DUF2140 - PFAM28P - GREMLIN Contacts

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DUF2140 - Uncharacterized protein conserved in bacteria (DUF2140)

PFAM:	PF09911	Sequences: NKWKWAFLILLALNLLVIIVLFILIFSPSEDTELPPSTKSTEEGAVFTVSTTKEQLNALINYYLKDEQKDSPIDYKVYLDDDVELYGTLKVFGQEVPFSLTFEPEVLENGNLVLKQKSISVGTLPLPVSYVLKYIKKSYKLPEWVTINPKEETIYVDLTEIKLKSGLKVKAKKIDLKNDDISFEIYV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	187 (186)
Sequences:	597 (466)
Seq/√Len:	34.2
META:	0.219

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_D	178_N	6.619	1.00
173_K	180_D	4.883	1.00
57_N	61_N	4.614	1.00
112_L	174_I	3.890	1.00
172_K	184_E	3.572	1.00
111_N	159_T	3.128	1.00
176_L	181_I	3.054	1.00
11_L	14_N	2.979	1.00
88_T	95_E	2.860	1.00
148_N	151_E	2.797	1.00
2_K	6_A	2.449	1.00
8_L	12_A	2.350	0.99
121_V	124_L	2.262	0.99
49_V	185_I	2.197	0.99
77_V	83_V	2.078	0.99
3_W	10_L	1.860	0.97
1_N	4_K	1.853	0.97
7_F	10_L	1.841	0.97
111_N	157_D	1.823	0.97
7_F	11_L	1.783	0.96
61_N	85_L	1.690	0.95
1_N	14_N	1.677	0.94
75_Y	145_V	1.675	0.94
10_L	175_D	1.636	0.94
3_W	7_F	1.634	0.94
45_A	184_E	1.621	0.93
148_N	153_T	1.552	0.92
110_G	127_P	1.530	0.91
132_L	141_L	1.528	0.91
53_K	79_L	1.524	0.91
104_P	110_G	1.514	0.91
117_K	160_E	1.494	0.90
6_A	136_K	1.480	0.90
110_G	114_L	1.476	0.90
113_V	155_Y	1.435	0.88
60_I	185_I	1.412	0.87
128_V	152_E	1.402	0.87
16_L	20_V	1.395	0.87
72_P	150_K	1.393	0.87
57_N	75_Y	1.360	0.85
12_A	160_E	1.355	0.85
51_T	92_F	1.350	0.85
1_N	5_W	1.350	0.85
79_L	181_I	1.317	0.83
87_G	139_Y	1.302	0.83
52_T	147_I	1.291	0.82
119_I	128_V	1.288	0.82
172_K	182_S	1.272	0.81
75_Y	139_Y	1.265	0.81
87_G	98_F	1.260	0.81
52_T	55_Q	1.251	0.80
12_A	157_D	1.235	0.79
108_E	160_E	1.225	0.79
53_K	179_D	1.224	0.79
6_A	111_N	1.217	0.78
128_V	185_I	1.190	0.77
112_L	171_A	1.177	0.76
103_E	107_L	1.168	0.75
75_Y	119_I	1.165	0.75
103_E	117_K	1.165	0.75
17_V	21_L	1.154	0.74
91_V	145_V	1.152	0.74
73_I	102_F	1.151	0.74
63_Y	139_Y	1.151	0.74
88_T	119_I	1.143	0.74
61_N	119_I	1.139	0.73
14_N	17_V	1.124	0.72
113_V	153_T	1.123	0.72
125_P	151_E	1.120	0.72
23_I	26_F	1.112	0.72
2_K	5_W	1.105	0.71
63_Y	134_Y	1.103	0.71
82_D	118_S	1.102	0.71
116_Q	128_V	1.093	0.70
162_K	168_K	1.087	0.70
135_I	139_Y	1.086	0.70
56_L	119_I	1.081	0.69
132_L	185_I	1.080	0.69
107_L	111_N	1.059	0.68
6_A	14_N	1.054	0.67
60_I	160_E	1.054	0.67
29_S	99_S	1.053	0.67
83_V	109_N	1.045	0.67
103_E	106_V	1.043	0.67
56_L	183_F	1.037	0.66
116_Q	155_Y	1.023	0.65
40_S	78_Y	1.018	0.65
6_A	98_F	1.007	0.64
42_E	96_V	1.004	0.64
158_L	171_A	0.999	0.63
20_V	23_I	0.998	0.63
156_V	174_I	0.995	0.63
171_A	183_F	0.992	0.63
12_A	16_L	0.990	0.62
147_I	185_I	0.971	0.61
120_S	145_V	0.971	0.61
99_S	120_S	0.960	0.60
91_V	107_L	0.951	0.59
100_L	116_Q	0.943	0.59
19_I	22_F	0.936	0.58
128_V	174_I	0.936	0.58
14_N	98_F	0.928	0.57
86_Y	96_V	0.922	0.57
110_G	142_P	0.921	0.57
108_E	132_L	0.917	0.56
115_K	153_T	0.909	0.56
149_P	155_Y	0.908	0.56
5_W	8_L	0.906	0.56
161_I	168_K	0.905	0.55
98_F	102_F	0.893	0.54
79_L	117_K	0.889	0.54
82_D	117_K	0.887	0.54
3_W	6_A	0.886	0.54
25_I	133_K	0.883	0.54
75_Y	134_Y	0.879	0.53
121_V	126_L	0.875	0.53
143_E	161_I	0.865	0.52
116_Q	144_W	0.865	0.52
6_A	141_L	0.861	0.52
131_V	139_Y	0.859	0.52
19_I	23_I	0.857	0.51
9_I	17_V	0.856	0.51
53_K	106_V	0.854	0.51
64_L	185_I	0.851	0.51
105_E	117_K	0.847	0.51
134_Y	145_V	0.847	0.51
110_G	144_W	0.840	0.50
105_E	115_K	0.832	0.49
45_A	62_Y	0.828	0.49
105_E	113_V	0.826	0.49
80_D	178_N	0.823	0.49
137_K	150_K	0.820	0.48
82_D	101_T	0.813	0.48
60_I	77_V	0.812	0.48
143_E	160_E	0.811	0.48
33_E	96_V	0.811	0.48
156_V	163_L	0.805	0.47
57_N	78_Y	0.798	0.46
55_Q	67_E	0.793	0.46
128_V	132_L	0.789	0.46
85_L	141_L	0.788	0.46
47_F	185_I	0.788	0.46
11_L	20_V	0.787	0.46
130_Y	133_K	0.785	0.45
11_L	118_S	0.782	0.45
87_G	154_I	0.778	0.45
51_T	98_F	0.776	0.45
105_E	135_I	0.774	0.44
146_T	157_D	0.774	0.44
77_V	84_E	0.773	0.44
102_F	142_P	0.763	0.43
31_D	54_E	0.759	0.43
5_W	58_A	0.749	0.42
161_I	164_K	0.747	0.42
146_T	160_E	0.747	0.42
13_L	24_L	0.742	0.42
5_W	9_I	0.742	0.42
85_L	137_K	0.737	0.41
16_L	91_V	0.737	0.41
74_D	87_G	0.730	0.41
25_I	152_E	0.729	0.41
132_L	152_E	0.729	0.41
59_L	119_I	0.728	0.41
47_F	128_V	0.725	0.40
51_T	89_L	0.725	0.40
46_V	184_E	0.721	0.40
108_E	125_P	0.721	0.40
15_L	143_E	0.716	0.40
73_I	180_D	0.716	0.40
22_F	173_K	0.714	0.39
35_P	88_T	0.713	0.39
51_T	55_Q	0.711	0.39
83_V	121_V	0.710	0.39
8_L	74_D	0.710	0.39
64_L	70_D	0.707	0.39
9_I	36_P	0.704	0.39
79_L	83_V	0.702	0.38
134_Y	139_Y	0.698	0.38
52_T	128_V	0.697	0.38
104_P	142_P	0.694	0.38
80_D	125_P	0.694	0.38
10_L	50_S	0.694	0.38
19_I	80_D	0.694	0.38
129_S	147_I	0.690	0.38
87_G	120_S	0.689	0.37
12_A	25_I	0.688	0.37
102_F	114_L	0.687	0.37
6_A	115_K	0.679	0.37
55_Q	63_Y	0.679	0.37
61_N	141_L	0.676	0.36
11_L	34_L	0.675	0.36
76_K	175_D	0.674	0.36
141_L	154_I	0.672	0.36
64_L	77_V	0.672	0.36
18_I	151_E	0.671	0.36
9_I	136_K	0.669	0.36
89_L	175_D	0.669	0.36
92_F	130_Y	0.668	0.36
9_I	15_L	0.665	0.36
89_L	98_F	0.664	0.35
90_K	95_E	0.663	0.35
20_V	24_L	0.660	0.35
131_V	138_S	0.659	0.35
96_V	137_K	0.656	0.35
102_F	149_P	0.655	0.35
73_I	117_K	0.642	0.34
170_K	186_Y	0.641	0.34
149_P	169_V	0.641	0.34
9_I	49_V	0.638	0.34
165_S	168_K	0.635	0.33
67_E	72_P	0.635	0.33
171_A	181_I	0.633	0.33
162_K	170_K	0.629	0.33
73_I	89_L	0.629	0.33
43_E	48_T	0.627	0.33
83_V	149_P	0.616	0.32
123_T	126_L	0.614	0.32
81_D	172_K	0.612	0.32
45_A	49_V	0.611	0.31
142_P	171_A	0.609	0.31
48_T	131_V	0.606	0.31
87_G	145_V	0.605	0.31
9_I	13_L	0.601	0.31
59_L	79_L	0.600	0.31
162_K	166_G	0.598	0.31
76_K	133_K	0.596	0.30
169_V	179_D	0.591	0.30
112_L	134_Y	0.591	0.30
54_E	125_P	0.586	0.30
91_V	106_V	0.583	0.29
62_Y	121_V	0.581	0.29
20_V	117_K	0.574	0.29
55_Q	92_F	0.572	0.29
17_V	23_I	0.572	0.29
6_A	64_L	0.571	0.29
5_W	24_L	0.568	0.28
60_I	79_L	0.564	0.28
90_K	100_L	0.562	0.28
55_Q	116_Q	0.559	0.28
15_L	26_F	0.559	0.28
176_L	179_D	0.555	0.28
49_V	59_L	0.554	0.27
16_L	109_N	0.554	0.27
69_K	74_D	0.554	0.27
135_I	184_E	0.550	0.27
59_L	101_T	0.548	0.27
58_A	62_Y	0.546	0.27
126_L	142_P	0.544	0.27
90_K	119_I	0.540	0.27
86_Y	98_F	0.540	0.27
49_V	89_L	0.540	0.27
15_L	23_I	0.539	0.26
59_L	137_K	0.537	0.26
97_P	119_I	0.536	0.26
18_I	23_I	0.535	0.26
67_E	70_D	0.534	0.26
39_K	177_K	0.532	0.26
42_E	76_K	0.531	0.26
56_L	161_I	0.530	0.26
47_F	51_T	0.527	0.26
66_D	137_K	0.526	0.26
47_F	126_L	0.524	0.26
62_Y	147_I	0.524	0.26
146_T	179_D	0.522	0.25
13_L	23_I	0.521	0.25
70_D	108_E	0.521	0.25
56_L	61_N	0.518	0.25
41_T	50_S	0.516	0.25
22_F	93_G	0.512	0.25
172_K	185_I	0.512	0.25
9_I	160_E	0.509	0.25
5_W	12_A	0.507	0.24
87_G	117_K	0.507	0.24
45_A	72_P	0.506	0.24
172_K	177_K	0.503	0.24
11_L	175_D	0.500	0.24
149_P	176_L	0.500	0.24
144_W	158_L	0.500	0.24
29_S	132_L	0.500	0.24

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
2xtcA	4	0.3316	9.5	0.949	Contact Map
1q8kA	1	0.3904	8.8	0.95	Contact Map
4tr8A	2	0.7005	7.8	0.951	Contact Map
5agvA	3	0.6257	7.8	0.951	Contact Map
1wi5A	1	0.4278	7.5	0.952	Contact Map
4tphA	2	0.1711	7.4	0.952	Contact Map
4trtA	2	0.6203	6.7	0.953	Contact Map
4nngA	1	0.4011	6.2	0.953	Contact Map
2cqaA	1	0.508	5.8	0.954	Contact Map
3aevA	1	0.3476	5.3	0.955	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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