YRAF - BACSU - GREMLIN Contacts

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YRAF - Spore coat protein F-like protein YraF

UniProt:	O07949	Sequences: MNNDHLDPINSLNVPELADTTFAMDFLIRAKEGVRNTAVALTETASPDVRALLRKQLMQGIAMHQEITELMISKKWFHPYELSEQYKLDQLSAKNTIMVGNMNLFPDETNRKGMFDRTPDEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	122 (94)
Sequences:	131 (106)
Seq/√Len:	10.9

BACSU - YRAF YRAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_F	67_I	3.586	0.98
49_V	80_Y	2.608	0.89
24_M	50_R	2.559	0.88
86_Y	100_G	2.307	0.81
61_I	89_D	2.297	0.81
30_A	67_I	2.202	0.78
9_I	15_P	2.150	0.76
88_L	92_S	2.093	0.74
9_I	12_L	2.089	0.74
24_M	88_L	1.986	0.70
70_L	77_F	1.971	0.70
78_H	84_E	1.894	0.66
26_F	63_M	1.874	0.66
18_A	77_F	1.865	0.65
17_L	63_M	1.830	0.64
35_R	90_Q	1.819	0.63
35_R	76_W	1.753	0.60
68_T	74_K	1.728	0.59
11_S	99_V	1.660	0.56
25_D	60_G	1.595	0.53
34_V	96_T	1.592	0.53
72_I	79_P	1.553	0.51
50_R	93_A	1.520	0.49
41_L	51_A	1.506	0.48
50_R	100_G	1.499	0.48
13_N	95_N	1.494	0.48
55_K	59_Q	1.424	0.45
49_V	83_S	1.344	0.41
20_T	77_F	1.321	0.40
10_N	73_S	1.313	0.39
33_G	48_D	1.294	0.38
20_T	99_V	1.274	0.38
32_E	75_K	1.222	0.35
35_R	39_V	1.220	0.35
81_E	84_E	1.165	0.33
33_G	40_A	1.134	0.32
50_R	92_S	1.113	0.31
63_M	76_W	1.099	0.30
9_I	75_K	1.097	0.30
60_G	86_Y	1.097	0.30
32_E	86_Y	1.092	0.30
45_A	61_I	1.031	0.27
24_M	92_S	0.990	0.26
46_S	57_L	0.984	0.26
64_H	75_K	0.976	0.25
21_T	77_F	0.972	0.25
78_H	87_K	0.962	0.25
54_R	69_E	0.959	0.25
15_P	70_L	0.954	0.25
9_I	32_E	0.952	0.25
22_F	90_Q	0.926	0.24
20_T	70_L	0.911	0.23
24_M	99_V	0.905	0.23
17_L	75_K	0.902	0.23
34_V	41_L	0.901	0.23
58_M	82_L	0.901	0.23
17_L	89_D	0.897	0.23
30_A	60_G	0.893	0.22
78_H	95_N	0.893	0.22
76_W	88_L	0.886	0.22
12_L	29_R	0.866	0.22
11_S	77_F	0.848	0.21
62_A	83_S	0.840	0.21
32_E	66_E	0.836	0.21
34_V	65_Q	0.817	0.20
73_S	83_S	0.809	0.20
38_A	46_S	0.807	0.20
44_T	99_V	0.805	0.20
11_S	20_T	0.804	0.20
47_P	58_M	0.802	0.20
11_S	76_W	0.798	0.19
83_S	94_K	0.795	0.19
94_K	98_M	0.793	0.19
14_V	98_M	0.787	0.19
84_E	87_K	0.786	0.19
46_S	70_L	0.785	0.19
15_P	99_V	0.782	0.19
91_L	100_G	0.781	0.19
37_T	59_Q	0.781	0.19
19_D	56_Q	0.775	0.19
70_L	84_E	0.765	0.19
36_N	57_L	0.745	0.18
26_F	79_P	0.735	0.18
81_E	101_N	0.735	0.18
10_N	54_R	0.728	0.17
26_F	35_R	0.727	0.17
29_R	99_V	0.727	0.17
51_A	54_R	0.725	0.17
73_S	94_K	0.720	0.17
24_M	76_W	0.709	0.17
22_F	96_T	0.707	0.17
32_E	101_N	0.702	0.17
12_L	16_E	0.701	0.17
8_P	75_K	0.688	0.16
35_R	66_E	0.683	0.16
66_E	74_K	0.683	0.16
49_V	65_Q	0.678	0.16
70_L	81_E	0.675	0.16
38_A	53_L	0.672	0.16
11_S	15_P	0.671	0.16
55_K	82_L	0.669	0.16
13_N	21_T	0.668	0.16
46_S	98_M	0.661	0.16
10_N	93_A	0.654	0.16
76_W	92_S	0.648	0.15
33_G	91_L	0.643	0.15
65_Q	95_N	0.640	0.15
91_L	94_K	0.637	0.15
80_Y	83_S	0.623	0.15
14_V	81_E	0.616	0.15
26_F	89_D	0.603	0.14
9_I	17_L	0.596	0.14
25_D	77_F	0.593	0.14
46_S	56_Q	0.593	0.14
29_R	51_A	0.588	0.14
69_E	79_P	0.588	0.14
8_P	70_L	0.584	0.14
32_E	98_M	0.583	0.14
80_Y	97_I	0.583	0.14
62_A	96_T	0.572	0.14
29_R	75_K	0.568	0.13
65_Q	91_L	0.567	0.13
45_A	50_R	0.563	0.13
64_H	71_M	0.563	0.13
24_M	93_A	0.562	0.13
25_D	29_R	0.557	0.13
34_V	66_E	0.556	0.13
44_T	61_I	0.555	0.13
40_A	80_Y	0.554	0.13
79_P	99_V	0.546	0.13
12_L	20_T	0.544	0.13
59_Q	68_T	0.543	0.13
65_Q	69_E	0.534	0.13
16_E	32_E	0.527	0.13
16_E	46_S	0.525	0.13
38_A	93_A	0.524	0.13
62_A	80_Y	0.520	0.12
12_L	77_F	0.520	0.12
13_N	48_D	0.515	0.12
77_F	99_V	0.509	0.12
22_F	61_I	0.500	0.12

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	0.6967	99.5	0.753	Contact Map
4etrA	1	0.4754	25.3	0.95	Contact Map
2k9mA	1	0.5902	21.3	0.951	Contact Map
3fdqA	2	0.7459	12.9	0.956	Contact Map
3bwgA	2	0.5082	12.8	0.956	Contact Map
2g39A	2	0.7213	12.7	0.956	Contact Map
4eu9A	2	0.6639	12	0.957	Contact Map
4wsoA	1	0.6475	9	0.959	Contact Map
1oefA	1	0.1803	7.9	0.96	Contact Map
3nuhB	1	0.4508	7.8	0.96	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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