YVYF - BACSU - GREMLIN Contacts

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YVYF - Uncharacterized protein YvyF

UniProt:	P39807	Sequences: MGELANCPKCNALFLKTKLQTVCQACIKEEEKSFETVYKFLRKQENRQSTLSRITEETGVEEELILKFIRQKRIQITHLPNLAYPCERCGTSIREGKFCKACQSDIKDQMDHLNHEDALKIEKENSKKDTYYAYNTKNS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	139 (122)
Sequences:	406 (346)
Seq/√Len:	31.3

BACSU - YVYF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_A	16_K	3.795	1.00
53_R	57_E	3.206	1.00
78_H	94_R	3.166	1.00
9_K	29_E	3.045	1.00
91_T	101_A	2.932	1.00
33_S	36_T	2.734	1.00
40_F	46_N	2.720	1.00
87_E	97_K	2.603	1.00
30_E	64_L	2.308	0.99
76_I	94_R	2.171	0.99
83_A	92_S	2.167	0.98
69_I	75_Q	2.159	0.98
118_A	121_I	2.011	0.98
88_R	105_D	1.999	0.97
14_F	17_T	1.987	0.97
4_L	13_L	1.911	0.97
12_A	25_A	1.886	0.96
58_T	68_F	1.827	0.96
34_F	37_V	1.768	0.95
14_F	64_L	1.645	0.92
108_D	120_K	1.636	0.92
50_T	88_R	1.618	0.92
49_S	54_I	1.594	0.91
34_F	68_F	1.542	0.90
36_T	60_V	1.494	0.88
85_P	92_S	1.493	0.88
16_K	19_L	1.476	0.87
65_I	93_I	1.405	0.85
50_T	82_L	1.403	0.85
39_K	112_H	1.373	0.83
9_K	22_V	1.369	0.83
21_T	67_K	1.359	0.83
42_R	85_P	1.359	0.83
121_I	124_E	1.352	0.82
61_E	66_L	1.351	0.82
7_C	10_C	1.346	0.82
75_Q	94_R	1.343	0.82
34_F	38_Y	1.327	0.81
6_N	11_N	1.314	0.80
4_L	15_L	1.299	0.80
38_Y	74_I	1.280	0.79
115_H	118_A	1.258	0.77
3_E	48_Q	1.257	0.77
37_V	98_F	1.254	0.77
69_I	76_I	1.245	0.77
51_L	66_L	1.214	0.75
40_F	57_E	1.202	0.74
48_Q	79_L	1.184	0.73
69_I	84_Y	1.174	0.72
38_Y	79_L	1.150	0.71
61_E	101_A	1.142	0.70
24_Q	36_T	1.139	0.70
47_R	84_Y	1.115	0.68
47_R	80_P	1.098	0.67
45_E	123_K	1.077	0.65
64_L	67_K	1.075	0.65
117_D	120_K	1.069	0.65
41_L	48_Q	1.066	0.65
75_Q	79_L	1.050	0.63
64_L	69_I	1.040	0.63
122_E	125_N	1.014	0.61
23_C	26_C	1.001	0.60
37_V	54_I	0.995	0.59
100_K	104_S	0.977	0.58
33_S	64_L	0.964	0.57
52_S	62_E	0.961	0.57
49_S	110_M	0.957	0.56
41_L	46_N	0.951	0.56
113_L	117_D	0.945	0.55
35_E	75_Q	0.935	0.54
37_V	97_K	0.889	0.51
110_M	125_N	0.888	0.51
51_L	59_G	0.882	0.50
65_I	71_Q	0.870	0.49
14_F	22_V	0.862	0.49
24_Q	70_R	0.862	0.49
42_R	84_Y	0.860	0.48
35_E	94_R	0.851	0.48
42_R	45_E	0.850	0.48
60_V	73_R	0.843	0.47
68_F	72_K	0.838	0.47
20_Q	72_K	0.830	0.46
32_K	35_E	0.821	0.45
40_F	53_R	0.819	0.45
34_F	101_A	0.819	0.45
13_L	27_I	0.813	0.45
40_F	52_S	0.813	0.45
20_Q	42_R	0.804	0.44
8_P	59_G	0.803	0.44
57_E	115_H	0.802	0.44
21_T	77_T	0.790	0.43
54_I	92_S	0.789	0.43
35_E	106_I	0.774	0.42
69_I	94_R	0.772	0.41
31_E	35_E	0.771	0.41
41_L	74_I	0.768	0.41
9_K	70_R	0.765	0.41
38_Y	47_R	0.757	0.40
100_K	111_D	0.756	0.40
22_V	31_E	0.749	0.40
71_Q	93_I	0.748	0.39
54_I	76_I	0.735	0.38
120_K	123_K	0.728	0.38
29_E	32_K	0.726	0.38
124_E	127_K	0.724	0.38
72_K	103_Q	0.714	0.37
37_V	60_V	0.713	0.37
52_S	56_E	0.705	0.36
10_C	23_C	0.670	0.34
7_C	23_C	0.670	0.34
7_C	26_C	0.670	0.34
10_C	26_C	0.670	0.34
25_A	48_Q	0.669	0.34
9_K	68_F	0.663	0.33
119_L	123_K	0.662	0.33
5_A	13_L	0.661	0.33
30_E	62_E	0.659	0.33
79_L	82_L	0.655	0.33
103_Q	106_I	0.652	0.32
86_C	102_C	0.650	0.32
99_C	102_C	0.650	0.32
86_C	89_C	0.650	0.32
89_C	99_C	0.650	0.32
89_C	102_C	0.650	0.32
86_C	99_C	0.650	0.32
80_P	84_Y	0.641	0.32
24_Q	27_I	0.638	0.31
36_T	68_F	0.634	0.31
112_H	115_H	0.633	0.31
72_K	76_I	0.625	0.30
53_R	87_E	0.622	0.30
115_H	127_K	0.618	0.30
40_F	62_E	0.616	0.30
65_I	111_D	0.615	0.30
117_D	123_K	0.611	0.29
16_K	54_I	0.609	0.29
3_E	61_E	0.600	0.29
119_L	122_E	0.600	0.29
79_L	98_F	0.598	0.29
12_A	112_H	0.596	0.28
19_L	96_G	0.596	0.28
50_T	118_A	0.595	0.28
4_L	114_N	0.594	0.28
120_K	126_S	0.584	0.28
107_K	126_S	0.580	0.27
49_S	53_R	0.575	0.27
45_E	48_Q	0.572	0.27
20_Q	39_K	0.572	0.27
14_F	42_R	0.568	0.27
101_A	121_I	0.567	0.27
38_Y	97_K	0.560	0.26
42_R	47_R	0.554	0.26
52_S	59_G	0.552	0.26
30_E	69_I	0.539	0.25
36_T	59_G	0.536	0.25
52_S	98_F	0.536	0.25
104_S	108_D	0.535	0.25
123_K	127_K	0.532	0.24
19_L	108_D	0.531	0.24
37_V	47_R	0.531	0.24
101_A	105_D	0.530	0.24
40_F	119_L	0.527	0.24
101_A	104_S	0.527	0.24
8_P	106_I	0.524	0.24
24_Q	63_E	0.520	0.24
30_E	63_E	0.520	0.24
12_A	24_Q	0.520	0.24
13_L	22_V	0.517	0.24
13_L	24_Q	0.516	0.23
30_E	68_F	0.512	0.23
42_R	69_I	0.512	0.23
82_L	107_K	0.510	0.23
35_E	103_Q	0.508	0.23
15_L	51_L	0.503	0.23
105_D	109_Q	0.502	0.23
14_F	19_L	0.502	0.23
108_D	115_H	0.500	0.23
26_C	99_C	0.500	0.23
23_C	102_C	0.500	0.23
23_C	89_C	0.500	0.23
26_C	102_C	0.500	0.23
23_C	99_C	0.500	0.23
26_C	86_C	0.500	0.23

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
3o9xA	2	0.6619	90.9	0.893	Contact Map
3qt1I	1	0.2878	88.2	0.899	Contact Map
1twfI	1	0.7194	86.1	0.902	Contact Map
3h0gI	1	0.6403	86.1	0.902	Contact Map
1y02A	1	0.4604	78.5	0.91	Contact Map
4c2mI	1	0.7338	77.2	0.911	Contact Map
3u6pA	1	0.5036	76.4	0.912	Contact Map
2og0A	1	0.3525	74.7	0.913	Contact Map
2gmgA	1	0.2878	73.5	0.914	Contact Map
4awxB	1	0.4245	69.5	0.916	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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