YRAD - BACSU - GREMLIN Contacts

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YRAD - Spore coat protein F-like protein YraD

UniProt:	O06010	Sequences: MNPIIEYLTGMNVLTDQIIAMDLLISAKNGVRNYAMAATEAGTPEVKEVLIRHLEEALDMHEQLSSYMMEKGWYHPWNPDEQVKLNLKNIDTAIQLPTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	99 (89)
Sequences:	202 (165)
Seq/√Len:	17.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_L	64_L	3.000	0.99
58_L	86_N	2.620	0.97
23_L	60_M	2.478	0.96
78_N	81_E	2.342	0.94
21_M	85_L	2.330	0.94
67_Y	74_Y	2.321	0.94
85_L	89_N	2.251	0.93
65_S	76_P	2.147	0.91
10_G	92_T	1.976	0.87
32_R	87_L	1.938	0.86
69_M	76_P	1.928	0.85
8_L	12_N	1.893	0.84
59_D	63_Q	1.889	0.84
34_Y	53_H	1.813	0.82
42_G	58_L	1.720	0.78
75_H	81_E	1.668	0.76
16_D	53_H	1.649	0.75
57_A	83_V	1.629	0.74
19_I	45_E	1.522	0.69
66_S	76_P	1.475	0.66
31_V	39_T	1.427	0.64
21_M	47_K	1.405	0.62
62_E	66_S	1.363	0.60
47_K	90_I	1.342	0.59
16_D	82_Q	1.341	0.59
27_A	57_A	1.333	0.58
9_T	13_V	1.289	0.55
41_A	58_L	1.287	0.55
14_L	60_M	1.283	0.55
10_G	15_T	1.283	0.55
32_R	36_M	1.282	0.55
15_T	74_Y	1.253	0.53
44_P	55_E	1.242	0.53
17_Q	73_W	1.227	0.52
46_V	79_P	1.219	0.51
17_Q	96_L	1.210	0.51
36_M	81_E	1.196	0.50
58_L	78_N	1.163	0.48
29_N	72_G	1.158	0.48
78_N	95_Q	1.137	0.46
34_Y	70_E	1.117	0.45
46_V	77_W	1.112	0.45
8_L	74_Y	1.064	0.42
69_M	82_Q	1.059	0.42
52_R	56_E	1.058	0.42
80_D	91_D	1.046	0.41
29_N	65_S	1.032	0.40
69_M	75_H	1.030	0.40
13_V	43_T	1.009	0.39
10_G	14_L	0.997	0.38
38_A	47_K	0.987	0.37
8_L	17_Q	0.976	0.37
39_T	77_W	0.946	0.35
30_G	96_L	0.945	0.35
14_L	86_N	0.931	0.34
51_I	66_S	0.927	0.34
27_A	35_A	0.917	0.34
65_S	95_Q	0.916	0.34
56_E	87_L	0.909	0.33
31_V	38_A	0.900	0.33
46_V	80_D	0.897	0.32
75_H	82_Q	0.889	0.32
59_D	93_A	0.886	0.32
23_L	32_R	0.873	0.31
19_I	22_D	0.862	0.31
21_M	96_L	0.826	0.29
19_I	82_Q	0.815	0.28
49_V	83_V	0.806	0.28
63_Q	71_K	0.803	0.28
71_K	89_N	0.788	0.27
20_A	35_A	0.780	0.27
27_A	49_V	0.772	0.26
74_Y	96_L	0.765	0.26
70_E	84_K	0.750	0.25
47_K	62_E	0.748	0.25
42_G	77_W	0.745	0.25
67_Y	73_W	0.731	0.24
29_N	95_Q	0.724	0.24
35_A	61_H	0.720	0.24
71_K	85_L	0.719	0.24
27_A	30_G	0.715	0.24
21_M	89_N	0.715	0.24
47_K	89_N	0.708	0.23
38_A	51_I	0.704	0.23
38_A	42_G	0.701	0.23
35_A	67_Y	0.693	0.23
81_E	84_K	0.689	0.23
9_T	12_N	0.689	0.23
12_N	74_Y	0.678	0.22
49_V	62_E	0.672	0.22
22_D	62_E	0.670	0.22
65_S	75_H	0.669	0.22
9_T	72_G	0.659	0.21
12_N	96_L	0.652	0.21
61_H	72_G	0.641	0.21
62_E	88_K	0.636	0.20
73_W	85_L	0.635	0.20
22_D	58_L	0.635	0.20
18_I	74_Y	0.632	0.20
13_V	96_L	0.617	0.20
21_M	73_W	0.615	0.20
30_G	91_D	0.613	0.19
43_T	53_H	0.602	0.19
35_A	45_E	0.602	0.19
77_W	94_I	0.602	0.19
59_D	88_K	0.597	0.19
49_V	69_M	0.591	0.19
42_G	68_M	0.590	0.19
8_L	96_L	0.590	0.19
41_A	46_V	0.582	0.18
22_D	26_S	0.576	0.18
48_E	92_T	0.567	0.18
13_V	29_N	0.562	0.18
46_V	75_H	0.561	0.18
23_L	33_N	0.560	0.18
43_T	75_H	0.553	0.17
20_A	36_M	0.551	0.17
88_K	91_D	0.546	0.17
53_H	79_P	0.535	0.17
9_T	74_Y	0.532	0.17
41_A	62_E	0.529	0.16
55_E	58_L	0.528	0.16
70_E	80_D	0.527	0.16
63_Q	95_Q	0.525	0.16
22_D	81_E	0.523	0.16
18_I	82_Q	0.521	0.16
15_T	87_L	0.519	0.16
26_S	48_E	0.519	0.16
36_M	65_S	0.515	0.16
26_S	82_Q	0.514	0.16
20_A	68_M	0.512	0.16
45_E	71_K	0.511	0.16
64_L	88_K	0.506	0.16
27_A	64_L	0.500	0.16

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
2rbdA	4	0.8283	99.5	0.651	Contact Map
4etrA	1	0.7071	17.8	0.935	Contact Map
1oefA	1	0.2222	10.3	0.941	Contact Map
4wsoA	1	0.7677	9.3	0.943	Contact Map
2ltlA	1	0.5859	7.3	0.945	Contact Map
4g2kA	3	0.6162	7.3	0.945	Contact Map
3uo9A	3	0.9899	6.5	0.946	Contact Map
1k4mA	3	0.7273	6.4	0.947	Contact Map
4iggA	2	0.9899	6.3	0.947	Contact Map
2ebfX	1	0.4242	5.6	0.948	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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