YCSF - BACSU - GREMLIN Contacts

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YCSF - UPF0271 protein YcsF

UniProt:	P42963	Sequences: MFQIDLNCDLGESFGAYKIGLDQDILEYVTSANIACGFHAGDPSVMRKTVALAAERGVKMGAHPGLPDLLGFGRRNMAISPEEAYDLVVYQIGALSGFLKAEGLHMQHVKPHGALYNMAAVDQKLSDAIAKAVYKVDPGLILFGLAESELVKAGERIGLQTANEVFADRTYQSDGTLTPRSQPDALIESDDAAVTQVIKMVKEGAVKSQQGHDVSLKADTVCIHGDGAHALTFAQKIRKQLKAAGIEVTAISEQRST	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	257 (247)
Sequences:	2309 (1582)
Seq/√Len:	100.6

ECOLI - YBGL
BACSU - YCSF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_A	104_L	3.360	1.00
44_S	86_D	3.072	1.00
27_E	56_R	3.024	1.00
173_S	210_Q	2.955	1.00
173_S	212_H	2.794	1.00
96_S	100_K	2.769	1.00
30_T	248_V	2.555	1.00
66_L	118_M	2.443	1.00
199_K	213_D	2.424	1.00
173_S	208_S	2.378	1.00
208_S	212_H	2.332	1.00
16_A	19_I	2.325	1.00
205_A	213_D	2.317	1.00
93_G	97_G	2.278	1.00
76_N	118_M	2.242	1.00
143_F	220_T	2.209	1.00
46_M	95_L	2.152	1.00
199_K	203_E	2.128	1.00
89_V	136_V	2.116	1.00
123_Q	149_E	2.078	1.00
149_E	152_K	2.077	1.00
96_S	136_V	2.069	1.00
47_R	102_E	2.049	1.00
51_A	102_E	2.030	1.00
141_I	162_A	2.028	1.00
170_T	178_T	2.020	1.00
197_V	221_V	1.996	1.00
165_V	218_A	1.987	1.00
85_Y	135_K	1.958	1.00
85_Y	131_K	1.944	1.00
172_Q	179_P	1.906	1.00
67_P	77_M	1.897	1.00
50_V	98_F	1.863	1.00
170_T	184_D	1.819	1.00
127_D	156_R	1.798	1.00
47_R	86_D	1.783	1.00
71_G	75_R	1.782	1.00
207_K	213_D	1.715	1.00
29_V	32_A	1.708	1.00
5_D	31_S	1.681	1.00
172_Q	182_Q	1.662	1.00
170_T	186_L	1.654	1.00
21_L	24_D	1.644	1.00
60_M	104_L	1.631	1.00
199_K	205_A	1.628	1.00
26_L	29_V	1.613	1.00
38_F	90_Y	1.613	1.00
172_Q	176_T	1.612	1.00
13_S	45_V	1.611	1.00
130_A	153_A	1.607	1.00
238_R	242_K	1.605	1.00
190_D	194_V	1.586	1.00
119_A	129_I	1.567	1.00
172_Q	178_T	1.545	1.00
99_L	104_L	1.542	1.00
223_I	234_A	1.540	1.00
50_V	99_L	1.530	1.00
144_G	161_T	1.510	1.00
193_A	233_F	1.504	1.00
84_A	125_L	1.482	1.00
67_P	87_L	1.477	1.00
121_V	176_T	1.475	1.00
47_R	51_A	1.442	1.00
79_I	84_A	1.440	1.00
162_A	219_D	1.406	1.00
194_V	240_Q	1.405	1.00
179_P	182_Q	1.404	1.00
131_K	135_K	1.403	1.00
144_G	151_V	1.402	1.00
170_T	196_Q	1.402	1.00
205_A	215_S	1.391	1.00
151_V	163_N	1.385	1.00
198_I	240_Q	1.382	0.99
170_T	209_Q	1.372	0.99
199_K	207_K	1.370	0.99
191_D	236_K	1.355	0.99
76_N	122_D	1.354	0.99
5_D	30_T	1.323	0.99
151_V	161_T	1.313	0.99
76_N	121_V	1.304	0.99
92_I	136_V	1.295	0.99
203_E	213_D	1.292	0.99
227_G	233_F	1.289	0.99
127_D	157_I	1.273	0.99
187_I	193_A	1.273	0.99
23_Q	52_L	1.273	0.99
127_D	153_A	1.270	0.99
70_L	87_L	1.267	0.99
118_M	125_L	1.267	0.99
190_D	236_K	1.233	0.99
232_T	235_Q	1.228	0.99
3_Q	249_T	1.226	0.99
26_L	56_R	1.225	0.99
240_Q	244_A	1.220	0.99
149_E	153_A	1.215	0.99
119_A	150_L	1.210	0.99
167_A	221_V	1.209	0.99
110_K	222_C	1.205	0.99
206_V	214_V	1.189	0.98
109_V	133_V	1.175	0.98
50_V	60_M	1.172	0.98
202_K	244_A	1.171	0.98
59_K	107_Q	1.148	0.98
14_F	69_L	1.144	0.98
118_M	122_D	1.143	0.98
90_Y	94_A	1.134	0.98
52_L	56_R	1.125	0.98
79_I	87_L	1.121	0.98
127_D	131_K	1.107	0.98
50_V	95_L	1.107	0.98
153_A	156_R	1.106	0.98
52_L	55_E	1.095	0.97
208_S	214_V	1.092	0.97
242_K	248_V	1.090	0.97
130_A	159_L	1.089	0.97
163_N	219_D	1.086	0.97
108_H	143_F	1.081	0.97
189_S	192_A	1.078	0.97
99_L	106_M	1.078	0.97
44_S	83_E	1.068	0.97
131_K	157_I	1.066	0.97
154_G	161_T	1.065	0.97
48_K	52_L	1.060	0.97
82_E	86_D	1.055	0.97
130_A	157_I	1.054	0.97
239_K	243_A	1.053	0.97
151_V	155_E	1.051	0.97
80_S	83_E	1.039	0.96
144_G	150_L	1.039	0.96
164_E	222_C	1.014	0.96
134_Y	157_I	1.014	0.96
137_D	140_L	1.011	0.96
178_T	209_Q	1.010	0.96
130_A	154_G	1.003	0.96
239_K	242_K	1.002	0.96
38_F	87_L	1.002	0.96
89_V	101_A	0.994	0.95
123_Q	153_A	0.988	0.95
110_K	164_E	0.987	0.95
186_L	227_G	0.986	0.95
4_I	201_V	0.982	0.95
92_I	109_V	0.981	0.95
54_A	60_M	0.974	0.95
197_V	201_V	0.970	0.95
14_F	17_Y	0.962	0.94
198_I	202_K	0.954	0.94
128_A	132_A	0.952	0.94
165_V	200_M	0.950	0.94
191_D	195_T	0.949	0.94
90_Y	93_G	0.949	0.94
160_Q	219_D	0.946	0.94
34_I	49_T	0.946	0.94
143_F	162_A	0.939	0.94
24_D	27_E	0.935	0.94
155_E	217_K	0.922	0.93
51_A	55_E	0.922	0.93
162_A	220_T	0.920	0.93
32_A	58_V	0.905	0.92
23_Q	48_K	0.888	0.92
167_A	197_V	0.883	0.92
105_H	137_D	0.876	0.91
200_M	218_A	0.871	0.91
137_D	160_Q	0.859	0.90
120_A	176_T	0.859	0.90
34_I	60_M	0.854	0.90
65_G	77_M	0.849	0.90
107_Q	143_F	0.846	0.90
133_V	159_L	0.845	0.90
192_A	196_Q	0.844	0.90
28_Y	234_A	0.844	0.90
3_Q	247_E	0.843	0.90
59_K	108_H	0.834	0.89
48_K	51_A	0.825	0.89
123_Q	127_D	0.817	0.88
26_L	53_A	0.817	0.88
169_R	180_R	0.816	0.88
13_S	49_T	0.816	0.88
192_A	195_T	0.815	0.88
123_Q	152_K	0.813	0.88
141_I	160_Q	0.811	0.88
117_N	180_R	0.809	0.88
98_F	102_E	0.803	0.87
11_G	49_T	0.803	0.87
10_L	26_L	0.801	0.87
85_Y	89_V	0.791	0.86
15_G	71_G	0.789	0.86
43_P	90_Y	0.783	0.86
241_L	246_I	0.781	0.86
195_T	240_Q	0.778	0.85
66_L	84_A	0.776	0.85
165_V	221_V	0.775	0.85
130_A	134_Y	0.771	0.85
119_A	125_L	0.770	0.85
108_H	141_I	0.770	0.85
70_L	79_I	0.765	0.84
172_Q	209_Q	0.764	0.84
206_V	216_L	0.762	0.84
81_P	128_A	0.762	0.84
54_A	99_L	0.761	0.84
196_Q	200_M	0.758	0.84
42_D	71_G	0.757	0.84
36_C	62_A	0.750	0.83
146_A	163_N	0.749	0.83
202_K	246_I	0.748	0.83
13_S	25_I	0.747	0.83
155_E	163_N	0.746	0.83
200_M	206_V	0.746	0.83
163_N	217_K	0.739	0.82
17_Y	45_V	0.737	0.82
116_Y	166_F	0.732	0.82
148_S	151_V	0.732	0.82
198_I	244_A	0.730	0.82
111_P	129_I	0.729	0.82
110_K	116_Y	0.727	0.81
235_Q	239_K	0.726	0.81
27_E	235_Q	0.725	0.81
8_C	25_I	0.723	0.81
89_V	135_K	0.720	0.81
67_P	70_L	0.720	0.81
126_S	153_A	0.719	0.81
28_Y	238_R	0.715	0.80
193_A	196_Q	0.715	0.80
28_Y	231_L	0.713	0.80
53_A	60_M	0.708	0.80
111_P	116_Y	0.705	0.79
46_M	63_H	0.702	0.79
188_E	229_H	0.702	0.79
15_G	69_L	0.701	0.79
142_L	150_L	0.697	0.79
84_A	87_L	0.696	0.78
191_D	240_Q	0.691	0.78
19_I	63_H	0.690	0.78
96_S	137_D	0.685	0.77
121_V	174_D	0.683	0.77
145_L	166_F	0.678	0.77
117_N	177_L	0.678	0.77
189_S	196_Q	0.675	0.76
26_L	32_A	0.674	0.76
182_Q	209_Q	0.671	0.76
60_M	99_L	0.668	0.76
116_Y	164_E	0.664	0.75
190_D	229_H	0.662	0.75
117_N	120_A	0.662	0.75
201_V	246_I	0.662	0.75
167_A	237_I	0.662	0.75
10_L	32_A	0.661	0.75
14_F	71_G	0.659	0.75
116_Y	144_G	0.658	0.74
194_V	236_K	0.654	0.74
153_A	157_I	0.653	0.74
117_N	179_P	0.653	0.74
83_E	181_S	0.651	0.74
50_V	104_L	0.649	0.73
117_N	169_R	0.649	0.73
142_L	154_G	0.645	0.73
4_I	221_V	0.644	0.73
100_K	105_H	0.641	0.73
116_Y	145_L	0.638	0.72
120_A	148_S	0.633	0.72
13_S	20_G	0.633	0.72
79_I	83_E	0.632	0.71
14_F	42_D	0.631	0.71
8_C	29_V	0.629	0.71
203_E	206_V	0.629	0.71
28_Y	235_Q	0.628	0.71
177_L	180_R	0.624	0.71
47_R	101_A	0.623	0.70
50_V	102_E	0.622	0.70
84_A	88_V	0.621	0.70
134_Y	138_P	0.621	0.70
14_F	70_L	0.620	0.70
142_L	159_L	0.615	0.69
97_G	136_V	0.614	0.69
89_V	132_A	0.610	0.69
170_T	187_I	0.610	0.69
88_V	128_A	0.609	0.69
110_K	166_F	0.608	0.69
93_G	98_F	0.607	0.68
81_P	124_K	0.605	0.68
100_K	136_V	0.605	0.68
84_A	128_A	0.604	0.68
90_Y	97_G	0.604	0.68
126_S	150_L	0.600	0.68
177_L	185_A	0.600	0.68
7_N	110_K	0.598	0.67
8_C	223_I	0.596	0.67
139_G	160_Q	0.594	0.67
198_I	241_L	0.593	0.67
5_D	59_K	0.593	0.67
67_P	79_I	0.592	0.67
47_R	98_F	0.592	0.67
236_K	240_Q	0.589	0.66
192_A	207_K	0.589	0.66
180_R	185_A	0.586	0.66
166_F	222_C	0.585	0.66
195_T	199_K	0.582	0.65
15_G	42_D	0.582	0.65
7_N	222_C	0.581	0.65
43_P	94_A	0.581	0.65
152_K	156_R	0.579	0.65
169_R	179_P	0.579	0.65
60_M	106_M	0.576	0.64
66_L	79_I	0.576	0.64
194_V	233_F	0.574	0.64
25_I	234_A	0.574	0.64
93_G	101_A	0.573	0.64
32_A	53_A	0.573	0.64
228_A	232_T	0.571	0.64
35_A	42_D	0.571	0.64
94_A	97_G	0.570	0.64
180_R	184_D	0.569	0.63
54_A	103_G	0.569	0.63
231_L	234_A	0.569	0.63
65_G	69_L	0.568	0.63
227_G	230_A	0.567	0.63
178_T	182_Q	0.566	0.63
201_V	241_L	0.565	0.63
25_I	28_Y	0.561	0.62
170_T	185_A	0.558	0.62
92_I	96_S	0.554	0.61
52_L	58_V	0.554	0.61
133_V	137_D	0.554	0.61
38_F	43_P	0.553	0.61
104_L	107_Q	0.553	0.61
150_L	154_G	0.553	0.61
66_L	76_N	0.552	0.61
22_D	49_T	0.552	0.61
238_R	248_V	0.551	0.61
64_P	88_V	0.551	0.61
81_P	131_K	0.550	0.61
152_K	155_E	0.549	0.61
116_Y	222_C	0.549	0.61
15_G	19_I	0.546	0.60
75_R	83_E	0.546	0.60
15_G	75_R	0.545	0.60
49_T	197_V	0.544	0.60
170_T	181_S	0.542	0.60
145_L	148_S	0.541	0.60
232_T	239_K	0.540	0.59
111_P	150_L	0.540	0.59
242_K	247_E	0.539	0.59
89_V	96_S	0.538	0.59
80_S	84_A	0.538	0.59
125_L	220_T	0.537	0.59
240_Q	243_A	0.536	0.59
178_T	196_Q	0.533	0.59
184_D	209_Q	0.531	0.58
132_A	136_V	0.530	0.58
48_K	82_E	0.530	0.58
197_V	200_M	0.529	0.58
42_D	45_V	0.529	0.58
17_Y	20_G	0.529	0.58
50_V	63_H	0.528	0.58
111_P	119_A	0.527	0.58
45_V	70_L	0.526	0.58
8_C	225_G	0.525	0.57
145_L	165_V	0.518	0.56
106_M	221_V	0.517	0.56
6_L	223_I	0.515	0.56
63_H	77_M	0.513	0.56
166_F	177_L	0.510	0.55
82_E	85_Y	0.510	0.55
15_G	70_L	0.509	0.55
11_G	35_A	0.508	0.55
186_L	193_A	0.507	0.55
234_A	237_I	0.506	0.55
10_L	28_Y	0.506	0.55
124_K	127_D	0.504	0.54
201_V	215_S	0.501	0.54
180_R	183_P	0.500	0.54

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
2dfaA	4	0.9611	100	0.037	Contact Map
1v6tA	4	0.9689	100	0.037	Contact Map
2xu2A	4	0.9261	100	0.061	Contact Map
1xw8A	2	0.8949	100	0.067	Contact Map
2i5iA	4	0.8638	96.3	0.937	Contact Map
4m1bA	1	0.6965	93.3	0.947	Contact Map
2vyoA	1	0.7276	87.4	0.954	Contact Map
1ny1A	1	0.7082	86.6	0.954	Contact Map
3kwsA	2	0.8288	86	0.955	Contact Map
2nlyA	1	0.7938	79.5	0.958	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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