YtxC - PFAM28P - GREMLIN Contacts

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YtxC - YtxC-like family

PFAM:	PF08812	Sequences: HYIANALADYIIEEYEKKLLRKIIRKNYFYFDEEEREEILEIALSILNGEKGEDEDSLYRINRKNKILEKILEYLEENNELNLDGFIRFRLKEYLEELEEIVDKAVDEYLMEKEYQEFIKLLRYFVDIQEPKIDEVHVVIKGDGEFILLDENGNPITNELLEEFDAELSDIEINYEDLLISALITLAPKKIIIHTDEPEEPKELIETIKNVFEERVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	217 (215)
Sequences:	1213 (1005)
Seq/√Len:	68.5
META:	0.617

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_E	63_R	5.310	1.00
16_E	94_Y	4.972	1.00
208_I	216_V	4.189	1.00
7_L	71_I	4.083	1.00
150_D	154_N	3.799	1.00
70_K	93_E	3.510	1.00
193_I	205_I	3.405	1.00
24_I	40_L	3.316	1.00
67_I	91_L	3.204	1.00
94_Y	98_L	2.824	1.00
124_Y	184_I	2.747	1.00
24_I	102_V	2.681	1.00
20_L	43_A	2.578	1.00
134_D	151_E	2.571	1.00
135_E	190_K	2.471	1.00
11_I	71_I	2.247	1.00
137_H	194_H	2.245	1.00
124_Y	181_S	2.219	1.00
31_F	39_I	2.192	1.00
9_D	64_K	2.182	1.00
43_A	105_A	2.117	1.00
135_E	192_I	2.107	1.00
139_V	149_L	2.053	1.00
123_R	213_E	2.026	1.00
125_F	129_Q	1.973	1.00
103_D	106_V	1.883	1.00
46_I	105_A	1.827	1.00
63_R	94_Y	1.817	1.00
28_Y	106_V	1.789	1.00
138_V	179_L	1.782	1.00
114_E	211_V	1.735	1.00
138_V	193_I	1.725	1.00
99_E	102_V	1.721	1.00
85_G	117_E	1.637	0.99
28_Y	103_D	1.623	0.99
8_A	68_L	1.601	0.99
7_L	83_L	1.540	0.99
25_R	36_R	1.539	0.99
137_H	153_G	1.517	0.99
85_G	194_H	1.513	0.99
124_Y	129_Q	1.471	0.99
23_I	98_L	1.470	0.99
20_L	40_L	1.464	0.99
23_I	102_V	1.448	0.98
172_E	177_D	1.442	0.98
125_F	181_S	1.442	0.98
134_D	189_K	1.406	0.98
118_F	181_S	1.402	0.98
161_L	178_L	1.391	0.98
10_Y	137_H	1.367	0.98
21_R	40_L	1.343	0.97
131_P	189_K	1.335	0.97
178_L	181_S	1.324	0.97
198_P	201_P	1.310	0.97
124_Y	128_I	1.279	0.97
52_G	56_D	1.279	0.97
74_Y	81_L	1.249	0.96
173_I	180_I	1.244	0.96
3_I	46_I	1.242	0.96
46_I	191_I	1.239	0.96
136_V	150_D	1.217	0.95
42_I	109_Y	1.202	0.95
118_F	122_L	1.198	0.95
207_T	211_V	1.187	0.95
30_Y	106_V	1.177	0.95
87_I	91_L	1.169	0.94
9_D	13_E	1.146	0.94
137_H	192_I	1.142	0.94
175_Y	179_L	1.140	0.94
30_Y	39_I	1.139	0.94
67_I	71_I	1.134	0.93
49_G	56_D	1.119	0.93
113_K	121_L	1.114	0.93
8_A	16_E	1.106	0.93
115_Y	207_T	1.104	0.92
74_Y	78_N	1.091	0.92
139_V	189_K	1.083	0.92
117_E	177_D	1.076	0.91
71_I	144_G	1.075	0.91
119_I	207_T	1.069	0.91
46_I	123_R	1.068	0.91
177_D	181_S	1.062	0.91
33_E	37_E	1.057	0.91
135_E	151_E	1.055	0.91
146_F	179_L	1.039	0.90
121_L	194_H	1.035	0.90
46_I	108_E	1.032	0.90
85_G	177_D	1.031	0.90
49_G	54_D	1.026	0.89
30_Y	107_D	1.025	0.89
117_E	121_L	1.025	0.89
24_I	67_I	1.023	0.89
183_L	191_I	1.023	0.89
27_N	30_Y	1.022	0.89
126_V	216_V	1.021	0.89
50_E	56_D	1.017	0.89
181_S	184_I	1.013	0.89
45_S	201_P	1.013	0.89
69_E	73_E	1.007	0.89
206_E	209_K	1.007	0.89
138_V	205_I	0.988	0.88
107_D	204_L	0.986	0.87
43_A	145_E	0.986	0.87
74_Y	86_F	0.984	0.87
176_E	181_S	0.973	0.87
136_V	156_I	0.965	0.86
96_E	154_N	0.963	0.86
69_E	136_V	0.962	0.86
4_A	72_L	0.962	0.86
106_V	110_L	0.951	0.86
80_E	123_R	0.948	0.85
38_E	102_V	0.947	0.85
85_G	90_R	0.939	0.85
129_Q	185_T	0.932	0.84
117_E	194_H	0.931	0.84
182_A	194_H	0.930	0.84
53_E	56_D	0.929	0.84
188_P	191_I	0.928	0.84
68_L	72_L	0.921	0.84
33_E	96_E	0.920	0.84
28_Y	31_F	0.918	0.83
120_K	124_Y	0.914	0.83
168_L	173_I	0.910	0.83
106_V	109_Y	0.909	0.83
74_Y	204_L	0.903	0.82
177_D	185_T	0.901	0.82
7_L	36_R	0.900	0.82
82_N	153_G	0.899	0.82
83_L	189_K	0.897	0.82
118_F	207_T	0.883	0.81
118_F	125_F	0.883	0.81
70_K	86_F	0.881	0.81
11_I	19_L	0.879	0.81
177_D	194_H	0.879	0.81
128_I	185_T	0.873	0.80
85_G	121_L	0.873	0.80
24_I	74_Y	0.869	0.80
117_E	184_I	0.868	0.80
19_L	94_Y	0.866	0.80
58_L	193_I	0.860	0.79
8_A	77_E	0.860	0.79
46_I	214_E	0.851	0.79
185_T	207_T	0.847	0.78
16_E	75_L	0.833	0.77
160_L	176_E	0.833	0.77
71_I	125_F	0.830	0.77
145_E	151_E	0.820	0.76
50_E	53_E	0.818	0.76
3_I	139_V	0.818	0.76
36_R	95_L	0.817	0.76
47_L	94_Y	0.815	0.75
104_K	108_E	0.809	0.75
121_L	129_Q	0.804	0.74
13_E	191_I	0.802	0.74
24_I	28_Y	0.796	0.74
7_L	67_I	0.792	0.73
15_Y	204_L	0.790	0.73
5_N	68_L	0.788	0.73
140_I	195_T	0.786	0.73
19_L	74_Y	0.786	0.73
107_D	111_M	0.783	0.72
153_G	211_V	0.780	0.72
195_T	199_E	0.780	0.72
97_E	121_L	0.777	0.72
172_E	181_S	0.770	0.71
163_E	167_E	0.768	0.71
25_R	38_E	0.766	0.71
124_Y	130_E	0.765	0.71
118_F	121_L	0.764	0.71
35_E	38_E	0.764	0.71
8_A	97_E	0.762	0.70
10_Y	20_L	0.759	0.70
83_L	162_E	0.759	0.70
7_L	15_Y	0.755	0.70
94_Y	194_H	0.750	0.69
39_I	98_L	0.748	0.69
129_Q	181_S	0.746	0.69
210_N	213_E	0.746	0.69
141_K	210_N	0.737	0.68
98_L	139_V	0.730	0.67
40_L	211_V	0.729	0.67
96_E	130_E	0.724	0.67
63_R	97_E	0.722	0.66
195_T	203_E	0.721	0.66
143_D	193_I	0.717	0.66
207_T	215_R	0.715	0.66
31_F	107_D	0.711	0.65
49_G	52_G	0.710	0.65
134_D	156_I	0.703	0.64
85_G	125_F	0.702	0.64
161_L	179_L	0.700	0.64
123_R	176_E	0.700	0.64
188_P	212_F	0.699	0.64
116_Q	203_E	0.698	0.64
119_I	211_V	0.697	0.64
20_L	102_V	0.696	0.63
170_D	174_N	0.694	0.63
12_I	101_I	0.689	0.63
48_N	133_I	0.687	0.62
121_L	181_S	0.685	0.62
82_N	176_E	0.684	0.62
95_L	136_V	0.683	0.62
76_E	87_I	0.683	0.62
7_L	81_L	0.681	0.62
7_L	62_N	0.676	0.61
124_Y	185_T	0.675	0.61
149_L	153_G	0.672	0.61
146_F	211_V	0.670	0.61
17_K	199_E	0.667	0.60
4_A	21_R	0.667	0.60
77_E	138_V	0.667	0.60
71_I	192_I	0.661	0.59
193_I	209_K	0.659	0.59
109_Y	207_T	0.659	0.59
81_L	86_F	0.658	0.59
51_K	55_E	0.657	0.59
205_I	211_V	0.654	0.59
209_K	214_E	0.649	0.58
38_E	41_E	0.643	0.57
22_K	87_I	0.642	0.57
117_E	122_L	0.642	0.57
28_Y	118_F	0.639	0.57
41_E	147_I	0.638	0.57
171_I	179_L	0.636	0.57
44_L	109_Y	0.635	0.56
85_G	181_S	0.633	0.56
116_Q	210_N	0.631	0.56
118_F	184_I	0.628	0.56
36_R	150_D	0.628	0.56
28_Y	35_E	0.625	0.55
123_R	214_E	0.623	0.55
49_G	57_S	0.620	0.55
21_R	37_E	0.616	0.54
11_I	22_K	0.616	0.54
27_N	73_E	0.615	0.54
85_G	89_F	0.614	0.54
99_E	103_D	0.613	0.54
123_R	205_I	0.613	0.54
78_N	190_K	0.612	0.54
84_D	123_R	0.609	0.53
58_L	78_N	0.609	0.53
182_A	201_P	0.608	0.53
3_I	191_I	0.607	0.53
122_L	207_T	0.602	0.53
104_K	208_I	0.602	0.53
92_K	136_V	0.601	0.52
9_D	84_D	0.599	0.52
133_I	215_R	0.598	0.52
181_S	185_T	0.596	0.52
115_Y	118_F	0.595	0.52
26_K	92_K	0.594	0.52
161_L	176_E	0.591	0.51
163_E	166_A	0.591	0.51
181_S	187_A	0.591	0.51
35_E	51_K	0.589	0.51
140_I	146_F	0.588	0.51
51_K	56_D	0.588	0.51
15_Y	180_I	0.587	0.51
124_Y	180_I	0.585	0.50
122_L	211_V	0.583	0.50
117_E	129_Q	0.580	0.50
106_V	162_E	0.580	0.50
107_D	180_I	0.575	0.49
126_V	163_E	0.575	0.49
80_E	83_L	0.573	0.49
115_Y	126_V	0.572	0.49
33_E	106_V	0.566	0.48
84_D	88_R	0.566	0.48
17_K	84_D	0.564	0.48
122_L	129_Q	0.564	0.48
19_L	95_L	0.563	0.48
103_D	214_E	0.563	0.48
151_E	154_N	0.562	0.48
16_E	98_L	0.561	0.48
106_V	207_T	0.557	0.47
156_I	177_D	0.555	0.47
167_E	171_I	0.555	0.47
2_Y	5_N	0.554	0.47
206_E	214_E	0.552	0.47
17_K	44_L	0.551	0.46
64_K	97_E	0.550	0.46
74_Y	85_G	0.550	0.46
96_E	151_E	0.549	0.46
8_A	12_I	0.548	0.46
50_E	54_D	0.547	0.46
58_L	173_I	0.546	0.46
111_M	201_P	0.545	0.46
41_E	156_I	0.545	0.46
49_G	55_E	0.544	0.46
98_L	189_K	0.543	0.45
138_V	209_K	0.536	0.45
116_Q	120_K	0.535	0.44
131_P	187_A	0.534	0.44
66_K	101_I	0.526	0.43
63_R	208_I	0.525	0.43
162_E	211_V	0.524	0.43
21_R	36_R	0.523	0.43
186_L	195_T	0.520	0.43
132_K	213_E	0.519	0.43
2_Y	6_A	0.519	0.43
24_I	82_N	0.519	0.43
129_Q	187_A	0.517	0.42
37_E	152_N	0.516	0.42
145_E	175_Y	0.514	0.42
6_A	127_D	0.513	0.42
49_G	84_D	0.513	0.42
72_L	76_E	0.512	0.42
101_I	120_K	0.510	0.42
147_I	155_P	0.509	0.41
13_E	151_E	0.508	0.41
6_A	10_Y	0.507	0.41
90_R	114_E	0.506	0.41
115_Y	132_K	0.506	0.41
54_D	156_I	0.506	0.41
57_S	68_L	0.505	0.41
35_E	109_Y	0.505	0.41
109_Y	113_K	0.503	0.41
167_E	178_L	0.502	0.41
205_I	208_I	0.502	0.41
196_D	205_I	0.501	0.41
99_E	123_R	0.500	0.40
11_I	177_D	0.500	0.40

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
4peoA	2	0.4009	6.5	0.954	Contact Map
1tm9A	1	0.2673	4.1	0.958	Contact Map
3s44A	1	0.4286	3.8	0.959	Contact Map
3o1fA	1	0.1429	3.8	0.959	Contact Map
3mmiA	2	0.3041	3.1	0.96	Contact Map
1a0cA	4	0.3502	2.8	0.961	Contact Map
2adlA	2	0.2995	2.8	0.961	Contact Map
3j3wT	1	0.212	2.6	0.962	Contact Map
2hyvA	1	0.2903	2.6	0.962	Contact Map
4d2uA	3	0.5668	2.4	0.962	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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