EII-Sor - PFAM28P - GREMLIN Contacts

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EII-Sor - PTS system sorbose-specific iic component

PFAM:	PF03609	Sequences: IIQAILIALVAGLAGLDGLLGQFMLSRPLVAGTLVGLILGDLQTGLIIGATLELIYLGVVPIGGAVPPDAALAGVIGTALAILSGQGPEAAIALAVPLALLGQLLDILVRTINSFFVHRADKAAEEGNFKGIERLHLLGPLLLGFLLRAIPVFLALYFGADAVQALLNAIPAWLTNGLSVAGGMLPAVGFAMLLNMMLKKKLWPFFFLGFVLAAYLGLPLIAIAIIGVAIALI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	233 (231)
Sequences:	3974 (2556)
Seq/√Len:	168.1
META:	0.609

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_D	44_T	5.449	1.00
27_R	53_E	4.534	1.00
128_N	131_G	4.079	1.00
208_L	229_A	4.027	1.00
10_V	34_L	3.277	1.00
218_L	222_A	3.225	1.00
119_R	122_K	3.076	1.00
211_V	226_I	2.982	1.00
122_K	126_E	2.922	1.00
123_A	131_G	2.860	1.00
37_L	42_L	2.856	1.00
32_G	45_G	2.787	1.00
211_V	225_I	2.650	1.00
172_A	176_N	2.498	1.00
4_A	8_A	2.427	1.00
118_H	121_D	2.369	1.00
123_A	135_L	2.322	1.00
123_A	128_N	2.318	1.00
130_K	134_R	2.312	1.00
164_Q	168_N	2.282	1.00
10_V	38_I	2.241	1.00
7_I	35_V	2.186	1.00
219_P	222_A	2.130	1.00
12_G	145_F	2.063	1.00
43_Q	47_I	2.050	1.00
11_A	152_V	1.982	1.00
39_L	83_L	1.959	1.00
6_L	38_I	1.956	1.00
119_R	123_A	1.943	1.00
161_D	164_Q	1.910	1.00
33_T	42_L	1.879	1.00
8_A	153_F	1.865	1.00
44_T	47_I	1.847	1.00
213_A	223_I	1.814	1.00
12_G	149_A	1.747	1.00
122_K	125_E	1.723	1.00
119_R	135_L	1.717	1.00
123_A	126_E	1.664	1.00
32_G	74_G	1.651	1.00
39_L	82_I	1.643	1.00
207_F	225_I	1.621	1.00
72_L	102_G	1.617	1.00
44_T	48_I	1.611	1.00
145_F	149_A	1.586	1.00
215_Y	219_P	1.562	1.00
45_G	49_G	1.527	1.00
44_T	82_I	1.493	1.00
203_W	207_F	1.485	1.00
128_N	134_R	1.472	1.00
215_Y	222_A	1.463	1.00
212_L	216_L	1.441	1.00
2_I	5_I	1.421	1.00
124_A	127_G	1.400	1.00
218_L	223_I	1.400	1.00
176_N	179_S	1.389	1.00
33_T	37_L	1.377	1.00
69_D	72_L	1.376	1.00
134_R	138_L	1.375	1.00
47_I	50_A	1.374	1.00
8_A	149_A	1.368	1.00
228_V	232_L	1.346	1.00
87_G	90_A	1.345	1.00
52_L	74_G	1.309	1.00
29_L	33_T	1.307	1.00
93_A	97_P	1.302	1.00
170_I	174_L	1.289	1.00
177_G	181_A	1.285	1.00
131_G	134_R	1.278	1.00
198_L	203_W	1.277	1.00
120_A	136_H	1.257	1.00
34_L	38_I	1.254	1.00
176_N	180_V	1.250	1.00
120_A	124_A	1.246	1.00
165_A	168_N	1.239	1.00
106_D	110_R	1.222	1.00
166_L	169_A	1.219	1.00
73_A	99_A	1.215	1.00
180_V	183_G	1.213	1.00
73_A	77_G	1.213	1.00
161_D	165_A	1.211	1.00
32_G	78_T	1.208	1.00
86_Q	90_A	1.197	1.00
69_D	106_D	1.196	1.00
69_D	148_R	1.187	1.00
165_A	169_A	1.179	1.00
130_K	133_E	1.169	1.00
216_L	219_P	1.167	1.00
68_P	99_A	1.134	1.00
79_A	83_L	1.123	1.00
30_V	33_T	1.104	1.00
51_T	55_I	1.099	1.00
78_T	82_I	1.098	1.00
126_E	131_G	1.085	1.00
153_F	157_Y	1.080	1.00
172_A	175_T	1.073	1.00
13_L	25_L	1.072	1.00
11_A	75_V	1.068	1.00
14_A	31_A	1.053	0.99
134_R	139_G	1.044	0.99
68_P	103_Q	1.040	0.99
162_A	166_L	1.038	0.99
10_V	31_A	1.031	0.99
43_Q	46_L	1.022	0.99
33_T	46_L	1.003	0.99
129_F	133_E	1.003	0.99
131_G	135_L	1.002	0.99
46_L	49_G	0.997	0.99
76_I	155_A	0.992	0.99
224_A	227_G	0.988	0.99
181_A	185_L	0.985	0.99
9_L	13_L	0.984	0.99
144_G	147_L	0.981	0.99
173_W	177_G	0.977	0.99
10_V	75_V	0.975	0.99
201_K	205_F	0.972	0.99
90_A	175_T	0.965	0.99
116_F	119_R	0.965	0.99
10_V	14_A	0.960	0.99
124_A	128_N	0.957	0.99
142_L	145_F	0.955	0.99
90_A	93_A	0.954	0.99
81_A	91_A	0.950	0.99
111_T	114_S	0.949	0.99
4_A	156_L	0.945	0.99
17_D	22_Q	0.940	0.99
225_I	228_V	0.936	0.99
191_A	195_N	0.933	0.99
48_I	78_T	0.930	0.99
52_L	73_A	0.929	0.99
154_L	162_A	0.927	0.99
2_I	6_L	0.916	0.98
107_I	110_R	0.905	0.98
114_S	117_V	0.902	0.98
162_A	165_A	0.902	0.98
217_G	220_L	0.899	0.98
31_A	74_G	0.894	0.98
204_P	232_L	0.894	0.98
35_V	78_T	0.876	0.98
158_F	161_D	0.876	0.98
149_A	153_F	0.866	0.98
27_R	30_V	0.864	0.98
3_Q	83_L	0.858	0.98
124_A	132_I	0.857	0.98
74_G	78_T	0.848	0.97
77_G	81_A	0.844	0.97
202_L	206_F	0.842	0.97
91_A	97_P	0.841	0.97
31_A	75_V	0.836	0.97
5_I	153_F	0.832	0.97
100_L	104_L	0.830	0.97
229_A	232_L	0.829	0.97
24_M	53_E	0.821	0.97
211_V	218_L	0.817	0.97
98_L	163_V	0.802	0.96
215_Y	221_I	0.798	0.96
171_P	177_G	0.796	0.96
121_D	125_E	0.796	0.96
227_G	230_I	0.794	0.96
33_T	78_T	0.790	0.96
216_L	221_I	0.787	0.96
121_D	124_A	0.782	0.96
172_A	217_G	0.781	0.96
42_L	45_G	0.781	0.96
154_L	157_Y	0.778	0.96
36_G	49_G	0.773	0.96
124_A	129_F	0.773	0.96
76_I	80_L	0.767	0.95
25_L	28_P	0.767	0.95
22_Q	26_S	0.765	0.95
14_A	71_A	0.763	0.95
24_M	27_R	0.759	0.95
158_F	162_A	0.758	0.95
207_F	232_L	0.756	0.95
59_V	70_A	0.753	0.95
112_I	143_L	0.751	0.95
193_L	196_M	0.748	0.95
210_F	214_A	0.745	0.95
207_F	229_A	0.740	0.95
100_L	103_Q	0.740	0.95
104_L	108_L	0.738	0.94
141_L	144_G	0.738	0.94
7_I	10_V	0.733	0.94
215_Y	218_L	0.732	0.94
15_G	18_G	0.729	0.94
175_T	184_M	0.729	0.94
109_V	139_G	0.729	0.94
164_Q	217_G	0.728	0.94
81_A	87_G	0.724	0.94
14_A	26_S	0.722	0.94
7_I	75_V	0.717	0.94
99_A	190_F	0.712	0.93
35_V	82_I	0.704	0.93
79_A	156_L	0.703	0.93
199_K	202_L	0.703	0.93
4_A	157_Y	0.701	0.93
191_A	194_L	0.701	0.93
105_L	151_P	0.700	0.93
8_A	156_L	0.700	0.93
5_I	8_A	0.689	0.92
34_L	45_G	0.689	0.92
175_T	178_L	0.685	0.92
154_L	158_F	0.684	0.92
109_V	113_N	0.683	0.92
8_A	12_G	0.682	0.92
84_S	157_Y	0.682	0.92
186_P	189_G	0.680	0.92
37_L	41_D	0.679	0.92
225_I	229_A	0.678	0.92
35_V	75_V	0.675	0.91
3_Q	38_I	0.675	0.91
85_G	89_E	0.674	0.91
6_L	9_L	0.673	0.91
143_L	146_L	0.673	0.91
29_L	50_A	0.672	0.91
120_A	132_I	0.670	0.91
116_F	143_L	0.668	0.91
76_I	79_A	0.667	0.91
14_A	34_L	0.667	0.91
11_A	15_G	0.663	0.91
127_G	132_I	0.663	0.91
198_L	206_F	0.663	0.91
204_P	229_A	0.661	0.91
110_R	113_N	0.661	0.91
33_T	43_Q	0.659	0.90
212_L	226_I	0.658	0.90
171_P	181_A	0.656	0.90
153_F	158_F	0.655	0.90
31_A	71_A	0.654	0.90
150_I	154_L	0.652	0.90
35_V	79_A	0.650	0.90
104_L	107_I	0.647	0.90
12_G	144_G	0.647	0.90
3_Q	6_L	0.647	0.90
146_L	150_I	0.645	0.89
89_E	217_G	0.643	0.89
137_L	140_P	0.641	0.89
202_L	207_F	0.640	0.89
151_P	155_A	0.639	0.89
98_L	155_A	0.637	0.89
47_I	51_T	0.634	0.89
152_V	156_L	0.632	0.88
21_G	27_R	0.632	0.88
111_T	115_F	0.630	0.88
10_V	13_L	0.629	0.88
17_D	26_S	0.628	0.88
42_L	46_L	0.628	0.88
75_V	79_A	0.626	0.88
39_L	79_A	0.625	0.88
226_I	230_I	0.623	0.88
32_G	49_G	0.620	0.88
26_S	71_A	0.617	0.87
115_F	119_R	0.617	0.87
133_E	136_H	0.614	0.87
142_L	146_L	0.610	0.87
220_L	224_A	0.609	0.87
132_I	135_L	0.609	0.87
56_Y	70_A	0.607	0.86
3_Q	39_L	0.606	0.86
57_L	76_I	0.605	0.86
44_T	85_G	0.600	0.86
76_I	98_L	0.600	0.86
3_Q	7_I	0.598	0.86
13_L	17_D	0.598	0.86
22_Q	30_V	0.593	0.85
214_A	217_G	0.591	0.85
28_P	31_A	0.588	0.85
102_G	113_N	0.587	0.85
9_L	149_A	0.585	0.84
193_L	197_M	0.584	0.84
211_V	215_Y	0.583	0.84
113_N	116_F	0.582	0.84
83_L	156_L	0.581	0.84
219_P	225_I	0.579	0.84
140_P	146_L	0.577	0.84
94_L	97_P	0.574	0.83
151_P	154_L	0.574	0.83
117_V	121_D	0.573	0.83
119_R	126_E	0.573	0.83
212_L	218_L	0.573	0.83
14_A	25_L	0.571	0.83
113_N	144_G	0.571	0.83
56_Y	96_V	0.569	0.83
208_L	226_I	0.568	0.83
80_L	98_L	0.568	0.83
80_L	163_V	0.567	0.82
169_A	176_N	0.566	0.82
89_E	164_Q	0.564	0.82
26_S	31_A	0.563	0.82
207_F	211_V	0.563	0.82
150_I	200_K	0.562	0.82
171_P	174_L	0.561	0.82
120_A	131_G	0.560	0.82
20_L	55_I	0.558	0.81
69_D	103_Q	0.558	0.81
132_I	139_G	0.558	0.81
103_Q	107_I	0.557	0.81
135_L	138_L	0.554	0.81
178_L	181_A	0.553	0.81
32_G	52_L	0.553	0.81
65_A	110_R	0.552	0.81
56_Y	94_L	0.550	0.81
73_A	100_L	0.546	0.80
148_R	152_V	0.546	0.80
194_L	198_L	0.545	0.80
99_A	106_D	0.543	0.80
89_E	168_N	0.542	0.80
22_Q	61_P	0.541	0.79
39_L	44_T	0.537	0.79
22_Q	60_V	0.536	0.79
73_A	180_V	0.536	0.79
124_A	131_G	0.535	0.79
119_R	134_R	0.534	0.79
48_I	52_L	0.532	0.78
48_I	163_V	0.530	0.78
17_D	68_P	0.530	0.78
16_L	22_Q	0.529	0.78
9_L	55_I	0.527	0.78
21_G	46_L	0.527	0.78
161_D	168_N	0.526	0.78
217_G	222_A	0.525	0.77
157_Y	162_A	0.525	0.77
228_V	231_A	0.520	0.77
12_G	141_L	0.519	0.77
80_L	178_L	0.519	0.77
153_F	156_L	0.518	0.77
148_R	155_A	0.516	0.76
157_Y	166_L	0.516	0.76
68_P	75_V	0.516	0.76
214_A	222_A	0.514	0.76
19_L	22_Q	0.514	0.76
32_G	77_G	0.510	0.75
164_Q	172_A	0.510	0.75
72_L	152_V	0.508	0.75
38_I	106_D	0.507	0.75
20_L	23_F	0.507	0.75
135_L	220_L	0.507	0.75
33_T	45_G	0.507	0.75
127_G	136_H	0.507	0.75
221_I	225_I	0.504	0.75
192_M	197_M	0.504	0.75
218_L	229_A	0.504	0.75
146_L	151_P	0.503	0.74
68_P	188_V	0.503	0.74
64_G	68_P	0.502	0.74
74_G	77_G	0.502	0.74
17_D	23_F	0.500	0.74

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
3j1zP	8	0.7167	4	0.957	Contact Map
3qnqA	2	0.4764	2.5	0.962	Contact Map
2a9hA	4	0.3863	2.4	0.962	Contact Map
2vpbB	1	0.1502	2.4	0.962	Contact Map
3zpvB	2	0.1588	2.1	0.963	Contact Map
3tx3A	2	0.3734	1.7	0.965	Contact Map
4lz6A	1	0.7682	1.5	0.966	Contact Map
1jb0I	1	0.1631	1.5	0.966	Contact Map
4lh9A	4	0.1717	1.5	0.966	Contact Map
3o7qA	1	0.4206	1.4	0.966	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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