YPIP - BACSU - GREMLIN Contacts

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YPIP - Uncharacterized protein YpiP

UniProt:	P54171	Sequences: MITTSYRPSEHTIKTAKQLSKELNMPYCGRNKQTVEHLLKSAERDLLVVGKERFELYTKQGAKFFFHPNTAMFRAKRFLQGEKEPMLRAAGLSEGDTFLDCTLGLGSDAIIASMAVGETGSVVGIEKNHLVSVLVRTGLHSWETGIEELQAAMRRIQVKNGDCFEHIKQLPDNSVDVVYFDPMFHEPVETSDGIAPLRDLAEDSVLHEGCINEAVRVARKSVVLKDHWKSPRFEQFGFNVMKRKTALFHYGVIQTSP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	257 (211)
Sequences:	947 (677)
Seq/√Len:	46.6

ECOLI - RSMJ
BACSU - YPIP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_L	175_V	4.721	1.00
127_K	202_E	3.482	1.00
103_L	124_G	3.423	1.00
125_I	161_G	3.369	1.00
87_L	115_A	3.178	1.00
161_G	166_H	2.937	1.00
125_I	166_H	2.588	1.00
124_G	156_I	2.517	1.00
137_T	141_S	2.475	1.00
106_G	135_V	2.459	1.00
53_R	63_K	2.430	1.00
176_D	219_R	2.406	1.00
90_A	112_A	2.368	1.00
184_F	246_A	2.325	1.00
98_F	112_A	2.211	1.00
161_G	165_E	2.178	1.00
132_S	158_V	2.098	1.00
213_E	217_V	2.093	1.00
96_D	220_K	2.065	1.00
89_A	223_V	2.058	1.00
239_N	252_V	2.023	0.99
166_H	170_L	1.997	0.99
123_V	175_V	1.948	0.99
64_F	138_G	1.931	0.99
215_V	236_F	1.918	0.99
103_L	158_V	1.903	0.99
86_M	112_A	1.868	0.99
127_K	162_D	1.841	0.99
162_D	165_E	1.821	0.99
186_E	198_R	1.811	0.99
184_F	231_P	1.807	0.99
185_H	227_H	1.805	0.99
232_R	241_M	1.772	0.99
73_F	78_F	1.758	0.98
85_P	246_A	1.754	0.98
75_A	111_I	1.718	0.98
97_T	121_S	1.687	0.98
50_G	55_E	1.683	0.98
103_L	135_V	1.640	0.98
90_A	120_G	1.632	0.97
71_A	84_E	1.605	0.97
99_L	167_I	1.596	0.97
164_F	209_G	1.589	0.97
168_K	209_G	1.588	0.97
215_V	222_V	1.582	0.97
70_T	248_F	1.557	0.97
147_E	151_A	1.549	0.96
75_A	114_M	1.544	0.96
101_C	180_F	1.513	0.96
163_C	210_C	1.498	0.96
121_S	157_Q	1.470	0.95
123_V	157_Q	1.442	0.95
178_V	217_V	1.396	0.94
224_L	233_F	1.389	0.94
116_V	120_G	1.383	0.93
185_H	226_D	1.370	0.93
240_V	250_Y	1.356	0.93
113_S	244_K	1.349	0.93
232_R	235_Q	1.327	0.92
187_P	198_R	1.323	0.92
180_F	210_C	1.306	0.91
187_P	190_T	1.305	0.91
54_F	133_V	1.302	0.91
97_T	123_V	1.297	0.91
184_F	245_T	1.291	0.91
198_R	203_D	1.269	0.90
129_H	160_N	1.264	0.90
82_E	86_M	1.246	0.89
81_G	111_I	1.235	0.89
226_D	232_R	1.233	0.89
97_T	175_V	1.227	0.88
167_I	217_V	1.225	0.88
243_R	246_A	1.217	0.88
109_A	124_G	1.201	0.87
66_F	74_R	1.200	0.87
243_R	247_L	1.188	0.87
58_T	61_G	1.181	0.86
178_V	222_V	1.177	0.86
50_G	63_K	1.161	0.85
123_V	178_V	1.134	0.84
170_L	175_V	1.134	0.84
87_L	90_A	1.125	0.84
98_F	116_V	1.122	0.83
164_F	168_K	1.119	0.83
50_G	53_R	1.117	0.83
149_L	152_A	1.116	0.83
227_H	249_H	1.107	0.83
92_L	116_V	1.104	0.82
149_L	153_M	1.101	0.82
69_N	72_M	1.095	0.82
110_I	152_A	1.094	0.82
107_S	193_G	1.085	0.81
127_K	206_L	1.084	0.81
85_P	243_R	1.079	0.81
92_L	115_A	1.077	0.81
92_L	96_D	1.070	0.80
198_R	201_A	1.069	0.80
144_T	150_Q	1.062	0.80
75_A	110_I	1.054	0.79
90_A	177_V	1.052	0.79
194_I	197_L	1.051	0.79
91_G	221_S	1.043	0.79
228_W	243_R	1.041	0.79
226_D	249_H	1.022	0.77
47_L	56_L	1.016	0.77
38_L	42_A	1.000	0.76
83_K	194_I	0.999	0.76
55_E	63_K	0.992	0.75
190_T	247_L	0.990	0.75
64_F	135_V	0.987	0.75
209_G	212_N	0.985	0.75
86_M	90_A	0.983	0.74
176_D	220_K	0.978	0.74
112_A	226_D	0.975	0.74
122_V	209_G	0.973	0.74
125_I	159_K	0.971	0.74
208_E	212_N	0.970	0.73
99_L	166_H	0.965	0.73
167_I	218_A	0.962	0.73
75_A	81_G	0.959	0.73
184_F	243_R	0.956	0.72
92_L	120_G	0.952	0.72
99_L	125_I	0.951	0.72
113_S	155_R	0.949	0.72
232_R	236_F	0.941	0.71
211_I	215_V	0.939	0.71
211_I	224_L	0.933	0.70
174_S	216_R	0.924	0.70
89_A	221_S	0.916	0.69
218_A	222_V	0.914	0.69
70_T	73_F	0.907	0.68
214_A	222_V	0.906	0.68
186_E	195_A	0.903	0.68
54_F	137_T	0.902	0.68
71_A	111_I	0.897	0.67
82_E	93_S	0.894	0.67
69_N	193_G	0.889	0.67
46_L	49_V	0.888	0.67
131_V	149_L	0.882	0.66
105_L	138_G	0.881	0.66
84_E	111_I	0.879	0.66
110_I	142_W	0.875	0.66
128_N	201_A	0.872	0.65
90_A	221_S	0.871	0.65
136_R	140_H	0.868	0.65
82_E	194_I	0.857	0.64
156_I	220_K	0.856	0.64
213_E	235_Q	0.849	0.63
162_D	166_H	0.831	0.61
212_N	236_F	0.828	0.61
142_W	152_A	0.828	0.61
131_V	201_A	0.822	0.61
228_W	249_H	0.806	0.59
47_L	54_F	0.799	0.58
106_G	137_T	0.799	0.58
75_A	79_L	0.795	0.58
45_D	58_T	0.794	0.58
215_V	253_I	0.787	0.57
213_E	216_R	0.780	0.57
140_H	165_E	0.769	0.56
45_D	178_V	0.765	0.55
165_E	168_K	0.765	0.55
243_R	249_H	0.764	0.55
84_E	152_A	0.763	0.55
151_A	155_R	0.758	0.54
102_T	181_D	0.757	0.54
150_Q	154_R	0.753	0.54
172_D	216_R	0.749	0.54
168_K	216_R	0.749	0.54
146_I	149_L	0.746	0.53
230_S	233_F	0.745	0.53
99_L	170_L	0.743	0.53
202_E	206_L	0.743	0.53
152_A	155_R	0.741	0.53
48_V	57_Y	0.739	0.53
93_S	120_G	0.736	0.52
66_F	73_F	0.731	0.52
69_N	107_S	0.726	0.51
224_L	238_F	0.725	0.51
59_K	62_A	0.723	0.51
185_H	249_H	0.723	0.51
142_W	156_I	0.716	0.50
94_E	239_N	0.711	0.50
66_F	110_I	0.711	0.50
162_D	202_E	0.704	0.49
75_A	80_Q	0.704	0.49
106_G	142_W	0.703	0.49
89_A	243_R	0.701	0.49
240_V	252_V	0.699	0.49
140_H	143_E	0.696	0.48
133_V	137_T	0.693	0.48
67_H	109_A	0.687	0.47
132_S	160_N	0.684	0.47
69_N	105_L	0.683	0.47
66_F	81_G	0.681	0.47
194_I	201_A	0.678	0.47
170_L	217_V	0.676	0.46
204_S	207_H	0.673	0.46
52_E	97_T	0.669	0.46
210_C	224_L	0.667	0.45
83_K	88_R	0.666	0.45
240_V	245_T	0.666	0.45
92_L	124_G	0.664	0.45
89_A	244_K	0.661	0.45
46_L	50_G	0.657	0.44
73_F	84_E	0.656	0.44
210_C	214_A	0.655	0.44
232_R	237_G	0.651	0.44
193_G	201_A	0.651	0.44
65_F	68_P	0.651	0.44
180_F	214_A	0.650	0.44
210_C	223_V	0.649	0.44
192_D	221_S	0.647	0.44
152_A	156_I	0.646	0.43
180_F	226_D	0.642	0.43
177_V	218_A	0.641	0.43
198_R	228_W	0.640	0.43
86_M	240_V	0.639	0.43
193_G	196_P	0.638	0.43
176_D	179_Y	0.638	0.43
178_V	200_L	0.637	0.43
227_H	247_L	0.635	0.42
231_P	235_Q	0.635	0.42
127_K	204_S	0.635	0.42
125_I	167_I	0.634	0.42
208_E	213_E	0.625	0.41
84_E	115_A	0.625	0.41
220_K	253_I	0.622	0.41
92_L	112_A	0.621	0.41
211_I	222_V	0.620	0.41
242_K	248_F	0.617	0.41
70_T	179_Y	0.616	0.41
165_E	171_P	0.612	0.40
84_E	128_N	0.612	0.40
229_K	245_T	0.612	0.40
97_T	164_F	0.610	0.40
140_H	144_T	0.606	0.40
188_V	247_L	0.603	0.39
81_G	84_E	0.601	0.39
193_G	226_D	0.600	0.39
125_I	162_D	0.599	0.39
203_D	234_E	0.597	0.39
139_L	153_M	0.596	0.39
90_A	115_A	0.594	0.38
148_E	151_A	0.592	0.38
179_Y	250_Y	0.592	0.38
171_P	216_R	0.591	0.38
95_G	120_G	0.590	0.38
194_I	204_S	0.589	0.38
102_T	180_F	0.586	0.38
76_K	238_F	0.581	0.37
54_F	194_I	0.580	0.37
43_E	220_K	0.579	0.37
174_S	219_R	0.574	0.37
116_V	192_D	0.573	0.36
103_L	116_V	0.569	0.36
67_H	250_Y	0.568	0.36
106_G	139_L	0.567	0.36
78_F	84_E	0.567	0.36
68_P	153_M	0.566	0.36
185_H	247_L	0.565	0.36
186_E	197_L	0.565	0.36
233_F	249_H	0.563	0.36
185_H	194_I	0.562	0.35
97_T	157_Q	0.562	0.35
149_L	243_R	0.561	0.35
151_A	154_R	0.561	0.35
56_L	130_L	0.560	0.35
123_V	159_K	0.557	0.35
111_I	115_A	0.556	0.35
113_S	135_V	0.552	0.35
49_V	52_E	0.552	0.35
60_Q	243_R	0.551	0.34
198_R	236_F	0.550	0.34
224_L	251_G	0.547	0.34
194_I	224_L	0.546	0.34
150_Q	153_M	0.544	0.34
164_F	234_E	0.544	0.34
95_G	232_R	0.543	0.34
79_L	134_L	0.541	0.34
185_H	231_P	0.540	0.34
123_V	176_D	0.533	0.33
98_F	109_A	0.533	0.33
208_E	234_E	0.532	0.33
50_G	136_R	0.532	0.33
183_M	225_K	0.531	0.33
185_H	232_R	0.530	0.33
130_L	200_L	0.530	0.33
59_K	197_L	0.529	0.33
125_I	142_W	0.528	0.32
122_V	237_G	0.527	0.32
137_T	189_E	0.525	0.32
84_E	246_A	0.525	0.32
107_S	190_T	0.523	0.32
85_P	229_K	0.523	0.32
121_S	171_P	0.523	0.32
166_H	217_V	0.522	0.32
56_L	200_L	0.522	0.32
65_F	158_V	0.520	0.32
161_G	222_V	0.519	0.32
134_L	249_H	0.518	0.32
97_T	144_T	0.516	0.31
69_N	83_K	0.516	0.31
167_I	214_A	0.515	0.31
142_W	247_L	0.513	0.31
147_E	150_Q	0.513	0.31
80_Q	87_L	0.512	0.31
100_D	104_G	0.512	0.31
100_D	126_E	0.512	0.31
104_G	126_E	0.512	0.31
80_Q	84_E	0.505	0.31
216_R	237_G	0.503	0.30
159_K	165_E	0.502	0.30
47_L	116_V	0.501	0.30
136_R	148_E	0.501	0.30
88_R	249_H	0.500	0.30

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
2r6zA	2	0.8949	100	0.557	Contact Map
2oyrA	1	0.9144	100	0.566	Contact Map
1uwvA	1	0.8054	99	0.854	Contact Map
2as0A	2	0.9144	98.9	0.858	Contact Map
3c0kA	2	0.9339	98.9	0.858	Contact Map
3bt7A	1	0.821	98.8	0.862	Contact Map
2dulA	2	0.6848	98.8	0.863	Contact Map
3ll7A	1	0.856	98.8	0.864	Contact Map
3vywA	1	0.9183	98.7	0.867	Contact Map
3axsA	2	0.6848	98.7	0.869	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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