DUF3874 - PFAM28P - GREMLIN Contacts

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DUF3874 - Domain of unknonw function from B. Theta Gene description (DUF3874)

PFAM:	PF12990	Sequences: QSPEEELFLACFRKPEEGEEGEWLSATEILERLQKKYPIKLSHSTKVKLGRALKKLGFERKHTRRGNVYLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (68)
Sequences:	1072 (808)
Seq/√Len:	98.0
META:	0.906

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_R	19_E	3.781	1.00
62_H	66_G	2.790	1.00
62_H	67_N	2.626	1.00
12_F	32_R	2.592	1.00
8_F	49_L	2.559	1.00
30_L	49_L	2.409	1.00
11_C	37_Y	2.297	1.00
59_E	70_L	2.291	1.00
7_L	37_Y	1.903	1.00
48_K	51_R	1.802	1.00
12_F	24_L	1.755	1.00
7_L	38_P	1.587	1.00
30_L	41_L	1.535	1.00
8_F	58_F	1.491	1.00
8_F	53_L	1.456	1.00
61_K	68_V	1.400	0.99
65_R	68_V	1.398	0.99
28_E	31_E	1.378	0.99
39_I	44_S	1.364	0.99
24_L	32_R	1.322	0.99
39_I	42_S	1.301	0.99
8_F	52_A	1.295	0.99
54_K	60_R	1.292	0.99
25_S	28_E	1.276	0.99
15_P	58_F	1.230	0.99
5_E	52_A	1.202	0.98
4_E	33_L	1.200	0.98
11_C	33_L	1.166	0.98
11_C	32_R	1.154	0.98
28_E	68_V	1.053	0.96
29_I	53_L	1.052	0.96
34_Q	40_K	1.051	0.96
43_H	47_V	1.043	0.96
31_E	34_Q	1.032	0.96
49_L	58_F	0.974	0.94
5_E	55_K	0.962	0.94
39_I	54_K	0.943	0.93
21_G	32_R	0.912	0.92
42_S	54_K	0.890	0.91
26_A	46_K	0.884	0.91
63_T	68_V	0.879	0.91
61_K	67_N	0.870	0.90
23_W	29_I	0.845	0.89
14_K	58_F	0.835	0.88
23_W	70_L	0.831	0.88
63_T	66_G	0.829	0.88
4_E	10_A	0.823	0.88
6_E	27_T	0.817	0.87
15_P	19_E	0.812	0.87
8_F	12_F	0.800	0.86
16_E	21_G	0.784	0.85
47_V	50_G	0.772	0.84
17_E	20_E	0.752	0.83
23_W	61_K	0.748	0.82
13_R	18_G	0.744	0.82
45_T	55_K	0.740	0.82
39_I	55_K	0.726	0.80
9_L	56_L	0.694	0.77
36_K	44_S	0.672	0.75
41_L	45_T	0.667	0.74
12_F	69_Y	0.667	0.74
7_L	11_C	0.665	0.74
18_G	59_E	0.653	0.73
4_E	27_T	0.653	0.73
47_V	65_R	0.648	0.72
5_E	53_L	0.642	0.72
22_E	68_V	0.639	0.71
18_G	35_K	0.634	0.71
14_K	59_E	0.632	0.70
14_K	19_E	0.627	0.70
47_V	58_F	0.626	0.70
3_P	16_E	0.625	0.70
6_E	46_K	0.623	0.69
10_A	27_T	0.620	0.69
3_P	6_E	0.619	0.69
53_L	67_N	0.615	0.68
15_P	59_E	0.609	0.68
31_E	47_V	0.608	0.67
44_S	47_V	0.600	0.66
15_P	18_G	0.599	0.66
52_A	55_K	0.596	0.66
63_T	67_N	0.594	0.66
33_L	41_L	0.593	0.66
4_E	43_H	0.592	0.65
23_W	28_E	0.576	0.63
13_R	16_E	0.575	0.63
16_E	36_K	0.572	0.63
45_T	48_K	0.567	0.62
6_E	59_E	0.558	0.61
3_P	31_E	0.554	0.60
34_Q	45_T	0.552	0.60
30_L	56_L	0.546	0.59
17_E	22_E	0.542	0.59
3_P	14_K	0.538	0.58
25_S	60_R	0.537	0.58
10_A	28_E	0.536	0.58
21_G	29_I	0.531	0.57
4_E	7_L	0.516	0.55
9_L	55_K	0.513	0.55
3_P	17_E	0.509	0.54
27_T	32_R	0.507	0.54
13_R	70_L	0.500	0.53

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
1nhaA	1	0.8873	49.8	0.823	Contact Map
1i27A	1	0.8873	48.6	0.824	Contact Map
3lapA	6	0.8028	29.3	0.844	Contact Map
4mtdA	2	0.9014	28	0.846	Contact Map
3zqjA	1	0.9859	27.3	0.846	Contact Map
3mwmA	2	0.9155	26.9	0.847	Contact Map
3pihA	2	0.5493	23.8	0.851	Contact Map
2o4cA	2	0.8592	21.4	0.854	Contact Map
1mzbA	4	0.9155	20.7	0.855	Contact Map
2r6fA	2	0.5493	20.7	0.855	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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