YKYA - BACSU - GREMLIN Contacts

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YKYA - Uncharacterized lipoprotein YkyA

UniProt:	P21884	Sequences: MKDAIKRRPGIKIGAFCAMALILTGCMGQDPVDSLHHSLEKAAESEKPFQEEQNTLKELEAKENQLYDSVMKLNMDDYKKIVALSNKALENVSKREEHLKLENDSMKKSETEFEEAKTSAEHIKEKDIKEKADAAANHMEKRYTSYGTMYKEYKKALELNKKLYMQLKDKDLTRDDLDQQIDKVNASYEKILKYSGEFNEQTEKYNKAREDLYDAAGYRVKKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	223 (207)
Sequences:	189 (162)
Seq/√Len:	11.3

BACSU - YKYA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_N	168_K	4.732	1.00
92_V	157_L	3.700	0.99
202_T	206_N	3.228	0.97
159_L	162_K	2.663	0.90
55_T	160_N	2.504	0.87
60_E	95_R	2.471	0.87
40_E	213_Y	2.435	0.86
142_R	202_T	2.395	0.85
145_S	194_Y	2.387	0.85
185_N	199_N	2.372	0.84
58_E	62_K	2.366	0.84
51_E	169_D	2.306	0.82
63_E	160_N	2.300	0.82
185_N	206_N	2.267	0.81
199_N	202_T	2.055	0.74
96_E	161_K	2.051	0.74
142_R	198_F	1.980	0.71
198_F	202_T	1.925	0.69
129_K	133_D	1.916	0.69
103_N	107_K	1.876	0.67
49_F	105_S	1.846	0.66
185_N	202_T	1.834	0.65
75_M	78_Y	1.791	0.63
146_Y	205_Y	1.788	0.63
73_L	139_M	1.773	0.62
81_I	175_D	1.731	0.61
59_L	110_E	1.720	0.60
67_Y	185_N	1.698	0.59
62_K	129_K	1.691	0.59
97_E	207_K	1.685	0.58
53_Q	63_E	1.675	0.58
96_E	193_K	1.666	0.57
146_Y	181_I	1.664	0.57
142_R	206_N	1.663	0.57
42_A	106_M	1.657	0.57
61_A	125_E	1.649	0.57
76_D	146_Y	1.648	0.57
110_E	114_E	1.618	0.55
111_T	133_D	1.606	0.55
97_E	130_E	1.589	0.54
39_L	113_F	1.586	0.54
49_F	53_Q	1.538	0.51
199_N	206_N	1.522	0.51
63_E	164_Y	1.516	0.50
142_R	199_N	1.515	0.50
82_V	168_K	1.514	0.50
156_A	188_Y	1.507	0.50
136_A	140_E	1.468	0.48
180_Q	183_K	1.461	0.48
111_T	151_K	1.420	0.46
198_F	206_N	1.418	0.45
11_I	79_K	1.407	0.45
38_S	112_E	1.397	0.44
207_K	211_D	1.391	0.44
15_A	203_E	1.387	0.44
53_Q	139_M	1.355	0.42
130_E	191_I	1.352	0.42
53_Q	177_L	1.349	0.42
64_N	76_D	1.314	0.40
43_A	205_Y	1.312	0.40
25_G	124_K	1.307	0.40
142_R	185_N	1.306	0.40
32_V	35_L	1.304	0.40
49_F	139_M	1.302	0.40
39_L	105_S	1.299	0.40
113_F	139_M	1.297	0.40
68_D	186_A	1.273	0.39
59_L	195_S	1.255	0.38
77_D	216_A	1.246	0.37
12_K	155_K	1.243	0.37
130_E	214_D	1.237	0.37
67_Y	146_Y	1.228	0.37
39_L	177_L	1.216	0.36
112_E	115_E	1.204	0.35
40_E	212_L	1.201	0.35
32_V	120_A	1.200	0.35
56_L	61_A	1.200	0.35
18_A	179_Q	1.190	0.35
67_Y	71_M	1.189	0.35
70_V	120_A	1.168	0.34
95_R	163_L	1.156	0.33
91_N	123_I	1.146	0.33
53_Q	105_S	1.145	0.33
63_E	177_L	1.119	0.32
93_S	127_D	1.118	0.32
212_L	216_A	1.115	0.32
58_E	100_K	1.102	0.31
67_Y	168_K	1.094	0.31
110_E	136_A	1.090	0.31
101_L	146_Y	1.079	0.30
41_K	79_K	1.077	0.30
176_D	190_K	1.072	0.30
41_K	181_I	1.069	0.30
44_E	70_V	1.062	0.29
164_Y	199_N	1.057	0.29
149_M	188_Y	1.046	0.29
24_T	115_E	1.044	0.29
106_M	181_I	1.043	0.29
47_K	154_K	1.032	0.28
67_Y	132_A	1.023	0.28
15_A	186_A	1.021	0.28
209_R	213_Y	1.017	0.28
81_I	177_L	1.016	0.28
99_L	109_S	1.016	0.28
40_E	205_Y	1.015	0.28
67_Y	206_N	1.013	0.27
70_V	82_V	1.005	0.27
40_E	43_A	1.004	0.27
67_Y	199_N	1.002	0.27
56_L	168_K	0.999	0.27
75_M	178_D	0.979	0.26
155_K	197_E	0.978	0.26
69_S	189_E	0.973	0.26
53_Q	73_L	0.965	0.26
109_S	201_Q	0.962	0.26
22_I	179_Q	0.957	0.25
51_E	151_K	0.955	0.25
51_E	115_E	0.947	0.25
85_S	187_S	0.937	0.25
166_Q	207_K	0.934	0.25
213_Y	216_A	0.930	0.24
63_E	73_L	0.928	0.24
91_N	184_V	0.923	0.24
49_F	160_N	0.922	0.24
185_N	198_F	0.919	0.24
182_D	194_Y	0.915	0.24
143_Y	171_D	0.906	0.24
13_I	155_K	0.904	0.23
100_K	204_K	0.899	0.23
81_I	181_I	0.896	0.23
21_L	137_N	0.896	0.23
88_A	160_N	0.894	0.23
64_N	86_N	0.889	0.23
99_L	149_M	0.884	0.23
109_S	137_N	0.867	0.22
24_T	147_G	0.864	0.22
123_I	164_Y	0.863	0.22
94_K	196_G	0.855	0.22
24_T	93_S	0.851	0.22
20_A	25_G	0.850	0.22
19_M	23_L	0.845	0.21
64_N	82_V	0.841	0.21
205_Y	213_Y	0.840	0.21
63_E	105_S	0.839	0.21
69_S	167_L	0.836	0.21
70_V	92_V	0.836	0.21
132_A	164_Y	0.834	0.21
69_S	147_G	0.828	0.21
118_T	141_K	0.825	0.21
86_N	94_K	0.825	0.21
71_M	124_K	0.825	0.21
32_V	200_E	0.824	0.21
112_E	116_A	0.823	0.21
53_Q	146_Y	0.822	0.21
42_A	59_L	0.816	0.21
73_L	177_L	0.815	0.20
21_L	90_E	0.810	0.20
126_K	208_A	0.805	0.20
117_K	120_A	0.805	0.20
25_G	214_D	0.803	0.20
193_K	203_E	0.798	0.20
119_S	167_L	0.793	0.20
144_T	154_K	0.791	0.20
62_K	104_D	0.790	0.20
77_D	80_K	0.788	0.20
63_E	113_F	0.787	0.20
117_K	140_E	0.787	0.20
94_K	97_E	0.783	0.19
100_K	104_D	0.777	0.19
27_M	192_L	0.776	0.19
63_E	139_M	0.772	0.19
67_Y	205_Y	0.772	0.19
63_E	146_Y	0.771	0.19
51_E	133_D	0.771	0.19
177_L	199_N	0.768	0.19
115_E	141_K	0.766	0.19
68_D	104_D	0.764	0.19
21_L	24_T	0.763	0.19
177_L	180_Q	0.760	0.19
80_K	118_T	0.760	0.19
41_K	89_L	0.756	0.19
59_L	143_Y	0.756	0.19
109_S	113_F	0.754	0.19
121_E	162_K	0.752	0.19
151_K	184_V	0.749	0.18
58_E	155_K	0.748	0.18
50_Q	140_E	0.746	0.18
49_F	177_L	0.744	0.18
49_F	71_M	0.744	0.18
94_K	144_T	0.742	0.18
68_D	110_E	0.742	0.18
129_K	191_I	0.741	0.18
54_N	140_E	0.734	0.18
149_M	195_S	0.730	0.18
111_T	193_K	0.729	0.18
173_T	176_D	0.726	0.18
205_Y	212_L	0.725	0.18
116_A	208_A	0.724	0.18
174_R	178_D	0.723	0.18
16_F	156_A	0.723	0.18
150_Y	204_K	0.716	0.18
115_E	121_E	0.714	0.17
49_F	63_E	0.711	0.17
96_E	174_R	0.706	0.17
156_A	173_T	0.703	0.17
87_K	194_Y	0.700	0.17
60_E	163_L	0.700	0.17
23_L	41_K	0.700	0.17
63_E	88_A	0.700	0.17
22_I	154_K	0.699	0.17
79_K	101_L	0.699	0.17
122_H	127_D	0.698	0.17
24_T	98_H	0.698	0.17
38_S	116_A	0.698	0.17
22_I	108_K	0.695	0.17
143_Y	213_Y	0.694	0.17
59_L	70_V	0.693	0.17
122_H	171_D	0.690	0.17
141_K	144_T	0.679	0.16
85_S	203_E	0.675	0.16
165_M	168_K	0.673	0.16
44_E	130_E	0.667	0.16
79_K	157_L	0.666	0.16
35_L	47_K	0.664	0.16
54_N	170_K	0.663	0.16
60_E	143_Y	0.660	0.16
107_K	171_D	0.655	0.16
196_G	200_E	0.655	0.16
63_E	199_N	0.651	0.16
128_I	212_L	0.644	0.16
57_K	91_N	0.642	0.16
100_K	103_N	0.641	0.15
46_E	95_R	0.640	0.15
36_H	209_R	0.639	0.15
39_L	63_E	0.637	0.15
64_N	195_S	0.636	0.15
142_R	164_Y	0.635	0.15
32_V	59_L	0.630	0.15
99_L	145_S	0.626	0.15
84_L	195_S	0.625	0.15
47_K	54_N	0.625	0.15
63_E	102_E	0.622	0.15
165_M	183_K	0.621	0.15
39_L	49_F	0.619	0.15
17_C	24_T	0.617	0.15
114_E	180_Q	0.617	0.15
71_M	81_I	0.615	0.15
53_Q	160_N	0.611	0.15
59_L	161_K	0.611	0.15
38_S	146_Y	0.610	0.15
39_L	53_Q	0.610	0.15
125_E	216_A	0.605	0.15
123_I	197_E	0.605	0.15
76_D	104_D	0.603	0.15
61_A	203_E	0.598	0.14
75_M	159_L	0.598	0.14
122_H	133_D	0.596	0.14
45_S	146_Y	0.593	0.14
122_H	137_N	0.591	0.14
107_K	126_K	0.590	0.14
11_I	163_L	0.589	0.14
22_I	81_I	0.589	0.14
78_Y	172_L	0.588	0.14
171_D	191_I	0.585	0.14
188_Y	195_S	0.581	0.14
107_K	147_G	0.577	0.14
48_P	138_H	0.577	0.14
84_L	188_Y	0.577	0.14
19_M	158_E	0.576	0.14
147_G	215_A	0.575	0.14
135_A	156_A	0.573	0.14
74_N	167_L	0.573	0.14
144_T	155_K	0.572	0.14
182_D	186_A	0.571	0.14
32_V	128_I	0.571	0.14
72_K	115_E	0.571	0.14
94_K	147_G	0.568	0.14
78_Y	170_K	0.565	0.14
16_F	111_T	0.562	0.14
67_Y	142_R	0.559	0.14
20_A	190_K	0.558	0.13
20_A	24_T	0.558	0.13
143_Y	209_R	0.557	0.13
141_K	158_E	0.556	0.13
171_D	190_K	0.552	0.13
71_M	169_D	0.547	0.13
85_S	92_V	0.544	0.13
75_M	85_S	0.542	0.13
211_D	215_A	0.541	0.13
11_I	51_E	0.540	0.13
146_Y	177_L	0.539	0.13
88_A	139_M	0.538	0.13
13_I	58_E	0.536	0.13
86_N	157_L	0.533	0.13
174_R	208_A	0.532	0.13
182_D	215_A	0.529	0.13
17_C	183_K	0.527	0.13
74_N	120_A	0.521	0.13
145_S	197_E	0.519	0.13
136_A	210_E	0.518	0.13
73_L	160_N	0.514	0.13
43_A	81_I	0.513	0.13
25_G	216_A	0.511	0.12
103_N	156_A	0.511	0.12
138_H	208_A	0.509	0.12
43_A	108_K	0.504	0.12
42_A	93_S	0.502	0.12
21_L	165_M	0.501	0.12
52_E	55_T	0.500	0.12
18_A	137_N	0.500	0.12

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
2ap3A	1	0.8565	100	0.268	Contact Map
4cgkA	3	0.6771	93.8	0.91	Contact Map
4q4gX	1	0	78.7	0.931	Contact Map
4r9fA	1	0.2915	63.6	0.938	Contact Map
3uorA	1	0.278	49.9	0.943	Contact Map
1i84S	2	0.4395	41.7	0.946	Contact Map
4r2fA	1	0.3991	40.6	0.946	Contact Map
3zbiC	1	0.1256	36.4	0.948	Contact Map
3cqxC	2	0.3274	36	0.948	Contact Map
4n01A	1	0.7444	27.2	0.951	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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