PXA - PFAM28P - GREMLIN Contacts

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PXA - PXA domain

PFAM:	PF02194	Sequences: PEVDAALDELLDLILRDFVLSWYSKISPDPEFPNEVRQTIRHALRELSQRLRKVDLVLLLTTRLVPLLTAHLRDFRQAEAAVRGKSVTESEELDLALASKYREGKLHPALSSKEAELAYLRLLVEGLLPLLLPPEDLESRPVRVLLREILACAVLLPVIDKLSDPDFINQLIVKLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (171)
Sequences:	1299 (947)
Seq/√Len:	72.4
META:	0.164

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_A	101_Y	3.741	1.00
15_L	19_V	3.391	1.00
125_E	147_R	3.183	1.00
97_L	101_Y	3.152	1.00
97_L	100_K	3.111	1.00
23_Y	27_S	3.096	1.00
13_L	16_R	3.039	1.00
104_G	107_H	2.809	1.00
166_D	169_N	2.750	1.00
98_A	102_R	2.661	1.00
121_R	148_E	2.288	1.00
158_V	163_S	2.152	1.00
136_D	142_V	2.108	1.00
162_L	171_L	2.051	1.00
104_G	108_P	2.050	1.00
124_V	155_L	2.003	1.00
167_F	171_L	1.982	1.00
94_D	98_A	1.956	1.00
148_E	169_N	1.953	1.00
112_S	116_E	1.915	1.00
3_V	7_L	1.883	1.00
125_E	143_R	1.858	1.00
132_L	137_L	1.845	1.00
127_L	131_L	1.824	1.00
148_E	152_C	1.821	1.00
162_L	167_F	1.758	1.00
23_Y	32_F	1.714	1.00
12_D	37_R	1.683	1.00
150_L	154_V	1.613	0.99
46_E	50_R	1.612	0.99
7_L	105_K	1.552	0.99
47_L	131_L	1.549	0.99
100_K	103_E	1.534	0.99
37_R	40_I	1.462	0.99
31_E	34_N	1.462	0.99
120_L	155_L	1.462	0.99
139_S	142_V	1.452	0.99
43_A	131_L	1.420	0.99
71_H	119_Y	1.413	0.99
169_N	173_V	1.409	0.98
8_D	41_R	1.407	0.98
43_A	142_V	1.340	0.98
32_F	36_V	1.337	0.98
112_S	134_P	1.334	0.98
153_A	157_P	1.334	0.98
142_V	145_L	1.333	0.98
8_D	12_D	1.314	0.98
10_L	17_D	1.310	0.98
9_E	13_L	1.299	0.97
124_V	127_L	1.287	0.97
103_E	154_V	1.272	0.97
94_D	97_L	1.260	0.97
99_S	102_R	1.258	0.97
114_E	159_I	1.256	0.97
92_E	96_A	1.256	0.97
4_D	8_D	1.248	0.97
14_I	154_V	1.245	0.97
35_E	38_Q	1.236	0.96
95_L	98_A	1.235	0.96
93_L	96_A	1.227	0.96
19_V	102_R	1.227	0.96
166_D	170_Q	1.217	0.96
26_I	164_D	1.217	0.96
73_R	136_D	1.195	0.96
59_L	64_L	1.184	0.96
13_L	17_D	1.170	0.95
15_L	33_P	1.153	0.95
105_K	108_P	1.152	0.95
11_L	40_I	1.151	0.95
96_A	102_R	1.141	0.95
91_E	95_L	1.134	0.94
92_E	97_L	1.129	0.94
102_R	106_L	1.129	0.94
76_R	97_L	1.125	0.94
75_F	79_E	1.117	0.94
91_E	94_D	1.093	0.93
117_L	121_R	1.089	0.93
79_E	82_V	1.075	0.93
92_E	99_S	1.071	0.92
20_L	33_P	1.068	0.92
21_S	25_K	1.063	0.92
3_V	65_V	1.056	0.92
76_R	136_D	1.055	0.92
81_A	113_K	1.053	0.92
71_H	75_F	1.051	0.92
104_G	109_A	1.032	0.91
78_A	111_S	1.010	0.90
12_D	40_I	0.993	0.89
45_R	48_S	0.986	0.89
112_S	126_G	0.985	0.89
4_D	10_L	0.982	0.89
6_A	10_L	0.979	0.89
155_L	158_V	0.975	0.88
5_A	19_V	0.974	0.88
168_I	172_I	0.970	0.88
92_E	95_L	0.959	0.88
136_D	139_S	0.957	0.87
66_P	69_T	0.955	0.87
97_L	102_R	0.948	0.87
31_E	99_S	0.945	0.87
123_L	133_P	0.938	0.86
90_S	93_L	0.936	0.86
95_L	100_K	0.936	0.86
94_D	100_K	0.932	0.86
158_V	161_K	0.923	0.85
70_A	103_E	0.920	0.85
68_L	154_V	0.919	0.85
90_S	94_D	0.918	0.85
43_A	60_L	0.918	0.85
96_A	101_Y	0.910	0.85
19_V	22_W	0.907	0.84
156_L	159_I	0.895	0.84
7_L	70_A	0.890	0.83
22_W	27_S	0.882	0.83
50_R	116_E	0.877	0.82
18_F	27_S	0.876	0.82
36_V	162_L	0.866	0.82
61_T	132_L	0.855	0.81
81_A	84_G	0.850	0.80
31_E	158_V	0.850	0.80
11_L	15_L	0.847	0.80
19_V	23_Y	0.841	0.80
124_V	150_L	0.833	0.79
46_E	131_L	0.832	0.79
24_S	28_P	0.831	0.79
90_S	95_L	0.822	0.78
164_D	169_N	0.819	0.78
101_Y	104_G	0.817	0.78
96_A	100_K	0.807	0.77
17_D	157_P	0.804	0.77
143_R	151_A	0.799	0.76
78_A	82_V	0.796	0.76
67_L	75_F	0.792	0.75
94_D	99_S	0.791	0.75
47_L	52_R	0.788	0.75
159_I	168_I	0.784	0.75
72_L	85_K	0.783	0.75
48_S	137_L	0.777	0.74
6_A	161_K	0.774	0.74
106_L	110_L	0.773	0.74
170_Q	173_V	0.770	0.73
95_L	99_S	0.768	0.73
143_R	147_R	0.754	0.72
93_L	98_A	0.751	0.72
21_S	29_D	0.741	0.71
114_E	158_V	0.739	0.70
18_F	22_W	0.736	0.70
10_L	134_P	0.735	0.70
99_S	103_E	0.729	0.69
62_T	159_I	0.725	0.69
98_A	105_K	0.723	0.69
13_L	163_S	0.715	0.68
50_R	130_L	0.714	0.68
73_R	127_L	0.712	0.67
20_L	24_S	0.708	0.67
19_V	46_E	0.706	0.67
79_E	98_A	0.706	0.67
13_L	18_F	0.705	0.67
63_R	66_P	0.697	0.66
18_F	21_S	0.683	0.64
145_L	149_I	0.680	0.64
22_W	29_D	0.680	0.64
6_A	69_T	0.672	0.63
11_L	20_L	0.672	0.63
128_L	132_L	0.668	0.63
39_T	136_D	0.667	0.62
95_L	101_Y	0.666	0.62
85_K	103_E	0.665	0.62
138_E	143_R	0.662	0.62
49_Q	108_P	0.661	0.62
68_L	80_A	0.660	0.62
42_H	47_L	0.658	0.61
105_K	151_A	0.658	0.61
11_L	41_R	0.653	0.61
53_K	138_E	0.652	0.61
77_Q	171_L	0.652	0.61
16_R	165_P	0.651	0.61
152_C	157_P	0.649	0.60
79_E	83_R	0.649	0.60
66_P	168_I	0.637	0.59
39_T	147_R	0.632	0.58
105_K	118_A	0.629	0.58
54_V	137_L	0.628	0.58
74_D	77_Q	0.619	0.57
68_L	108_P	0.614	0.56
103_E	159_I	0.613	0.56
93_L	101_Y	0.610	0.56
157_P	169_N	0.607	0.55
64_L	134_P	0.607	0.55
76_R	167_F	0.603	0.55
23_Y	60_L	0.597	0.54
81_A	135_E	0.597	0.54
135_E	158_V	0.596	0.54
51_L	54_V	0.590	0.53
151_A	160_D	0.588	0.53
158_V	162_L	0.587	0.53
4_D	11_L	0.582	0.52
3_V	6_A	0.580	0.52
32_F	141_P	0.578	0.52
27_S	156_L	0.577	0.52
153_A	168_I	0.576	0.51
65_V	167_F	0.575	0.51
60_L	163_S	0.573	0.51
115_A	172_I	0.568	0.50
109_A	119_Y	0.566	0.50
157_P	161_K	0.565	0.50
127_L	134_P	0.565	0.50
2_E	5_A	0.565	0.50
163_S	173_V	0.563	0.50
61_T	166_D	0.563	0.50
44_L	132_L	0.561	0.50
129_P	150_L	0.559	0.49
25_K	153_A	0.558	0.49
4_D	119_Y	0.552	0.49
16_R	78_A	0.551	0.48
85_K	96_A	0.549	0.48
55_D	67_L	0.547	0.48
61_T	66_P	0.545	0.48
12_D	60_L	0.545	0.48
17_D	148_E	0.543	0.47
74_D	78_A	0.542	0.47
15_L	36_V	0.541	0.47
19_V	161_K	0.540	0.47
80_A	150_L	0.540	0.47
5_A	52_R	0.539	0.47
47_L	111_S	0.536	0.47
124_V	151_A	0.535	0.46
93_L	97_L	0.532	0.46
71_H	146_L	0.532	0.46
55_D	70_A	0.528	0.46
26_I	154_V	0.527	0.45
53_K	127_L	0.526	0.45
167_F	174_K	0.525	0.45
59_L	65_V	0.525	0.45
83_R	173_V	0.524	0.45
66_P	79_E	0.524	0.45
14_I	125_E	0.523	0.45
121_R	166_D	0.517	0.44
130_L	134_P	0.517	0.44
40_I	147_R	0.514	0.44
73_R	118_A	0.514	0.44
74_D	81_A	0.510	0.43
9_E	12_D	0.510	0.43
66_P	107_H	0.509	0.43
34_N	160_D	0.508	0.43
35_E	119_Y	0.508	0.43
163_S	171_L	0.507	0.43
19_V	113_K	0.505	0.43
4_D	61_T	0.503	0.43
151_A	157_P	0.502	0.42
115_A	175_L	0.501	0.42
29_D	159_I	0.501	0.42
121_R	152_C	0.501	0.42
45_R	49_Q	0.500	0.42
50_R	132_L	0.500	0.42
136_D	143_R	0.500	0.42

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
2fji1	1	0.9773	9.6	0.934	Contact Map
3v3tA	1	0.0909	6.7	0.939	Contact Map
3r9rA	1	0.3409	6.2	0.94	Contact Map
2a7oA	1	0.5	3.9	0.945	Contact Map
2p7vA	1	0.5966	3.9	0.945	Contact Map
3o4zA	2	0.9375	3.8	0.945	Contact Map
1h3lA	1	0.4375	3.7	0.946	Contact Map
1fp3A	2	0.375	3	0.948	Contact Map
4qikA	2	0.8466	2.8	0.949	Contact Map
1vsy5	1	0.858	2.8	0.949	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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