YRKF - BACSU - GREMLIN Contacts

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YRKF - UPF0033 protein YrkF

UniProt:	P54433	Sequences: MMKATIVLDAKGLACPMPIVKTKKRMKDLKAGEVLEIHATDKGSTADLEAWAKSTGHEYLGTEAEGEILRHFLRKGGEHSSENASSIPEISLEAFKQKVDSDESLNILDVREIEEYEKAHIPGVVHIPLGEVEKRANELNENDEIYIICHSGRRSEMAARTMKKQGFKKVINVVPGMRDWTGKTE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (145)
Sequences:	1156 (911)
Seq/√Len:	75.7

BACSU - YRKF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_K	56_G	3.392	1.00
129_L	158_A	3.319	1.00
91_S	94_A	3.300	1.00
52_A	56_G	3.102	1.00
59_Y	62_T	3.078	1.00
107_I	148_I	2.932	1.00
135_R	138_E	2.876	1.00
95_F	146_Y	2.828	1.00
119_A	177_M	2.595	1.00
59_Y	63_E	2.482	1.00
51_W	54_S	2.369	1.00
115_E	150_H	2.359	1.00
141_E	167_F	2.308	1.00
113_I	117_E	2.228	1.00
51_W	55_T	2.207	1.00
88_P	98_K	2.099	1.00
112_E	115_E	2.080	1.00
105_L	146_Y	1.914	1.00
110_V	150_H	1.887	1.00
145_I	167_F	1.886	1.00
66_G	69_L	1.873	1.00
51_W	56_G	1.841	1.00
140_N	143_D	1.742	1.00
94_A	97_Q	1.733	1.00
59_Y	64_A	1.690	1.00
61_G	65_E	1.677	1.00
124_V	177_M	1.676	1.00
60_L	63_E	1.635	1.00
44_S	48_L	1.610	1.00
67_E	70_R	1.606	1.00
110_V	158_A	1.604	1.00
45_T	50_A	1.560	0.99
44_S	47_D	1.560	0.99
62_T	65_E	1.552	0.99
52_A	57_H	1.534	0.99
75_K	79_H	1.526	0.99
99_V	107_I	1.457	0.99
149_C	155_S	1.447	0.99
116_Y	126_H	1.429	0.99
147_I	158_A	1.316	0.98
38_H	42_K	1.313	0.98
130_G	154_R	1.307	0.98
94_A	98_K	1.292	0.98
127_I	135_R	1.282	0.98
72_F	75_K	1.270	0.97
99_V	103_E	1.249	0.97
116_Y	120_H	1.232	0.97
152_G	155_S	1.227	0.97
90_I	95_F	1.200	0.96
70_R	80_S	1.188	0.96
77_G	80_S	1.186	0.96
134_K	138_E	1.166	0.96
66_G	70_R	1.147	0.95
113_I	126_H	1.142	0.95
99_V	105_L	1.141	0.95
38_H	45_T	1.140	0.95
177_M	181_T	1.124	0.95
133_E	165_Q	1.116	0.95
42_K	46_A	1.102	0.94
150_H	158_A	1.089	0.94
53_K	57_H	1.087	0.94
137_N	164_K	1.087	0.94
70_R	77_G	1.085	0.94
82_E	142_N	1.061	0.93
121_I	173_V	1.041	0.92
72_F	141_E	1.039	0.92
59_Y	69_L	1.023	0.92
133_E	161_T	1.022	0.91
121_I	148_I	1.021	0.91
52_A	55_T	1.017	0.91
117_E	126_H	1.014	0.91
178_R	182_G	1.012	0.91
110_V	139_L	0.997	0.90
139_L	145_I	0.996	0.90
37_I	40_T	0.967	0.89
96_K	99_V	0.966	0.89
40_T	44_S	0.961	0.89
88_P	94_A	0.961	0.89
60_L	64_A	0.948	0.88
159_A	172_N	0.934	0.87
92_L	179_D	0.928	0.87
54_S	57_H	0.911	0.86
175_P	179_D	0.909	0.86
144_E	168_K	0.907	0.86
71_H	74_R	0.903	0.86
98_K	105_L	0.902	0.85
70_R	168_K	0.893	0.85
108_L	127_I	0.889	0.85
116_Y	161_T	0.886	0.84
160_R	164_K	0.886	0.84
126_H	150_H	0.879	0.84
110_V	115_E	0.877	0.84
112_E	150_H	0.875	0.84
46_A	49_E	0.871	0.83
64_A	69_L	0.868	0.83
50_A	78_E	0.868	0.83
115_E	179_D	0.865	0.83
60_L	65_E	0.859	0.83
108_L	173_V	0.858	0.82
58_E	63_E	0.856	0.82
69_L	77_G	0.848	0.82
37_I	121_I	0.841	0.81
79_H	93_E	0.840	0.81
58_E	61_G	0.839	0.81
164_K	168_K	0.827	0.80
82_E	85_S	0.823	0.80
128_P	135_R	0.820	0.80
47_D	151_S	0.809	0.79
41_D	45_T	0.793	0.77
92_L	99_V	0.786	0.77
47_D	112_E	0.776	0.76
112_E	126_H	0.768	0.75
161_T	165_Q	0.763	0.74
90_I	105_L	0.749	0.73
91_S	97_Q	0.743	0.72
69_L	80_S	0.738	0.72
89_E	174_V	0.736	0.72
86_S	170_V	0.728	0.71
127_I	137_N	0.726	0.71
90_I	107_I	0.717	0.70
67_E	77_G	0.712	0.69
73_L	80_S	0.709	0.69
144_E	163_K	0.706	0.69
61_G	69_L	0.704	0.68
82_E	169_K	0.704	0.68
134_K	165_Q	0.703	0.68
41_D	46_A	0.698	0.68
61_G	142_N	0.695	0.67
44_S	112_E	0.682	0.66
157_M	161_T	0.678	0.65
119_A	181_T	0.678	0.65
97_Q	100_D	0.676	0.65
62_T	69_L	0.673	0.65
104_S	143_D	0.668	0.64
136_A	167_F	0.666	0.64
108_L	162_M	0.664	0.64
115_E	118_K	0.659	0.63
82_E	93_E	0.656	0.63
61_G	68_I	0.650	0.62
61_G	66_G	0.649	0.62
150_H	179_D	0.648	0.62
120_H	150_H	0.645	0.62
61_G	64_A	0.639	0.61
150_H	154_R	0.636	0.61
173_V	180_W	0.635	0.60
110_V	126_H	0.634	0.60
67_E	137_N	0.624	0.59
41_D	47_D	0.620	0.59
58_E	62_T	0.617	0.58
73_L	133_E	0.611	0.57
149_C	158_A	0.610	0.57
91_S	99_V	0.609	0.57
65_E	69_L	0.606	0.57
89_E	182_G	0.606	0.57
77_G	81_S	0.603	0.56
67_E	164_K	0.603	0.56
38_H	41_D	0.602	0.56
163_K	168_K	0.600	0.56
62_T	66_G	0.597	0.56
103_E	107_I	0.593	0.55
64_A	67_E	0.588	0.55
144_E	169_K	0.587	0.54
124_V	150_H	0.586	0.54
152_G	178_R	0.585	0.54
120_H	170_V	0.581	0.54
100_D	104_S	0.580	0.54
148_I	151_S	0.579	0.53
110_V	120_H	0.578	0.53
110_V	149_C	0.578	0.53
70_R	137_N	0.577	0.53
72_F	167_F	0.576	0.53
51_W	130_G	0.573	0.53
68_I	72_F	0.570	0.52
96_K	100_D	0.564	0.52
69_L	74_R	0.561	0.51
157_M	160_R	0.558	0.51
43_G	148_I	0.555	0.50
60_L	70_R	0.552	0.50
72_F	77_G	0.552	0.50
92_L	137_N	0.551	0.50
37_I	42_K	0.550	0.50
159_A	170_V	0.547	0.49
92_L	96_K	0.547	0.49
133_E	164_K	0.539	0.48
43_G	154_R	0.538	0.48
175_P	180_W	0.536	0.48
114_E	118_K	0.534	0.48
110_V	176_G	0.534	0.48
137_N	165_Q	0.532	0.48
151_S	155_S	0.530	0.47
38_H	43_G	0.529	0.47
111_R	126_H	0.527	0.47
97_Q	102_D	0.526	0.47
62_T	145_I	0.525	0.47
89_E	172_N	0.521	0.46
37_I	167_F	0.521	0.46
81_S	84_A	0.519	0.46
59_Y	74_R	0.518	0.46
46_A	77_G	0.517	0.46
95_F	98_K	0.517	0.46
127_I	152_G	0.516	0.46
136_A	144_E	0.515	0.45
64_A	70_R	0.514	0.45
39_A	42_K	0.514	0.45
58_E	64_A	0.514	0.45
96_K	147_I	0.513	0.45
42_K	49_E	0.512	0.45
90_I	146_Y	0.512	0.45
98_K	144_E	0.511	0.45
115_E	151_S	0.511	0.45
112_E	158_A	0.511	0.45
42_K	47_D	0.510	0.45
93_E	96_K	0.508	0.45
48_L	152_G	0.507	0.44
112_E	147_I	0.505	0.44
62_T	67_E	0.502	0.44
59_Y	70_R	0.500	0.44
96_K	123_G	0.500	0.44

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
3tp9A	2	0.9784	99.9	0.557	Contact Map
1gmxA	1	0.5459	99.9	0.568	Contact Map
3r2uA	4	0.5081	99.9	0.568	Contact Map
3iwhA	1	0.5297	99.9	0.575	Contact Map
3fojA	1	0.5297	99.9	0.578	Contact Map
1yt8A	1	0.5351	99.9	0.579	Contact Map
3ilmA	2	0.5189	99.9	0.582	Contact Map
3gk5A	1	0.5135	99.9	0.584	Contact Map
3icsA	2	0.9676	99.9	0.586	Contact Map
3d1pA	1	0.5351	99.9	0.587	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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