YKUK - BACSU - GREMLIN Contacts

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YKUK - Uncharacterized protein YkuK

UniProt:	O34776	Sequences: MADSFLFYNLSEAQMTFQDVMERLKAFVQKDPRSSYVLSIGTDSQVYRDYTKFITALHLHRTGKGAWGCLKNHTVDRPIHSLREKISLETAYSQETAAHILDGHLMDITDLLLPFTGEGADLTFEVHLDIGKKGLTKDLIQEMTGRITSMGIEAKIKPDSYTAFSYANRFTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (153)
Sequences:	224 (159)
Seq/√Len:	12.8

BACSU - YKUK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_V	57_L	5.657	1.00
38_L	59_L	4.271	1.00
55_T	96_T	2.774	0.94
85_K	90_T	2.714	0.94
23_R	69_C	2.679	0.93
146_R	149_S	2.535	0.91
16_T	19_D	2.500	0.91
79_I	85_K	2.478	0.90
53_F	171_T	2.413	0.89
25_K	160_S	2.410	0.89
12_E	23_R	2.222	0.84
141_Q	149_S	2.218	0.84
93_S	126_V	2.188	0.83
36_Y	61_R	2.024	0.78
56_A	128_L	2.007	0.77
27_F	38_L	1.964	0.76
90_T	128_L	1.943	0.75
86_I	156_I	1.903	0.73
40_I	93_S	1.831	0.70
17_F	85_K	1.814	0.70
68_G	166_Y	1.728	0.66
79_I	142_E	1.664	0.63
27_F	59_L	1.660	0.63
18_Q	59_L	1.655	0.62
134_G	140_I	1.603	0.60
136_T	156_I	1.562	0.58
95_E	99_H	1.514	0.55
67_W	166_Y	1.486	0.54
21_M	145_G	1.410	0.50
94_Q	168_N	1.393	0.49
13_A	93_S	1.372	0.48
54_I	146_R	1.370	0.48
46_V	51_T	1.368	0.48
45_Q	56_A	1.357	0.47
55_T	125_E	1.355	0.47
70_L	147_I	1.336	0.46
40_I	126_V	1.311	0.45
41_G	44_S	1.287	0.44
54_I	165_S	1.286	0.43
83_R	87_S	1.274	0.43
115_F	149_S	1.270	0.43
59_L	124_F	1.267	0.43
66_A	147_I	1.253	0.42
130_I	156_I	1.252	0.42
35_S	62_T	1.244	0.41
35_S	49_D	1.229	0.41
128_L	154_A	1.209	0.40
20_V	78_P	1.208	0.40
50_Y	96_T	1.185	0.38
102_D	170_F	1.178	0.38
90_T	147_I	1.170	0.38
57_L	97_A	1.158	0.37
88_L	92_Y	1.157	0.37
69_C	94_Q	1.141	0.36
68_G	170_F	1.135	0.36
42_T	53_F	1.131	0.36
142_E	168_N	1.126	0.36
131_G	134_G	1.123	0.35
68_G	140_I	1.117	0.35
86_I	136_T	1.117	0.35
13_A	152_I	1.094	0.34
73_H	92_Y	1.093	0.34
11_S	61_R	1.083	0.34
17_F	29_Q	1.082	0.33
56_A	68_G	1.072	0.33
16_T	149_S	1.066	0.33
37_V	164_F	1.066	0.33
37_V	169_R	1.063	0.33
9_N	135_L	1.054	0.32
148_T	154_A	1.051	0.32
147_I	151_G	1.049	0.32
16_T	61_R	1.048	0.32
152_I	161_Y	1.047	0.32
97_A	161_Y	1.040	0.32
13_A	168_N	1.018	0.31
136_T	140_I	1.012	0.30
67_W	143_M	1.010	0.30
71_K	92_Y	1.009	0.30
68_G	134_G	0.989	0.29
22_E	153_E	0.981	0.29
29_Q	138_D	0.979	0.29
125_E	130_I	0.974	0.29
57_L	102_D	0.965	0.28
57_L	75_V	0.965	0.28
84_E	101_L	0.961	0.28
126_V	151_G	0.959	0.28
37_V	125_E	0.959	0.28
18_Q	149_S	0.949	0.28
124_F	160_S	0.946	0.28
84_E	143_M	0.940	0.27
86_I	130_I	0.937	0.27
60_H	163_A	0.934	0.27
12_E	69_C	0.926	0.27
91_A	161_Y	0.920	0.26
97_A	126_V	0.917	0.26
143_M	166_Y	0.913	0.26
10_L	85_K	0.912	0.26
52_K	85_K	0.910	0.26
10_L	168_N	0.907	0.26
60_H	85_K	0.907	0.26
19_D	22_E	0.904	0.26
58_H	162_T	0.898	0.26
69_C	166_Y	0.890	0.25
67_W	162_T	0.883	0.25
119_G	171_T	0.876	0.25
127_H	130_I	0.873	0.25
82_L	137_K	0.864	0.24
36_Y	131_G	0.860	0.24
75_V	82_L	0.860	0.24
56_A	166_Y	0.858	0.24
9_N	67_W	0.831	0.23
84_E	164_F	0.831	0.23
140_I	156_I	0.830	0.23
128_L	144_T	0.830	0.23
23_R	52_K	0.819	0.23
58_H	171_T	0.809	0.22
40_I	147_I	0.801	0.22
24_L	63_G	0.797	0.22
56_A	143_M	0.792	0.22
40_I	100_I	0.790	0.22
60_H	66_A	0.789	0.22
52_K	72_N	0.788	0.21
103_G	160_S	0.788	0.21
39_S	58_H	0.786	0.21
163_A	170_F	0.780	0.21
25_K	153_E	0.780	0.21
17_F	152_I	0.777	0.21
67_W	154_A	0.766	0.21
64_K	96_T	0.765	0.21
130_I	137_K	0.765	0.21
127_H	134_G	0.764	0.21
131_G	136_T	0.762	0.21
18_Q	25_K	0.758	0.20
51_T	72_N	0.757	0.20
44_S	127_H	0.755	0.20
83_R	142_E	0.752	0.20
88_L	150_M	0.751	0.20
46_V	146_R	0.749	0.20
50_Y	165_S	0.746	0.20
27_F	32_P	0.745	0.20
94_Q	126_V	0.743	0.20
156_I	163_A	0.743	0.20
22_E	26_A	0.741	0.20
87_S	152_I	0.740	0.20
18_Q	26_A	0.739	0.20
25_K	29_Q	0.729	0.19
143_M	146_R	0.729	0.19
86_I	127_H	0.729	0.19
138_D	169_R	0.722	0.19
39_S	150_M	0.722	0.19
57_L	62_T	0.721	0.19
28_V	148_T	0.714	0.19
140_I	154_A	0.708	0.19
69_C	143_M	0.706	0.19
96_T	147_I	0.696	0.18
32_P	119_G	0.695	0.18
15_M	25_K	0.695	0.18
10_L	13_A	0.691	0.18
48_R	54_I	0.690	0.18
67_W	146_R	0.686	0.18
146_R	150_M	0.676	0.18
23_R	67_W	0.676	0.18
39_S	85_K	0.666	0.18
122_L	171_T	0.666	0.18
126_V	147_I	0.663	0.17
13_A	166_Y	0.656	0.17
14_Q	80_H	0.656	0.17
61_R	132_K	0.651	0.17
62_T	71_K	0.650	0.17
86_I	139_L	0.637	0.17
70_L	172_K	0.623	0.16
22_E	159_D	0.620	0.16
94_Q	146_R	0.615	0.16
56_A	170_F	0.614	0.16
15_M	165_S	0.611	0.16
63_G	149_S	0.610	0.16
66_A	128_L	0.609	0.16
100_I	169_R	0.607	0.16
59_L	98_A	0.606	0.16
20_V	90_T	0.606	0.16
93_S	149_S	0.603	0.16
70_L	126_V	0.603	0.16
45_Q	133_K	0.602	0.16
69_C	87_S	0.601	0.16
12_E	67_W	0.600	0.16
51_T	165_S	0.599	0.16
83_R	145_G	0.597	0.16
154_A	171_T	0.584	0.15
31_D	66_A	0.582	0.15
54_I	168_N	0.581	0.15
57_L	71_K	0.580	0.15
81_S	97_A	0.580	0.15
115_F	160_S	0.574	0.15
23_R	138_D	0.570	0.15
69_C	119_G	0.569	0.15
102_D	117_G	0.569	0.15
19_D	99_H	0.569	0.15
86_I	134_G	0.568	0.15
9_N	13_A	0.567	0.15
27_F	86_I	0.566	0.15
42_T	172_K	0.566	0.15
126_V	138_D	0.565	0.15
69_C	160_S	0.558	0.14
97_A	162_T	0.557	0.14
67_W	84_E	0.557	0.14
43_D	157_K	0.554	0.14
43_D	129_D	0.554	0.14
89_E	129_D	0.554	0.14
43_D	89_E	0.554	0.14
43_D	158_P	0.554	0.14
89_E	157_K	0.554	0.14
89_E	158_P	0.554	0.14
129_D	158_P	0.554	0.14
129_D	157_K	0.554	0.14
41_G	127_H	0.551	0.14
24_L	59_L	0.548	0.14
13_A	145_G	0.541	0.14
42_T	159_D	0.536	0.14
56_A	162_T	0.534	0.14
131_G	143_M	0.534	0.14
59_L	80_H	0.532	0.14
78_P	91_A	0.520	0.14
56_A	67_W	0.514	0.13
99_H	124_F	0.513	0.13
119_G	159_D	0.511	0.13
30_K	141_Q	0.508	0.13
77_R	128_L	0.505	0.13
85_K	140_I	0.504	0.13
34_S	46_V	0.500	0.13
31_D	97_A	0.500	0.13

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
4ljyA	1	0.6395	44.2	0.95	Contact Map
4c9bA	1	0.5465	41.5	0.95	Contact Map
3eiqA	1	0.4535	40.3	0.951	Contact Map
4d25A	1	0.593	39.7	0.951	Contact Map
4w7sA	2	0.657	33.7	0.953	Contact Map
2db3A	1	0.564	33.5	0.953	Contact Map
3fmpB	1	0	32.7	0.953	Contact Map
3fhoA	2	0.4302	32.1	0.953	Contact Map
3peyA	1	0.6221	31.5	0.953	Contact Map
3fhtA	1	0.5407	31.3	0.954	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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