YPUF - BACSU - GREMLIN Contacts

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YPUF - Uncharacterized protein YpuF

UniProt:	P17617	Sequences: MYPKAYIDYLVEFHATRDYFECHEILEEYWKEDPPKKRKRYWVGFIQLAVALYHHRRQNTAGAKRLMANSIRILQAEHRAVEDLGLDHGRLLELMQSVYEQIETVSAYKSIILPIKDEKLEEACRIECRKKKYTWGQPSALSNIFLIDKHRLRDRTDVIREREKEIERRKKSRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	174 (168)
Sequences:	255 (212)
Seq/√Len:	16.3

BACSU - YPUF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_E	16_T	4.553	1.00
44_G	74_L	3.528	1.00
66_L	69_N	3.424	0.99
124_C	135_W	3.010	0.98
86_L	115_I	2.810	0.98
12_E	25_I	2.797	0.97
38_R	47_Q	2.777	0.97
145_F	149_K	2.527	0.95
26_L	43_V	2.472	0.95
18_D	24_E	2.447	0.94
161_E	165_E	2.440	0.94
8_D	127_E	2.427	0.94
47_Q	66_L	2.326	0.93
48_L	111_I	2.262	0.92
140_A	143_N	2.134	0.89
34_P	37_K	2.082	0.88
149_K	165_E	1.973	0.85
163_E	166_I	1.941	0.84
18_D	21_E	1.937	0.84
21_E	24_E	1.937	0.84
86_L	113_L	1.928	0.83
57_R	148_D	1.926	0.83
51_A	66_L	1.864	0.81
65_R	69_N	1.815	0.79
98_V	111_I	1.787	0.78
117_D	120_L	1.732	0.76
155_R	162_R	1.720	0.75
64_K	99_Y	1.705	0.75
55_H	98_V	1.699	0.75
165_E	169_R	1.698	0.74
55_H	60_T	1.630	0.71
110_S	139_S	1.585	0.69
141_L	146_L	1.504	0.65
51_A	67_M	1.480	0.64
48_L	95_M	1.456	0.62
18_D	120_L	1.453	0.62
24_E	120_L	1.453	0.62
18_D	149_K	1.450	0.62
24_E	149_K	1.450	0.62
74_L	121_E	1.436	0.61
45_F	158_V	1.425	0.61
44_G	73_I	1.410	0.60
11_V	15_A	1.405	0.59
6_Y	42_W	1.335	0.55
102_I	110_S	1.319	0.55
14_H	42_W	1.294	0.53
7_I	124_C	1.283	0.52
47_Q	52_L	1.282	0.52
47_Q	50_V	1.273	0.52
38_R	66_L	1.255	0.51
6_Y	10_L	1.245	0.50
21_E	120_L	1.211	0.48
108_Y	136_G	1.210	0.48
19_Y	70_S	1.197	0.47
49_A	124_C	1.190	0.47
166_I	170_K	1.182	0.46
43_V	73_I	1.162	0.45
48_L	91_L	1.150	0.45
14_H	26_L	1.129	0.43
140_A	146_L	1.121	0.43
48_L	86_L	1.106	0.42
151_R	169_R	1.105	0.42
10_L	17_R	1.104	0.42
122_E	148_D	1.096	0.42
17_R	110_S	1.089	0.41
150_H	153_R	1.059	0.39
18_D	50_V	1.041	0.38
24_E	50_V	1.041	0.38
154_D	162_R	1.039	0.38
38_R	69_N	1.035	0.38
155_R	158_V	1.024	0.38
50_V	128_C	1.020	0.37
102_I	105_V	1.018	0.37
17_R	108_Y	1.018	0.37
50_V	85_G	1.015	0.37
18_D	42_W	1.011	0.37
24_E	42_W	1.011	0.37
25_I	154_D	1.007	0.37
9_Y	164_K	0.997	0.36
21_E	149_K	0.987	0.35
31_K	43_V	0.986	0.35
51_A	99_Y	0.980	0.35
8_D	148_D	0.973	0.35
2_Y	6_Y	0.973	0.35
145_F	152_L	0.967	0.34
14_H	31_K	0.960	0.34
6_Y	128_C	0.959	0.34
41_Y	45_F	0.957	0.34
139_S	143_N	0.955	0.34
15_A	128_C	0.955	0.34
38_R	52_L	0.954	0.34
13_F	26_L	0.952	0.34
98_V	109_K	0.945	0.33
3_P	108_Y	0.935	0.33
3_P	29_Y	0.935	0.33
63_A	148_D	0.932	0.33
47_Q	165_E	0.931	0.33
26_L	113_L	0.930	0.32
121_E	125_R	0.910	0.31
25_I	149_K	0.904	0.31
34_P	69_N	0.898	0.31
69_N	165_E	0.894	0.31
31_K	57_R	0.889	0.30
11_V	40_R	0.882	0.30
37_K	47_Q	0.877	0.30
154_D	158_V	0.874	0.30
2_Y	117_D	0.854	0.29
139_S	146_L	0.853	0.29
70_S	102_I	0.851	0.29
19_Y	110_S	0.846	0.28
100_E	122_E	0.845	0.28
10_L	117_D	0.845	0.28
49_A	74_L	0.844	0.28
42_W	50_V	0.843	0.28
10_L	120_L	0.839	0.28
6_Y	117_D	0.828	0.27
133_Y	143_N	0.823	0.27
10_L	42_W	0.818	0.27
97_S	122_E	0.816	0.27
71_I	99_Y	0.812	0.27
106_S	122_E	0.807	0.27
55_H	108_Y	0.807	0.27
9_Y	51_A	0.806	0.26
52_L	55_H	0.804	0.26
115_I	120_L	0.804	0.26
57_R	114_P	0.802	0.26
36_K	47_Q	0.802	0.26
5_A	33_D	0.802	0.26
98_V	101_Q	0.801	0.26
28_E	158_V	0.800	0.26
37_K	146_L	0.797	0.26
6_Y	84_L	0.792	0.26
14_H	114_P	0.790	0.26
81_V	103_E	0.786	0.26
6_Y	50_V	0.786	0.26
36_K	50_V	0.785	0.26
45_F	98_V	0.784	0.25
163_E	167_E	0.782	0.25
75_Q	96_Q	0.780	0.25
87_D	130_K	0.772	0.25
145_F	148_D	0.772	0.25
19_Y	46_I	0.769	0.25
45_F	84_L	0.768	0.25
165_E	168_R	0.768	0.25
57_R	150_H	0.758	0.24
60_T	105_V	0.750	0.24
123_A	168_R	0.749	0.24
4_K	28_E	0.749	0.24
121_E	127_E	0.747	0.24
61_A	84_L	0.738	0.23
21_E	42_W	0.734	0.23
100_E	107_A	0.734	0.23
15_A	124_C	0.732	0.23
156_T	163_E	0.722	0.23
20_F	23_H	0.721	0.23
57_R	63_A	0.721	0.23
38_R	41_Y	0.719	0.23
29_Y	151_R	0.716	0.23
28_E	162_R	0.712	0.22
18_D	91_L	0.712	0.22
24_E	91_L	0.712	0.22
4_K	8_D	0.712	0.22
57_R	155_R	0.706	0.22
7_I	76_A	0.703	0.22
12_E	159_I	0.702	0.22
102_I	108_Y	0.701	0.22
10_L	21_E	0.696	0.22
166_I	169_R	0.695	0.22
33_D	37_K	0.690	0.22
137_Q	156_T	0.689	0.21
123_A	160_R	0.682	0.21
3_P	42_W	0.676	0.21
9_Y	160_R	0.675	0.21
34_P	121_E	0.673	0.21
26_L	46_I	0.673	0.21
2_Y	10_L	0.669	0.21
7_I	28_E	0.661	0.20
17_R	112_I	0.659	0.20
47_Q	149_K	0.656	0.20
92_L	126_I	0.653	0.20
33_D	39_K	0.653	0.20
19_Y	26_L	0.651	0.20
10_L	18_D	0.651	0.20
10_L	24_E	0.651	0.20
21_E	50_V	0.645	0.20
146_L	149_K	0.644	0.20
101_Q	106_S	0.642	0.20
34_P	149_K	0.639	0.20
70_S	97_S	0.637	0.19
44_G	70_S	0.631	0.19
67_M	102_I	0.628	0.19
126_I	168_R	0.627	0.19
35_P	106_S	0.626	0.19
7_I	142_S	0.623	0.19
25_I	123_A	0.619	0.19
98_V	108_Y	0.618	0.19
4_K	148_D	0.610	0.19
25_I	73_I	0.602	0.18
53_Y	63_A	0.601	0.18
14_H	43_V	0.595	0.18
140_A	164_K	0.593	0.18
9_Y	17_R	0.590	0.18
15_A	67_M	0.589	0.18
94_L	112_I	0.589	0.18
7_I	32_E	0.588	0.18
9_Y	28_E	0.587	0.18
138_P	143_N	0.586	0.18
134_T	137_Q	0.584	0.18
48_L	113_L	0.582	0.18
52_L	149_K	0.582	0.18
55_H	67_M	0.582	0.18
82_E	157_D	0.581	0.18
9_Y	110_S	0.575	0.17
10_L	50_V	0.575	0.17
75_Q	93_E	0.575	0.17
5_A	147_I	0.569	0.17
44_G	66_L	0.567	0.17
45_F	96_Q	0.565	0.17
48_L	152_L	0.563	0.17
13_F	44_G	0.561	0.17
67_M	107_A	0.559	0.17
66_L	70_S	0.555	0.17
39_K	76_A	0.555	0.17
52_L	165_E	0.553	0.17
70_S	111_I	0.552	0.17
59_N	150_H	0.550	0.16
12_E	136_G	0.549	0.16
94_L	114_P	0.545	0.16
35_P	160_R	0.544	0.16
32_E	121_E	0.537	0.16
17_R	124_C	0.537	0.16
136_G	170_K	0.537	0.16
14_H	84_L	0.536	0.16
9_Y	61_A	0.535	0.16
68_A	103_E	0.535	0.16
158_V	161_E	0.533	0.16
158_V	165_E	0.533	0.16
5_A	14_H	0.531	0.16
6_Y	21_E	0.528	0.16
153_R	162_R	0.525	0.16
86_L	118_E	0.522	0.16
17_R	128_C	0.519	0.16
138_P	144_I	0.517	0.15
142_S	146_L	0.516	0.15
95_M	119_K	0.516	0.15
21_E	47_Q	0.514	0.15
48_L	120_L	0.514	0.15
37_K	40_R	0.510	0.15
93_E	97_S	0.502	0.15
44_G	91_L	0.502	0.15
26_L	73_I	0.502	0.15
43_V	77_E	0.500	0.15

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
2ijqA	1	0.7356	100	0.641	Contact Map
2cwyA	1	0.5402	99.9	0.684	Contact Map
4rykA	2	0.5747	77.2	0.94	Contact Map
4bt9A	2	0.5287	66.8	0.945	Contact Map
1qqeA	1	0.6782	65.5	0.945	Contact Map
3ro3A	1	0.4368	52.9	0.949	Contact Map
3ro2A	1	0.4138	43.1	0.952	Contact Map
1tjcA	2	0.523	43	0.952	Contact Map
4h7yA	1	0.5287	41.9	0.952	Contact Map
3nf1A	1	0.4195	41.3	0.953	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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