DUF2322 - PFAM28P - GREMLIN Contacts

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DUF2322 - Uncharacterized protein conserved in bacteria (DUF2322)

PFAM:	PF10084	Sequences: FADNLKQLPSIDHLAAIELLDADGAVVATIENKPGKQGSLAVYNHLAQKFGAIDAEAAEEGLELFAEHTADARANPGKHPNIDRLLAIIAGGETLRVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (98)
Sequences:	984 (583)
Seq/√Len:	58.9
META:	0.792

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_N	78_K	2.987	1.00
21_D	25_A	2.964	1.00
46_L	61_G	2.954	1.00
36_K	65_F	2.888	1.00
62_L	69_T	2.870	1.00
71_D	78_K	2.694	1.00
49_K	60_E	2.688	1.00
8_L	42_V	2.596	1.00
53_I	97_V	2.583	1.00
32_N	37_Q	2.326	1.00
4_N	7_Q	2.321	1.00
20_L	26_V	2.218	1.00
60_E	64_L	2.165	1.00
70_A	74_A	2.145	1.00
87_A	91_G	1.920	1.00
44_N	48_Q	1.829	1.00
18_E	29_T	1.796	0.99
68_H	71_D	1.640	0.99
42_V	64_L	1.635	0.99
16_A	29_T	1.583	0.99
14_L	40_L	1.515	0.98
4_N	64_L	1.449	0.97
18_E	26_V	1.443	0.97
18_E	98_K	1.433	0.97
2_A	6_K	1.399	0.97
10_S	41_A	1.351	0.96
91_G	94_T	1.298	0.95
26_V	29_T	1.293	0.95
19_L	28_A	1.268	0.94
87_A	93_E	1.266	0.94
42_V	69_T	1.226	0.93
47_A	53_I	1.191	0.92
72_A	83_D	1.191	0.92
34_P	37_Q	1.181	0.92
88_I	95_L	1.179	0.92
65_F	78_K	1.174	0.92
73_R	89_I	1.167	0.92
36_K	40_L	1.141	0.91
70_A	73_R	1.139	0.91
6_K	41_A	1.135	0.90
88_I	91_G	1.120	0.90
11_I	40_L	1.120	0.90
37_Q	40_L	1.110	0.89
82_I	86_L	1.086	0.88
40_L	65_F	1.085	0.88
50_F	60_E	1.081	0.88
38_G	42_V	1.078	0.88
31_E	40_L	1.036	0.86
34_P	40_L	1.017	0.85
42_V	68_H	1.004	0.84
31_E	36_K	0.966	0.82
37_Q	44_N	0.963	0.82
37_Q	65_F	0.962	0.81
64_L	69_T	0.947	0.80
1_F	5_L	0.944	0.80
77_G	83_D	0.919	0.78
45_H	64_L	0.868	0.74
88_I	94_T	0.860	0.74
59_E	63_E	0.853	0.73
39_S	65_F	0.852	0.73
41_A	53_I	0.850	0.73
71_D	75_N	0.850	0.73
33_K	36_K	0.842	0.72
55_A	59_E	0.836	0.71
72_A	77_G	0.832	0.71
44_N	47_A	0.828	0.71
73_R	86_L	0.826	0.71
68_H	81_N	0.822	0.70
14_L	17_I	0.815	0.70
4_N	8_L	0.813	0.69
38_G	67_E	0.789	0.67
49_K	56_E	0.778	0.66
49_K	96_R	0.777	0.66
38_G	68_H	0.771	0.65
86_L	89_I	0.771	0.65
65_F	71_D	0.770	0.65
10_S	44_N	0.769	0.65
4_N	66_A	0.761	0.64
9_P	45_H	0.752	0.63
67_E	81_N	0.726	0.61
7_Q	23_D	0.716	0.59
80_P	83_D	0.715	0.59
12_D	41_A	0.708	0.59
48_Q	60_E	0.691	0.57
17_I	86_L	0.691	0.57
11_I	60_E	0.688	0.56
6_K	44_N	0.676	0.55
45_H	49_K	0.671	0.55
11_I	41_A	0.652	0.52
30_I	59_E	0.649	0.52
33_K	65_F	0.647	0.52
3_D	7_Q	0.647	0.52
21_D	27_V	0.645	0.52
28_A	84_R	0.639	0.51
46_L	83_D	0.639	0.51
26_V	70_A	0.639	0.51
49_K	63_E	0.637	0.51
6_K	12_D	0.626	0.50
13_H	16_A	0.623	0.49
19_L	84_R	0.619	0.49
35_G	68_H	0.618	0.49
51_G	57_A	0.613	0.48
22_A	96_R	0.610	0.48
20_L	98_K	0.607	0.47
5_L	38_G	0.603	0.47
86_L	90_A	0.597	0.46
43_Y	67_E	0.597	0.46
38_G	46_L	0.588	0.45
38_G	66_A	0.583	0.45
46_L	50_F	0.581	0.45
93_E	96_R	0.576	0.44
35_G	81_N	0.567	0.43
2_A	78_K	0.566	0.43
30_I	49_K	0.562	0.43
35_G	79_H	0.558	0.42
73_R	98_K	0.556	0.42
61_G	67_E	0.555	0.42
47_A	52_A	0.554	0.42
11_I	17_I	0.554	0.42
48_Q	87_A	0.554	0.42
7_Q	70_A	0.550	0.41
40_L	87_A	0.550	0.41
46_L	67_E	0.547	0.41
13_H	45_H	0.542	0.40
1_F	38_G	0.539	0.40
16_A	45_H	0.538	0.40
32_N	76_P	0.538	0.40
66_A	71_D	0.535	0.40
56_E	59_E	0.535	0.40
55_A	89_I	0.529	0.39
60_E	63_E	0.529	0.39
19_L	97_V	0.528	0.39
31_E	65_F	0.520	0.38
28_A	32_N	0.520	0.38
88_I	93_E	0.519	0.38
33_K	51_G	0.518	0.38
17_I	47_A	0.515	0.38
42_V	65_F	0.511	0.37
22_A	90_A	0.510	0.37
12_D	44_N	0.506	0.37
52_A	94_T	0.505	0.36
27_V	63_E	0.505	0.36
3_D	60_E	0.503	0.36
13_H	44_N	0.501	0.36
52_A	56_E	0.501	0.36
59_E	89_I	0.500	0.36
20_L	96_R	0.500	0.36

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
2qhqA	2	0.9184	75.8	0.884	Contact Map
3j3bC	1	1	9.8	0.931	Contact Map
3lraA	1	0.4694	9.3	0.932	Contact Map
4pkfA	2	0.7857	8.5	0.933	Contact Map
1r9dA	2	0.8265	7.9	0.934	Contact Map
2du3A	4	0.898	7.4	0.934	Contact Map
1s4cA	2	0.5612	6.9	0.935	Contact Map
2f3oA	3	0.8571	6.9	0.935	Contact Map
1h16A	2	0.9184	6.9	0.935	Contact Map
1dmgA	1	0.6633	6.7	0.936	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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