PEX11 - PFAM28P - GREMLIN Contacts

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PEX11 - Peroxisomal biogenesis factor 11 (PEX11)

PFAM:	PF05648	Sequences: LDHLVKFLATTDGRDKLLRLLQYFSRLLAWYLLRTGASKELAARLKALESQLSLARKLLRLGKFLEHLQAARSALDSKPPDPVLRLLAVLRNLGYALYLFLDHIVWLAKAGLLKLKSAKKWSKWSARFWLLGLLLSLVRDLYELRRLREREKKLRKSLKEGEGKEEEKLRKLRKERRALLLQLVKNLCDLLIPLHWLGLLKLNPGVVGLAGLVSSLIGLYQLW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	223 (222)
Sequences:	1290 (972)
Seq/√Len:	65.2
META:	0.179

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_R	215_S	5.246	1.00
55_A	59_L	4.692	1.00
81_D	142_Y	3.592	1.00
30_W	205_G	3.561	1.00
151_E	176_R	3.284	1.00
181_L	217_I	3.166	1.00
95_Y	132_G	2.698	1.00
19_R	189_D	2.660	1.00
129_W	133_L	2.572	1.00
61_L	103_H	2.550	1.00
97_L	128_F	2.457	1.00
57_K	102_D	2.436	1.00
7_F	219_L	2.434	1.00
2_D	6_K	2.335	1.00
94_G	135_L	2.242	1.00
20_L	212_L	2.132	1.00
189_D	193_P	2.131	1.00
188_C	214_S	2.117	1.00
125_S	132_G	2.099	1.00
159_K	165_E	2.062	1.00
108_A	115_L	2.032	1.00
189_D	214_S	2.004	1.00
185_K	189_D	1.980	1.00
23_Y	211_G	1.931	1.00
20_L	24_F	1.875	1.00
21_L	52_L	1.805	1.00
43_A	47_A	1.805	1.00
99_L	103_H	1.796	1.00
64_F	103_H	1.776	1.00
90_L	135_L	1.771	1.00
57_K	105_V	1.753	1.00
19_R	214_S	1.706	0.99
100_F	103_H	1.697	0.99
57_K	63_K	1.697	0.99
124_W	127_R	1.691	0.99
106_W	110_A	1.681	0.99
195_H	200_L	1.651	0.99
206_V	210_A	1.647	0.99
48_L	112_L	1.637	0.99
147_L	172_L	1.631	0.99
133_L	193_P	1.617	0.99
67_H	99_L	1.594	0.99
103_H	106_W	1.584	0.99
107_L	113_L	1.579	0.99
57_K	110_A	1.571	0.99
203_N	206_V	1.551	0.99
163_G	166_E	1.538	0.99
144_L	176_R	1.521	0.99
144_L	183_L	1.498	0.99
47_A	51_Q	1.476	0.98
208_G	211_G	1.470	0.98
66_E	193_P	1.452	0.98
40_E	44_R	1.452	0.98
4_L	8_L	1.421	0.98
101_L	124_W	1.400	0.98
23_Y	57_K	1.378	0.97
16_K	26_R	1.369	0.97
6_K	10_T	1.366	0.97
84_L	88_A	1.366	0.97
102_D	110_A	1.362	0.97
64_F	100_F	1.344	0.97
192_I	196_W	1.326	0.97
214_S	217_I	1.321	0.97
123_K	127_R	1.314	0.97
105_V	122_S	1.309	0.97
10_T	13_G	1.305	0.97
204_P	208_G	1.275	0.96
130_L	197_L	1.261	0.96
212_L	216_L	1.258	0.96
39_K	43_A	1.253	0.96
140_D	179_L	1.248	0.95
101_L	121_W	1.212	0.95
40_E	43_A	1.199	0.94
68_L	112_L	1.194	0.94
102_D	185_K	1.185	0.94
58_L	106_W	1.175	0.94
160_E	163_G	1.163	0.93
11_T	14_R	1.138	0.93
133_L	136_S	1.138	0.93
185_K	214_S	1.133	0.93
166_E	173_R	1.125	0.92
142_Y	146_R	1.114	0.92
115_L	119_K	1.113	0.92
160_E	165_E	1.101	0.91
18_L	58_L	1.094	0.91
147_L	151_E	1.093	0.91
81_D	85_R	1.090	0.91
130_L	194_L	1.086	0.91
137_L	183_L	1.077	0.90
40_E	65_L	1.073	0.90
193_P	197_L	1.064	0.90
63_K	99_L	1.059	0.90
15_D	106_W	1.058	0.90
137_L	186_N	1.047	0.89
193_P	196_W	1.046	0.89
151_E	155_R	1.045	0.89
180_L	184_V	1.041	0.89
69_Q	73_S	1.035	0.89
129_W	193_P	1.034	0.89
181_L	220_Y	1.033	0.89
74_A	88_A	1.032	0.88
161_G	165_E	1.032	0.88
14_R	102_D	1.029	0.88
51_Q	58_L	1.023	0.88
98_Y	101_L	1.021	0.88
7_F	18_L	1.008	0.87
94_G	132_G	1.007	0.87
97_L	114_K	1.005	0.87
187_L	191_L	1.003	0.87
102_D	196_W	1.001	0.87
189_D	195_H	0.982	0.86
98_Y	208_G	0.981	0.86
18_L	52_L	0.978	0.86
161_G	164_K	0.977	0.86
164_K	168_K	0.964	0.85
132_G	135_L	0.961	0.85
71_A	182_Q	0.960	0.85
213_V	217_I	0.959	0.85
181_L	221_Q	0.957	0.84
61_L	68_L	0.955	0.84
67_H	92_N	0.946	0.84
126_A	196_W	0.942	0.83
86_L	90_L	0.938	0.83
8_L	214_S	0.930	0.83
139_R	143_E	0.929	0.83
26_R	49_E	0.927	0.82
19_R	197_L	0.920	0.82
106_W	210_A	0.918	0.82
160_E	164_K	0.918	0.82
137_L	141_L	0.917	0.82
87_L	139_R	0.913	0.82
55_A	104_I	0.911	0.81
186_N	192_I	0.906	0.81
57_K	211_G	0.901	0.81
182_Q	186_N	0.898	0.80
93_L	187_L	0.897	0.80
117_S	131_L	0.897	0.80
136_S	186_N	0.890	0.80
150_R	175_E	0.883	0.79
19_R	193_P	0.882	0.79
212_L	219_L	0.874	0.79
62_G	189_D	0.873	0.79
7_F	20_L	0.871	0.78
27_L	31_Y	0.869	0.78
136_S	214_S	0.865	0.78
140_D	186_N	0.864	0.78
82_P	86_L	0.862	0.78
91_R	95_Y	0.861	0.78
28_L	45_L	0.860	0.77
155_R	158_L	0.859	0.77
62_G	214_S	0.854	0.77
148_R	151_E	0.852	0.77
22_Q	57_K	0.850	0.77
94_G	202_L	0.848	0.76
71_A	128_F	0.840	0.76
60_R	98_Y	0.838	0.76
60_R	129_W	0.831	0.75
188_C	210_A	0.831	0.75
73_S	104_I	0.830	0.75
143_E	175_E	0.828	0.75
181_L	185_K	0.827	0.75
150_R	153_K	0.825	0.74
26_R	189_D	0.821	0.74
20_L	219_L	0.817	0.74
163_G	184_V	0.816	0.74
61_L	110_A	0.813	0.73
122_S	125_S	0.812	0.73
64_F	68_L	0.808	0.73
18_L	59_L	0.804	0.73
150_R	159_K	0.803	0.72
162_E	165_E	0.802	0.72
47_A	112_L	0.789	0.71
151_E	154_L	0.783	0.71
20_L	218_G	0.780	0.70
99_L	102_D	0.779	0.70
211_G	215_S	0.759	0.68
141_L	155_R	0.759	0.68
64_F	102_D	0.756	0.68
54_L	110_A	0.755	0.68
116_K	119_K	0.753	0.68
153_K	168_K	0.749	0.67
163_G	167_E	0.747	0.67
81_D	84_L	0.743	0.67
64_F	214_S	0.742	0.66
38_S	41_L	0.741	0.66
162_E	166_E	0.741	0.66
157_S	170_R	0.741	0.66
145_R	149_E	0.739	0.66
123_K	213_V	0.737	0.66
151_E	162_E	0.737	0.66
58_L	117_S	0.732	0.65
83_V	142_Y	0.732	0.65
71_A	96_A	0.731	0.65
49_E	57_K	0.730	0.65
101_L	135_L	0.729	0.65
192_I	207_V	0.729	0.65
190_L	214_S	0.728	0.65
133_L	186_N	0.726	0.65
95_Y	129_W	0.726	0.65
192_I	200_L	0.724	0.65
67_H	70_A	0.724	0.65
102_D	211_G	0.718	0.64
15_D	26_R	0.717	0.64
96_A	140_D	0.717	0.64
83_V	138_V	0.715	0.64
55_A	58_L	0.710	0.63
90_L	184_V	0.707	0.63
21_L	31_Y	0.706	0.63
121_W	143_E	0.696	0.61
27_L	209_L	0.696	0.61
67_H	95_Y	0.695	0.61
21_L	78_K	0.695	0.61
25_S	45_L	0.694	0.61
141_L	144_L	0.694	0.61
28_L	37_A	0.693	0.61
175_E	187_L	0.692	0.61
181_L	188_C	0.690	0.61
9_A	66_E	0.687	0.60
107_L	112_L	0.687	0.60
33_L	38_S	0.684	0.60
181_L	214_S	0.678	0.59
11_T	22_Q	0.672	0.59
186_N	197_L	0.672	0.59
199_L	211_G	0.672	0.59
2_D	212_L	0.666	0.58
146_R	150_R	0.662	0.58
122_S	126_A	0.661	0.58
105_V	109_K	0.661	0.58
68_L	96_A	0.660	0.57
68_L	93_L	0.660	0.57
16_K	63_K	0.659	0.57
182_Q	185_K	0.657	0.57
194_L	207_V	0.655	0.57
92_N	95_Y	0.651	0.56
168_K	172_L	0.650	0.56
45_L	97_L	0.648	0.56
22_Q	102_D	0.647	0.56
82_P	149_E	0.646	0.56
209_L	213_V	0.642	0.55
212_L	215_S	0.639	0.55
80_P	156_K	0.638	0.55
51_Q	64_F	0.637	0.55
96_A	215_S	0.635	0.55
45_L	209_L	0.633	0.54
45_L	61_L	0.632	0.54
54_L	62_G	0.632	0.54
141_L	152_K	0.632	0.54
7_F	16_K	0.631	0.54
103_H	130_L	0.627	0.54
151_E	172_L	0.622	0.53
16_K	218_G	0.621	0.53
65_L	150_R	0.614	0.52
58_L	91_R	0.613	0.52
71_A	92_N	0.613	0.52
95_Y	210_A	0.610	0.52
45_L	210_A	0.608	0.51
89_V	94_G	0.606	0.51
52_L	55_A	0.605	0.51
208_G	213_V	0.603	0.51
21_L	51_Q	0.602	0.51
63_K	100_F	0.601	0.51
160_E	167_E	0.600	0.50
63_K	67_H	0.599	0.50
159_K	164_K	0.598	0.50
37_A	42_A	0.597	0.50
159_K	162_E	0.596	0.50
54_L	188_C	0.593	0.50
65_L	210_A	0.593	0.50
15_D	20_L	0.593	0.50
92_N	99_L	0.592	0.49
57_K	126_A	0.590	0.49
152_K	164_K	0.590	0.49
84_L	143_E	0.588	0.49
126_A	132_G	0.587	0.49
149_E	160_E	0.585	0.49
98_Y	103_H	0.583	0.48
46_K	50_S	0.581	0.48
71_A	127_R	0.579	0.48
174_K	178_A	0.576	0.48
132_G	189_D	0.572	0.47
191_L	210_A	0.571	0.47
191_L	212_L	0.569	0.47
160_E	168_K	0.568	0.47
88_A	91_R	0.564	0.46
64_F	67_H	0.563	0.46
40_E	174_K	0.561	0.46
20_L	23_Y	0.556	0.45
14_R	19_R	0.553	0.45
24_F	27_L	0.551	0.45
219_L	222_L	0.551	0.45
94_G	186_N	0.550	0.45
28_L	31_Y	0.547	0.44
78_K	168_K	0.540	0.43
12_D	19_R	0.538	0.43
70_A	100_F	0.537	0.43
130_L	193_P	0.536	0.43
28_L	38_S	0.535	0.43
199_L	212_L	0.535	0.43
102_D	194_L	0.534	0.43
26_R	102_D	0.534	0.43
22_Q	56_R	0.532	0.43
14_R	215_S	0.530	0.42
50_S	53_S	0.529	0.42
198_G	207_V	0.529	0.42
108_A	215_S	0.529	0.42
76_D	79_P	0.528	0.42
154_L	209_L	0.528	0.42
152_K	157_S	0.527	0.42
14_R	23_Y	0.527	0.42
98_Y	114_K	0.526	0.42
54_L	214_S	0.526	0.42
144_L	180_L	0.526	0.42
29_A	33_L	0.525	0.42
51_Q	62_G	0.524	0.42
88_A	218_G	0.524	0.42
120_K	125_S	0.524	0.42
100_F	109_K	0.523	0.41
99_L	106_W	0.521	0.41
61_L	106_W	0.519	0.41
106_W	121_W	0.518	0.41
186_N	198_G	0.516	0.41
156_K	159_K	0.515	0.41
98_Y	192_I	0.514	0.40
101_L	130_L	0.512	0.40
87_L	152_K	0.511	0.40
128_F	220_Y	0.511	0.40
88_A	139_R	0.508	0.40
157_S	160_E	0.506	0.40
159_K	202_L	0.504	0.39
59_L	129_W	0.504	0.39
115_L	118_A	0.503	0.39
76_D	102_D	0.501	0.39
13_G	23_Y	0.500	0.39

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
2a9hA	4	0.3543	7.3	0.945	Contact Map
3g43E	2	0.278	4	0.951	Contact Map
4opcA	1	0.3408	3.6	0.952	Contact Map
4i77Z	1	0.2646	2.6	0.956	Contact Map
2kmfA	1	0.2825	2.5	0.956	Contact Map
3lk5A	2	0.2422	2.3	0.957	Contact Map
1xkpA	1	0.2332	2.1	0.958	Contact Map
2bgcA	2	0.4843	1.9	0.958	Contact Map
1wmwA	2	0.2825	1.9	0.959	Contact Map
3mk4A	1	0.3812	1.8	0.959	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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