TORD - ECOLI - GREMLIN Contacts

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TORD - Chaperone protein TorD

UniProt:	P36662	Sequences: MTTLTAQQIACVYAWLAQLFSRELDDEQLTQIASAQMAEWFSLLKSEPPLTAAVNELENRIATLTVRDDARLELAADFCGLFLMTDKQAALPYASAYKQDEQEIKRLLVEAGMETSGNFNEPADHLAIYLELLSHLHFSLGEGTVPARRIDSLRQKTLTALWQWLPEFVARCRQYDSFGFYAALSQLLLVLVECDHQNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12195
Length:	199 (176)
Sequences:	1311 (1034)
Seq/√Len:	78.0

ECOLI - TORD DMSD
HALSA - DMSD
SULSO - Q97XY2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_L	132_L	4.157	1.00
20_F	188_L	3.310	1.00
77_D	178_F	3.134	1.00
105_K	123_A	3.097	1.00
169_V	188_L	2.665	1.00
126_L	165_L	2.626	1.00
173_R	189_L	2.606	1.00
168_F	172_C	2.599	1.00
94_A	160_A	2.589	1.00
9_I	153_L	2.570	1.00
9_I	13_Y	2.485	1.00
13_Y	195_D	2.449	1.00
9_I	195_D	2.323	1.00
133_L	153_L	2.316	1.00
94_A	129_Y	2.168	1.00
21_S	127_A	2.164	1.00
16_L	188_L	2.163	1.00
111_A	152_S	2.139	1.00
74_L	180_F	2.137	1.00
165_L	192_V	2.061	1.00
173_R	186_Q	1.989	1.00
97_Y	171_R	1.921	1.00
172_C	185_S	1.905	1.00
79_C	83_L	1.896	1.00
26_D	30_T	1.870	1.00
133_L	157_T	1.864	1.00
19_L	184_L	1.778	1.00
137_H	153_L	1.766	1.00
94_A	104_I	1.754	1.00
92_P	168_F	1.751	1.00
132_L	156_K	1.749	1.00
20_F	184_L	1.728	1.00
94_A	163_Q	1.724	1.00
17_A	131_E	1.656	1.00
165_L	169_V	1.621	1.00
13_Y	153_L	1.584	1.00
179_G	182_A	1.584	1.00
113_M	135_H	1.549	0.99
134_S	138_F	1.528	0.99
77_D	176_D	1.523	0.99
91_L	96_A	1.512	0.99
166_P	189_L	1.506	0.99
155_Q	159_T	1.494	0.99
104_I	108_L	1.474	0.99
14_A	134_S	1.468	0.99
14_A	138_F	1.460	0.99
158_L	196_H	1.454	0.99
104_I	129_Y	1.436	0.99
78_F	125_H	1.417	0.99
95_S	122_P	1.415	0.99
57_L	183_A	1.391	0.99
130_L	192_V	1.382	0.99
13_Y	191_L	1.381	0.99
133_L	191_L	1.373	0.99
53_A	190_V	1.357	0.98
85_T	88_Q	1.303	0.98
126_L	168_F	1.300	0.98
101_E	104_I	1.270	0.98
161_L	165_L	1.263	0.98
137_H	195_D	1.257	0.97
17_A	93_Y	1.255	0.97
18_Q	25_D	1.237	0.97
9_I	191_L	1.214	0.97
170_A	189_L	1.191	0.97
126_L	188_L	1.186	0.96
24_L	28_Q	1.184	0.96
129_Y	132_L	1.178	0.96
93_Y	121_E	1.175	0.96
19_L	180_F	1.146	0.96
20_F	82_F	1.143	0.96
164_W	168_F	1.141	0.96
110_E	155_Q	1.133	0.95
23_E	83_L	1.123	0.95
137_H	140_L	1.111	0.95
93_Y	122_P	1.095	0.94
64_L	74_L	1.092	0.94
10_A	138_F	1.088	0.94
83_L	88_Q	1.087	0.94
20_F	126_L	1.079	0.94
90_A	96_A	1.064	0.94
75_A	79_C	1.062	0.93
176_D	179_G	1.059	0.93
126_L	169_V	1.050	0.93
160_A	163_Q	1.039	0.93
104_I	156_K	1.032	0.92
9_I	133_L	1.032	0.92
184_L	188_L	1.031	0.92
167_E	171_R	1.009	0.92
53_A	183_A	1.008	0.92
77_D	80_G	1.005	0.91
176_D	182_A	0.999	0.91
101_E	123_A	0.974	0.90
25_D	31_Q	0.945	0.89
189_L	193_E	0.940	0.88
21_S	128_I	0.930	0.88
97_Y	181_Y	0.929	0.88
110_E	152_S	0.927	0.88
130_L	188_L	0.918	0.87
92_P	126_L	0.907	0.87
85_T	93_Y	0.905	0.86
13_Y	133_L	0.900	0.86
125_H	128_I	0.893	0.86
140_L	150_I	0.891	0.86
111_A	132_L	0.889	0.85
92_P	122_P	0.887	0.85
78_F	82_F	0.883	0.85
162_W	192_V	0.876	0.85
108_L	128_I	0.876	0.85
56_E	187_L	0.874	0.85
51_T	55_N	0.872	0.84
85_T	101_E	0.855	0.83
129_Y	156_K	0.852	0.83
76_A	79_C	0.848	0.83
90_A	97_Y	0.840	0.82
56_E	59_N	0.835	0.82
94_A	98_K	0.835	0.82
156_K	164_W	0.834	0.82
169_V	185_S	0.832	0.81
23_E	79_C	0.830	0.81
110_E	117_G	0.830	0.81
84_M	88_Q	0.819	0.80
106_R	110_E	0.819	0.80
81_L	187_L	0.816	0.80
59_N	63_T	0.810	0.80
93_Y	101_E	0.810	0.80
35_A	39_E	0.803	0.79
49_P	53_A	0.798	0.79
101_E	105_K	0.796	0.79
24_L	78_F	0.795	0.78
133_L	195_D	0.795	0.78
108_L	129_Y	0.787	0.78
71_R	75_A	0.785	0.78
9_I	137_H	0.783	0.77
153_L	195_D	0.779	0.77
107_L	111_A	0.775	0.77
12_V	54_V	0.772	0.76
26_D	71_R	0.768	0.76
84_M	122_P	0.750	0.74
173_R	182_A	0.749	0.74
97_Y	167_E	0.748	0.74
85_T	98_K	0.742	0.74
50_L	53_A	0.740	0.73
23_E	98_K	0.737	0.73
78_F	92_P	0.735	0.73
129_Y	161_L	0.733	0.73
157_T	162_W	0.732	0.73
157_T	195_D	0.730	0.72
171_R	174_Q	0.726	0.72
77_D	182_A	0.722	0.71
83_L	125_H	0.718	0.71
56_E	186_Q	0.717	0.71
79_C	88_Q	0.706	0.70
170_A	173_R	0.706	0.70
58_E	62_A	0.706	0.70
104_I	172_C	0.703	0.69
129_Y	140_L	0.699	0.69
23_E	71_R	0.694	0.68
193_E	196_H	0.689	0.68
103_E	159_T	0.686	0.68
35_A	133_L	0.676	0.66
81_L	175_Y	0.675	0.66
167_E	170_A	0.668	0.66
60_R	183_A	0.667	0.65
18_Q	74_L	0.666	0.65
51_T	58_E	0.662	0.65
123_A	160_A	0.654	0.64
185_S	188_L	0.652	0.64
76_A	105_K	0.647	0.63
107_L	156_K	0.646	0.63
36_Q	74_L	0.644	0.63
183_A	187_L	0.643	0.63
110_E	177_S	0.640	0.62
104_I	132_L	0.640	0.62
191_L	195_D	0.640	0.62
77_D	172_C	0.639	0.62
93_Y	131_E	0.636	0.62
12_V	18_Q	0.633	0.61
72_L	76_A	0.633	0.61
20_F	172_C	0.630	0.61
99_Q	114_E	0.629	0.61
131_E	135_H	0.629	0.61
16_L	191_L	0.627	0.61
117_G	120_N	0.626	0.61
18_Q	21_S	0.619	0.60
94_A	132_L	0.616	0.59
49_P	52_A	0.613	0.59
135_H	138_F	0.609	0.58
14_A	131_E	0.607	0.58
161_L	184_L	0.605	0.58
56_E	60_R	0.605	0.58
57_L	184_L	0.603	0.58
156_K	163_Q	0.602	0.58
77_D	177_S	0.602	0.58
8_Q	113_M	0.601	0.57
106_R	109_V	0.598	0.57
166_P	193_E	0.598	0.57
10_A	134_S	0.593	0.56
82_F	172_C	0.593	0.56
79_C	85_T	0.585	0.55
125_H	168_F	0.585	0.55
53_A	56_E	0.583	0.55
23_E	73_E	0.582	0.55
108_L	123_A	0.582	0.55
183_A	190_V	0.578	0.55
62_A	139_S	0.578	0.55
31_Q	116_S	0.576	0.54
82_F	90_A	0.575	0.54
77_D	112_G	0.574	0.54
153_L	191_L	0.571	0.54
13_Y	131_E	0.571	0.54
52_A	186_Q	0.569	0.53
96_A	101_E	0.565	0.53
71_R	74_L	0.565	0.53
17_A	134_S	0.563	0.53
113_M	138_F	0.563	0.53
17_A	191_L	0.561	0.52
78_F	127_A	0.560	0.52
78_F	185_S	0.557	0.52
13_Y	29_L	0.557	0.52
20_F	185_S	0.557	0.52
57_L	159_T	0.553	0.51
18_Q	126_L	0.553	0.51
33_A	38_A	0.552	0.51
39_E	43_L	0.551	0.51
111_A	136_L	0.551	0.51
100_D	104_I	0.549	0.51
139_S	149_R	0.547	0.51
64_L	186_Q	0.545	0.50
12_V	191_L	0.543	0.50
17_A	127_A	0.543	0.50
135_H	139_S	0.540	0.50
16_L	187_L	0.538	0.49
90_A	165_L	0.537	0.49
129_Y	163_Q	0.537	0.49
157_T	192_V	0.537	0.49
126_L	142_E	0.536	0.49
107_L	191_L	0.535	0.49
32_I	91_L	0.533	0.49
24_L	83_L	0.532	0.49
163_Q	166_P	0.532	0.49
104_I	137_H	0.532	0.49
77_D	89_A	0.531	0.49
10_A	141_G	0.530	0.48
15_W	32_I	0.529	0.48
21_S	87_K	0.529	0.48
30_T	36_Q	0.528	0.48
106_R	190_V	0.527	0.48
90_A	122_P	0.525	0.48
33_A	62_A	0.523	0.47
162_W	195_D	0.522	0.47
83_L	92_P	0.519	0.47
79_C	104_I	0.517	0.47
23_E	74_L	0.516	0.47
60_R	64_L	0.512	0.46
24_L	104_I	0.510	0.46
102_Q	123_A	0.510	0.46
73_E	94_A	0.509	0.46
63_T	174_Q	0.509	0.46
14_A	97_Y	0.504	0.45
189_L	192_V	0.503	0.45
10_A	18_Q	0.502	0.45
77_D	107_L	0.502	0.45
65_T	106_R	0.502	0.45
186_Q	193_E	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
1n1cA	2	0.9347	100	0.242	Contact Map
1s9uA	1	0.8744	100	0.287	Contact Map
2o9xA	2	0.7688	100	0.406	Contact Map
2xolA	2	0.7739	100	0.412	Contact Map
3e56A	2	0.2915	7.3	0.95	Contact Map
2zqmA	5	0.3568	4.5	0.954	Contact Map
4jzaA	2	0.4171	4.4	0.954	Contact Map
3iu5A	1	0.5126	3.4	0.957	Contact Map
3c4rA	4	0.397	3	0.958	Contact Map
3mb4A	1	0.5126	2.4	0.96	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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