PRA1 - PFAM28P - GREMLIN Contacts

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PRA1 - PRA1 family protein

PFAM:	PF03208	Sequences: RLAPLRPWSEFFDRSRFSKPASFSEATSRVRYNLSYFRTNYALVFLLLLALSLLTNPLSLIVLLLLVAAWLFLYFLRDEPLVIFGRRFSDRQVLTGLLVVTVVLLFLTSVGSTLLWALGASLVLVLLHAAFRDPEDLFLDEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	142 (139)
Sequences:	1489 (1029)
Seq/√Len:	87.2
META:	0.233

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_V	130_A	2.859	1.00
36_Y	40_N	2.710	1.00
26_A	130_A	2.579	1.00
37_F	133_D	2.543	1.00
82_V	85_G	2.353	1.00
48_L	124_L	2.346	1.00
41_Y	128_H	2.325	1.00
121_S	125_V	2.295	1.00
100_V	103_V	2.287	1.00
137_L	140_D	2.276	1.00
127_L	131_F	2.257	1.00
6_R	36_Y	2.123	1.00
11_F	14_R	2.103	1.00
45_F	121_S	1.914	1.00
40_N	132_R	1.889	1.00
5_L	43_L	1.849	1.00
46_L	113_T	1.840	1.00
7_P	10_E	1.750	1.00
17_F	132_R	1.714	1.00
23_F	119_G	1.685	1.00
40_N	57_P	1.654	1.00
37_F	132_R	1.612	1.00
51_L	116_W	1.608	1.00
49_L	117_A	1.562	1.00
70_W	97_L	1.519	1.00
109_S	112_S	1.510	1.00
10_E	23_F	1.472	0.99
36_Y	132_R	1.466	0.99
92_Q	104_L	1.462	0.99
135_E	140_D	1.461	0.99
37_F	136_D	1.434	0.99
95_T	98_L	1.428	0.99
60_L	117_A	1.405	0.99
70_W	73_L	1.385	0.99
112_S	119_G	1.382	0.99
49_L	55_T	1.371	0.99
60_L	68_A	1.358	0.99
17_F	131_F	1.358	0.99
60_L	70_W	1.325	0.99
34_L	129_A	1.316	0.99
112_S	116_W	1.305	0.99
34_L	46_L	1.295	0.99
45_F	125_V	1.293	0.99
6_R	10_E	1.290	0.99
61_I	95_T	1.276	0.98
13_D	16_R	1.265	0.98
95_T	105_L	1.261	0.98
66_L	104_L	1.234	0.98
88_F	91_R	1.233	0.98
23_F	27_T	1.233	0.98
85_G	88_F	1.232	0.98
61_I	81_L	1.214	0.98
43_L	79_E	1.210	0.98
9_S	12_F	1.199	0.98
116_W	120_A	1.192	0.98
110_V	114_L	1.169	0.97
26_A	37_F	1.168	0.97
99_V	103_V	1.160	0.97
57_P	60_L	1.146	0.97
67_V	71_L	1.142	0.97
14_R	30_V	1.141	0.97
13_D	17_F	1.121	0.96
26_A	30_V	1.115	0.96
37_F	137_L	1.113	0.96
19_K	96_G	1.108	0.96
88_F	105_L	1.099	0.96
106_F	109_S	1.097	0.96
65_L	109_S	1.096	0.96
27_T	37_F	1.091	0.96
18_S	133_D	1.077	0.96
30_V	129_A	1.065	0.95
65_L	100_V	1.060	0.95
105_L	108_T	1.057	0.95
33_N	41_Y	1.054	0.95
102_V	123_V	1.048	0.95
59_S	110_V	1.041	0.95
59_S	62_V	1.035	0.94
74_Y	90_D	1.023	0.94
51_L	55_T	1.021	0.94
68_A	71_L	1.018	0.94
65_L	69_A	1.008	0.94
52_S	120_A	0.997	0.93
82_V	87_R	0.993	0.93
53_L	117_A	0.987	0.93
60_L	63_L	0.983	0.93
53_L	93_V	0.977	0.93
33_N	128_H	0.963	0.92
134_P	137_L	0.958	0.92
135_E	139_L	0.957	0.92
6_R	82_V	0.950	0.92
94_L	123_V	0.945	0.91
16_R	25_E	0.928	0.91
91_R	95_T	0.918	0.90
17_F	36_Y	0.916	0.90
61_I	68_A	0.916	0.90
43_L	73_L	0.912	0.90
92_Q	105_L	0.903	0.89
107_L	110_V	0.879	0.88
16_R	26_A	0.877	0.88
115_L	119_G	0.869	0.87
54_L	86_R	0.860	0.87
78_D	81_L	0.859	0.87
98_L	104_L	0.855	0.87
62_V	106_F	0.851	0.86
72_F	75_F	0.840	0.86
39_T	129_A	0.829	0.85
76_L	80_P	0.827	0.85
72_F	76_L	0.825	0.85
46_L	99_V	0.817	0.84
18_S	28_S	0.815	0.84
93_V	97_L	0.809	0.83
85_G	90_D	0.807	0.83
70_W	101_T	0.806	0.83
12_F	16_R	0.803	0.83
103_V	120_A	0.789	0.82
56_N	59_S	0.785	0.82
49_L	56_N	0.779	0.81
71_L	105_L	0.778	0.81
133_D	139_L	0.775	0.81
7_P	24_S	0.774	0.81
57_P	61_I	0.766	0.80
65_L	116_W	0.759	0.79
34_L	126_L	0.759	0.79
45_F	117_A	0.758	0.79
43_L	95_T	0.754	0.79
4_P	92_Q	0.745	0.78
48_L	108_T	0.737	0.77
64_L	71_L	0.736	0.77
38_R	129_A	0.727	0.76
101_T	109_S	0.726	0.76
9_S	13_D	0.714	0.75
81_L	96_G	0.713	0.75
65_L	118_L	0.710	0.75
4_P	39_T	0.706	0.74
70_W	77_R	0.705	0.74
66_L	101_T	0.698	0.73
97_L	108_T	0.696	0.73
96_G	99_V	0.691	0.73
35_S	38_R	0.684	0.72
43_L	91_R	0.683	0.72
58_L	107_L	0.680	0.71
43_L	98_L	0.672	0.70
9_S	119_G	0.667	0.70
52_S	113_T	0.660	0.69
57_P	70_W	0.654	0.68
132_R	135_E	0.652	0.68
100_V	107_L	0.652	0.68
61_I	127_L	0.642	0.67
31_R	97_L	0.641	0.67
123_V	131_F	0.640	0.67
39_T	98_L	0.640	0.67
88_F	92_Q	0.638	0.67
6_R	40_N	0.635	0.66
83_I	88_F	0.633	0.66
96_G	112_S	0.623	0.65
8_W	44_V	0.621	0.64
9_S	28_S	0.617	0.64
14_R	17_F	0.615	0.64
26_A	36_Y	0.614	0.64
15_S	127_L	0.614	0.64
67_V	98_L	0.609	0.63
101_T	114_L	0.609	0.63
71_L	122_L	0.602	0.62
12_F	27_T	0.597	0.61
102_V	116_W	0.596	0.61
58_L	62_V	0.592	0.61
48_L	52_S	0.592	0.61
122_L	130_A	0.591	0.61
6_R	16_R	0.590	0.61
34_L	64_L	0.588	0.60
52_S	56_N	0.588	0.60
110_V	132_R	0.588	0.60
15_S	104_L	0.588	0.60
3_A	6_R	0.588	0.60
53_L	76_L	0.588	0.60
38_R	121_S	0.583	0.60
49_L	122_L	0.580	0.59
67_V	104_L	0.573	0.58
134_P	138_F	0.571	0.58
119_G	126_L	0.567	0.57
127_L	130_A	0.566	0.57
56_N	110_V	0.560	0.57
52_S	121_S	0.559	0.56
59_S	63_L	0.558	0.56
17_F	85_G	0.558	0.56
64_L	98_L	0.556	0.56
3_A	39_T	0.554	0.56
22_S	77_R	0.553	0.56
30_V	35_S	0.549	0.55
50_A	65_L	0.547	0.55
78_D	99_V	0.545	0.55
17_F	82_V	0.544	0.54
8_W	12_F	0.542	0.54
4_P	98_L	0.540	0.54
4_P	9_S	0.539	0.54
42_A	51_L	0.539	0.54
107_L	115_L	0.539	0.54
28_S	130_A	0.533	0.53
76_L	99_V	0.532	0.53
73_L	100_V	0.530	0.53
45_F	95_T	0.528	0.52
45_F	52_S	0.524	0.52
90_D	137_L	0.518	0.51
83_I	86_R	0.511	0.50
50_A	68_A	0.511	0.50
10_E	40_N	0.506	0.49
94_L	98_L	0.504	0.49
64_L	69_A	0.500	0.48

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
5c4iC	2	0.3239	3.8	0.931	Contact Map
4qtnA	3	0.8028	3.6	0.932	Contact Map
4ognA	1	0.2535	3.5	0.932	Contact Map
4pj6A	2	0.338	3.4	0.933	Contact Map
4bpmA	3	0.9155	2.9	0.935	Contact Map
2m1mA	1	0.2535	2.8	0.935	Contact Map
4mndA	2	0.7535	2.3	0.938	Contact Map
2oyzA	2	0.2817	2	0.94	Contact Map
3j01B	1	0.4155	2	0.94	Contact Map
2lm1A	1	0.331	1.9	0.941	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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