gerPA - PFAM28P - GREMLIN Contacts

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gerPA - Spore germination protein gerPA/gerPF

PFAM:	PF10676	Sequences: MPAIVGPIKINSVGSSGVVNFGDTLQISPKSNSKTFAGSGSFNTGDFISTNNGVSATNTLDPDVIDQPIVGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (71)
Sequences:	962 (622)
Seq/√Len:	73.8
META:	0.407

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_I	68_P	4.528	1.00
37_A	42_F	4.158	1.00
9_K	46_D	4.025	1.00
36_F	57_T	3.056	1.00
2_P	23_D	2.746	1.00
29_P	40_G	2.320	1.00
13_V	19_V	2.165	1.00
8_I	21_F	2.140	1.00
10_I	19_V	2.108	1.00
18_V	27_I	1.905	1.00
43_N	48_I	1.841	1.00
63_D	66_D	1.598	0.99
43_N	50_T	1.471	0.99
61_D	66_D	1.330	0.98
13_V	17_G	1.256	0.97
47_F	54_V	1.245	0.97
34_K	61_D	1.245	0.97
41_S	53_G	1.238	0.97
35_T	42_F	1.237	0.97
39_S	52_N	1.229	0.97
64_V	68_P	1.219	0.96
34_K	66_D	1.196	0.96
24_T	27_I	1.173	0.96
7_P	21_F	1.151	0.95
35_T	44_T	1.123	0.94
63_D	71_G	1.120	0.94
39_S	57_T	1.114	0.94
20_N	25_L	1.033	0.91
8_I	19_V	1.032	0.91
39_S	51_N	1.031	0.91
4_I	9_K	1.017	0.91
32_N	67_Q	1.005	0.90
38_G	55_S	1.005	0.90
9_K	68_P	0.982	0.89
48_I	67_Q	0.946	0.87
17_G	27_I	0.942	0.87
32_N	69_I	0.937	0.87
11_N	48_I	0.934	0.87
54_V	58_N	0.919	0.86
36_F	59_T	0.892	0.84
49_S	53_G	0.892	0.84
10_I	28_S	0.888	0.84
43_N	67_Q	0.878	0.83
22_G	61_D	0.875	0.83
23_D	38_G	0.869	0.82
19_V	47_F	0.859	0.82
29_P	32_N	0.838	0.80
35_T	55_S	0.831	0.80
26_Q	67_Q	0.803	0.77
51_N	62_P	0.773	0.74
6_G	23_D	0.757	0.73
15_S	19_V	0.748	0.72
46_D	63_D	0.747	0.72
15_S	18_V	0.743	0.71
17_G	28_S	0.738	0.71
64_V	69_I	0.732	0.70
25_L	32_N	0.720	0.69
19_V	64_V	0.714	0.68
8_I	43_N	0.712	0.68
10_I	23_D	0.712	0.68
52_N	55_S	0.711	0.68
17_G	43_N	0.691	0.66
60_L	70_V	0.691	0.66
17_G	29_P	0.670	0.64
7_P	25_L	0.650	0.61
11_N	14_G	0.642	0.60
18_V	40_G	0.621	0.58
12_S	38_G	0.617	0.57
50_T	53_G	0.617	0.57
47_F	56_A	0.614	0.57
42_F	68_P	0.614	0.57
16_S	26_Q	0.605	0.56
38_G	59_T	0.604	0.56
29_P	44_T	0.602	0.55
14_G	35_T	0.599	0.55
30_K	58_N	0.597	0.55
9_K	48_I	0.596	0.55
54_V	68_P	0.595	0.55
6_G	42_F	0.587	0.54
13_V	50_T	0.582	0.53
56_A	65_I	0.580	0.53
12_S	61_D	0.577	0.52
62_P	67_Q	0.575	0.52
13_V	34_K	0.572	0.52
24_T	29_P	0.570	0.51
45_G	50_T	0.566	0.51
40_G	55_S	0.562	0.50
52_N	58_N	0.560	0.50
27_I	49_S	0.556	0.50
55_S	59_T	0.554	0.49
61_D	65_I	0.546	0.48
3_A	10_I	0.545	0.48
24_T	71_G	0.543	0.48
4_I	7_P	0.540	0.48
9_K	71_G	0.535	0.47
20_N	26_Q	0.531	0.47
20_N	24_T	0.529	0.46
23_D	29_P	0.529	0.46
41_S	55_S	0.525	0.46
28_S	32_N	0.522	0.45
11_N	49_S	0.518	0.45
45_G	55_S	0.507	0.44
32_N	44_T	0.506	0.44
18_V	29_P	0.505	0.43
12_S	46_D	0.502	0.43
22_G	34_K	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
3wv7A	3	0.5972	1.5	0.908	Contact Map
4axgC	1	0	1.1	0.915	Contact Map
4tw1A	3	0.8889	1.1	0.915	Contact Map
1bkuA	1	0.1389	1	0.917	Contact Map
2jxzA	1	0.1389	1	0.917	Contact Map
3w1eA	1	0.4306	0.7	0.926	Contact Map
4tw1B	1	0.7917	0.7	0.926	Contact Map
5a1uG	1	0.4722	0.7	0.927	Contact Map
1mkfA	4	0.3333	0.6	0.929	Contact Map
3f83A	1	0.8611	0.6	0.929	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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