YRKC - BACSU - GREMLIN Contacts

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YRKC - Uncharacterized protein YrkC

UniProt:	P54430	Sequences: MYYNPFSPQCYYYVTVPMYNDGRSVYWTIPNEMEKVHRGADLRSSYEDRNLLLKDYGPKPFVVNINRATKQNNTFRTALWTGKHFQVTLMSLGIGEDIGLEIHPNVDQFLRIEQGRGIVKMGKSKDHLNFQRNVYDDSAIVVPAGTWHNVINTGNTPLKLYSIYAPPNHPFGTVHETKADAVAAED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	186 (157)
Sequences:	228 (181)
Seq/√Len:	14.5

BACSU - YRKC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
123_K	146_T	6.093	1.00
87_V	141_V	4.778	1.00
120_K	151_I	4.776	1.00
110_L	142_V	3.752	1.00
176_E	180_D	3.467	0.99
102_I	168_N	3.273	0.99
114_Q	156_T	3.030	0.98
93_G	96_E	2.986	0.98
58_P	79_L	2.975	0.97
179_A	183_A	2.855	0.97
150_V	158_L	2.331	0.90
120_K	131_Q	2.281	0.89
106_V	168_N	2.251	0.89
140_I	158_L	2.118	0.85
74_T	77_T	1.996	0.81
89_L	162_S	1.977	0.81
75_F	151_I	1.868	0.77
58_P	171_F	1.846	0.76
85_F	162_S	1.722	0.71
75_F	175_H	1.696	0.69
53_L	56_Y	1.685	0.69
134_V	160_L	1.673	0.68
31_N	34_E	1.622	0.66
51_L	63_V	1.618	0.66
53_L	71_Q	1.616	0.66
92_L	96_E	1.601	0.65
110_L	118_I	1.538	0.62
79_L	171_F	1.458	0.57
106_V	162_S	1.428	0.56
58_P	168_N	1.422	0.55
146_T	168_N	1.400	0.54
61_F	96_E	1.376	0.53
64_N	67_R	1.358	0.52
110_L	160_L	1.354	0.52
102_I	162_S	1.342	0.51
112_I	160_L	1.335	0.51
136_D	184_A	1.328	0.50
66_N	134_V	1.300	0.49
67_R	116_R	1.289	0.48
63_V	182_V	1.276	0.47
140_I	150_V	1.263	0.47
51_L	56_Y	1.258	0.46
38_R	43_R	1.253	0.46
34_E	38_R	1.249	0.46
139_A	158_L	1.247	0.46
74_T	79_L	1.234	0.45
141_V	150_V	1.227	0.45
175_H	184_A	1.213	0.44
151_I	171_F	1.200	0.43
33_M	37_H	1.188	0.43
75_F	106_V	1.165	0.41
105_N	168_N	1.137	0.40
33_M	38_R	1.131	0.39
32_E	38_R	1.114	0.39
66_N	74_T	1.108	0.38
59_K	171_F	1.096	0.38
69_T	87_V	1.091	0.37
62_V	140_I	1.087	0.37
131_Q	151_I	1.086	0.37
29_I	39_G	1.077	0.37
96_E	132_R	1.063	0.36
56_Y	61_F	1.061	0.36
138_S	160_L	1.054	0.35
35_K	41_D	1.049	0.35
59_K	146_T	1.048	0.35
48_D	118_I	1.035	0.35
123_K	132_R	1.021	0.34
67_R	118_I	1.016	0.34
116_R	153_T	1.012	0.33
117_G	150_V	1.009	0.33
97_D	182_V	0.995	0.33
33_M	40_A	0.978	0.32
56_Y	79_L	0.977	0.32
102_I	131_Q	0.969	0.31
129_N	146_T	0.963	0.31
33_M	36_V	0.960	0.31
31_N	38_R	0.957	0.31
92_L	114_Q	0.944	0.30
78_A	153_T	0.939	0.30
32_E	44_S	0.931	0.30
41_D	45_S	0.925	0.29
100_L	172_G	0.921	0.29
75_F	184_A	0.918	0.29
78_A	167_P	0.917	0.29
66_N	158_L	0.910	0.29
96_E	141_V	0.910	0.29
61_F	64_N	0.905	0.28
133_N	138_S	0.894	0.28
111_R	161_Y	0.881	0.27
79_L	92_L	0.877	0.27
29_I	33_M	0.872	0.27
30_P	35_K	0.871	0.27
32_E	36_V	0.862	0.26
85_F	160_L	0.860	0.26
31_N	35_K	0.859	0.26
67_R	136_D	0.859	0.26
134_V	162_S	0.858	0.26
138_S	146_T	0.850	0.26
66_N	136_D	0.849	0.26
35_K	39_G	0.847	0.26
85_F	134_V	0.841	0.26
46_Y	50_N	0.835	0.25
74_T	176_E	0.834	0.25
118_I	138_S	0.833	0.25
61_F	181_A	0.832	0.25
63_V	141_V	0.832	0.25
58_P	131_Q	0.830	0.25
92_L	146_T	0.824	0.25
51_L	79_L	0.819	0.25
29_I	38_R	0.818	0.25
155_N	176_E	0.818	0.25
30_P	34_E	0.804	0.24
87_V	160_L	0.801	0.24
32_E	35_K	0.790	0.24
116_R	133_N	0.788	0.23
32_E	41_D	0.784	0.23
124_S	129_N	0.782	0.23
29_I	32_E	0.782	0.23
75_F	102_I	0.779	0.23
61_F	129_N	0.775	0.23
78_A	104_P	0.770	0.23
37_H	73_N	0.766	0.23
29_I	37_H	0.757	0.22
68_A	89_L	0.757	0.22
69_T	112_I	0.755	0.22
142_V	162_S	0.753	0.22
137_D	142_V	0.749	0.22
67_R	104_P	0.728	0.21
168_N	174_V	0.724	0.21
126_D	172_G	0.721	0.21
45_S	125_K	0.721	0.21
46_Y	127_H	0.719	0.21
100_L	128_L	0.716	0.21
74_T	175_H	0.712	0.21
58_P	180_D	0.712	0.21
94_I	141_V	0.711	0.21
133_N	183_A	0.704	0.20
63_V	84_H	0.701	0.20
104_P	144_A	0.696	0.20
71_Q	142_V	0.695	0.20
31_N	36_V	0.691	0.20
94_I	133_N	0.689	0.20
35_K	49_R	0.681	0.19
110_L	185_E	0.680	0.19
66_N	156_T	0.678	0.19
41_D	66_N	0.676	0.19
124_S	162_S	0.673	0.19
70_K	136_D	0.669	0.19
35_K	135_Y	0.667	0.19
29_I	50_N	0.665	0.19
41_D	47_E	0.662	0.19
29_I	34_E	0.662	0.19
39_G	43_R	0.661	0.19
75_F	93_G	0.661	0.19
84_H	104_P	0.660	0.19
39_G	47_E	0.660	0.19
98_I	117_G	0.656	0.19
102_I	110_L	0.652	0.18
52_L	131_Q	0.646	0.18
112_I	128_L	0.643	0.18
68_A	78_A	0.642	0.18
59_K	142_V	0.642	0.18
70_K	73_N	0.639	0.18
62_V	71_Q	0.635	0.18
36_V	39_G	0.629	0.18
62_V	70_K	0.628	0.18
98_I	167_P	0.626	0.18
35_K	45_S	0.623	0.18
61_F	134_V	0.623	0.18
132_R	156_T	0.623	0.18
123_K	168_N	0.622	0.18
83_K	155_N	0.621	0.17
75_F	120_K	0.619	0.17
31_N	150_V	0.619	0.17
73_N	93_G	0.618	0.17
75_F	150_V	0.618	0.17
47_E	135_Y	0.616	0.17
62_V	168_N	0.615	0.17
132_R	138_S	0.614	0.17
96_E	160_L	0.613	0.17
37_H	42_L	0.612	0.17
84_H	153_T	0.611	0.17
35_K	44_S	0.610	0.17
107_D	144_A	0.607	0.17
70_K	155_N	0.607	0.17
141_V	146_T	0.605	0.17
48_D	125_K	0.604	0.17
49_R	125_K	0.604	0.17
65_I	161_Y	0.603	0.17
87_V	139_A	0.603	0.17
106_V	141_V	0.601	0.17
34_E	133_N	0.599	0.17
146_T	150_V	0.598	0.17
65_I	175_H	0.596	0.17
47_E	52_L	0.595	0.17
102_I	135_Y	0.588	0.16
79_L	131_Q	0.587	0.16
52_L	117_G	0.583	0.16
37_H	41_D	0.580	0.16
67_R	168_N	0.578	0.16
47_E	124_S	0.577	0.16
61_F	117_G	0.573	0.16
36_V	40_A	0.572	0.16
48_D	127_H	0.571	0.16
30_P	110_L	0.569	0.16
38_R	150_V	0.563	0.16
110_L	162_S	0.557	0.16
119_V	165_A	0.556	0.15
83_K	135_Y	0.554	0.15
36_V	47_E	0.552	0.15
53_L	68_A	0.549	0.15
33_M	49_R	0.548	0.15
116_R	135_Y	0.547	0.15
96_E	117_G	0.545	0.15
29_I	64_N	0.540	0.15
70_K	88_T	0.537	0.15
96_E	178_K	0.535	0.15
104_P	116_R	0.535	0.15
45_S	94_I	0.534	0.15
136_D	156_T	0.532	0.15
127_H	142_V	0.532	0.15
41_D	132_R	0.530	0.15
109_F	139_A	0.528	0.15
120_K	140_I	0.524	0.15
53_L	176_E	0.523	0.15
125_K	134_V	0.520	0.14
79_L	141_V	0.520	0.14
66_N	137_D	0.516	0.14
42_L	118_I	0.515	0.14
79_L	129_N	0.514	0.14
98_I	181_A	0.511	0.14
87_V	147_W	0.509	0.14
51_L	110_L	0.508	0.14
63_V	102_I	0.508	0.14
160_L	183_A	0.503	0.14
60_P	109_F	0.500	0.14

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
2oa2A	2	0.7097	99.9	0.766	Contact Map
2ea7A	3	0.7258	99.3	0.852	Contact Map
2cavA	3	0.672	99.3	0.855	Contact Map
2gu9A	2	0.586	99.2	0.857	Contact Map
1v70A	2	0.5538	99.1	0.863	Contact Map
1uijA	3	0.6989	99.1	0.864	Contact Map
1lr5A	2	0.6989	99	0.868	Contact Map
1dgwA	3	0.672	99	0.868	Contact Map
2fqpA	3	0.5215	98.9	0.875	Contact Map
2b8mA	2	0.586	98.9	0.876	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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