Pex2_Pex12 - PFAM28P - GREMLIN Contacts

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Pex2_Pex12 - Pex2 / Pex12 amino terminal region

PFAM:	PF04757	Sequences: DEELLSLLRPQLRYVLRVLAGARLPLLNWFDEIYLLLDLLYERLTLLSGNATLGEEYYGLKRVDAPSDSPTGRPLSRRQRLLYLLLLVLLPYLKAKLLDLLEARERLREEDLSDLSRSWRERLKSRLRRRLLKLYPSLNSLYELAALHLALFYLNGRYYSLSKRLLGIRYVRLTPQDPARSERRVSYELNRQLVWHAFTELLGFLLPLLLASIFFLKFLEWWYSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	225 (207)
Sequences:	1395 (965)
Seq/√Len:	67.1
META:	0.143

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_E	92_Y	6.646	1.00
92_Y	96_K	3.690	1.00
29_W	32_E	3.256	1.00
52_T	87_L	3.145	1.00
213_I	221_W	2.459	1.00
189_L	193_L	2.409	1.00
194_V	197_A	2.260	1.00
41_Y	51_A	2.098	1.00
190_N	194_V	2.091	1.00
201_L	204_F	2.086	1.00
32_E	96_K	2.082	1.00
149_L	164_R	2.040	1.00
35_L	88_V	2.024	1.00
46_L	62_R	1.976	1.00
43_R	47_L	1.901	1.00
192_Q	195_W	1.882	1.00
191_R	195_W	1.864	1.00
202_L	205_L	1.850	1.00
191_R	194_V	1.836	1.00
162_S	166_L	1.821	1.00
130_R	134_L	1.806	1.00
35_L	92_Y	1.781	1.00
31_D	96_K	1.770	1.00
215_F	218_F	1.761	1.00
55_E	159_Y	1.749	1.00
189_L	192_Q	1.744	1.00
190_N	197_A	1.700	0.99
76_S	79_Q	1.674	0.99
62_R	163_K	1.671	0.99
107_L	114_D	1.637	0.99
215_F	221_W	1.628	0.99
159_Y	163_K	1.591	0.99
192_Q	196_H	1.579	0.99
55_E	153_Y	1.578	0.99
214_F	219_L	1.577	0.99
63_V	171_V	1.571	0.99
158_Y	164_R	1.561	0.99
188_E	206_L	1.550	0.99
6_S	15_V	1.527	0.99
55_E	58_Y	1.504	0.99
119_W	122_R	1.502	0.99
218_F	221_W	1.497	0.99
83_Y	87_L	1.465	0.98
192_Q	197_A	1.461	0.98
194_V	199_T	1.448	0.98
191_R	196_H	1.448	0.98
4_L	7_L	1.426	0.98
214_F	218_F	1.419	0.98
192_Q	199_T	1.415	0.98
53_L	58_Y	1.412	0.98
51_A	55_E	1.399	0.98
46_L	51_A	1.398	0.98
53_L	94_K	1.384	0.98
210_L	214_F	1.377	0.98
82_L	86_L	1.373	0.98
21_G	24_L	1.371	0.98
42_E	62_R	1.358	0.97
189_L	196_H	1.353	0.97
21_G	25_P	1.342	0.97
115_L	118_S	1.341	0.97
217_K	221_W	1.338	0.97
197_A	203_G	1.327	0.97
88_V	147_L	1.305	0.97
61_K	177_D	1.300	0.97
82_L	166_L	1.289	0.97
190_N	193_L	1.288	0.97
191_R	197_A	1.286	0.97
213_I	217_K	1.277	0.96
163_K	170_Y	1.250	0.96
85_L	89_L	1.234	0.96
115_L	120_R	1.233	0.96
190_N	195_W	1.220	0.95
214_F	221_W	1.218	0.95
196_H	200_E	1.188	0.95
129_R	133_K	1.187	0.95
217_K	220_E	1.186	0.94
209_L	212_S	1.185	0.94
195_W	198_F	1.182	0.94
115_L	119_W	1.177	0.94
131_L	135_Y	1.173	0.94
193_L	200_E	1.173	0.94
86_L	166_L	1.167	0.94
190_N	200_E	1.157	0.94
7_L	11_Q	1.155	0.94
31_D	35_L	1.136	0.93
67_S	72_G	1.134	0.93
118_S	122_R	1.115	0.92
10_P	14_Y	1.106	0.92
148_H	152_F	1.098	0.92
201_L	207_P	1.094	0.92
193_L	196_H	1.092	0.92
75_L	78_R	1.090	0.92
10_P	18_V	1.085	0.91
194_V	200_E	1.085	0.91
50_N	61_K	1.082	0.91
189_L	195_W	1.081	0.91
124_K	127_L	1.078	0.91
196_H	199_T	1.071	0.91
152_F	156_G	1.062	0.90
55_E	62_R	1.059	0.90
35_L	38_D	1.052	0.90
74_P	144_L	1.044	0.90
51_A	86_L	1.041	0.90
31_D	62_R	1.031	0.89
141_L	165_L	1.031	0.89
29_W	97_L	1.022	0.89
214_F	217_K	1.020	0.89
116_S	119_W	1.016	0.88
210_L	213_I	1.011	0.88
185_V	188_E	1.006	0.88
2_E	14_Y	1.001	0.88
122_R	126_R	0.998	0.88
193_L	198_F	0.994	0.87
36_L	151_L	0.983	0.87
203_G	207_P	0.980	0.87
42_E	83_Y	0.978	0.86
190_N	198_F	0.974	0.86
9_R	17_R	0.966	0.86
146_A	150_A	0.964	0.86
133_K	137_S	0.960	0.85
195_W	199_T	0.959	0.85
193_L	197_A	0.949	0.85
8_L	15_V	0.946	0.85
36_L	93_L	0.945	0.85
20_A	23_R	0.943	0.84
214_F	222_W	0.942	0.84
83_Y	168_I	0.940	0.84
198_F	203_G	0.938	0.84
199_T	202_L	0.938	0.84
62_R	83_Y	0.937	0.84
122_R	147_L	0.931	0.84
153_Y	159_Y	0.930	0.84
196_H	202_L	0.920	0.83
6_S	10_P	0.918	0.83
42_E	45_T	0.909	0.82
120_R	123_L	0.908	0.82
210_L	217_K	0.906	0.82
39_L	43_R	0.906	0.82
52_T	159_Y	0.903	0.82
118_S	121_E	0.902	0.82
189_L	197_A	0.898	0.81
96_K	161_L	0.887	0.81
199_T	203_G	0.879	0.80
39_L	84_L	0.876	0.80
32_E	90_L	0.874	0.80
45_T	57_Y	0.869	0.79
71_T	77_R	0.866	0.79
191_R	200_E	0.866	0.79
89_L	122_R	0.863	0.79
131_L	137_S	0.860	0.78
212_S	219_L	0.859	0.78
192_Q	203_G	0.855	0.78
191_R	208_L	0.853	0.78
29_W	92_Y	0.852	0.78
58_Y	163_K	0.851	0.78
7_L	10_P	0.841	0.77
108_R	114_D	0.839	0.77
68_D	72_G	0.830	0.76
100_L	137_S	0.826	0.76
75_L	80_R	0.826	0.76
204_F	207_P	0.818	0.75
190_N	203_G	0.817	0.75
41_Y	152_F	0.815	0.75
195_W	200_E	0.815	0.75
192_Q	198_F	0.810	0.74
127_L	130_R	0.806	0.74
116_S	120_R	0.803	0.74
152_F	155_N	0.801	0.73
42_E	46_L	0.800	0.73
116_S	123_L	0.799	0.73
216_L	221_W	0.795	0.73
190_N	199_T	0.794	0.73
31_D	147_L	0.794	0.73
173_L	177_D	0.792	0.73
55_E	192_Q	0.792	0.73
40_L	169_R	0.784	0.72
76_S	123_L	0.781	0.71
219_L	222_W	0.779	0.71
12_L	33_I	0.777	0.71
2_E	11_Q	0.775	0.71
149_L	161_L	0.770	0.70
16_L	19_L	0.767	0.70
51_A	56_E	0.766	0.70
216_L	222_W	0.766	0.70
58_Y	62_R	0.765	0.70
193_L	199_T	0.758	0.69
66_P	70_P	0.756	0.69
42_E	101_L	0.756	0.69
97_L	160_S	0.752	0.69
14_Y	18_V	0.750	0.68
52_T	178_P	0.748	0.68
119_W	123_L	0.746	0.68
212_S	215_F	0.739	0.67
9_R	93_L	0.735	0.67
76_S	80_R	0.734	0.67
34_Y	161_L	0.734	0.67
66_P	72_G	0.733	0.67
146_A	161_L	0.730	0.66
83_Y	163_K	0.730	0.66
14_Y	136_P	0.723	0.66
149_L	158_Y	0.721	0.65
120_R	133_K	0.720	0.65
56_E	162_S	0.717	0.65
45_T	80_R	0.717	0.65
126_R	130_R	0.714	0.65
41_Y	201_L	0.708	0.64
121_E	128_R	0.705	0.64
158_Y	169_R	0.705	0.64
50_N	70_P	0.703	0.63
75_L	79_Q	0.702	0.63
3_E	7_L	0.698	0.63
97_L	131_L	0.697	0.63
9_R	95_A	0.697	0.63
82_L	169_R	0.696	0.63
202_L	208_L	0.693	0.62
55_E	83_Y	0.691	0.62
132_L	135_Y	0.689	0.62
195_W	207_P	0.688	0.62
153_Y	158_Y	0.687	0.62
116_S	122_R	0.684	0.61
120_R	124_K	0.680	0.61
1_D	54_G	0.678	0.61
117_R	122_R	0.675	0.60
210_L	220_E	0.673	0.60
115_L	123_L	0.670	0.60
192_Q	200_E	0.666	0.59
45_T	56_E	0.664	0.59
13_R	25_P	0.663	0.59
46_L	84_L	0.663	0.59
215_F	219_L	0.662	0.59
74_P	80_R	0.661	0.59
14_Y	132_L	0.644	0.57
19_L	23_R	0.642	0.56
51_A	163_K	0.642	0.56
85_L	93_L	0.640	0.56
135_Y	139_N	0.639	0.56
131_L	165_L	0.638	0.56
189_L	200_E	0.637	0.56
45_T	49_G	0.636	0.56
89_L	208_L	0.627	0.55
69_S	72_G	0.626	0.55
125_S	130_R	0.624	0.54
12_L	60_L	0.622	0.54
37_L	148_H	0.621	0.54
162_S	168_I	0.621	0.54
189_L	198_F	0.616	0.53
215_F	222_W	0.615	0.53
191_R	198_F	0.615	0.53
46_L	91_P	0.615	0.53
194_V	198_F	0.613	0.53
127_L	139_N	0.596	0.51
108_R	117_R	0.596	0.51
42_E	59_G	0.595	0.51
160_S	163_K	0.595	0.51
6_S	22_A	0.593	0.51
7_L	12_L	0.592	0.51
32_E	60_L	0.584	0.50
16_L	217_K	0.583	0.49
22_A	25_P	0.583	0.49
146_A	160_S	0.582	0.49
189_L	194_V	0.573	0.48
14_Y	101_L	0.573	0.48
32_E	39_L	0.572	0.48
2_E	19_L	0.572	0.48
84_L	88_V	0.566	0.47
212_S	217_K	0.566	0.47
116_S	125_S	0.560	0.47
143_E	153_Y	0.557	0.46
132_L	137_S	0.555	0.46
29_W	38_D	0.550	0.46
117_R	120_R	0.550	0.46
41_Y	56_E	0.550	0.46
133_K	167_G	0.549	0.45
14_Y	151_L	0.546	0.45
118_S	123_L	0.542	0.45
132_L	139_N	0.539	0.44
101_L	131_L	0.537	0.44
131_L	139_N	0.534	0.44
55_E	163_K	0.534	0.44
67_S	70_P	0.534	0.44
53_L	214_F	0.533	0.44
197_A	202_L	0.532	0.43
124_K	138_L	0.531	0.43
54_G	164_R	0.529	0.43
211_A	216_L	0.529	0.43
135_Y	138_L	0.529	0.43
13_R	93_L	0.524	0.43
83_Y	153_Y	0.524	0.43
76_S	85_L	0.524	0.43
114_D	198_F	0.522	0.42
37_L	170_Y	0.522	0.42
44_L	53_L	0.521	0.42
187_Y	200_E	0.520	0.42
4_L	16_L	0.518	0.42
90_L	201_L	0.518	0.42
69_S	118_S	0.516	0.42
126_R	131_L	0.516	0.42
95_A	151_L	0.513	0.41
33_I	85_L	0.513	0.41
30_F	38_D	0.512	0.41
41_Y	193_L	0.506	0.40
118_S	125_S	0.506	0.40
153_Y	195_W	0.506	0.40
53_L	163_K	0.506	0.40
107_L	125_S	0.505	0.40
76_S	138_L	0.503	0.40
190_N	201_L	0.502	0.40
51_A	62_R	0.501	0.40
49_G	80_R	0.501	0.40
85_L	127_L	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
1l8kA	1	0.2	2.6	0.956	Contact Map
5bu6A	2	0.3067	1.5	0.962	Contact Map
2ce7A	3	0.2356	1.4	0.962	Contact Map
3kalA	2	0.3556	1.3	0.963	Contact Map
4ww0A	4	0.2356	1.3	0.963	Contact Map
2kmtA	2	0.1644	1.3	0.963	Contact Map
4q9hA	1	0.2711	1.3	0.963	Contact Map
2di4A	3	0.2667	1.2	0.963	Contact Map
4m8nA	2	0.2889	1.2	0.964	Contact Map
3vubA	2	0.1644	1.1	0.965	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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