DUF2262 - PFAM28P - GREMLIN Contacts

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DUF2262 - Uncharacterized protein conserved in bacteria (DUF2262)

PFAM:	PF10020	Sequences: DEVLGEFTLDRDLDWFEGEIDWLGEEIELSLDVDEDDEEDLEKALATAKKLLANQEEWDKKIREFAAEELLELANDWLEEDEEDEEAPEITEEEFAKRISLESISIYSDGSFEFYFDDGDLFWGHSIIVSGDLDGGFTDADI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	142 (135)
Sequences:	1266 (1022)
Seq/√Len:	88.0
META:	0.825

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_D	63_R	4.409	1.00
118_D	124_G	3.432	1.00
59_D	116_F	2.730	1.00
99_I	127_I	2.691	1.00
132_D	136_G	2.577	1.00
68_E	92_E	2.552	1.00
7_F	18_G	2.499	1.00
10_D	17_E	2.410	1.00
112_F	131_G	2.390	1.00
131_G	136_G	2.278	1.00
4_L	52_L	2.219	1.00
29_L	48_A	2.165	1.00
98_R	119_G	2.145	1.00
74_A	78_L	2.141	1.00
78_L	88_P	2.081	1.00
67_A	96_A	2.050	1.00
22_W	55_Q	1.997	1.00
101_L	114_F	1.929	1.00
22_W	58_W	1.927	1.00
77_W	125_H	1.852	1.00
113_E	128_I	1.844	1.00
66_A	129_V	1.838	1.00
70_L	127_I	1.837	1.00
58_W	112_F	1.805	1.00
62_I	114_F	1.776	1.00
19_E	26_E	1.701	1.00
9_L	16_F	1.677	1.00
120_D	124_G	1.629	1.00
71_L	75_N	1.570	1.00
133_L	136_G	1.567	1.00
3_V	7_F	1.526	1.00
21_D	24_G	1.526	1.00
132_D	135_G	1.481	0.99
64_E	96_A	1.480	0.99
54_N	57_E	1.475	0.99
57_E	61_K	1.424	0.99
54_N	58_W	1.385	0.99
115_Y	126_S	1.380	0.99
66_A	99_I	1.370	0.99
115_Y	128_I	1.328	0.99
64_E	92_E	1.326	0.99
51_L	106_I	1.319	0.99
9_L	14_D	1.314	0.99
101_L	116_F	1.301	0.99
90_I	121_L	1.247	0.98
62_I	137_F	1.241	0.98
77_W	122_F	1.226	0.98
75_N	78_L	1.221	0.98
48_A	62_I	1.207	0.98
92_E	96_A	1.200	0.98
65_F	69_E	1.196	0.98
51_L	131_G	1.185	0.98
91_T	94_E	1.177	0.97
22_W	59_D	1.173	0.97
98_R	118_D	1.160	0.97
99_I	118_D	1.133	0.97
75_N	121_L	1.115	0.96
120_D	123_W	1.112	0.96
71_L	121_L	1.101	0.96
102_E	117_D	1.093	0.96
78_L	123_W	1.084	0.96
47_T	112_F	1.083	0.96
30_S	115_Y	1.037	0.95
51_L	55_Q	1.024	0.94
10_D	13_L	1.009	0.94
67_A	71_L	1.009	0.94
11_R	15_W	0.957	0.92
56_E	59_D	0.937	0.91
60_K	64_E	0.932	0.91
107_Y	113_E	0.923	0.90
49_K	53_A	0.915	0.90
118_D	121_L	0.903	0.90
93_E	97_K	0.900	0.89
104_I	114_F	0.898	0.89
94_E	98_R	0.896	0.89
3_V	53_A	0.896	0.89
17_E	28_E	0.893	0.89
37_D	40_D	0.887	0.89
11_R	16_F	0.887	0.89
74_A	122_F	0.874	0.88
51_L	112_F	0.861	0.87
74_A	82_E	0.857	0.87
31_L	44_A	0.856	0.87
113_E	130_S	0.855	0.87
73_L	77_W	0.848	0.86
58_W	62_I	0.846	0.86
112_F	133_L	0.843	0.86
66_A	70_L	0.840	0.86
38_E	41_L	0.837	0.86
71_L	91_T	0.832	0.85
28_E	103_S	0.831	0.85
29_L	49_K	0.827	0.85
69_E	72_E	0.826	0.85
119_G	124_G	0.825	0.85
63_R	67_A	0.821	0.85
70_L	73_L	0.813	0.84
7_F	48_A	0.798	0.83
98_R	121_L	0.797	0.83
55_Q	58_W	0.796	0.83
122_F	125_H	0.795	0.83
19_E	100_S	0.782	0.82
58_W	131_G	0.775	0.81
26_E	97_K	0.759	0.80
128_I	141_D	0.757	0.79
94_E	97_K	0.750	0.79
130_S	139_D	0.744	0.78
132_D	137_F	0.743	0.78
32_D	105_S	0.742	0.78
17_E	30_S	0.741	0.78
96_A	99_I	0.737	0.78
76_D	81_D	0.735	0.77
13_L	108_S	0.732	0.77
4_L	67_A	0.730	0.77
101_L	104_I	0.729	0.77
32_D	107_Y	0.727	0.77
105_S	115_Y	0.722	0.76
45_L	116_F	0.720	0.76
22_W	51_L	0.715	0.75
31_L	105_S	0.715	0.75
27_I	31_L	0.706	0.74
20_I	52_L	0.705	0.74
64_E	101_L	0.696	0.73
55_Q	62_I	0.692	0.73
23_L	27_I	0.690	0.73
18_G	48_A	0.686	0.72
58_W	61_K	0.683	0.72
41_L	44_A	0.681	0.72
73_L	76_D	0.681	0.72
88_P	93_E	0.681	0.72
63_R	96_A	0.671	0.71
51_L	62_I	0.670	0.71
21_D	93_E	0.668	0.70
77_W	82_E	0.655	0.69
50_K	53_A	0.649	0.68
58_W	114_F	0.637	0.67
31_L	79_E	0.634	0.66
78_L	81_D	0.631	0.66
42_E	46_A	0.629	0.66
50_K	54_N	0.624	0.65
51_L	114_F	0.619	0.65
95_F	127_I	0.619	0.65
55_Q	101_L	0.614	0.64
118_D	123_W	0.611	0.64
82_E	88_P	0.610	0.63
23_L	56_E	0.609	0.63
78_L	86_E	0.606	0.63
67_A	116_F	0.603	0.63
16_F	59_D	0.597	0.62
95_F	122_F	0.595	0.61
103_S	126_S	0.592	0.61
74_A	90_I	0.591	0.61
75_N	95_F	0.591	0.61
121_L	128_I	0.589	0.61
33_V	41_L	0.589	0.61
99_I	121_L	0.585	0.60
69_E	109_D	0.585	0.60
43_K	72_E	0.583	0.60
71_L	90_I	0.581	0.60
8_T	18_G	0.581	0.60
70_L	125_H	0.579	0.59
7_F	31_L	0.575	0.59
127_I	140_A	0.574	0.59
75_N	94_E	0.572	0.58
114_F	131_G	0.572	0.58
7_F	106_I	0.571	0.58
22_W	131_G	0.569	0.58
41_L	48_A	0.569	0.58
78_L	89_E	0.565	0.58
108_S	111_S	0.564	0.57
98_R	120_D	0.558	0.57
115_Y	118_D	0.551	0.56
102_E	110_G	0.551	0.56
134_D	137_F	0.546	0.55
99_I	116_F	0.544	0.55
23_L	59_D	0.544	0.55
73_L	122_F	0.544	0.55
62_I	131_G	0.541	0.54
48_A	52_L	0.533	0.53
72_E	130_S	0.532	0.53
102_E	115_Y	0.529	0.53
16_F	74_A	0.529	0.53
116_F	126_S	0.524	0.52
22_W	133_L	0.522	0.52
129_V	133_L	0.519	0.51
59_D	72_E	0.519	0.51
90_I	94_E	0.518	0.51
26_E	76_D	0.517	0.51
30_S	42_E	0.514	0.51
56_E	93_E	0.512	0.50
62_I	116_F	0.511	0.50
71_L	96_A	0.510	0.50
70_L	95_F	0.510	0.50
11_R	61_K	0.509	0.50
3_V	56_E	0.509	0.50
71_L	74_A	0.508	0.50
131_G	135_G	0.507	0.50
41_L	55_Q	0.507	0.50
90_I	98_R	0.503	0.49
46_A	49_K	0.503	0.49
71_L	92_E	0.502	0.49
95_F	120_D	0.501	0.49
71_L	122_F	0.500	0.49

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
3epuA	3	0.3803	13.2	0.912	Contact Map
1k3eA	2	0.3803	8	0.92	Contact Map
2cqkA	1	0.3662	6.9	0.923	Contact Map
3r6fA	2	0.3662	5.5	0.926	Contact Map
3f02A	1	0.9014	5.1	0.928	Contact Map
3ddcB	2	0.3592	4.4	0.929	Contact Map
3op1A	4	0.4225	3.7	0.932	Contact Map
2h4pA	1	0.9155	3.4	0.933	Contact Map
3pzfA	1	0.8803	3.3	0.934	Contact Map
3efyA	2	0.5211	3.2	0.934	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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