RebB - PFAM28P - GREMLIN Contacts

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RebB - Killing trait

PFAM:	PF11747	Sequences: ITDAVTQANVKVLGEAPAMAMGNLYQATAQALGLAAHNAVAAQQQANITAQAATTQGVALLYSLDTAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (66)
Sequences:	1600 (959)
Seq/√Len:	118.0
META:	0.813

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_K	15_E	5.379	1.00
2_T	7_Q	3.151	1.00
57_G	62_Y	2.654	1.00
27_A	33_G	2.368	1.00
16_A	22_G	2.073	1.00
45_Q	48_I	1.969	1.00
28_T	36_A	1.901	1.00
35_A	40_V	1.884	1.00
30_Q	37_H	1.856	1.00
28_T	32_L	1.713	1.00
56_Q	63_S	1.703	1.00
56_Q	59_A	1.616	1.00
56_Q	60_L	1.609	1.00
34_L	37_H	1.566	1.00
2_T	6_T	1.538	1.00
12_V	18_A	1.408	1.00
59_A	63_S	1.353	1.00
41_A	44_Q	1.336	1.00
19_M	23_N	1.242	0.99
53_A	58_V	1.224	0.99
28_T	31_A	1.205	0.99
32_L	35_A	1.181	0.99
41_A	47_N	1.137	0.99
25_Y	29_A	1.127	0.99
21_M	25_Y	1.116	0.99
42_A	47_N	1.115	0.99
3_D	6_T	1.068	0.98
34_L	40_V	1.066	0.98
16_A	25_Y	1.023	0.98
26_Q	29_A	1.015	0.97
13_L	18_A	1.014	0.97
26_Q	62_Y	1.004	0.97
46_A	50_A	0.981	0.97
49_T	59_A	0.975	0.97
3_D	14_G	0.936	0.96
32_L	52_A	0.905	0.95
62_Y	65_D	0.903	0.95
41_A	49_T	0.900	0.95
29_A	32_L	0.899	0.95
45_Q	51_Q	0.898	0.95
19_M	24_L	0.887	0.95
55_T	59_A	0.871	0.94
32_L	37_H	0.846	0.93
53_A	57_G	0.845	0.93
6_T	10_V	0.844	0.93
9_N	12_V	0.824	0.92
31_A	60_L	0.813	0.92
31_A	37_H	0.812	0.91
24_L	29_A	0.799	0.91
23_N	26_Q	0.795	0.91
58_V	61_L	0.785	0.90
53_A	59_A	0.775	0.89
2_T	10_V	0.756	0.88
36_A	46_A	0.747	0.88
30_Q	36_A	0.743	0.87
41_A	45_Q	0.735	0.87
24_L	36_A	0.734	0.87
31_A	34_L	0.733	0.87
4_A	15_E	0.733	0.87
21_M	24_L	0.727	0.86
3_D	7_Q	0.725	0.86
1_I	7_Q	0.706	0.85
32_L	36_A	0.692	0.83
12_V	16_A	0.685	0.83
48_I	53_A	0.678	0.82
19_M	51_Q	0.671	0.82
42_A	58_V	0.668	0.81
6_T	20_A	0.662	0.81
14_G	18_A	0.646	0.79
41_A	46_A	0.635	0.78
39_A	43_Q	0.633	0.78
13_L	57_G	0.627	0.77
16_A	21_M	0.620	0.76
42_A	45_Q	0.614	0.75
30_Q	34_L	0.603	0.74
45_Q	54_T	0.600	0.74
24_L	44_Q	0.591	0.73
23_N	29_A	0.591	0.73
60_L	66_T	0.588	0.72
28_T	35_A	0.585	0.72
27_A	31_A	0.584	0.72
6_T	11_K	0.574	0.71
33_G	50_A	0.569	0.70
51_Q	55_T	0.567	0.70
44_Q	48_I	0.566	0.69
60_L	65_D	0.565	0.69
34_L	49_T	0.560	0.69
14_G	19_M	0.560	0.69
4_A	10_V	0.559	0.69
1_I	44_Q	0.555	0.68
20_A	51_Q	0.553	0.68
6_T	52_A	0.545	0.67
17_P	24_L	0.532	0.65
31_A	36_A	0.531	0.65
24_L	32_L	0.529	0.64
23_N	61_L	0.514	0.62
30_Q	39_A	0.504	0.61
52_A	56_Q	0.502	0.60
54_T	58_V	0.500	0.60

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
4b6iA	2	0.5147	1.5	0.904	Contact Map
2x4iA	2	0.6912	1.4	0.906	Contact Map
4dzdA	1	0.4559	1.2	0.909	Contact Map
3qrpA	1	0.4412	1	0.913	Contact Map
2y8yA	1	0.4412	1	0.913	Contact Map
2j85A	2	0.6912	0.9	0.917	Contact Map
2j6bA	2	0.6765	0.8	0.918	Contact Map
3dahA	5	0.5294	0.8	0.919	Contact Map
1dkuA	5	0.5147	0.6	0.925	Contact Map
4twbA	2	0.3382	0.6	0.927	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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