YDJH - BACSU - GREMLIN Contacts

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YDJH - UPF0603 protein YdjH

UniProt:	O35004	Sequences: MRGFFGKAIFVVLAVFIMMPLLGIEAVRASELQQHVYDRAHLLSKAEIGKLESLSAKLGAKRDTDFIIITTKSTNGEDIADYTGDFYDRYGKGSTAILTIDMTNREVFIAGFKKAEQYLDNSRLNSIRNTISSDLSNENYFEAFETYIQLSYKDMGIKPGVNPDNIFFTWWFQLIAAIAVGGIAVSIMLYHAGGKVTVNGSTYMDQRTSDVIDQYDTYIRTTVTRERKPSDKDSGSDGGVTKGGTSYSGSRGSF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (236)
Sequences:	2138 (1986)
Seq/√Len:	129.3

ECOLI - YGCG
BACSU - YDJH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_N	142_E	5.153	1.00
87_Y	247_Y	4.406	1.00
135_L	143_A	3.772	1.00
40_A	70_T	3.690	1.00
125_N	129_N	3.539	1.00
54_L	149_Q	3.524	1.00
47_E	141_F	3.474	1.00
98_L	131_I	3.432	1.00
69_I	86_F	3.108	1.00
41_H	48_I	3.053	1.00
119_L	124_L	2.791	1.00
120_D	124_L	2.590	1.00
134_D	146_T	2.547	1.00
54_L	145_E	2.494	1.00
44_S	47_E	2.409	1.00
96_A	119_L	2.379	1.00
61_K	156_G	2.326	1.00
87_Y	97_I	2.307	1.00
131_I	147_Y	2.306	1.00
44_S	141_F	2.243	1.00
80_A	108_F	2.195	1.00
96_A	151_S	2.184	1.00
100_I	144_F	2.118	1.00
55_S	148_I	2.117	1.00
42_L	102_M	2.038	1.00
119_L	154_D	2.005	1.00
63_D	94_S	1.963	1.00
58_L	152_Y	1.954	1.00
101_D	104_N	1.951	1.00
113_K	248_S	1.936	1.00
134_D	139_N	1.934	1.00
215_Y	218_Y	1.916	1.00
111_G	115_A	1.846	1.00
35_H	59_G	1.829	1.00
128_R	131_I	1.816	1.00
98_L	144_F	1.757	1.00
83_T	99_T	1.735	1.00
57_K	61_K	1.729	1.00
120_D	123_R	1.699	1.00
79_I	99_T	1.680	1.00
78_D	81_D	1.672	1.00
84_G	87_Y	1.630	1.00
216_D	219_I	1.601	1.00
35_H	56_A	1.594	1.00
107_V	128_R	1.588	1.00
107_V	132_S	1.553	1.00
68_I	144_F	1.547	1.00
107_V	131_I	1.534	1.00
182_G	186_S	1.504	1.00
77_E	85_D	1.502	1.00
84_G	247_Y	1.487	1.00
80_A	110_A	1.483	1.00
183_I	187_I	1.475	1.00
124_L	252_G	1.473	1.00
84_G	110_A	1.454	1.00
142_E	146_T	1.443	1.00
119_L	151_S	1.431	1.00
134_D	142_E	1.422	1.00
74_T	104_N	1.418	1.00
79_I	108_F	1.417	1.00
42_L	70_T	1.413	1.00
50_K	145_E	1.381	1.00
123_R	154_D	1.322	1.00
84_G	88_D	1.321	1.00
109_I	151_S	1.318	1.00
116_E	248_S	1.315	1.00
88_D	93_G	1.306	1.00
58_L	64_T	1.283	1.00
214_Q	217_T	1.241	1.00
132_S	136_S	1.229	1.00
134_D	137_N	1.227	1.00
56_A	60_A	1.199	0.99
224_T	229_P	1.194	0.99
231_D	234_S	1.191	0.99
34_Q	52_E	1.189	0.99
70_T	74_T	1.182	0.99
111_G	121_N	1.180	0.99
102_M	140_Y	1.179	0.99
58_L	66_F	1.159	0.99
113_K	116_E	1.149	0.99
175_I	179_A	1.141	0.99
81_D	84_G	1.137	0.99
212_I	216_D	1.127	0.99
98_L	107_V	1.117	0.99
29_A	86_F	1.114	0.99
145_E	149_Q	1.108	0.99
74_T	101_D	1.101	0.99
215_Y	219_I	1.100	0.99
54_L	152_Y	1.090	0.99
74_T	79_I	1.085	0.99
51_L	141_F	1.084	0.99
47_E	51_L	1.078	0.99
86_F	90_Y	1.068	0.99
177_A	181_G	1.067	0.99
173_Q	177_A	1.065	0.99
230_S	233_D	1.064	0.99
48_I	52_E	1.055	0.99
43_L	141_F	1.045	0.98
217_T	220_R	1.041	0.98
223_V	228_K	1.026	0.98
81_D	85_D	1.019	0.98
132_S	147_Y	1.007	0.98
178_I	182_G	0.986	0.98
111_G	248_S	0.986	0.98
43_L	144_F	0.986	0.98
228_K	231_D	0.982	0.98
110_A	247_Y	0.976	0.98
141_F	145_E	0.969	0.97
85_D	89_R	0.969	0.97
221_T	224_T	0.965	0.97
66_F	151_S	0.964	0.97
146_T	149_Q	0.962	0.97
213_D	216_D	0.960	0.97
216_D	220_R	0.957	0.97
37_Y	67_I	0.942	0.97
40_A	102_M	0.939	0.97
211_V	215_Y	0.939	0.97
154_D	157_I	0.937	0.97
184_A	188_M	0.935	0.97
36_V	51_L	0.933	0.97
87_Y	246_S	0.932	0.97
226_E	229_P	0.929	0.97
222_T	225_R	0.928	0.97
39_R	70_T	0.927	0.97
43_L	47_E	0.924	0.97
212_I	215_Y	0.922	0.97
79_I	83_T	0.920	0.97
83_T	87_Y	0.917	0.96
91_G	242_K	0.911	0.96
73_S	76_G	0.906	0.96
66_F	152_Y	0.904	0.96
82_Y	99_T	0.904	0.96
23_G	26_A	0.897	0.96
49_G	53_S	0.896	0.96
128_R	252_G	0.895	0.96
111_G	116_E	0.892	0.96
10_F	17_I	0.886	0.96
108_F	251_R	0.884	0.96
128_R	147_Y	0.881	0.96
29_A	69_I	0.877	0.95
32_L	37_Y	0.876	0.95
32_L	35_H	0.872	0.95
223_V	226_E	0.871	0.95
35_H	52_E	0.871	0.95
109_I	128_R	0.870	0.95
213_D	217_T	0.866	0.95
135_L	140_Y	0.862	0.95
224_T	227_R	0.849	0.95
42_L	100_I	0.849	0.95
47_E	50_K	0.845	0.94
211_V	214_Q	0.842	0.94
93_G	112_F	0.838	0.94
233_D	236_S	0.829	0.94
74_T	106_E	0.828	0.94
179_A	183_I	0.828	0.94
43_L	70_T	0.826	0.94
96_A	115_A	0.824	0.94
219_I	222_T	0.814	0.93
109_I	127_I	0.808	0.93
66_F	96_A	0.806	0.93
195_K	198_V	0.805	0.93
98_L	147_Y	0.799	0.93
122_S	126_S	0.797	0.93
126_S	130_T	0.797	0.93
128_R	132_S	0.796	0.93
112_F	116_E	0.795	0.92
232_K	235_G	0.794	0.92
56_A	59_G	0.794	0.92
82_Y	86_F	0.789	0.92
164_D	168_F	0.783	0.92
73_S	101_D	0.775	0.91
185_V	189_L	0.773	0.91
218_Y	223_V	0.771	0.91
170_W	180_V	0.767	0.91
212_I	218_Y	0.765	0.91
62_R	155_M	0.764	0.91
171_W	175_I	0.763	0.91
107_V	147_Y	0.758	0.91
50_K	54_L	0.753	0.90
70_T	102_M	0.751	0.90
45_K	48_I	0.749	0.90
70_T	144_F	0.747	0.90
100_I	135_L	0.745	0.90
63_D	157_I	0.744	0.90
222_T	226_E	0.743	0.90
93_G	113_K	0.740	0.90
194_G	200_G	0.739	0.89
47_E	145_E	0.739	0.89
223_V	227_R	0.738	0.89
150_L	153_K	0.737	0.89
47_E	144_F	0.736	0.89
186_S	189_L	0.733	0.89
111_G	120_D	0.732	0.89
214_Q	218_Y	0.732	0.89
229_P	232_K	0.730	0.89
181_G	185_V	0.727	0.89
47_E	139_N	0.726	0.89
64_T	155_M	0.725	0.89
214_Q	219_I	0.724	0.88
55_S	59_G	0.724	0.88
59_G	63_D	0.723	0.88
225_R	228_K	0.721	0.88
43_L	48_I	0.720	0.88
226_E	231_D	0.720	0.88
33_Q	37_Y	0.717	0.88
84_G	97_I	0.713	0.88
83_T	247_Y	0.713	0.88
212_I	217_T	0.712	0.88
241_T	246_S	0.709	0.87
67_I	70_T	0.707	0.87
83_T	108_F	0.707	0.87
238_G	241_T	0.703	0.87
58_L	155_M	0.701	0.87
113_K	246_S	0.699	0.87
40_A	74_T	0.699	0.87
115_A	155_M	0.697	0.87
71_T	101_D	0.697	0.87
53_S	57_K	0.697	0.87
20_P	23_G	0.697	0.87
197_T	200_G	0.695	0.86
20_P	25_E	0.695	0.86
100_I	107_V	0.692	0.86
85_D	88_D	0.690	0.86
124_L	250_S	0.689	0.86
162_N	165_N	0.683	0.85
225_R	229_P	0.682	0.85
97_I	110_A	0.682	0.85
112_F	245_T	0.681	0.85
227_R	231_D	0.679	0.85
57_K	60_A	0.673	0.85
83_T	110_A	0.673	0.85
93_G	114_K	0.671	0.84
77_E	100_I	0.667	0.84
77_E	81_D	0.666	0.84
245_T	251_R	0.666	0.84
64_T	115_A	0.666	0.84
124_L	128_R	0.661	0.84
116_E	121_N	0.658	0.83
183_I	186_S	0.658	0.83
220_R	223_V	0.658	0.83
189_L	193_G	0.656	0.83
171_W	174_L	0.655	0.83
28_R	31_E	0.654	0.83
122_S	125_N	0.654	0.83
123_R	129_N	0.653	0.83
72_K	103_T	0.652	0.83
64_T	94_S	0.651	0.83
209_S	213_D	0.651	0.83
100_I	131_I	0.651	0.83
219_I	223_V	0.650	0.82
45_K	49_G	0.645	0.82
30_S	90_Y	0.644	0.82
51_L	68_I	0.643	0.82
215_Y	220_R	0.641	0.82
214_Q	220_R	0.639	0.81
215_Y	221_T	0.639	0.81
185_V	188_M	0.630	0.81
101_D	105_R	0.629	0.80
84_G	108_F	0.627	0.80
221_T	229_P	0.622	0.80
127_I	147_Y	0.619	0.79
32_L	59_G	0.618	0.79
79_I	101_D	0.614	0.79
196_V	199_N	0.610	0.78
14_A	17_I	0.610	0.78
227_R	230_S	0.609	0.78
149_Q	152_Y	0.608	0.78
80_A	83_T	0.607	0.78
62_R	94_S	0.606	0.78
239_G	242_K	0.603	0.78
129_N	132_S	0.602	0.77
97_I	247_Y	0.602	0.77
127_I	151_S	0.601	0.77
127_I	150_L	0.601	0.77
67_I	90_Y	0.599	0.77
147_Y	150_L	0.597	0.77
226_E	230_S	0.596	0.77
223_V	229_P	0.596	0.77
64_T	118_Y	0.596	0.77
218_Y	226_E	0.593	0.76
134_D	147_Y	0.591	0.76
84_G	111_G	0.591	0.76
134_D	138_E	0.588	0.76
172_F	176_A	0.583	0.75
22_L	25_E	0.583	0.75
59_G	65_D	0.583	0.75
52_E	56_A	0.579	0.75
133_S	147_Y	0.578	0.75
106_E	132_S	0.577	0.74
228_K	236_S	0.575	0.74
76_G	106_E	0.574	0.74
229_P	235_G	0.573	0.74
69_I	82_Y	0.573	0.74
29_A	32_L	0.572	0.74
186_S	190_Y	0.571	0.74
18_M	23_G	0.571	0.74
79_I	110_A	0.571	0.74
42_L	155_M	0.566	0.73
177_A	185_V	0.564	0.73
110_A	124_L	0.561	0.72
170_W	187_I	0.560	0.72
123_R	126_S	0.558	0.72
37_Y	86_F	0.554	0.71
173_Q	187_I	0.550	0.71
88_D	113_K	0.547	0.70
158_K	163_P	0.545	0.70
118_Y	155_M	0.544	0.70
90_Y	147_Y	0.544	0.70
36_V	52_E	0.543	0.70
17_I	20_P	0.541	0.70
64_T	126_S	0.540	0.70
32_L	52_E	0.538	0.69
46_A	50_K	0.538	0.69
105_R	136_S	0.538	0.69
42_L	143_A	0.538	0.69
66_F	148_I	0.537	0.69
11_V	14_A	0.537	0.69
153_K	157_I	0.536	0.69
213_D	218_Y	0.535	0.69
209_S	216_D	0.535	0.69
42_L	140_Y	0.534	0.69
225_R	231_D	0.531	0.68
123_R	127_I	0.530	0.68
170_W	175_I	0.529	0.68
100_I	143_A	0.528	0.68
170_W	176_A	0.526	0.68
101_D	106_E	0.525	0.67
35_H	65_D	0.523	0.67
74_T	82_Y	0.523	0.67
87_Y	112_F	0.521	0.67
84_G	246_S	0.520	0.67
93_G	140_Y	0.519	0.67
119_L	147_Y	0.519	0.67
31_E	34_Q	0.518	0.66
208_T	211_V	0.518	0.66
220_R	224_T	0.518	0.66
228_K	232_K	0.517	0.66
187_I	190_Y	0.513	0.66
225_R	232_K	0.513	0.66
122_S	154_D	0.512	0.65
242_K	245_T	0.511	0.65
51_L	55_S	0.511	0.65
84_G	113_K	0.511	0.65
240_V	245_T	0.511	0.65
216_D	221_T	0.510	0.65
93_G	246_S	0.509	0.65
21_L	180_V	0.507	0.65
225_R	230_S	0.506	0.65
235_G	239_G	0.506	0.65
148_I	152_Y	0.505	0.64
171_W	178_I	0.504	0.64
182_G	189_L	0.504	0.64
173_Q	180_V	0.500	0.64
34_Q	91_G	0.500	0.64

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
2kptA	1	0.5827	99.9	0.569	Contact Map
2kw7A	1	0.5945	99.9	0.572	Contact Map
4oa3A	1	0.5354	99.9	0.583	Contact Map
3pvhA	1	0.563	99.9	0.59	Contact Map
2pk2A	3	0.6654	94.3	0.903	Contact Map
4fybB	1	0.4528	84.6	0.922	Contact Map
4kblA	2	0	82.8	0.923	Contact Map
2zvfA	2	0.5118	69.9	0.931	Contact Map
4oe8C	1	0.126	62.1	0.935	Contact Map
1w7fA	1	0.3268	55.5	0.937	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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