DUF3322 - PFAM28P - GREMLIN Contacts

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DUF3322 - Uncharacterized protein conserved in bacteria N-term (DUF3322)

PFAM:	PF11795	Sequences: PADIRAQLRRRWDRGELLRALLTGEPFFPLRLPLKGPTAAELLEDFDAVRAWIAALRAWSKEYRVEWREVNHRVLGRQRLPARIWFDTLDDALALIGKEREARRFRALAELTRARFPALLPWLAKRPLRLLELADDWADYSDADFPRLLAVVAWLRAHPRPGLYLRQLPIPGVDTKFIERHRGLLAELLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	190 (182)
Sequences:	2612 (2107)
Seq/√Len:	156.2
META:	0.828

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_F	95_L	4.404	1.00
45_D	48_A	4.024	1.00
64_R	87_D	3.592	1.00
115_R	153_A	3.177	1.00
93_L	102_A	3.164	1.00
31_R	83_R	3.006	1.00
69_E	79_R	2.995	1.00
66_E	83_R	2.982	1.00
68_R	82_A	2.734	1.00
69_E	77_R	2.617	1.00
88_T	91_D	2.469	1.00
118_A	156_R	2.459	1.00
137_W	188_L	2.333	1.00
98_K	101_E	2.287	1.00
9_R	13_D	2.130	1.00
57_R	79_R	2.125	1.00
4_I	32_L	1.905	1.00
66_E	85_W	1.901	1.00
168_L	178_I	1.864	1.00
170_I	173_V	1.861	1.00
115_R	150_A	1.835	1.00
111_L	146_P	1.820	1.00
147_R	174_D	1.786	1.00
47_D	50_R	1.773	1.00
38_T	41_E	1.761	1.00
67_W	79_R	1.741	1.00
21_L	102_A	1.740	1.00
47_D	51_A	1.736	1.00
64_R	85_W	1.726	1.00
52_W	56_L	1.708	1.00
11_R	30_L	1.701	1.00
133_L	184_L	1.679	1.00
109_A	113_R	1.652	1.00
99_E	103_R	1.624	1.00
113_R	120_L	1.596	1.00
136_D	181_H	1.581	1.00
7_Q	33_P	1.567	1.00
151_V	170_I	1.566	1.00
153_A	157_A	1.560	1.00
20_A	25_E	1.553	1.00
71_N	77_R	1.539	1.00
65_V	84_I	1.506	1.00
94_A	99_E	1.492	1.00
104_R	134_A	1.491	1.00
116_F	153_A	1.487	1.00
163_L	167_Q	1.483	1.00
8_L	96_I	1.445	1.00
186_A	190_D	1.406	1.00
154_W	168_L	1.391	1.00
59_W	63_Y	1.359	1.00
110_E	114_A	1.355	1.00
86_F	92_A	1.341	1.00
50_R	54_A	1.333	1.00
146_P	150_A	1.327	1.00
90_D	99_E	1.306	1.00
53_I	75_L	1.297	1.00
5_R	9_R	1.287	1.00
53_I	67_W	1.277	1.00
21_L	106_R	1.275	1.00
154_W	158_H	1.272	1.00
49_V	52_W	1.252	1.00
89_L	93_L	1.250	1.00
148_L	184_L	1.245	1.00
89_L	106_R	1.231	1.00
129_R	187_E	1.209	1.00
16_E	19_R	1.208	1.00
129_R	132_E	1.205	1.00
31_R	66_E	1.195	1.00
116_F	152_V	1.176	1.00
54_A	57_R	1.174	1.00
54_A	58_A	1.174	1.00
151_V	173_V	1.172	1.00
5_R	95_L	1.117	1.00
120_L	124_A	1.112	1.00
6_A	10_R	1.111	1.00
178_I	185_L	1.107	1.00
72_H	75_L	1.100	0.99
51_A	54_A	1.083	0.99
164_Y	167_Q	1.083	0.99
8_L	92_A	1.077	0.99
154_W	161_P	1.073	0.99
63_Y	91_D	1.059	0.99
89_L	102_A	1.055	0.99
18_L	105_F	1.047	0.99
123_L	130_L	1.041	0.99
60_S	63_Y	1.028	0.99
6_A	9_R	1.020	0.99
151_V	168_L	1.016	0.99
104_R	107_A	1.015	0.99
22_L	109_A	1.006	0.99
8_L	95_L	0.997	0.99
7_Q	11_R	0.994	0.99
147_R	150_A	0.994	0.99
182_R	186_A	0.987	0.99
136_D	147_R	0.973	0.99
174_D	180_R	0.969	0.99
104_R	108_L	0.964	0.99
57_R	67_W	0.960	0.99
126_R	129_R	0.948	0.98
116_F	156_R	0.939	0.98
112_T	149_L	0.938	0.98
2_A	55_A	0.931	0.98
40_A	44_E	0.929	0.98
61_K	91_D	0.926	0.98
56_L	60_S	0.919	0.98
56_L	63_Y	0.915	0.98
42_L	49_V	0.898	0.98
158_H	161_P	0.894	0.98
165_L	175_T	0.892	0.98
112_T	137_W	0.891	0.98
7_Q	32_L	0.883	0.98
126_R	187_E	0.881	0.98
17_L	27_F	0.879	0.97
155_L	189_L	0.878	0.97
87_D	91_D	0.870	0.97
112_T	130_L	0.870	0.97
57_R	62_E	0.866	0.97
57_R	65_V	0.866	0.97
31_R	85_W	0.858	0.97
150_A	170_I	0.856	0.97
155_L	163_L	0.853	0.97
112_T	123_L	0.837	0.97
46_F	50_R	0.833	0.96
75_L	78_Q	0.830	0.96
181_H	185_L	0.829	0.96
11_R	14_R	0.826	0.96
12_W	39_A	0.821	0.96
41_E	45_D	0.818	0.96
108_L	112_T	0.816	0.96
53_I	81_P	0.811	0.96
183_G	187_E	0.808	0.96
42_L	75_L	0.795	0.95
56_L	61_K	0.782	0.95
103_R	107_A	0.779	0.95
147_R	173_V	0.779	0.95
71_N	74_V	0.773	0.95
49_V	75_L	0.766	0.94
155_L	170_I	0.760	0.94
70_V	80_L	0.757	0.94
106_R	110_E	0.755	0.94
4_I	84_I	0.753	0.94
36_G	68_R	0.746	0.94
165_L	177_F	0.746	0.94
4_I	56_L	0.739	0.93
33_P	83_R	0.739	0.93
42_L	72_H	0.739	0.93
65_V	81_P	0.739	0.93
151_V	155_L	0.739	0.93
53_I	80_L	0.738	0.93
164_Y	177_F	0.728	0.93
3_D	6_A	0.725	0.93
166_R	176_K	0.725	0.93
52_W	154_W	0.717	0.92
20_A	26_P	0.716	0.92
108_L	134_A	0.710	0.92
159_P	163_L	0.705	0.92
10_R	19_R	0.705	0.92
23_T	124_A	0.703	0.91
175_T	179_E	0.697	0.91
171_P	175_T	0.697	0.91
63_Y	84_I	0.691	0.91
150_A	172_G	0.691	0.91
177_F	181_H	0.690	0.91
119_L	164_Y	0.689	0.91
17_L	92_A	0.679	0.90
108_L	135_D	0.678	0.90
130_L	137_W	0.677	0.90
17_L	93_L	0.670	0.89
43_L	74_V	0.668	0.89
167_Q	170_I	0.665	0.89
163_L	168_L	0.664	0.89
66_E	82_A	0.662	0.89
57_R	75_L	0.660	0.89
105_F	108_L	0.651	0.88
51_A	55_A	0.651	0.88
102_A	106_R	0.650	0.88
52_W	76_G	0.647	0.88
32_L	86_F	0.646	0.88
104_R	135_D	0.644	0.88
52_W	167_Q	0.644	0.88
133_L	181_H	0.644	0.88
93_L	98_K	0.643	0.87
10_R	13_D	0.642	0.87
40_A	43_L	0.640	0.87
165_L	178_I	0.639	0.87
57_R	60_S	0.639	0.87
52_W	57_R	0.634	0.87
150_A	153_A	0.633	0.87
127_P	131_L	0.633	0.87
19_R	78_Q	0.630	0.86
116_F	119_L	0.626	0.86
112_T	188_L	0.624	0.86
34_L	37_P	0.624	0.86
19_R	23_T	0.622	0.86
43_L	46_F	0.621	0.86
36_G	56_L	0.621	0.86
111_L	115_R	0.619	0.85
84_I	95_L	0.618	0.85
112_T	148_L	0.616	0.85
17_L	21_L	0.615	0.85
167_Q	179_E	0.615	0.85
39_A	72_H	0.614	0.85
185_L	189_L	0.612	0.85
4_I	7_Q	0.611	0.85
49_V	78_Q	0.607	0.84
100_R	103_R	0.601	0.84
7_Q	30_L	0.592	0.83
3_D	7_Q	0.592	0.83
109_A	120_L	0.592	0.83
34_L	84_I	0.590	0.83
122_W	126_R	0.589	0.82
20_A	27_F	0.588	0.82
108_L	130_L	0.586	0.82
153_A	156_R	0.584	0.82
21_L	89_L	0.584	0.82
12_W	72_H	0.583	0.82
46_F	49_V	0.583	0.82
150_A	171_P	0.583	0.82
148_L	185_L	0.582	0.82
111_L	135_D	0.577	0.81
174_D	177_F	0.576	0.81
119_L	187_E	0.572	0.81
98_K	105_F	0.570	0.80
111_L	149_L	0.569	0.80
66_E	149_L	0.568	0.80
105_F	131_L	0.564	0.80
108_L	131_L	0.564	0.80
116_F	149_L	0.564	0.80
9_R	98_K	0.562	0.79
173_V	177_F	0.561	0.79
4_I	175_T	0.559	0.79
2_A	25_E	0.558	0.79
159_P	167_Q	0.557	0.79
24_G	48_A	0.554	0.78
90_D	106_R	0.551	0.78
154_W	169_P	0.546	0.77
78_Q	152_V	0.533	0.76
28_F	92_A	0.533	0.76
169_P	174_D	0.532	0.76
8_L	12_W	0.532	0.76
63_Y	86_F	0.530	0.75
72_H	78_Q	0.529	0.75
30_L	78_Q	0.528	0.75
127_P	137_W	0.528	0.75
109_A	130_L	0.525	0.75
173_V	179_E	0.524	0.75
12_W	15_G	0.524	0.75
128_L	184_L	0.523	0.74
41_E	44_E	0.522	0.74
101_E	121_P	0.522	0.74
36_G	39_A	0.520	0.74
68_R	114_A	0.519	0.74
22_L	124_A	0.517	0.74
3_D	110_E	0.517	0.74
37_P	41_E	0.516	0.73
39_A	73_R	0.516	0.73
41_E	75_L	0.515	0.73
170_I	178_I	0.514	0.73
63_Y	78_Q	0.513	0.73
6_A	13_D	0.509	0.72
76_G	102_A	0.509	0.72
168_L	174_D	0.507	0.72
165_L	174_D	0.506	0.72
119_L	122_W	0.506	0.72
81_P	167_Q	0.505	0.72
92_A	95_L	0.505	0.72
186_A	189_L	0.505	0.72
74_V	162_G	0.504	0.72
38_T	107_A	0.503	0.72
74_V	130_L	0.502	0.71
4_I	63_Y	0.501	0.71
148_L	188_L	0.501	0.71
81_P	173_V	0.500	0.71

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
2yd0A	1	0.9105	27.2	0.929	Contact Map
4jbsA	1	0.9105	22.5	0.932	Contact Map
3rjoA	1	0.9	22.4	0.932	Contact Map
4pj6A	2	0.9053	12.5	0.939	Contact Map
4kx7A	1	0.9105	10.5	0.941	Contact Map
4jc0A	1	0.9368	5.6	0.948	Contact Map
2b4jC	1	0.0947	5.4	0.949	Contact Map
3r84A	2	0.4	4.7	0.95	Contact Map
2qgqA	1	0.8789	4.4	0.951	Contact Map
4kmoB	1	0.4421	4	0.952	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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