DUF2145 - PFAM28P - GREMLIN Contacts

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DUF2145 - Uncharacterized protein conserved in bacteria (DUF2145)

PFAM:	PF09916	Sequences: ELDASGARVALVARAGQDLSRYGLRYSHAGFALRDSPDGPWRVRHLYNACGTARSRLYDQGLGGFFLDDPFRYEASIVVPPPELQARLLAALLDSPRALRLHEPRYSAVAYPFSTRYQNCNQWVLETLAAAWGPTATTRAQAQAWLRAQGYEPTTLRVGPLTRLGARMFVANVAFDDHPNEDRFAGRIETVTVDSIEAFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	200 (199)
Sequences:	1399 (1001)
Seq/√Len:	71.0
META:	0.847

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
182_D	189_E	5.381	1.00
66_F	75_A	3.474	1.00
117_Y	176_D	3.083	1.00
136_A	141_Q	2.649	1.00
101_L	130_A	2.592	1.00
55_S	102_H	2.561	1.00
24_L	156_L	2.531	1.00
49_A	56_R	2.428	1.00
21_R	162_T	2.427	1.00
2_L	10_A	2.391	1.00
180_N	184_F	2.385	1.00
105_R	117_Y	2.384	1.00
57_L	99_L	2.106	1.00
84_L	132_W	2.103	1.00
8_R	89_L	2.082	1.00
81_P	84_L	2.023	1.00
108_A	173_V	2.021	1.00
138_T	141_Q	1.994	1.00
175_F	188_I	1.990	1.00
70_P	73_Y	1.906	1.00
158_V	162_T	1.863	1.00
117_Y	174_A	1.851	1.00
129_A	199_F	1.850	1.00
19_L	27_S	1.831	1.00
159_G	162_T	1.810	1.00
133_G	148_A	1.785	1.00
25_R	74_E	1.778	1.00
80_P	84_L	1.776	1.00
24_L	192_T	1.754	1.00
12_V	43_V	1.724	1.00
45_H	120_C	1.700	1.00
45_H	60_Q	1.700	1.00
156_L	192_T	1.697	1.00
13_A	76_S	1.694	1.00
105_R	116_R	1.682	1.00
155_T	182_D	1.682	1.00
80_P	85_Q	1.613	0.99
115_T	126_E	1.612	0.99
160_P	186_G	1.602	0.99
113_F	153_P	1.595	0.99
91_A	131_A	1.584	0.99
2_L	5_S	1.575	0.99
98_A	123_W	1.557	0.99
38_D	42_R	1.556	0.99
42_R	59_D	1.519	0.99
162_T	165_G	1.508	0.99
60_Q	64_G	1.506	0.99
137_T	141_Q	1.504	0.99
47_Y	120_C	1.498	0.99
107_S	112_P	1.496	0.99
48_N	172_N	1.437	0.99
155_T	189_E	1.419	0.98
161_L	165_G	1.406	0.98
29_A	193_V	1.406	0.98
7_A	85_Q	1.401	0.98
9_V	89_L	1.390	0.98
83_E	87_R	1.388	0.98
110_A	114_S	1.385	0.98
135_T	141_Q	1.352	0.98
141_Q	144_A	1.348	0.98
36_S	40_P	1.347	0.98
115_T	130_A	1.337	0.98
29_A	124_V	1.337	0.98
125_L	196_I	1.326	0.98
9_V	30_G	1.305	0.97
92_L	127_T	1.292	0.97
181_E	184_F	1.283	0.97
66_F	70_P	1.278	0.97
133_G	149_Q	1.260	0.97
18_D	21_R	1.258	0.97
139_R	145_W	1.227	0.96
107_S	177_D	1.216	0.96
44_R	98_A	1.203	0.96
89_L	93_L	1.176	0.95
50_C	61_G	1.171	0.95
167_R	183_R	1.161	0.95
77_I	104_P	1.160	0.95
181_E	186_G	1.149	0.94
155_T	187_R	1.139	0.94
15_A	72_R	1.130	0.94
8_R	86_A	1.114	0.93
31_F	127_T	1.106	0.93
30_G	43_V	1.104	0.93
33_L	92_L	1.089	0.93
184_F	188_I	1.088	0.93
100_R	137_T	1.085	0.93
122_Q	126_E	1.063	0.92
12_V	75_A	1.060	0.92
3_D	7_A	1.054	0.91
8_R	85_Q	1.053	0.91
63_G	110_A	1.044	0.91
165_G	175_F	1.038	0.91
129_A	142_A	1.035	0.91
135_T	148_A	1.026	0.90
160_P	165_G	1.024	0.90
167_R	175_F	1.016	0.90
152_E	155_T	1.010	0.90
79_V	85_Q	1.008	0.89
54_R	104_P	0.996	0.89
46_L	119_N	0.995	0.89
133_G	141_Q	0.984	0.88
97_R	100_R	0.979	0.88
163_R	167_R	0.977	0.88
13_A	49_A	0.976	0.88
112_P	177_D	0.973	0.88
49_A	52_T	0.967	0.87
113_F	146_L	0.966	0.87
66_F	73_Y	0.964	0.87
31_F	92_L	0.964	0.87
76_S	197_E	0.963	0.87
94_D	97_R	0.960	0.87
162_T	166_A	0.941	0.86
195_S	198_A	0.940	0.86
3_D	34_R	0.936	0.86
113_F	143_Q	0.934	0.86
78_V	197_E	0.922	0.85
43_V	62_L	0.914	0.84
109_V	166_A	0.914	0.84
57_L	180_N	0.912	0.84
139_R	142_A	0.910	0.84
59_D	199_F	0.904	0.84
45_H	48_N	0.904	0.84
97_R	130_A	0.903	0.84
95_S	99_L	0.902	0.83
165_G	184_F	0.888	0.83
34_R	87_R	0.884	0.82
126_E	139_R	0.883	0.82
117_Y	177_D	0.880	0.82
78_V	200_L	0.876	0.82
107_S	178_H	0.874	0.82
102_H	132_W	0.872	0.81
108_A	122_Q	0.868	0.81
167_R	173_V	0.860	0.80
77_I	110_A	0.851	0.80
154_T	198_A	0.849	0.80
116_R	176_D	0.846	0.79
13_A	29_A	0.840	0.79
163_R	188_I	0.838	0.79
9_V	32_A	0.835	0.78
110_A	122_Q	0.834	0.78
184_F	187_R	0.826	0.78
147_R	181_E	0.825	0.78
35_D	40_P	0.821	0.77
24_L	154_T	0.816	0.77
55_S	103_E	0.815	0.77
15_A	19_L	0.813	0.77
157_R	181_E	0.813	0.77
35_D	38_D	0.808	0.76
84_L	200_L	0.803	0.76
126_E	142_A	0.795	0.75
183_R	188_I	0.792	0.75
10_A	32_A	0.786	0.74
90_A	93_L	0.786	0.74
34_R	41_W	0.780	0.74
80_P	136_A	0.777	0.73
171_A	174_A	0.775	0.73
122_Q	139_R	0.771	0.73
15_A	25_R	0.770	0.73
161_L	186_G	0.765	0.72
90_A	95_S	0.764	0.72
26_Y	101_L	0.761	0.72
11_L	36_S	0.761	0.72
64_G	76_S	0.755	0.71
4_A	9_V	0.752	0.71
9_V	33_L	0.748	0.70
84_L	128_L	0.745	0.70
142_A	145_W	0.744	0.70
11_L	124_V	0.743	0.70
159_G	180_N	0.739	0.70
17_Q	27_S	0.739	0.70
175_F	183_R	0.736	0.69
126_E	143_Q	0.735	0.69
95_S	136_A	0.734	0.69
176_D	188_I	0.734	0.69
91_A	101_L	0.731	0.69
15_A	76_S	0.731	0.69
36_S	42_R	0.730	0.69
48_N	120_C	0.725	0.68
31_F	91_A	0.723	0.68
33_L	59_D	0.723	0.68
34_R	40_P	0.721	0.68
188_I	195_S	0.718	0.67
91_A	123_W	0.716	0.67
11_L	31_F	0.714	0.67
153_P	195_S	0.714	0.67
18_D	71_F	0.706	0.66
136_A	142_A	0.705	0.66
67_L	96_P	0.703	0.66
105_R	110_A	0.703	0.66
57_L	133_G	0.703	0.66
111_Y	122_Q	0.702	0.66
22_Y	124_V	0.701	0.65
64_G	119_N	0.698	0.65
76_S	80_P	0.698	0.65
6_G	30_G	0.697	0.65
91_A	97_R	0.694	0.65
38_D	59_D	0.692	0.64
2_L	7_A	0.689	0.64
33_L	40_P	0.681	0.63
130_A	166_A	0.679	0.63
22_Y	47_Y	0.679	0.63
166_A	169_F	0.676	0.63
111_Y	177_D	0.674	0.62
180_N	186_G	0.674	0.62
46_L	55_S	0.672	0.62
160_P	164_L	0.663	0.61
87_R	90_A	0.662	0.61
161_L	184_F	0.659	0.61
20_S	23_G	0.658	0.61
140_A	147_R	0.655	0.60
53_A	172_N	0.649	0.59
95_S	98_A	0.648	0.59
157_R	187_R	0.632	0.57
17_Q	22_Y	0.631	0.57
88_L	115_T	0.629	0.57
60_Q	98_A	0.628	0.57
182_D	188_I	0.628	0.57
111_Y	145_W	0.627	0.57
152_E	198_A	0.627	0.57
22_Y	27_S	0.624	0.57
164_L	188_I	0.624	0.57
135_T	138_T	0.623	0.56
88_L	99_L	0.621	0.56
15_A	71_F	0.617	0.56
156_L	166_A	0.616	0.56
107_S	118_Q	0.611	0.55
22_Y	120_C	0.605	0.54
124_V	127_T	0.605	0.54
193_V	197_E	0.604	0.54
35_D	77_I	0.603	0.54
112_P	132_W	0.603	0.54
43_V	129_A	0.595	0.53
105_R	112_P	0.594	0.53
9_V	92_L	0.594	0.53
83_E	144_A	0.591	0.53
70_P	75_A	0.590	0.52
135_T	147_R	0.588	0.52
81_P	200_L	0.587	0.52
109_V	158_V	0.586	0.52
19_L	25_R	0.584	0.52
84_L	101_L	0.581	0.51
57_L	101_L	0.581	0.51
164_L	185_A	0.579	0.51
128_L	196_I	0.578	0.51
43_V	199_F	0.578	0.51
32_A	163_R	0.577	0.51
162_T	172_N	0.576	0.51
165_G	186_G	0.575	0.51
7_A	79_V	0.572	0.50
86_A	149_Q	0.572	0.50
144_A	148_A	0.570	0.50
168_M	184_F	0.570	0.50
125_L	146_L	0.567	0.50
24_L	68_D	0.567	0.50
36_S	39_G	0.564	0.49
10_A	31_F	0.563	0.49
64_G	95_S	0.562	0.49
80_P	102_H	0.562	0.49
24_L	153_P	0.562	0.49
42_R	61_G	0.561	0.49
71_F	77_I	0.561	0.49
143_Q	178_H	0.561	0.49
158_V	188_I	0.561	0.49
141_Q	148_A	0.559	0.49
111_Y	179_P	0.557	0.48
116_R	137_T	0.557	0.48
19_L	129_A	0.555	0.48
114_S	180_N	0.554	0.48
194_D	199_F	0.552	0.48
31_F	124_V	0.548	0.47
113_F	119_N	0.546	0.47
12_V	17_Q	0.544	0.47
121_N	129_A	0.543	0.47
25_R	69_D	0.543	0.47
40_P	44_R	0.540	0.46
192_T	195_S	0.540	0.46
4_A	77_I	0.539	0.46
182_D	186_G	0.539	0.46
87_R	95_S	0.538	0.46
141_Q	145_W	0.536	0.46
168_M	186_G	0.536	0.46
89_L	196_I	0.533	0.45
92_L	95_S	0.532	0.45
164_L	167_R	0.529	0.45
107_S	117_Y	0.527	0.45
165_G	168_M	0.526	0.45
161_L	164_L	0.526	0.45
170_V	173_V	0.526	0.45
30_G	124_V	0.521	0.44
15_A	37_P	0.521	0.44
15_A	18_D	0.518	0.44
69_D	101_L	0.517	0.44
87_R	181_E	0.514	0.43
34_R	77_I	0.511	0.43
132_W	135_T	0.510	0.43
59_D	122_Q	0.507	0.42
139_R	143_Q	0.504	0.42
24_L	27_S	0.500	0.41

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
3kw0A	3	0.72	75.9	0.941	Contact Map
2if6A	1	0.78	72.7	0.942	Contact Map
4q68A	1	0.355	67.7	0.944	Contact Map
2p1gA	1	0.345	41.3	0.952	Contact Map
2im9A	1	0.41	38.5	0.953	Contact Map
3jrnA	1	0.645	15.7	0.961	Contact Map
4mtdA	2	0.33	15.4	0.961	Contact Map
4dotA	1	0.48	14.7	0.962	Contact Map
2xigA	4	0.34	14.2	0.962	Contact Map
4rifA	2	0.625	12.6	0.963	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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