411	2.2	0.94	Contact Map
1p4qA	1	0.3288	1.7	0.944	Contact Map
3vx8D	1	0.3151	1.6	0.945	Contact Map
2x3hA	3	0.6438	1.4	0.947	Contact Map
1qqp4	3	0.3699	1.4	0.947	Contact Map
3uaqA	2	0.0822	1.2	0.949	Contact Map
3j8eG	3	0.5342	1.2	0.949	Contact Map
2ey4C	1	0.3836	1.2	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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