YKOP - BACSU - GREMLIN Contacts

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YKOP - Uncharacterized protein YkoP

UniProt:	O34495	Sequences: MKTCFLSIWRVVDPIYFFFSRLSLIDNDQKSVFRVRLTKYKGHHVVLSDGTHIRKNDVLVKIHLHNIKLIRELQSIESAVRKGIIIYQKVYQSMPLLLDYINNHKKSEKIKGIIGITMLDKGVERLGFDVITPVNPFYRCFKKVSHVPILYLTSKPVSLRHLPNSSYLFISKEKLQKTYQKKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	183 (178)
Sequences:	183 (151)
Seq/√Len:	11.3

BACSU - YKOP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
154_S	157_V	4.884	1.00
145_S	149_I	3.101	0.96
53_I	112_G	3.021	0.95
36_R	47_L	2.850	0.93
132_T	166_S	2.773	0.92
117_T	168_L	2.709	0.91
174_K	178_T	2.539	0.88
25_I	110_I	2.474	0.87
13_D	16_Y	2.464	0.87
150_L	160_R	2.464	0.87
138_Y	142_K	2.412	0.85
13_D	142_K	2.127	0.77
13_D	65_H	2.126	0.77
120_D	170_I	2.068	0.75
12_V	155_K	2.060	0.75
77_E	81_R	2.053	0.74
154_S	160_R	2.034	0.74
32_V	118_M	1.965	0.71
81_R	119_L	1.962	0.71
64_L	165_S	1.952	0.70
33_F	97_L	1.940	0.70
61_K	142_K	1.923	0.69
120_D	147_V	1.904	0.68
94_M	130_V	1.861	0.67
62_I	149_I	1.848	0.66
68_K	173_E	1.763	0.62
60_V	101_I	1.751	0.62
2_K	19_F	1.742	0.61
65_H	142_K	1.691	0.59
133_P	165_S	1.676	0.58
47_L	70_I	1.675	0.58
61_K	65_H	1.642	0.57
53_I	171_S	1.636	0.56
47_L	116_I	1.605	0.55
100_Y	104_H	1.587	0.54
16_Y	61_K	1.586	0.54
158_S	164_N	1.584	0.54
16_Y	119_L	1.559	0.53
104_H	135_N	1.516	0.50
34_R	114_I	1.494	0.49
49_D	171_S	1.440	0.47
53_I	72_E	1.414	0.45
47_L	69_L	1.408	0.45
35_V	100_Y	1.380	0.44
113_I	121_K	1.379	0.44
13_D	61_K	1.373	0.43
33_F	90_V	1.346	0.42
16_Y	142_K	1.335	0.42
64_L	126_L	1.279	0.39
144_V	168_L	1.277	0.39
16_Y	83_G	1.268	0.39
17_F	22_L	1.266	0.38
70_I	116_I	1.265	0.38
39_K	177_K	1.250	0.38
50_G	101_I	1.243	0.37
97_L	118_M	1.239	0.37
161_H	166_S	1.235	0.37
31_S	34_R	1.231	0.37
9_W	175_L	1.223	0.36
21_R	94_M	1.206	0.36
69_L	78_S	1.206	0.36
135_N	172_K	1.206	0.36
65_H	107_S	1.194	0.35
16_Y	110_I	1.185	0.35
146_H	155_K	1.180	0.35
34_R	65_H	1.180	0.35
35_V	104_H	1.174	0.34
48_S	121_K	1.164	0.34
5_F	44_H	1.142	0.33
34_R	142_K	1.139	0.33
145_S	150_L	1.136	0.33
13_D	167_Y	1.131	0.32
43_H	116_I	1.110	0.32
133_P	142_K	1.103	0.31
62_I	111_K	1.099	0.31
67_I	149_I	1.098	0.31
20_S	36_R	1.081	0.30
28_D	177_K	1.076	0.30
17_F	61_K	1.075	0.30
137_F	172_K	1.073	0.30
19_F	64_L	1.072	0.30
83_G	148_P	1.064	0.30
123_V	130_V	1.054	0.29
35_V	65_H	1.054	0.29
81_R	117_T	1.029	0.28
70_I	84_I	1.028	0.28
25_I	55_K	1.025	0.28
86_I	168_L	1.023	0.28
44_H	103_N	1.023	0.28
169_F	179_Y	1.023	0.28
32_V	97_L	1.021	0.28
16_Y	149_I	1.005	0.27
36_R	112_G	1.004	0.27
36_R	170_I	1.004	0.27
14_P	117_T	1.004	0.27
63_H	128_F	1.000	0.27
63_H	127_G	1.000	0.27
35_V	93_S	0.993	0.27
102_N	180_Q	0.989	0.27
98_L	176_Q	0.988	0.27
21_R	166_S	0.985	0.27
36_R	87_Y	0.975	0.26
90_V	95_P	0.935	0.25
87_Y	91_Y	0.929	0.24
150_L	157_V	0.918	0.24
105_K	121_K	0.905	0.24
46_V	105_K	0.902	0.23
114_I	119_L	0.901	0.23
126_L	129_D	0.899	0.23
5_F	179_Y	0.894	0.23
81_R	150_L	0.889	0.23
121_K	165_S	0.876	0.23
69_L	94_M	0.874	0.23
86_I	160_R	0.870	0.22
61_K	149_I	0.869	0.22
20_S	119_L	0.866	0.22
91_Y	166_S	0.859	0.22
4_C	177_K	0.859	0.22
44_H	108_E	0.850	0.22
7_S	71_R	0.848	0.22
100_Y	110_I	0.846	0.22
138_Y	152_L	0.838	0.21
157_V	160_R	0.837	0.21
105_K	125_R	0.832	0.21
8_I	99_D	0.832	0.21
2_K	152_L	0.823	0.21
77_E	98_L	0.820	0.21
60_V	98_L	0.812	0.20
20_S	142_K	0.811	0.20
23_S	31_S	0.811	0.20
2_K	79_A	0.809	0.20
150_L	155_K	0.807	0.20
10_R	119_L	0.806	0.20
17_F	35_V	0.804	0.20
34_R	179_Y	0.803	0.20
45_V	55_K	0.802	0.20
92_Q	99_D	0.801	0.20
92_Q	108_E	0.798	0.20
9_W	16_Y	0.797	0.20
22_L	169_F	0.792	0.20
13_D	133_P	0.791	0.20
125_R	146_H	0.789	0.20
14_P	110_I	0.783	0.20
12_V	146_H	0.780	0.19
33_F	95_P	0.777	0.19
151_Y	158_S	0.776	0.19
32_V	90_V	0.775	0.19
103_N	131_I	0.773	0.19
120_D	150_L	0.771	0.19
145_S	160_R	0.770	0.19
44_H	54_R	0.768	0.19
58_V	109_K	0.757	0.19
130_V	154_S	0.756	0.19
158_S	180_Q	0.746	0.18
31_S	91_Y	0.744	0.18
17_F	142_K	0.741	0.18
91_Y	112_G	0.740	0.18
15_I	75_S	0.737	0.18
25_I	130_V	0.736	0.18
83_G	163_P	0.736	0.18
99_D	177_K	0.735	0.18
116_I	167_Y	0.730	0.18
162_L	179_Y	0.728	0.18
88_Q	118_M	0.728	0.18
91_Y	105_K	0.727	0.18
97_L	172_K	0.724	0.18
96_L	143_K	0.721	0.18
40_Y	115_G	0.718	0.18
32_V	141_F	0.712	0.17
117_T	129_D	0.702	0.17
42_G	49_D	0.701	0.17
66_N	122_G	0.696	0.17
123_V	165_S	0.694	0.17
35_V	60_V	0.686	0.17
108_E	173_E	0.685	0.17
64_L	129_D	0.684	0.17
45_V	157_V	0.682	0.17
170_I	180_Q	0.677	0.16
69_L	130_V	0.676	0.16
13_D	82_K	0.668	0.16
49_D	66_N	0.667	0.16
21_R	25_I	0.667	0.16
9_W	138_Y	0.665	0.16
152_L	179_Y	0.663	0.16
62_I	88_Q	0.655	0.16
159_L	162_L	0.654	0.16
38_T	126_L	0.652	0.16
26_D	130_V	0.650	0.16
72_E	82_K	0.647	0.16
30_K	120_D	0.643	0.16
8_I	155_K	0.637	0.15
88_Q	166_S	0.636	0.15
56_N	105_K	0.634	0.15
12_V	107_S	0.628	0.15
53_I	98_L	0.623	0.15
48_S	97_L	0.622	0.15
6_L	123_V	0.621	0.15
94_M	151_Y	0.619	0.15
49_D	140_C	0.617	0.15
136_P	146_H	0.617	0.15
170_I	179_Y	0.616	0.15
73_L	117_T	0.615	0.15
12_V	68_K	0.612	0.15
4_C	7_S	0.605	0.15
68_K	146_H	0.605	0.15
114_I	146_H	0.604	0.15
119_L	175_L	0.604	0.15
8_I	163_P	0.593	0.14
10_R	13_D	0.593	0.14
52_H	103_N	0.592	0.14
42_G	128_F	0.592	0.14
42_G	63_H	0.592	0.14
42_G	127_G	0.592	0.14
66_N	171_S	0.588	0.14
34_R	86_I	0.584	0.14
24_L	31_S	0.580	0.14
32_V	79_A	0.578	0.14
83_G	175_L	0.577	0.14
4_C	111_K	0.576	0.14
138_Y	148_P	0.575	0.14
8_I	162_L	0.574	0.14
46_V	78_S	0.574	0.14
41_K	48_S	0.574	0.14
13_D	138_Y	0.572	0.14
14_P	169_F	0.572	0.14
49_D	150_L	0.572	0.14
10_R	17_F	0.572	0.14
30_K	58_V	0.571	0.14
16_Y	145_S	0.571	0.14
83_G	138_Y	0.570	0.14
117_T	174_K	0.570	0.14
113_I	155_K	0.570	0.14
60_V	85_I	0.567	0.14
45_V	177_K	0.567	0.14
108_E	177_K	0.564	0.14
149_I	153_T	0.562	0.14
112_G	167_Y	0.562	0.14
40_Y	97_L	0.562	0.14
23_S	137_F	0.558	0.14
44_H	101_I	0.551	0.13
41_K	62_I	0.549	0.13
59_L	67_I	0.549	0.13
37_L	46_V	0.548	0.13
45_V	59_L	0.546	0.13
112_G	169_F	0.543	0.13
31_S	136_P	0.543	0.13
76_I	84_I	0.541	0.13
32_V	143_K	0.540	0.13
9_W	83_G	0.539	0.13
26_D	170_I	0.536	0.13
32_V	131_I	0.533	0.13
34_R	126_L	0.532	0.13
61_K	112_G	0.532	0.13
47_L	115_G	0.529	0.13
94_M	132_T	0.527	0.13
95_P	98_L	0.523	0.13
54_R	103_N	0.519	0.13
77_E	80_V	0.519	0.13
20_S	114_I	0.519	0.13
51_T	173_E	0.518	0.13
84_I	120_D	0.509	0.12
147_V	155_K	0.507	0.12
21_R	129_D	0.507	0.12
79_A	156_P	0.506	0.12
56_N	62_I	0.504	0.12
111_K	148_P	0.500	0.12
21_R	59_L	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
2pwwA	1	0.5027	38.6	0.947	Contact Map
2r5xA	1	0.5082	38	0.947	Contact Map
4ftsA	6	0.4973	25.5	0.952	Contact Map
4ga6A	2	0.459	8.8	0.961	Contact Map
4h0aA	1	0.2295	6.1	0.964	Contact Map
2pqnB	1	0.1093	5.1	0.965	Contact Map
3na6A	4	0.5082	4.9	0.965	Contact Map
1vsy5	1	0.6393	3.7	0.967	Contact Map
1v0dA	2	0.4863	3.6	0.968	Contact Map
4ry2A	2	0.5301	3.3	0.968	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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