YKVT - BACSU - GREMLIN Contacts

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YKVT - Uncharacterized protein YkvT

UniProt:	O31685	Sequences: MTTKFTALAVFLLCFMPAAKIEHTQASLLSAKKTKHEEAKWLTHIDRNTNESFPSLSADKDKKIKPIKLSAHTEKKEKDKPDKTNDEKETYTQSEKELLSRLVHAEAKGESYKGKVAVASVVLNRTEKKGFPDTIRGVIYQKNAFEPVANGSINQKPDKESIEAAEEALSSKNRETDAIFFYNPKTASDNWIRSRKIVEKIGRHVFAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	208 (175)
Sequences:	471 (399)
Seq/√Len:	30.2

BACSU - YKVT SLEB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_V	119_A	6.085	1.00
103_V	165_A	4.198	1.00
114_G	204_H	3.678	1.00
112_Y	167_E	3.505	1.00
110_E	203_R	3.117	1.00
102_L	122_V	3.056	1.00
115_K	160_E	2.924	1.00
99_L	122_V	2.791	1.00
119_A	165_A	2.684	1.00
104_H	158_D	2.433	0.99
126_T	133_D	2.255	0.99
131_F	180_F	2.193	0.98
144_A	192_I	2.032	0.97
105_A	147_P	1.993	0.97
126_T	138_V	1.988	0.97
36_H	40_K	1.892	0.96
96_K	166_E	1.877	0.96
120_S	174_R	1.876	0.96
102_L	147_P	1.857	0.96
104_H	115_K	1.846	0.95
132_P	141_Q	1.836	0.95
117_A	201_I	1.831	0.95
95_E	136_R	1.736	0.94
110_E	204_H	1.722	0.93
147_P	181_F	1.692	0.93
110_E	115_K	1.679	0.92
140_Y	154_N	1.565	0.89
34_T	40_K	1.558	0.89
144_A	186_T	1.476	0.86
73_T	77_E	1.474	0.86
175_E	178_A	1.449	0.85
49_T	56_L	1.444	0.85
115_K	161_S	1.431	0.85
37_E	40_K	1.423	0.84
65_K	69_L	1.406	0.83
112_Y	116_V	1.402	0.83
150_N	154_N	1.376	0.82
59_D	62_K	1.361	0.81
105_A	153_I	1.349	0.81
70_S	74_E	1.342	0.80
39_A	42_L	1.328	0.80
73_T	76_K	1.324	0.80
200_K	205_V	1.323	0.80
98_L	139_I	1.311	0.79
52_S	55_S	1.292	0.78
70_S	73_T	1.252	0.76
173_N	177_D	1.250	0.75
96_K	169_L	1.239	0.75
40_K	45_I	1.234	0.75
54_P	57_S	1.223	0.74
120_S	173_N	1.219	0.74
160_E	163_E	1.219	0.74
54_P	58_A	1.210	0.73
89_E	123_L	1.192	0.72
55_S	58_A	1.191	0.72
119_A	168_A	1.189	0.72
46_D	51_E	1.169	0.70
201_I	204_H	1.142	0.69
41_W	44_H	1.141	0.68
110_E	164_A	1.139	0.68
46_D	49_T	1.135	0.68
182_Y	205_V	1.134	0.68
140_Y	157_P	1.131	0.68
71_A	75_K	1.126	0.67
184_P	204_H	1.123	0.67
55_S	62_K	1.107	0.66
104_H	108_K	1.096	0.65
39_A	46_D	1.089	0.65
97_E	157_P	1.083	0.64
146_E	150_N	1.076	0.64
45_I	48_N	1.075	0.64
100_S	157_P	1.073	0.64
126_T	159_K	1.070	0.63
171_S	174_R	1.066	0.63
119_A	164_A	1.066	0.63
42_L	56_L	1.064	0.63
131_F	179_I	1.062	0.63
43_T	50_N	1.051	0.62
183_N	204_H	1.049	0.62
40_K	60_K	1.044	0.61
126_T	135_I	1.037	0.61
178_A	198_V	1.031	0.60
114_G	183_N	1.030	0.60
111_S	139_I	1.027	0.60
60_K	64_I	1.026	0.60
97_E	101_R	1.024	0.60
91_Y	123_L	1.020	0.60
173_N	178_A	1.009	0.59
38_E	41_W	1.005	0.59
74_E	81_P	1.000	0.58
98_L	140_Y	0.999	0.58
38_E	42_L	0.990	0.57
159_K	163_E	0.989	0.57
192_I	195_R	0.986	0.57
147_P	152_S	0.982	0.57
116_V	174_R	0.979	0.56
51_E	57_S	0.969	0.56
104_H	161_S	0.968	0.56
34_T	43_T	0.940	0.53
120_S	168_A	0.935	0.53
57_S	62_K	0.919	0.52
46_D	60_K	0.917	0.52
58_A	64_I	0.917	0.52
140_Y	148_V	0.917	0.52
34_T	42_L	0.911	0.51
182_Y	207_A	0.908	0.51
146_E	181_F	0.894	0.50
40_K	49_T	0.893	0.50
184_P	201_I	0.892	0.50
173_N	176_T	0.888	0.49
35_K	42_L	0.887	0.49
195_R	198_V	0.883	0.49
120_S	176_T	0.882	0.49
115_K	204_H	0.880	0.49
189_D	192_I	0.879	0.49
36_H	41_W	0.870	0.48
174_R	178_A	0.865	0.47
132_P	137_G	0.857	0.47
35_K	39_A	0.855	0.47
120_S	171_S	0.853	0.46
167_E	172_K	0.851	0.46
64_I	69_L	0.850	0.46
152_S	207_A	0.849	0.46
42_L	49_T	0.846	0.46
44_H	59_D	0.842	0.46
63_K	67_I	0.838	0.45
183_N	207_A	0.835	0.45
97_E	177_D	0.833	0.45
122_V	202_G	0.831	0.45
120_S	178_A	0.829	0.45
34_T	46_D	0.828	0.45
59_D	74_E	0.826	0.44
134_T	137_G	0.820	0.44
40_K	43_T	0.804	0.43
152_S	181_F	0.802	0.42
42_L	46_D	0.801	0.42
108_K	115_K	0.800	0.42
140_Y	153_I	0.799	0.42
111_S	172_K	0.797	0.42
121_V	145_F	0.789	0.41
100_S	117_A	0.781	0.41
116_V	172_K	0.781	0.41
49_T	60_K	0.779	0.41
47_R	54_P	0.779	0.41
111_S	180_F	0.779	0.41
37_E	42_L	0.767	0.40
92_T	123_L	0.763	0.39
105_A	198_V	0.762	0.39
99_L	144_A	0.759	0.39
36_H	39_A	0.758	0.39
53_F	57_S	0.757	0.39
36_H	60_K	0.754	0.39
110_E	114_G	0.748	0.38
110_E	201_I	0.745	0.38
42_L	50_N	0.745	0.38
95_E	153_I	0.744	0.38
193_R	197_I	0.744	0.38
181_F	207_A	0.742	0.38
129_K	149_A	0.730	0.37
101_R	156_K	0.729	0.37
34_T	39_A	0.722	0.36
129_K	133_D	0.718	0.36
102_L	139_I	0.715	0.36
101_R	155_Q	0.713	0.36
100_S	161_S	0.709	0.35
109_G	115_K	0.707	0.35
114_G	206_F	0.704	0.35
108_K	171_S	0.703	0.35
98_L	164_A	0.695	0.34
117_A	165_A	0.694	0.34
141_Q	169_L	0.693	0.34
120_S	175_E	0.689	0.34
39_A	60_K	0.688	0.34
102_L	105_A	0.683	0.34
41_W	60_K	0.682	0.33
41_W	51_E	0.680	0.33
80_K	93_Q	0.678	0.33
57_S	69_L	0.673	0.33
37_E	45_I	0.671	0.33
61_D	66_P	0.669	0.33
61_D	64_I	0.668	0.33
53_F	62_K	0.668	0.33
128_K	133_D	0.666	0.32
47_R	61_D	0.666	0.32
103_V	110_E	0.663	0.32
47_R	52_S	0.661	0.32
43_T	64_I	0.656	0.32
122_V	139_I	0.656	0.32
102_L	205_V	0.655	0.32
34_T	45_I	0.655	0.32
98_L	112_Y	0.653	0.31
43_T	49_T	0.652	0.31
44_H	61_D	0.650	0.31
112_Y	201_I	0.638	0.30
111_S	201_I	0.637	0.30
118_V	121_V	0.636	0.30
49_T	67_I	0.631	0.30
124_N	145_F	0.629	0.30
46_D	52_S	0.628	0.30
102_L	140_Y	0.627	0.30
39_A	43_T	0.620	0.29
66_P	69_L	0.619	0.29
120_S	146_E	0.619	0.29
92_T	95_E	0.619	0.29
49_T	52_S	0.616	0.29
62_K	73_T	0.612	0.29
94_S	97_E	0.609	0.29
114_G	201_I	0.604	0.28
51_E	60_K	0.599	0.28
38_E	45_I	0.599	0.28
98_L	189_D	0.594	0.28
137_G	144_A	0.594	0.28
60_K	107_A	0.592	0.27
33_K	37_E	0.590	0.27
39_A	56_L	0.590	0.27
71_A	135_I	0.589	0.27
77_E	81_P	0.589	0.27
33_K	45_I	0.585	0.27
71_A	74_E	0.584	0.27
41_W	67_I	0.582	0.27
133_D	150_N	0.582	0.27
88_K	169_L	0.581	0.27
102_L	151_G	0.580	0.27
36_H	43_T	0.580	0.27
57_S	65_K	0.572	0.26
56_L	60_K	0.571	0.26
40_K	51_E	0.569	0.26
70_S	83_K	0.568	0.26
182_Y	193_R	0.567	0.26
52_S	65_K	0.566	0.26
116_V	120_S	0.566	0.26
51_E	54_P	0.558	0.25
94_S	136_R	0.555	0.25
163_E	167_E	0.553	0.25
139_I	164_A	0.553	0.25
57_S	60_K	0.551	0.25
197_I	207_A	0.544	0.24
41_W	46_D	0.543	0.24
101_R	154_N	0.543	0.24
105_A	187_A	0.543	0.24
116_V	167_E	0.541	0.24
197_I	200_K	0.540	0.24
40_K	69_L	0.532	0.24
58_A	61_D	0.530	0.24
49_T	63_K	0.527	0.24
46_D	50_N	0.527	0.24
50_N	60_K	0.523	0.23
96_K	157_P	0.522	0.23
157_P	162_I	0.522	0.23
137_G	159_K	0.520	0.23
128_K	132_P	0.520	0.23
33_K	44_H	0.517	0.23
119_A	123_L	0.516	0.23
95_E	102_L	0.513	0.23
52_S	67_I	0.512	0.23
47_R	58_A	0.512	0.23
164_A	187_A	0.511	0.23
50_N	54_P	0.508	0.22
117_A	174_R	0.505	0.22
43_T	67_I	0.503	0.22
36_H	45_I	0.501	0.22
119_A	174_R	0.500	0.22

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
4f55A	1	0.6154	100	0.334	Contact Map
4fetB	1	0.5913	100	0.419	Contact Map
2r1fA	4	0.8558	91.8	0.915	Contact Map
4iiwA	4	0.8606	91	0.917	Contact Map
3a68A	7	0.3317	56.4	0.94	Contact Map
3vnxA	6	0.2885	42.8	0.945	Contact Map
2mkxA	1	0.2452	33.3	0.948	Contact Map
2djpA	1	0.3654	19.5	0.953	Contact Map
1e0gA	1	0.2308	19	0.954	Contact Map
4o9aA	4	0.3654	13.2	0.957	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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