SRR1 - PFAM28P - GREMLIN Contacts

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SRR1 - SRR1

PFAM:	PF07985	Sequences: IVCLGLGSFSSSRRSRYQLALLLLLRELLGIPGSSEVYAYDPVFTELDKEFLESL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (53)
Sequences:	882 (734)
Seq/√Len:	100.8
META:	0.338

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_S	48_D	3.651	1.00
9_F	48_D	2.884	1.00
6_L	44_F	2.370	1.00
1_I	22_L	2.262	1.00
2_V	5_G	2.046	1.00
39_A	52_L	2.037	1.00
22_L	26_R	1.911	1.00
3_C	22_L	1.835	1.00
19_L	44_F	1.780	1.00
6_L	19_L	1.735	1.00
46_E	49_K	1.530	1.00
4_L	40_Y	1.506	1.00
1_I	26_R	1.447	1.00
6_L	41_D	1.435	1.00
39_A	44_F	1.402	1.00
50_E	53_E	1.386	1.00
30_G	34_S	1.355	0.99
44_F	52_L	1.267	0.99
8_S	45_T	1.251	0.99
22_L	37_V	1.242	0.99
30_G	33_G	1.234	0.99
10_S	47_L	1.162	0.98
22_L	44_F	1.155	0.98
29_L	40_Y	1.134	0.98
10_S	45_T	1.020	0.96
2_V	38_Y	1.011	0.96
24_L	27_E	0.973	0.95
17_Y	21_L	0.934	0.94
3_C	6_L	0.932	0.94
46_E	53_E	0.932	0.94
21_L	40_Y	0.920	0.93
9_F	52_L	0.913	0.93
23_L	27_E	0.895	0.92
2_V	50_E	0.846	0.90
6_L	9_F	0.845	0.90
31_I	35_S	0.798	0.87
34_S	50_E	0.797	0.87
4_L	9_F	0.791	0.86
47_L	53_E	0.788	0.86
47_L	51_F	0.780	0.86
5_G	12_S	0.778	0.85
4_L	38_Y	0.767	0.85
23_L	49_K	0.763	0.84
12_S	15_S	0.763	0.84
27_E	54_S	0.741	0.83
21_L	25_L	0.707	0.80
3_C	19_L	0.706	0.79
15_S	40_Y	0.706	0.79
34_S	46_E	0.701	0.79
33_G	53_E	0.697	0.79
6_L	52_L	0.668	0.76
41_D	44_F	0.668	0.76
5_G	17_Y	0.666	0.75
43_V	48_D	0.663	0.75
12_S	40_Y	0.651	0.74
27_E	35_S	0.649	0.74
35_S	46_E	0.648	0.73
26_R	30_G	0.643	0.73
44_F	48_D	0.641	0.73
9_F	19_L	0.626	0.71
27_E	33_G	0.613	0.69
28_L	47_L	0.611	0.69
3_C	44_F	0.603	0.68
47_L	54_S	0.601	0.68
22_L	43_V	0.582	0.65
10_S	25_L	0.578	0.65
16_R	21_L	0.575	0.64
46_E	54_S	0.557	0.62
16_R	44_F	0.549	0.61
32_P	41_D	0.548	0.61
28_L	31_I	0.530	0.58
22_L	41_D	0.519	0.57
4_L	24_L	0.519	0.57
30_G	53_E	0.517	0.56
4_L	19_L	0.517	0.56
13_R	16_R	0.512	0.56
5_G	11_S	0.512	0.56
3_C	26_R	0.509	0.55
5_G	18_Q	0.503	0.54
13_R	49_K	0.500	0.54

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
2y0cA	4	0.9455	16.3	0.821	Contact Map
4xr9A	2	0.9455	14.4	0.825	Contact Map
1mszA	1	0.6727	14.2	0.826	Contact Map
4a7pA	2	0.9455	14.1	0.826	Contact Map
3vtfA	2	0.9455	12.2	0.831	Contact Map
3ojoA	2	0.9273	11	0.834	Contact Map
2o3jA	4	0.9818	7.7	0.846	Contact Map
3gg2A	3	0.9455	7.7	0.846	Contact Map
3i9v3	1	0.9273	7.6	0.846	Contact Map
2q3eA	5	0.9455	7.4	0.847	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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