PgaD - PFAM28P - GREMLIN Contacts

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PgaD - PgaD-like protein

PFAM:	PF13994	Sequences: LIIDRPRLQPRRQRLLDGLLTLLAWALWLYLWLPLLTLLAWLLGVRLFYDEMLAGLFAGGSAPELGGYLALLELLLLYLLVILVLALLLLLWALYNRRRFRGRERRKAPPPVTDEELARSFGLDPEELAALRQARVLVVHHDEDGRII	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	148 (136)
Sequences:	1233 (974)
Seq/√Len:	83.5
META:	0.788

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_D	132_R	3.499	1.00
139_V	147_I	3.326	1.00
142_D	146_R	3.262	1.00
28_W	34_P	3.108	1.00
113_T	116_E	3.014	1.00
96_N	100_F	2.604	1.00
115_E	119_R	2.430	1.00
28_W	33_L	2.300	1.00
86_A	89_L	2.299	1.00
21_T	25_W	2.259	1.00
131_L	137_L	2.225	1.00
37_T	41_W	2.203	1.00
96_N	105_R	2.130	1.00
41_W	48_F	2.067	1.00
96_N	99_R	1.975	1.00
100_F	106_R	1.868	1.00
124_D	127_E	1.857	1.00
9_Q	13_Q	1.798	1.00
17_D	28_W	1.794	1.00
92_W	96_N	1.762	1.00
21_T	24_A	1.736	1.00
112_V	117_L	1.659	1.00
94_L	97_R	1.623	1.00
46_R	51_E	1.584	1.00
28_W	141_H	1.574	1.00
40_A	44_G	1.545	1.00
95_Y	100_F	1.540	1.00
26_A	29_L	1.538	1.00
48_F	52_M	1.521	0.99
100_F	105_R	1.507	0.99
96_N	106_R	1.496	0.99
127_E	130_A	1.486	0.99
141_H	145_G	1.469	0.99
9_Q	17_D	1.454	0.99
115_E	125_P	1.450	0.99
5_R	8_L	1.420	0.99
10_P	13_Q	1.402	0.99
6_P	9_Q	1.373	0.99
16_L	117_L	1.352	0.99
131_L	139_V	1.347	0.99
78_Y	85_L	1.334	0.99
78_Y	81_V	1.325	0.99
4_D	9_Q	1.323	0.99
118_A	128_L	1.320	0.99
92_W	106_R	1.306	0.98
11_R	15_L	1.303	0.98
116_E	119_R	1.290	0.98
132_R	145_G	1.280	0.98
19_L	23_L	1.245	0.98
125_P	129_A	1.241	0.98
49_Y	53_L	1.236	0.98
108_A	111_P	1.232	0.98
32_W	40_A	1.227	0.98
47_L	53_L	1.223	0.98
51_E	65_L	1.212	0.97
89_L	93_A	1.147	0.96
13_Q	17_D	1.145	0.96
82_I	86_A	1.131	0.96
37_T	40_A	1.129	0.96
86_A	90_L	1.109	0.96
123_L	137_L	1.106	0.96
48_F	53_L	1.104	0.96
123_L	131_L	1.098	0.95
70_A	73_E	1.074	0.95
41_W	44_G	1.058	0.94
112_V	132_R	1.037	0.94
116_E	120_S	1.031	0.94
87_L	125_P	0.986	0.92
30_Y	33_L	0.961	0.91
36_L	43_L	0.952	0.91
38_L	41_W	0.940	0.90
3_I	6_P	0.924	0.89
22_L	102_G	0.922	0.89
24_A	82_I	0.921	0.89
17_D	40_A	0.915	0.89
143_E	146_R	0.902	0.88
41_W	51_E	0.895	0.88
6_P	10_P	0.885	0.87
45_V	48_F	0.879	0.87
28_W	79_L	0.875	0.87
94_L	98_R	0.870	0.86
76_L	79_L	0.868	0.86
27_L	140_H	0.865	0.86
92_W	95_Y	0.864	0.86
127_E	131_L	0.858	0.85
117_L	132_R	0.837	0.84
42_L	45_V	0.836	0.84
9_Q	14_R	0.836	0.84
133_Q	143_E	0.833	0.84
101_R	135_R	0.832	0.84
46_R	50_D	0.824	0.83
118_A	125_P	0.823	0.83
22_L	80_L	0.821	0.83
78_Y	82_I	0.810	0.82
92_W	121_F	0.808	0.82
129_A	133_Q	0.808	0.82
138_V	141_H	0.804	0.82
129_A	137_L	0.804	0.82
134_A	141_H	0.797	0.81
29_L	65_L	0.793	0.81
28_W	44_G	0.790	0.80
87_L	111_P	0.788	0.80
35_L	41_W	0.788	0.80
34_P	38_L	0.788	0.80
12_R	40_A	0.784	0.80
21_T	32_W	0.780	0.80
85_L	88_L	0.780	0.80
37_T	44_G	0.774	0.79
21_T	89_L	0.773	0.79
82_I	128_L	0.768	0.79
34_P	41_W	0.766	0.78
93_A	97_R	0.758	0.78
97_R	100_F	0.757	0.78
30_Y	78_Y	0.756	0.77
114_D	128_L	0.752	0.77
95_Y	101_R	0.751	0.77
46_R	78_Y	0.745	0.76
107_K	110_P	0.743	0.76
34_P	37_T	0.738	0.76
29_L	132_R	0.733	0.75
37_T	51_E	0.727	0.75
38_L	52_M	0.727	0.75
67_G	71_L	0.715	0.73
16_L	33_L	0.697	0.72
71_L	77_L	0.696	0.71
135_R	144_D	0.684	0.70
33_L	37_T	0.680	0.70
74_L	81_V	0.678	0.69
35_L	38_L	0.674	0.69
43_L	47_L	0.674	0.69
6_P	34_P	0.673	0.69
29_L	84_V	0.671	0.69
130_A	134_A	0.670	0.69
72_L	91_L	0.670	0.69
17_D	131_L	0.668	0.68
114_D	118_A	0.665	0.68
15_L	18_G	0.663	0.68
26_A	117_L	0.658	0.67
25_W	31_L	0.658	0.67
114_D	129_A	0.646	0.66
23_L	70_A	0.643	0.65
93_A	99_R	0.635	0.64
23_L	26_A	0.634	0.64
83_L	125_P	0.632	0.64
30_Y	38_L	0.632	0.64
93_A	100_F	0.631	0.64
90_L	94_L	0.624	0.63
45_V	49_Y	0.621	0.63
101_R	104_E	0.621	0.63
30_Y	93_A	0.620	0.63
44_G	53_L	0.616	0.62
128_L	132_R	0.616	0.62
23_L	107_K	0.614	0.62
114_D	125_P	0.611	0.61
52_M	67_G	0.609	0.61
128_L	145_G	0.609	0.61
52_M	78_Y	0.607	0.61
89_L	99_R	0.607	0.61
29_L	33_L	0.605	0.61
112_V	116_E	0.602	0.60
45_V	80_L	0.601	0.60
92_W	105_R	0.593	0.59
102_G	106_R	0.592	0.59
6_P	35_L	0.590	0.59
130_A	133_Q	0.586	0.58
96_N	101_R	0.584	0.58
26_A	129_A	0.584	0.58
79_L	90_L	0.580	0.57
13_Q	28_W	0.579	0.57
76_L	88_L	0.576	0.57
134_A	137_L	0.572	0.56
74_L	86_A	0.571	0.56
65_L	71_L	0.566	0.56
30_Y	71_L	0.564	0.55
131_L	134_A	0.564	0.55
22_L	69_L	0.561	0.55
115_E	133_Q	0.559	0.55
17_D	20_L	0.556	0.54
31_L	34_P	0.555	0.54
10_P	17_D	0.551	0.54
122_G	146_R	0.549	0.53
18_G	91_L	0.546	0.53
31_L	99_R	0.546	0.53
42_L	46_R	0.546	0.53
71_L	128_L	0.539	0.52
46_R	121_F	0.533	0.51
131_L	141_H	0.527	0.50
66_G	82_I	0.526	0.50
69_L	73_E	0.525	0.50
24_A	93_A	0.523	0.50
17_D	34_P	0.523	0.50
108_A	147_I	0.522	0.50
24_A	97_R	0.522	0.50
123_L	147_I	0.521	0.50
16_L	127_E	0.519	0.49
126_E	130_A	0.518	0.49
109_P	115_E	0.518	0.49
31_L	53_L	0.514	0.49
69_L	114_D	0.513	0.49
19_L	28_W	0.510	0.48
71_L	75_L	0.507	0.48
25_W	92_W	0.503	0.47
83_L	132_R	0.501	0.47
14_R	31_L	0.500	0.47

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
3f2gA	1	0.4865	48.8	0.893	Contact Map
4r4eB	2	0.3243	27	0.907	Contact Map
2jmlA	1	0.2838	23.4	0.91	Contact Map
1j9iA	2	0.2635	23.2	0.91	Contact Map
4r24B	2	0.3041	17.2	0.915	Contact Map
4j2nA	4	0.2905	15.6	0.917	Contact Map
3ucsA	2	0.2905	15.5	0.917	Contact Map
3g74A	3	0.3986	13.7	0.919	Contact Map
4a0zA	2	0.3716	12	0.921	Contact Map
4i5sA	2	0.4122	11.3	0.922	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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