DBP10CT - PFAM28P - GREMLIN Contacts

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DBP10CT - DBP10CT (NUC160) domain

PFAM:	PF08147	Sequences: DLTGDDGEGLRKQKRVMKMRWDKKKKKYVKRTNGDEDGSKKIRTESGAKIPASYKSGRYDKWKKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (62)
Sequences:	634 (446)
Seq/√Len:	56.7
META:	0.44

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_D	38_G	2.663	1.00
41_K	49_K	2.645	1.00
43_R	49_K	2.631	1.00
42_I	52_A	2.498	1.00
60_D	64_K	2.395	1.00
60_D	63_K	2.303	1.00
23_K	28_Y	2.118	1.00
51_P	54_Y	1.657	0.99
17_M	30_K	1.638	0.99
58_R	61_K	1.608	0.99
22_D	26_K	1.587	0.98
57_G	60_D	1.507	0.98
4_G	7_G	1.498	0.98
40_K	53_S	1.433	0.97
44_T	48_A	1.409	0.97
13_Q	17_M	1.365	0.96
6_D	28_Y	1.350	0.96
59_Y	62_W	1.344	0.96
14_K	17_M	1.292	0.94
4_G	9_G	1.231	0.93
3_T	27_K	1.227	0.93
9_G	12_K	1.189	0.92
44_T	50_I	1.122	0.89
10_L	13_Q	1.119	0.89
36_E	40_K	1.115	0.89
28_Y	41_K	1.109	0.88
23_K	59_Y	1.089	0.88
53_S	56_S	1.082	0.87
17_M	28_Y	1.075	0.87
44_T	51_P	1.031	0.85
4_G	11_R	1.029	0.84
8_E	11_R	1.027	0.84
7_G	14_K	1.009	0.83
46_S	49_K	1.007	0.83
15_R	57_G	0.999	0.83
14_K	18_K	0.930	0.78
6_D	34_G	0.911	0.76
33_N	36_E	0.898	0.75
37_D	49_K	0.891	0.75
31_R	37_D	0.885	0.74
12_K	15_R	0.884	0.74
6_D	9_G	0.875	0.73
44_T	54_Y	0.874	0.73
23_K	26_K	0.823	0.69
25_K	48_A	0.809	0.67
55_K	60_D	0.807	0.67
28_Y	50_I	0.796	0.66
16_V	30_K	0.793	0.66
13_Q	16_V	0.790	0.66
7_G	18_K	0.787	0.65
28_Y	31_R	0.784	0.65
44_T	52_A	0.765	0.63
18_K	32_T	0.762	0.63
24_K	42_I	0.754	0.62
6_D	22_D	0.753	0.62
4_G	13_Q	0.745	0.61
22_D	43_R	0.738	0.60
35_D	39_S	0.726	0.59
9_G	39_S	0.722	0.59
12_K	16_V	0.707	0.57
44_T	56_S	0.702	0.56
14_K	30_K	0.700	0.56
32_T	41_K	0.694	0.56
6_D	40_K	0.692	0.55
7_G	11_R	0.686	0.55
23_K	61_K	0.684	0.55
15_R	26_K	0.675	0.54
15_R	32_T	0.674	0.53
12_K	60_D	0.668	0.53
55_K	61_K	0.661	0.52
23_K	29_V	0.661	0.52
24_K	28_Y	0.661	0.52
37_D	40_K	0.656	0.51
24_K	54_Y	0.651	0.51
41_K	44_T	0.649	0.51
28_Y	63_K	0.648	0.51
26_K	33_N	0.635	0.49
39_S	46_S	0.614	0.47
6_D	46_S	0.612	0.47
28_Y	61_K	0.610	0.46
4_G	12_K	0.605	0.46
57_G	63_K	0.603	0.46
42_I	51_P	0.596	0.45
29_V	42_I	0.578	0.43
52_A	56_S	0.577	0.43
2_L	9_G	0.562	0.41
15_R	30_K	0.553	0.40
14_K	43_R	0.532	0.38
31_R	34_G	0.519	0.37
33_N	50_I	0.517	0.37
9_G	29_V	0.511	0.36
21_W	47_G	0.509	0.36
27_K	31_R	0.500	0.35

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
2cs2A	1	0.6769	11.6	0.866	Contact Map
3j60B	1	0.7538	3.5	0.896	Contact Map
4ujpC	1	0.7538	3.4	0.896	Contact Map
1ynxA	1	0.9231	3.4	0.896	Contact Map
3j20A	1	0.7538	3.1	0.897	Contact Map
3j7aB	1	0.7538	2.7	0.901	Contact Map
3j38B	1	0.7846	2.5	0.903	Contact Map
1jmcA	1	0.9231	1.9	0.908	Contact Map
4gnxC	1	0.9231	1.9	0.909	Contact Map
4bpe4	1	0.7538	1.6	0.913	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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