YKAA - BACSU - GREMLIN Contacts

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YKAA - UPF0111 protein YkaA

UniProt:	O34454	Sequences: MIRRKKDKFSLLLTEIAKNIDETAEYFVNFKVTNQTTLKEFADTLKEYETKGDNHVHVMIKELNKAFITPIEREDILQLTNSLDDVLDGIEHFSAMMEIFSITSSDEHIDKFSGYIRECAKEILITIELLAENRLKDIQPHAIKIKEYEHSCDNLHRKSLKNLFGNETDPIKVIQYREIYETLEEIADSCQSVANNLETIIMKNA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (195)
Sequences:	1521 (1112)
Seq/√Len:	79.6

BACSU - YKAA
SULSO - Q97ZY2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_K	147_E	3.431	1.00
152_C	187_A	3.345	1.00
53_D	84_D	2.975	1.00
149_E	188_D	2.940	1.00
59_M	80_T	2.922	1.00
49_E	53_D	2.863	1.00
52_G	87_L	2.779	1.00
19_N	52_G	2.658	1.00
23_T	87_L	2.656	1.00
49_E	84_D	2.599	1.00
45_L	94_S	2.525	1.00
34_N	37_T	2.481	1.00
153_D	188_D	2.435	1.00
115_Y	148_Y	2.384	1.00
149_E	153_D	2.360	1.00
19_N	51_K	2.280	1.00
22_E	51_K	2.258	1.00
15_E	58_V	2.258	1.00
108_H	162_N	2.190	1.00
25_E	121_K	2.176	1.00
122_E	141_H	2.168	1.00
101_S	165_G	2.128	1.00
47_E	50_T	2.114	1.00
145_I	194_A	2.110	1.00
86_V	123_I	2.083	1.00
32_V	110_D	1.986	1.00
43_D	47_E	1.953	1.00
116_I	186_I	1.928	1.00
44_T	47_E	1.891	1.00
37_T	40_E	1.862	1.00
122_E	144_K	1.828	1.00
162_N	166_N	1.812	1.00
118_E	151_S	1.758	1.00
18_K	124_L	1.715	1.00
14_T	131_A	1.702	1.00
111_K	114_G	1.678	1.00
26_Y	44_T	1.675	1.00
19_N	22_E	1.658	1.00
151_S	154_N	1.616	1.00
28_V	114_G	1.583	1.00
57_H	146_K	1.557	0.99
127_I	130_L	1.547	0.99
31_K	113_S	1.530	0.99
57_H	143_I	1.520	0.99
74_E	203_K	1.512	0.99
122_E	125_I	1.508	0.99
119_C	148_Y	1.486	0.99
21_D	121_K	1.478	0.99
9_F	76_I	1.467	0.99
21_D	124_L	1.462	0.99
120_A	190_C	1.446	0.99
146_K	191_Q	1.439	0.99
49_E	88_D	1.433	0.99
28_V	117_R	1.424	0.99
16_I	52_G	1.417	0.99
126_T	197_L	1.410	0.99
95_A	157_R	1.409	0.99
24_A	90_I	1.408	0.99
17_A	124_L	1.382	0.99
159_S	180_Y	1.375	0.99
46_K	91_E	1.348	0.99
53_D	88_D	1.334	0.98
67_F	72_E	1.328	0.98
85_D	88_D	1.323	0.98
86_V	193_V	1.304	0.98
134_R	138_I	1.262	0.98
58_V	62_E	1.250	0.98
75_D	203_K	1.244	0.97
40_E	44_T	1.232	0.97
184_E	188_D	1.220	0.97
9_F	69_T	1.214	0.97
106_D	180_Y	1.178	0.97
169_D	172_K	1.173	0.96
30_F	94_S	1.159	0.96
26_Y	41_F	1.152	0.96
84_D	88_D	1.152	0.96
30_F	38_L	1.135	0.96
14_T	128_E	1.131	0.96
109_I	176_Y	1.129	0.96
106_D	176_Y	1.128	0.96
129_L	137_D	1.111	0.95
47_E	51_K	1.102	0.95
29_N	44_T	1.092	0.95
21_D	25_E	1.079	0.94
157_R	177_R	1.065	0.94
146_K	195_N	1.046	0.93
26_Y	45_L	1.043	0.93
100_F	175_Q	1.038	0.93
19_N	48_Y	1.037	0.93
16_I	80_T	1.035	0.93
118_E	121_K	1.031	0.93
189_S	192_S	1.016	0.92
17_A	83_L	1.013	0.92
63_L	76_I	1.012	0.92
25_E	117_R	0.998	0.92
18_K	22_E	0.984	0.91
117_R	121_K	0.969	0.90
15_E	18_K	0.965	0.90
26_Y	48_Y	0.934	0.89
195_N	198_E	0.933	0.89
111_K	151_S	0.925	0.88
127_I	131_A	0.923	0.88
44_T	51_K	0.909	0.87
60_I	196_N	0.906	0.87
110_D	116_I	0.899	0.87
69_T	76_I	0.894	0.86
37_T	41_F	0.893	0.86
93_F	186_I	0.886	0.86
40_E	43_D	0.885	0.86
137_D	140_P	0.884	0.86
124_L	128_E	0.884	0.86
48_Y	51_K	0.881	0.86
140_P	144_K	0.875	0.85
121_K	125_I	0.875	0.85
50_T	54_N	0.872	0.85
176_Y	180_Y	0.868	0.85
13_L	76_I	0.867	0.85
41_F	44_T	0.857	0.84
20_I	87_L	0.852	0.84
69_T	72_E	0.850	0.83
178_E	181_E	0.849	0.83
121_K	124_L	0.846	0.83
9_F	67_F	0.834	0.82
84_D	149_E	0.825	0.82
156_H	184_E	0.823	0.81
192_S	195_N	0.821	0.81
153_D	184_E	0.813	0.81
79_L	193_V	0.810	0.80
66_A	69_T	0.806	0.80
172_K	175_Q	0.806	0.80
82_S	85_D	0.805	0.80
157_R	164_F	0.800	0.80
20_I	23_T	0.799	0.80
89_G	189_S	0.793	0.79
109_I	116_I	0.793	0.79
163_L	180_Y	0.792	0.79
32_V	114_G	0.790	0.79
143_I	191_Q	0.786	0.78
82_S	192_S	0.785	0.78
149_E	184_E	0.784	0.78
158_K	162_N	0.783	0.78
73_R	76_I	0.782	0.78
62_E	65_K	0.779	0.78
120_A	124_L	0.774	0.77
118_E	144_K	0.773	0.77
26_Y	29_N	0.770	0.77
116_I	120_A	0.769	0.77
57_H	198_E	0.766	0.77
27_F	90_I	0.766	0.77
112_F	156_H	0.760	0.76
29_N	41_F	0.753	0.75
156_H	181_E	0.753	0.75
16_I	186_I	0.751	0.75
163_L	179_I	0.750	0.75
59_M	133_N	0.746	0.75
136_K	140_P	0.745	0.75
145_I	166_N	0.740	0.74
45_L	48_Y	0.735	0.74
57_H	191_Q	0.733	0.73
86_V	190_C	0.731	0.73
71_I	74_E	0.731	0.73
25_E	29_N	0.729	0.73
143_I	150_H	0.723	0.72
28_V	113_S	0.722	0.72
22_E	32_V	0.722	0.72
126_T	141_H	0.720	0.72
98_E	161_K	0.720	0.72
99_I	160_L	0.718	0.72
187_A	199_T	0.714	0.71
144_K	148_Y	0.710	0.71
111_K	158_K	0.700	0.70
171_I	175_Q	0.699	0.70
49_E	149_E	0.696	0.70
99_I	157_R	0.696	0.70
115_Y	118_E	0.695	0.69
39_K	43_D	0.695	0.69
38_L	97_M	0.691	0.69
18_K	128_E	0.689	0.69
148_Y	152_C	0.683	0.68
12_L	55_H	0.682	0.68
29_N	32_V	0.681	0.68
8_K	62_E	0.679	0.68
119_C	187_A	0.678	0.68
35_Q	38_L	0.675	0.67
155_L	159_S	0.673	0.67
67_F	76_I	0.670	0.67
93_F	183_L	0.670	0.67
61_K	198_E	0.669	0.66
67_F	71_I	0.665	0.66
168_T	171_I	0.665	0.66
39_K	98_E	0.658	0.65
133_N	198_E	0.648	0.64
54_N	58_V	0.646	0.64
24_A	120_A	0.646	0.64
66_A	71_I	0.646	0.64
16_I	19_N	0.645	0.64
51_K	54_N	0.639	0.63
22_E	29_N	0.638	0.63
160_L	177_R	0.637	0.63
143_I	146_K	0.636	0.63
25_E	28_V	0.635	0.62
163_L	176_Y	0.634	0.62
112_F	119_C	0.633	0.62
118_E	148_Y	0.632	0.62
22_E	47_E	0.631	0.62
48_Y	94_S	0.631	0.62
150_H	154_N	0.628	0.62
167_E	173_V	0.628	0.62
113_S	117_R	0.626	0.61
181_E	185_E	0.622	0.61
57_H	150_H	0.620	0.61
83_L	86_V	0.618	0.60
31_K	97_M	0.615	0.60
148_Y	187_A	0.613	0.60
67_F	70_P	0.612	0.60
63_L	167_E	0.607	0.59
16_I	20_I	0.603	0.58
103_T	172_K	0.601	0.58
46_K	50_T	0.600	0.58
95_A	99_I	0.599	0.58
67_F	73_R	0.596	0.58
35_Q	55_H	0.596	0.58
37_T	44_T	0.596	0.58
79_L	200_I	0.593	0.57
20_I	27_F	0.593	0.57
80_T	196_N	0.590	0.57
56_V	80_T	0.589	0.57
125_I	141_H	0.588	0.57
42_A	157_R	0.588	0.57
89_G	182_T	0.582	0.56
115_Y	152_C	0.582	0.56
92_H	119_C	0.580	0.56
70_P	73_R	0.580	0.56
56_V	59_M	0.578	0.55
117_R	120_A	0.578	0.55
29_N	39_K	0.576	0.55
27_F	31_K	0.576	0.55
51_K	93_F	0.574	0.55
115_Y	122_E	0.574	0.55
40_E	103_T	0.573	0.55
13_L	23_T	0.573	0.55
63_L	70_P	0.572	0.55
59_M	76_I	0.571	0.54
164_F	177_R	0.571	0.54
123_I	185_E	0.570	0.54
114_G	118_E	0.569	0.54
88_D	146_K	0.566	0.54
92_H	182_T	0.566	0.54
130_L	157_R	0.561	0.53
10_S	174_I	0.559	0.53
156_H	182_T	0.556	0.52
59_M	89_G	0.552	0.52
56_V	84_D	0.550	0.52
38_L	200_I	0.545	0.51
64_N	203_K	0.544	0.51
116_I	122_E	0.542	0.51
92_H	96_M	0.542	0.51
123_I	127_I	0.540	0.50
36_T	110_D	0.539	0.50
46_K	94_S	0.539	0.50
80_T	83_L	0.538	0.50
30_F	45_L	0.537	0.50
32_V	117_R	0.537	0.50
12_L	15_E	0.534	0.50
27_F	93_F	0.533	0.50
177_R	181_E	0.533	0.50
93_F	182_T	0.532	0.49
32_V	113_S	0.532	0.49
159_S	190_C	0.529	0.49
11_L	138_I	0.528	0.49
11_L	131_A	0.524	0.48
23_T	123_I	0.523	0.48
10_S	191_Q	0.522	0.48
166_N	202_M	0.521	0.48
173_V	177_R	0.521	0.48
88_D	149_E	0.519	0.48
13_L	200_I	0.519	0.48
149_E	191_Q	0.517	0.47
45_L	90_I	0.517	0.47
60_I	77_L	0.517	0.47
69_T	100_F	0.516	0.47
112_F	155_L	0.516	0.47
193_V	196_N	0.513	0.47
102_I	194_A	0.512	0.47
24_A	184_E	0.510	0.47
52_G	90_I	0.509	0.46
97_M	112_F	0.508	0.46
56_V	60_I	0.507	0.46
43_D	162_N	0.504	0.46
67_F	184_E	0.502	0.46
108_H	180_Y	0.500	0.45
49_E	52_G	0.500	0.45

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
3l39A	3	1	100	0.159	Contact Map
2oltA	5	0.9805	100	0.404	Contact Map
1t72A	5	0.961	98.4	0.794	Contact Map
2i0mA	2	0.9268	98.2	0.803	Contact Map
1xwmA	2	0.9512	98.2	0.805	Contact Map
1sumB	2	0.961	98.1	0.808	Contact Map
4q25A	2	0.9317	98	0.813	Contact Map
2w72C	2	0.361	21.1	0.937	Contact Map
2r80A	2	0.361	18.8	0.938	Contact Map
3wctB	3	0.3805	18.4	0.938	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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