DUF4335 - PFAM28P - GREMLIN Contacts

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DUF4335 - Domain of unknown function (DUF4335)

PFAM:	PF14233	Sequences: RRYTLPSCTLELEGLPDPSRWASNNELKDLISILSNWELRLPGEKPLLEGGREHLEALMDAVSIYAQELLSGVPHPQESGSESEYLVKLIPIKADNLLIHRLVLGSSKPNVKPLVIKLSTVQLFDLVEALDQLNADSQTLPDLSLPLQPLSRRYLNNKVPLAKRAIPPWIGIASLALAAVALFLLPVP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (181)
Sequences:	630 (433)
Seq/√Len:	32.2
META:	0.649

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_R	56_E	5.724	1.00
65_Y	100_H	4.865	1.00
55_L	133_L	3.293	1.00
160_P	164_R	3.292	1.00
66_A	127_V	3.122	1.00
101_R	117_K	2.954	1.00
155_L	158_K	2.821	1.00
67_Q	141_P	2.704	1.00
179_A	183_F	2.539	1.00
95_D	172_I	2.489	1.00
43_G	132_Q	2.472	0.99
2_R	11_E	2.445	0.99
169_W	181_A	2.335	0.99
5_L	129_A	2.287	0.99
171_G	179_A	2.287	0.99
100_H	123_L	2.128	0.98
131_D	136_D	2.127	0.98
41_L	129_A	2.053	0.98
16_P	53_E	2.026	0.98
37_W	54_H	1.999	0.98
34_L	56_E	1.957	0.97
3_Y	10_L	1.909	0.97
109_P	113_P	1.905	0.97
11_E	40_R	1.827	0.96
16_P	131_D	1.773	0.95
150_L	154_Y	1.772	0.95
170_I	173_A	1.704	0.94
97_L	117_K	1.703	0.94
180_V	183_F	1.700	0.94
55_L	134_N	1.682	0.94
37_W	46_P	1.681	0.94
177_L	180_V	1.634	0.93
148_Q	152_R	1.617	0.92
166_I	170_I	1.567	0.91
43_G	122_Q	1.563	0.91
73_V	158_K	1.553	0.91
1_R	6_P	1.548	0.90
71_S	171_G	1.544	0.90
162_A	182_L	1.521	0.90
174_S	182_L	1.501	0.89
5_L	37_W	1.440	0.87
71_S	136_D	1.408	0.86
101_R	115_V	1.371	0.84
1_R	8_C	1.347	0.83
11_E	162_A	1.342	0.83
171_G	178_A	1.329	0.82
148_Q	154_Y	1.324	0.82
116_I	161_L	1.313	0.81
153_R	157_N	1.293	0.80
4_T	9_T	1.287	0.80
80_G	83_S	1.267	0.79
76_P	79_S	1.265	0.79
12_L	40_R	1.253	0.78
3_Y	136_D	1.223	0.76
26_E	32_S	1.212	0.76
1_R	5_L	1.198	0.75
9_T	133_L	1.176	0.73
71_S	120_T	1.163	0.73
62_V	126_L	1.131	0.70
149_P	154_Y	1.131	0.70
8_C	34_L	1.125	0.70
22_A	25_N	1.117	0.69
83_S	86_L	1.116	0.69
151_S	154_Y	1.093	0.68
16_P	23_S	1.085	0.67
79_S	89_L	1.076	0.67
65_Y	123_L	1.070	0.66
35_S	143_L	1.067	0.66
56_E	144_S	1.066	0.66
179_A	185_L	1.059	0.65
2_R	29_D	1.055	0.65
18_P	26_E	1.054	0.65
48_L	160_P	1.053	0.65
17_D	33_I	1.049	0.65
18_P	141_P	1.049	0.65
139_T	143_L	1.049	0.65
172_I	179_A	1.041	0.64
108_K	113_P	1.038	0.64
134_N	137_S	1.036	0.64
61_A	161_L	1.030	0.63
50_G	58_L	1.020	0.62
121_V	168_P	1.015	0.62
6_P	139_T	1.011	0.62
68_E	91_P	1.007	0.61
50_G	55_L	1.003	0.61
3_Y	12_L	0.999	0.61
14_G	17_D	0.993	0.60
136_D	171_G	0.981	0.59
6_P	152_R	0.978	0.59
120_T	171_G	0.976	0.59
6_P	129_A	0.973	0.59
2_R	9_T	0.964	0.58
138_Q	184_L	0.956	0.57
23_S	106_S	0.955	0.57
15_L	51_G	0.953	0.57
79_S	82_E	0.950	0.57
102_L	123_L	0.947	0.57
23_S	177_L	0.942	0.56
9_T	119_S	0.931	0.55
14_G	113_P	0.923	0.55
59_M	128_E	0.922	0.54
132_Q	175_L	0.919	0.54
102_L	116_I	0.917	0.54
64_I	114_L	0.905	0.53
60_D	166_I	0.903	0.53
150_L	153_R	0.899	0.53
14_G	143_L	0.899	0.53
6_P	140_L	0.898	0.53
4_T	37_W	0.897	0.52
88_K	96_N	0.893	0.52
68_E	79_S	0.893	0.52
118_L	122_Q	0.886	0.52
147_L	180_V	0.878	0.51
8_C	69_L	0.869	0.50
173_A	179_A	0.860	0.49
34_L	55_L	0.857	0.49
121_V	167_P	0.848	0.48
113_P	130_L	0.842	0.48
101_R	142_D	0.831	0.47
82_E	176_A	0.829	0.47
5_L	39_L	0.827	0.47
59_M	63_S	0.825	0.47
15_L	33_I	0.823	0.46
8_C	129_A	0.819	0.46
80_G	84_E	0.816	0.46
150_L	155_L	0.811	0.45
120_T	132_Q	0.810	0.45
121_V	128_E	0.809	0.45
24_N	74_P	0.807	0.45
154_Y	157_N	0.806	0.45
18_P	41_L	0.806	0.45
71_S	164_R	0.805	0.45
82_E	93_K	0.800	0.44
171_G	184_L	0.793	0.44
30_L	157_N	0.792	0.44
118_L	126_L	0.787	0.43
89_L	128_E	0.786	0.43
64_I	91_P	0.774	0.42
88_K	180_V	0.772	0.42
67_Q	136_D	0.771	0.42
43_G	153_R	0.770	0.42
8_C	143_L	0.768	0.42
91_P	96_N	0.764	0.42
153_R	156_N	0.762	0.41
51_G	129_A	0.761	0.41
78_E	96_N	0.761	0.41
59_M	133_L	0.760	0.41
175_L	178_A	0.758	0.41
171_G	186_P	0.757	0.41
6_P	141_P	0.756	0.41
34_L	181_A	0.755	0.41
148_Q	157_N	0.754	0.41
58_L	130_L	0.752	0.41
120_T	178_A	0.752	0.41
71_S	186_P	0.751	0.41
16_P	33_I	0.748	0.40
4_T	8_C	0.748	0.40
160_P	166_I	0.746	0.40
92_I	172_I	0.731	0.39
4_T	116_I	0.728	0.39
112_K	115_V	0.726	0.39
45_K	101_R	0.724	0.38
7_S	39_L	0.723	0.38
22_A	111_V	0.722	0.38
41_L	46_P	0.722	0.38
143_L	155_L	0.715	0.38
166_I	185_L	0.711	0.37
116_I	181_A	0.710	0.37
23_S	49_E	0.706	0.37
67_Q	140_L	0.704	0.37
8_C	38_E	0.704	0.37
102_L	118_L	0.703	0.37
16_P	64_I	0.699	0.36
72_G	131_D	0.699	0.36
6_P	51_G	0.692	0.36
73_V	113_P	0.690	0.36
124_F	129_A	0.685	0.35
120_T	167_P	0.681	0.35
168_P	171_G	0.678	0.35
116_I	171_G	0.678	0.35
87_V	104_L	0.677	0.35
61_A	137_S	0.676	0.35
44_E	55_L	0.676	0.35
163_K	182_L	0.673	0.35
65_Y	69_L	0.666	0.34
57_A	61_A	0.661	0.34
174_S	183_F	0.657	0.33
92_I	117_K	0.655	0.33
5_L	11_E	0.654	0.33
148_Q	156_N	0.654	0.33
33_I	121_V	0.645	0.32
102_L	131_D	0.640	0.32
61_A	140_L	0.638	0.32
18_P	155_L	0.637	0.32
120_T	128_E	0.637	0.32
129_A	152_R	0.634	0.32
16_P	106_S	0.633	0.32
30_L	148_Q	0.632	0.32
24_N	89_L	0.630	0.31
103_V	115_V	0.629	0.31
39_L	129_A	0.626	0.31
72_G	75_H	0.623	0.31
25_N	60_D	0.622	0.31
48_L	167_P	0.621	0.31
8_C	122_Q	0.620	0.31
40_R	47_L	0.619	0.31
131_D	175_L	0.617	0.30
54_H	120_T	0.615	0.30
39_L	54_H	0.612	0.30
130_L	174_S	0.611	0.30
37_W	42_P	0.611	0.30
77_Q	82_E	0.611	0.30
12_L	47_L	0.610	0.30
41_L	152_R	0.609	0.30
171_G	175_L	0.604	0.30
159_V	162_A	0.603	0.30
95_D	117_K	0.602	0.29
50_G	125_D	0.600	0.29
18_P	21_W	0.599	0.29
90_I	94_A	0.593	0.29
58_L	126_L	0.591	0.29
53_E	104_L	0.589	0.29
48_L	72_G	0.587	0.28
12_L	165_A	0.586	0.28
103_V	119_S	0.586	0.28
25_N	33_I	0.579	0.28
91_P	169_W	0.579	0.28
76_P	95_D	0.576	0.28
50_G	123_L	0.575	0.28
22_A	53_E	0.571	0.27
10_L	100_H	0.570	0.27
79_S	91_P	0.559	0.27
77_Q	81_S	0.559	0.27
170_I	175_L	0.557	0.26
22_A	131_D	0.555	0.26
74_P	161_L	0.553	0.26
137_S	186_P	0.551	0.26
3_Y	58_L	0.549	0.26
9_T	155_L	0.549	0.26
12_L	141_P	0.549	0.26
178_A	183_F	0.544	0.26
75_H	78_E	0.542	0.26
14_G	31_I	0.541	0.25
82_E	90_I	0.538	0.25
151_S	156_N	0.538	0.25
15_L	120_T	0.533	0.25
46_P	133_L	0.531	0.25
101_R	184_L	0.528	0.25
82_E	162_A	0.526	0.25
119_S	127_V	0.525	0.24
57_A	87_V	0.524	0.24
24_N	152_R	0.523	0.24
147_L	151_S	0.523	0.24
17_D	37_W	0.522	0.24
115_V	180_V	0.521	0.24
81_S	146_P	0.521	0.24
78_E	83_S	0.521	0.24
67_Q	126_L	0.519	0.24
4_T	7_S	0.519	0.24
54_H	128_E	0.516	0.24
95_D	124_F	0.515	0.24
10_L	14_G	0.515	0.24
81_S	88_K	0.513	0.24
16_P	31_I	0.512	0.24
79_S	84_E	0.510	0.24
30_L	141_P	0.509	0.24
69_L	150_L	0.508	0.23
63_S	176_A	0.507	0.23
26_E	31_I	0.506	0.23
56_E	110_N	0.503	0.23
94_A	97_L	0.502	0.23
12_L	133_L	0.500	0.23

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
2qztA	2	0.2766	7.3	0.954	Contact Map
3bkrA	1	0.2926	5.8	0.956	Contact Map
1iktA	1	0.3085	5.5	0.957	Contact Map
2y69G	1	0.1809	4.4	0.959	Contact Map
2ww9B	1	0.2872	4.4	0.959	Contact Map
4w252	1	0.2872	4.1	0.959	Contact Map
3ivrA	2	0.4309	3.7	0.96	Contact Map
1pz4A	1	0.2979	3.6	0.96	Contact Map
1c44A	1	0.3191	3.6	0.96	Contact Map
4pzpA	1	0.4362	3.3	0.961	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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