DUF1977 - PFAM28P - GREMLIN Contacts

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DUF1977 - Domain of unknown function (DUF1977)

PFAM:	PF09320	Sequences: FSSPSDPSYSFTPSPPYTVERTTPNLKVPYYVNPDFVSEYSGRKLRRLERSVEEDYVSNLRNECEREKQQKERLIYRARGWFFGDEEKLKKARAMPMPSCERLEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (100)
Sequences:	681 (534)
Seq/√Len:	53.4
META:	0.379

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_E	29_P	3.286	1.00
9_Y	52_V	3.201	1.00
75_I	89_L	2.914	1.00
18_T	34_P	2.913	1.00
96_P	101_E	2.834	1.00
90_K	94_A	2.766	1.00
21_R	45_L	2.646	1.00
78_A	92_A	2.513	1.00
74_L	95_M	2.328	1.00
101_E	104_E	2.238	1.00
32_V	36_F	2.161	1.00
44_K	47_R	1.980	1.00
28_V	53_E	1.951	1.00
67_E	98_P	1.799	0.99
92_A	97_M	1.726	0.99
59_N	63_E	1.646	0.98
71_K	97_M	1.595	0.98
36_F	40_Y	1.575	0.98
60_L	102_R	1.504	0.97
88_K	91_K	1.498	0.97
10_S	29_P	1.484	0.97
87_E	90_K	1.459	0.97
8_S	11_F	1.443	0.96
78_A	89_L	1.438	0.96
9_Y	14_S	1.428	0.96
67_E	97_M	1.427	0.96
81_W	84_G	1.425	0.96
78_A	97_M	1.413	0.96
30_Y	49_E	1.350	0.95
33_N	36_F	1.347	0.95
57_V	103_L	1.345	0.95
70_Q	74_L	1.260	0.93
6_D	33_N	1.239	0.92
80_G	85_D	1.220	0.91
71_K	93_R	1.213	0.91
85_D	88_K	1.187	0.90
67_E	78_A	1.179	0.90
49_E	65_E	1.177	0.90
73_R	77_R	1.152	0.89
21_R	66_R	1.123	0.88
90_K	93_R	1.084	0.86
31_Y	79_R	1.076	0.85
74_L	91_K	1.074	0.85
10_S	14_S	1.073	0.85
75_I	93_R	1.072	0.85
97_M	101_E	1.070	0.85
31_Y	47_R	1.069	0.85
19_V	27_K	1.035	0.83
66_R	70_Q	1.010	0.81
23_T	99_S	0.981	0.79
54_E	61_R	0.976	0.79
92_A	95_M	0.964	0.78
25_N	50_R	0.963	0.78
79_R	98_P	0.951	0.77
30_Y	41_S	0.951	0.77
14_S	18_T	0.937	0.76
42_G	50_R	0.921	0.75
47_R	51_S	0.919	0.75
13_P	31_Y	0.911	0.74
74_L	88_K	0.889	0.72
14_S	17_Y	0.886	0.72
84_G	89_L	0.881	0.72
82_F	85_D	0.873	0.71
18_T	67_E	0.869	0.70
6_D	16_P	0.866	0.70
63_E	67_E	0.863	0.70
38_S	50_R	0.862	0.70
86_E	90_K	0.857	0.69
9_Y	55_D	0.837	0.68
100_C	103_L	0.834	0.67
34_P	42_G	0.828	0.67
60_L	99_S	0.823	0.66
28_V	56_Y	0.811	0.65
17_Y	39_E	0.803	0.64
45_L	49_E	0.793	0.63
27_K	47_R	0.786	0.63
56_Y	102_R	0.777	0.62
24_P	49_E	0.767	0.61
50_R	55_D	0.758	0.60
77_R	102_R	0.755	0.60
22_T	29_P	0.754	0.59
19_V	34_P	0.740	0.58
15_P	104_E	0.726	0.57
9_Y	40_Y	0.713	0.55
89_L	93_R	0.710	0.55
67_E	92_A	0.708	0.55
13_P	20_E	0.706	0.54
62_N	104_E	0.699	0.54
12_T	59_N	0.694	0.53
31_Y	55_D	0.693	0.53
30_Y	86_E	0.692	0.53
65_E	73_R	0.690	0.53
11_F	80_G	0.687	0.52
38_S	60_L	0.671	0.51
9_Y	17_Y	0.668	0.50
48_L	52_V	0.668	0.50
34_P	76_Y	0.667	0.50
37_V	49_E	0.665	0.50
40_Y	51_S	0.659	0.50
64_C	100_C	0.659	0.50
19_V	46_R	0.657	0.49
63_E	99_S	0.656	0.49
72_E	76_Y	0.652	0.49
36_F	45_L	0.651	0.49
41_S	93_R	0.643	0.48
48_L	89_L	0.641	0.48
38_S	70_Q	0.639	0.47
21_R	30_Y	0.635	0.47
16_P	52_V	0.617	0.45
24_P	46_R	0.614	0.45
56_Y	97_M	0.613	0.45
61_R	92_A	0.611	0.44
55_D	63_E	0.609	0.44
11_F	54_E	0.608	0.44
40_Y	48_L	0.604	0.44
37_V	40_Y	0.594	0.43
87_E	94_A	0.590	0.42
31_Y	57_V	0.584	0.42
87_E	99_S	0.583	0.42
5_S	9_Y	0.582	0.41
81_W	85_D	0.582	0.41
60_L	103_L	0.576	0.41
41_S	49_E	0.576	0.41
24_P	62_N	0.566	0.40
36_F	81_W	0.552	0.38
59_N	66_R	0.551	0.38
87_E	91_K	0.548	0.38
48_L	82_F	0.548	0.38
58_S	104_E	0.543	0.38
22_T	26_L	0.536	0.37
75_I	79_R	0.536	0.37
21_R	68_K	0.529	0.36
67_E	81_W	0.526	0.36
8_S	17_Y	0.525	0.36
33_N	65_E	0.524	0.36
25_N	38_S	0.523	0.36
67_E	95_M	0.521	0.35
30_Y	34_P	0.520	0.35
61_R	71_K	0.519	0.35
11_F	33_N	0.518	0.35
56_Y	60_L	0.517	0.35
79_R	82_F	0.512	0.34
35_D	87_E	0.512	0.34
22_T	32_V	0.511	0.34
39_E	55_D	0.511	0.34
86_E	89_L	0.510	0.34
70_Q	91_K	0.509	0.34
30_Y	64_C	0.506	0.34
13_P	36_F	0.505	0.34
57_V	69_Q	0.500	0.33

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
4recA	2	0.7238	2.2	0.933	Contact Map
3bbnE	1	0.0381	2.1	0.934	Contact Map
1a9xA	3	0.5714	2.1	0.934	Contact Map
2yvqA	2	0.4	2	0.935	Contact Map
4b9gA	1	0.5048	1.8	0.936	Contact Map
1mlwA	1	0.4762	1.7	0.937	Contact Map
4r8aA	1	0.7429	1.6	0.938	Contact Map
4n78D	1	0.4857	1.6	0.938	Contact Map
3plwA	1	0	1.5	0.939	Contact Map
3dinE	1	0.3714	1.3	0.942	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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