YKOJ - BACSU - GREMLIN Contacts

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YKOJ - Uncharacterized protein YkoJ

UniProt:	O35012	Sequences: MLKKKWMVGLLAGCLAAGGFSYNAFATENNENRQASSKTDALTEQEAEAIAKTVVDGTVEDIDRDLYNGKEVYEVEIEKEGEDYDVYVDIHTKQALNDPLKEKAEQVAITKEEAEEIALKQTGGTVTESKLDEDDGAYIYEMEIQTKQGTETEFEISAKDGRIIKQEIDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	170 (156)
Sequences:	534 (480)
Seq/√Len:	38.4

BACSU - YKOJ YKOI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_G	77_I	4.439	1.00
109_I	114_A	3.577	1.00
137_A	157_S	3.131	1.00
157_S	160_D	3.071	1.00
124_G	144_I	3.007	1.00
114_A	118_A	2.832	1.00
119_L	144_I	2.814	1.00
51_A	77_I	2.713	1.00
115_E	126_V	2.390	1.00
113_E	116_E	2.306	1.00
154_F	166_Q	2.261	0.99
73_Y	140_Y	2.253	0.99
51_A	57_G	2.239	0.99
13_G	16_A	2.153	0.99
47_A	88_V	2.102	0.99
89_D	96_L	2.100	0.99
157_S	164_I	2.095	0.99
89_D	92_T	2.090	0.99
124_G	154_F	2.086	0.99
152_T	166_Q	2.039	0.99
109_I	117_I	2.021	0.99
20_F	23_N	1.908	0.98
43_T	46_E	1.868	0.98
117_I	156_I	1.860	0.98
118_A	156_I	1.789	0.97
17_A	20_F	1.676	0.96
111_K	129_S	1.664	0.96
42_L	50_I	1.632	0.95
122_T	154_F	1.616	0.95
126_V	144_I	1.570	0.94
52_K	77_I	1.560	0.94
109_I	161_G	1.558	0.94
110_T	113_E	1.513	0.93
42_L	47_A	1.509	0.93
118_A	142_M	1.507	0.93
121_Q	166_Q	1.478	0.92
74_E	93_K	1.464	0.92
121_Q	154_F	1.447	0.91
51_A	59_V	1.440	0.91
131_L	138_Y	1.409	0.90
129_S	142_M	1.374	0.89
6_W	21_S	1.369	0.89
59_V	68_N	1.364	0.89
89_D	157_S	1.362	0.89
47_A	155_E	1.308	0.87
82_E	100_L	1.303	0.86
8_V	14_C	1.274	0.85
12_A	25_F	1.262	0.85
122_T	144_I	1.249	0.84
65_D	68_N	1.243	0.84
50_I	88_V	1.238	0.83
73_Y	95_A	1.237	0.83
50_I	96_L	1.221	0.83
49_A	165_K	1.220	0.82
13_G	20_F	1.219	0.82
154_F	163_I	1.211	0.82
139_I	155_E	1.211	0.82
18_G	21_S	1.198	0.81
46_E	120_K	1.172	0.80
79_K	82_E	1.162	0.79
51_A	55_V	1.162	0.79
142_M	154_F	1.161	0.79
142_M	156_I	1.085	0.74
47_A	86_V	1.083	0.74
40_D	129_S	1.050	0.72
119_L	123_G	1.043	0.71
109_I	113_E	1.009	0.69
121_Q	156_I	1.008	0.69
5_K	116_E	0.992	0.67
38_K	130_K	0.984	0.67
10_L	23_N	0.979	0.66
47_A	51_A	0.963	0.65
40_D	71_E	0.962	0.65
12_A	15_L	0.949	0.64
152_T	168_I	0.933	0.63
153_E	161_G	0.930	0.62
73_Y	84_Y	0.923	0.62
147_K	150_T	0.912	0.61
141_E	155_E	0.902	0.60
51_A	75_V	0.899	0.60
137_A	156_I	0.899	0.60
65_D	74_E	0.899	0.60
71_E	129_S	0.898	0.60
85_D	135_D	0.894	0.59
5_K	10_L	0.893	0.59
55_V	86_V	0.885	0.59
117_I	161_G	0.878	0.58
126_V	142_M	0.877	0.58
16_A	137_A	0.872	0.57
41_A	91_H	0.870	0.57
115_E	129_S	0.866	0.57
47_A	65_D	0.866	0.57
128_E	142_M	0.856	0.56
77_I	86_V	0.855	0.56
122_T	152_T	0.851	0.56
5_K	8_V	0.845	0.55
133_E	138_Y	0.843	0.55
42_L	90_I	0.843	0.55
64_R	89_D	0.842	0.55
14_C	127_T	0.841	0.55
108_A	160_D	0.839	0.54
45_Q	91_H	0.830	0.54
10_L	15_L	0.829	0.54
13_G	23_N	0.824	0.53
8_V	18_G	0.819	0.53
135_D	155_E	0.818	0.53
11_L	14_C	0.809	0.52
58_T	72_V	0.808	0.52
13_G	103_K	0.807	0.52
94_Q	121_Q	0.805	0.51
48_E	52_K	0.804	0.51
62_I	112_E	0.804	0.51
137_A	162_R	0.804	0.51
114_A	169_D	0.800	0.51
119_L	126_V	0.799	0.51
10_L	121_Q	0.795	0.51
127_T	132_D	0.793	0.50
116_E	120_K	0.792	0.50
109_I	156_I	0.792	0.50
59_V	77_I	0.787	0.50
81_G	87_Y	0.781	0.49
144_I	154_F	0.781	0.49
115_E	119_L	0.774	0.49
126_V	140_Y	0.768	0.48
39_T	136_G	0.768	0.48
47_A	75_V	0.762	0.48
113_E	162_R	0.761	0.47
108_A	159_K	0.756	0.47
81_G	148_Q	0.754	0.47
143_E	151_E	0.751	0.47
37_S	110_T	0.750	0.46
42_L	88_V	0.749	0.46
67_Y	87_Y	0.748	0.46
49_A	53_T	0.748	0.46
66_L	128_E	0.740	0.46
43_T	125_T	0.740	0.46
42_L	46_E	0.738	0.45
9_G	15_L	0.734	0.45
52_K	57_G	0.732	0.45
51_A	114_A	0.730	0.45
67_Y	74_E	0.721	0.44
37_S	155_E	0.718	0.44
46_E	63_D	0.717	0.44
5_K	23_N	0.716	0.43
139_I	164_I	0.714	0.43
132_D	141_E	0.706	0.43
20_F	27_T	0.701	0.42
45_Q	49_A	0.697	0.42
134_D	139_I	0.693	0.41
41_A	64_R	0.693	0.41
88_V	167_E	0.690	0.41
19_G	22_Y	0.688	0.41
47_A	134_D	0.683	0.41
121_Q	163_I	0.682	0.40
153_E	167_E	0.681	0.40
42_L	53_T	0.680	0.40
146_T	150_T	0.665	0.39
49_A	91_H	0.663	0.39
53_T	108_A	0.658	0.38
113_E	161_G	0.653	0.38
153_E	160_D	0.652	0.38
98_D	161_G	0.648	0.38
47_A	60_E	0.645	0.37
134_D	141_E	0.640	0.37
126_V	154_F	0.628	0.36
44_E	117_I	0.627	0.36
141_E	168_I	0.625	0.36
39_T	113_E	0.619	0.35
8_V	119_L	0.619	0.35
11_L	39_T	0.619	0.35
18_G	23_N	0.617	0.35
11_L	26_A	0.616	0.35
47_A	73_Y	0.615	0.35
10_L	24_A	0.613	0.35
70_K	160_D	0.613	0.35
6_W	17_A	0.611	0.35
41_A	53_T	0.611	0.35
76_E	120_K	0.611	0.35
79_K	84_Y	0.609	0.34
86_V	95_A	0.605	0.34
18_G	169_D	0.605	0.34
9_G	20_F	0.603	0.34
115_E	140_Y	0.602	0.34
136_G	153_E	0.602	0.34
118_A	154_F	0.597	0.33
133_E	152_T	0.595	0.33
6_W	26_A	0.595	0.33
47_A	132_D	0.593	0.33
16_A	19_G	0.593	0.33
11_L	16_A	0.591	0.33
51_A	82_E	0.586	0.32
75_V	83_D	0.583	0.32
16_A	160_D	0.578	0.32
64_R	90_I	0.578	0.32
75_V	131_L	0.574	0.32
54_V	82_E	0.571	0.31
144_I	166_Q	0.569	0.31
108_A	133_E	0.569	0.31
42_L	93_K	0.566	0.31
24_A	45_Q	0.565	0.31
135_D	139_I	0.563	0.31
20_F	24_A	0.562	0.31
21_S	25_F	0.561	0.31
62_I	107_V	0.559	0.30
155_E	165_K	0.558	0.30
9_G	12_A	0.555	0.30
144_I	152_T	0.552	0.30
111_K	130_K	0.551	0.30
112_E	115_E	0.550	0.30
117_I	120_K	0.550	0.30
57_G	71_E	0.548	0.30
22_Y	117_I	0.547	0.30
40_D	77_I	0.545	0.29
49_A	160_D	0.544	0.29
53_T	80_E	0.542	0.29
13_G	49_A	0.539	0.29
9_G	26_A	0.535	0.29
78_E	113_E	0.534	0.29
61_D	139_I	0.528	0.28
123_G	148_Q	0.528	0.28
59_V	115_E	0.527	0.28
21_S	49_A	0.525	0.28
78_E	103_K	0.522	0.28
11_L	100_L	0.522	0.28
13_G	21_S	0.518	0.27
60_E	65_D	0.514	0.27
90_I	93_K	0.512	0.27
8_V	13_G	0.511	0.27
5_K	11_L	0.505	0.26
66_L	160_D	0.505	0.26
75_V	87_Y	0.503	0.26
61_D	122_T	0.502	0.26
47_A	95_A	0.500	0.26
24_A	48_E	0.500	0.26

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
4exrA	2	0.8059	99.9	0.405	Contact Map
2kgyA	1	0.5118	99.1	0.683	Contact Map
4ipbA	1	0.7118	98.5	0.744	Contact Map
4fr9A	1	0.6882	98.4	0.752	Contact Map
2gu3A	1	0.7294	97.9	0.787	Contact Map
4k90B	1	0.8765	97.2	0.814	Contact Map
4k61A	1	0.7235	97.1	0.815	Contact Map
3nqzA	1	0.7882	96.4	0.83	Contact Map
3u1wA	3	0.7176	96	0.837	Contact Map
4dsdA	1	0.7059	96	0.838	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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