Nodulin_late - PFAM28P - GREMLIN Contacts

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Nodulin_late - Late nodulin protein

PFAM:	PF07127	Sequences: MAKILKFVYVMIIFLSLFLVATNVDAYIPCKTDADCPKKCPPPLVPKCINGFCE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (53)
Sequences:	625 (582)
Seq/√Len:	80.0
META:	0.003

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_C	46_P	4.222	1.00
3_K	6_K	2.698	1.00
33_D	47_K	2.424	1.00
17_L	24_V	2.137	1.00
8_V	12_I	1.868	1.00
14_F	17_L	1.807	1.00
25_D	38_K	1.580	1.00
21_A	43_P	1.562	1.00
6_K	9_Y	1.561	1.00
12_I	20_V	1.406	0.99
36_C	53_C	1.399	0.99
48_C	53_C	1.390	0.99
2_A	8_V	1.376	0.99
15_L	46_P	1.332	0.98
6_K	11_M	1.326	0.98
41_P	47_K	1.257	0.98
12_I	19_L	1.232	0.97
18_F	23_N	1.216	0.97
5_L	13_I	1.204	0.97
33_D	46_P	1.197	0.97
32_T	42_P	1.182	0.97
30_C	35_D	1.132	0.96
5_L	48_C	1.109	0.95
28_I	52_F	1.078	0.94
11_M	20_V	1.051	0.94
14_F	25_D	1.037	0.93
9_Y	19_L	1.014	0.92
10_V	32_T	1.011	0.92
18_F	24_V	1.002	0.92
27_Y	45_V	0.955	0.90
10_V	24_V	0.954	0.90
31_K	39_K	0.939	0.89
5_L	11_M	0.938	0.89
31_K	34_A	0.932	0.89
8_V	26_A	0.903	0.87
42_P	52_F	0.877	0.85
4_I	39_K	0.872	0.85
29_P	52_F	0.844	0.83
15_L	45_V	0.843	0.83
15_L	37_P	0.820	0.81
34_A	38_K	0.811	0.81
34_A	50_N	0.796	0.79
7_F	25_D	0.794	0.79
19_L	41_P	0.792	0.79
13_I	40_C	0.790	0.79
27_Y	39_K	0.774	0.78
3_K	13_I	0.764	0.77
27_Y	52_F	0.762	0.76
10_V	37_P	0.743	0.75
11_M	21_A	0.740	0.74
25_D	52_F	0.740	0.74
9_Y	17_L	0.733	0.74
9_Y	16_S	0.732	0.73
14_F	44_L	0.732	0.73
4_I	13_I	0.709	0.71
11_M	14_F	0.706	0.71
1_M	6_K	0.702	0.70
8_V	19_L	0.700	0.70
17_L	47_K	0.700	0.70
15_L	42_P	0.681	0.68
47_K	52_F	0.669	0.67
1_M	4_I	0.622	0.61
28_I	44_L	0.622	0.61
10_V	34_A	0.602	0.59
36_C	48_C	0.601	0.58
21_A	24_V	0.596	0.58
28_I	51_G	0.587	0.57
25_D	43_P	0.583	0.56
1_M	5_L	0.578	0.56
30_C	36_C	0.575	0.55
4_I	22_T	0.570	0.54
45_V	52_F	0.569	0.54
10_V	28_I	0.555	0.53
30_C	53_C	0.552	0.52
25_D	35_D	0.548	0.52
12_I	22_T	0.543	0.51
4_I	23_N	0.529	0.49
16_S	19_L	0.512	0.47
22_T	37_P	0.503	0.46
4_I	40_C	0.500	0.45

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
1rjiA	1	0.5185	55.6	0.76	Contact Map
2axkA	1	0.5926	51.7	0.766	Contact Map
1tskA	1	0.5741	48.8	0.77	Contact Map
1m2sA	1	0.5926	48.7	0.77	Contact Map
1hp2A	1	0.5741	47.7	0.771	Contact Map
1n8mA	1	0.5556	47.7	0.771	Contact Map
1wmtA	1	0.5741	47.5	0.772	Contact Map
1bigA	1	0.5741	47.4	0.772	Contact Map
1wz5A	1	0.5185	46.9	0.772	Contact Map
1qkyA	1	0.5556	46.9	0.772	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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