DUF2170 - PFAM28P - GREMLIN Contacts

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DUF2170 - Uncharacterized protein conserved in bacteria (DUF2170)

PFAM:	PF09938	Sequences: NWTTESLAEALAESELVGGGFASVELIEGEEPVLQITMHEYGDLPIFLTVSGEQILVETYLWPVDEVKDRAAFNEALLRTHKLFPLSSFGIETVDGGDYYVMFGALSASSSLEDIVHEIETLADNAIDALEAYEEFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (136)
Sequences:	850 (527)
Seq/√Len:	45.2
META:	0.771

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_S	114_D	3.783	1.00
73_F	77_L	3.590	1.00
71_A	74_N	2.940	1.00
36_I	48_L	2.768	1.00
65_D	97_G	2.500	1.00
64_V	91_I	2.458	1.00
64_V	70_R	2.445	1.00
23_S	39_H	2.224	1.00
88_S	105_A	2.197	1.00
54_Q	105_A	2.188	1.00
29_G	32_P	2.053	0.99
11_L	119_I	2.033	0.99
106_L	110_S	2.010	0.99
75_E	79_R	1.937	0.99
8_A	12_A	1.889	0.99
71_A	75_E	1.865	0.99
67_V	120_E	1.862	0.99
84_F	102_M	1.823	0.99
70_R	74_N	1.793	0.98
40_E	44_L	1.763	0.98
50_V	55_I	1.745	0.98
63_P	66_E	1.733	0.98
3_T	10_A	1.703	0.98
90_G	103_F	1.698	0.98
59_T	126_A	1.675	0.98
53_E	115_I	1.667	0.98
122_L	125_N	1.639	0.97
114_D	117_H	1.544	0.96
80_T	88_S	1.522	0.96
46_I	59_T	1.500	0.95
14_S	116_V	1.493	0.95
4_T	8_A	1.461	0.95
42_G	73_F	1.453	0.94
48_L	69_D	1.431	0.94
77_L	133_Y	1.421	0.94
89_F	129_A	1.416	0.94
54_Q	85_P	1.378	0.93
103_F	119_I	1.342	0.92
41_Y	123_A	1.339	0.92
77_L	89_F	1.319	0.91
81_H	88_S	1.310	0.91
70_R	75_E	1.308	0.91
110_S	122_L	1.270	0.89
5_E	9_E	1.265	0.89
106_L	122_L	1.251	0.89
81_H	103_F	1.251	0.89
64_V	79_R	1.248	0.89
107_S	117_H	1.245	0.88
21_F	24_V	1.214	0.87
28_E	32_P	1.203	0.87
54_Q	103_F	1.199	0.86
80_T	133_Y	1.196	0.86
52_G	108_A	1.151	0.84
127_I	130_L	1.143	0.84
56_L	105_A	1.137	0.83
74_N	100_Y	1.106	0.82
42_G	130_L	1.093	0.81
120_E	133_Y	1.085	0.80
46_I	119_I	1.082	0.80
49_T	101_V	1.071	0.79
44_L	126_A	1.063	0.79
2_W	7_L	1.059	0.79
60_Y	101_V	1.043	0.78
81_H	105_A	1.042	0.78
48_L	57_V	1.030	0.77
115_I	136_F	1.023	0.76
55_I	108_A	1.020	0.76
8_A	34_L	1.019	0.76
34_L	132_A	1.018	0.76
64_V	74_N	1.014	0.76
109_S	117_H	1.005	0.75
60_Y	99_Y	0.992	0.74
21_F	25_E	0.985	0.73
118_E	121_T	0.978	0.73
15_E	23_S	0.973	0.72
109_S	114_D	0.953	0.71
16_L	19_G	0.949	0.71
87_S	125_N	0.940	0.70
36_I	97_G	0.930	0.69
3_T	9_E	0.925	0.69
38_M	73_F	0.919	0.68
77_L	80_T	0.919	0.68
43_D	73_F	0.918	0.68
54_Q	81_H	0.913	0.68
60_Y	90_G	0.910	0.67
15_E	18_G	0.906	0.67
89_F	92_E	0.900	0.66
83_L	105_A	0.895	0.66
62_W	74_N	0.891	0.66
81_H	89_F	0.885	0.65
22_A	25_E	0.876	0.64
4_T	34_L	0.876	0.64
19_G	24_V	0.869	0.64
48_L	124_D	0.866	0.63
41_Y	127_I	0.861	0.63
43_D	123_A	0.860	0.63
73_F	82_K	0.857	0.63
107_S	118_E	0.855	0.62
123_A	130_L	0.850	0.62
51_S	115_I	0.850	0.62
49_T	92_E	0.844	0.61
92_E	101_V	0.837	0.61
102_M	126_A	0.833	0.60
86_L	104_G	0.832	0.60
14_S	20_G	0.815	0.59
113_E	116_V	0.809	0.58
28_E	116_V	0.803	0.58
84_F	129_A	0.801	0.57
44_L	131_E	0.796	0.57
6_S	9_E	0.787	0.56
21_F	26_L	0.782	0.56
47_F	50_V	0.781	0.55
5_E	15_E	0.767	0.54
31_E	34_L	0.765	0.54
49_T	52_G	0.755	0.53
45_P	66_E	0.754	0.53
81_H	129_A	0.746	0.52
35_Q	92_E	0.739	0.51
65_D	134_E	0.736	0.51
12_A	15_E	0.736	0.51
56_L	88_S	0.736	0.51
46_I	87_S	0.730	0.51
53_E	68_K	0.720	0.50
82_K	101_V	0.713	0.49
64_V	95_D	0.703	0.48
56_L	103_F	0.700	0.48
57_V	106_L	0.700	0.48
26_L	115_I	0.700	0.48
14_S	17_V	0.700	0.48
58_E	81_H	0.699	0.48
24_V	32_P	0.699	0.48
52_G	114_D	0.691	0.47
38_M	123_A	0.689	0.47
121_T	124_D	0.683	0.46
82_K	90_G	0.681	0.46
35_Q	47_F	0.681	0.46
6_S	10_A	0.675	0.45
2_W	10_A	0.674	0.45
57_V	122_L	0.670	0.45
78_L	88_S	0.668	0.45
52_G	99_Y	0.657	0.43
58_E	77_L	0.655	0.43
4_T	49_T	0.648	0.43
65_D	115_I	0.647	0.43
5_E	51_S	0.639	0.42
103_F	110_S	0.639	0.42
67_V	90_G	0.620	0.40
20_G	24_V	0.617	0.40
68_K	115_I	0.617	0.40
6_S	15_E	0.617	0.40
58_E	88_S	0.616	0.40
30_E	69_D	0.610	0.39
57_V	133_Y	0.610	0.39
93_T	98_D	0.609	0.39
118_E	122_L	0.606	0.39
33_V	89_F	0.601	0.38
90_G	110_S	0.597	0.38
67_V	105_A	0.595	0.38
73_F	130_L	0.594	0.38
18_G	22_A	0.588	0.37
76_A	136_F	0.588	0.37
38_M	42_G	0.587	0.37
10_A	113_E	0.584	0.37
72_A	95_D	0.582	0.36
57_V	60_Y	0.582	0.36
32_P	113_E	0.578	0.36
93_T	134_E	0.576	0.36
59_T	99_Y	0.573	0.36
49_T	89_F	0.570	0.35
83_L	95_D	0.569	0.35
124_D	128_D	0.568	0.35
9_E	13_E	0.567	0.35
3_T	12_A	0.567	0.35
76_A	121_T	0.560	0.35
79_R	114_D	0.560	0.35
56_L	84_F	0.558	0.34
54_Q	87_S	0.550	0.34
27_I	66_E	0.548	0.33
91_I	97_G	0.548	0.33
117_H	133_Y	0.547	0.33
93_T	108_A	0.547	0.33
26_L	90_G	0.543	0.33
84_F	105_A	0.542	0.33
22_A	36_I	0.542	0.33
58_E	84_F	0.541	0.33
34_L	108_A	0.541	0.33
73_F	102_M	0.539	0.33
3_T	66_E	0.533	0.32
38_M	119_I	0.532	0.32
38_M	62_W	0.531	0.32
127_I	134_E	0.527	0.32
79_R	91_I	0.524	0.31
102_M	129_A	0.522	0.31
32_P	37_T	0.522	0.31
29_G	50_V	0.518	0.31
13_E	18_G	0.516	0.31
19_G	55_I	0.514	0.31
7_L	74_N	0.513	0.30
34_L	121_T	0.508	0.30
24_V	110_S	0.506	0.30
23_S	113_E	0.503	0.30
23_S	37_T	0.502	0.30
99_Y	115_I	0.500	0.29
64_V	98_D	0.500	0.29

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
2plgA	4	0.8978	50.1	0.918	Contact Map
1jyoA	2	0.9124	39.3	0.923	Contact Map
3epuA	3	0.8686	14.3	0.938	Contact Map
2xgaA	2	0.8175	12.7	0.939	Contact Map
2bp1A	2	0.2774	12.1	0.94	Contact Map
1ry9A	2	0.8467	11.8	0.94	Contact Map
1xkpC	1	0.8467	10.3	0.942	Contact Map
3cx5A	1	0.6569	9.6	0.943	Contact Map
1hr6B	1	0.7518	9.6	0.943	Contact Map
4mt1A	3	0.8759	8	0.944	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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