DUF4141 - PFAM28P - GREMLIN Contacts

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DUF4141 - Domain of unknown function (DUF4141)

PFAM:	PF13605	Sequences: KIIILALALLLFTGQAKAQWVVTDPANLAQSIVNTANEIVQTSSTASNMIKNF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (52)
Sequences:	793 (484)
Seq/√Len:	67.1
META:	0.868

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_A	49_M	2.832	1.00
28_L	31_S	2.736	1.00
35_T	38_E	2.627	1.00
49_M	52_N	2.312	1.00
21_V	25_P	2.291	1.00
31_S	34_N	1.980	1.00
23_T	28_L	1.884	1.00
20_W	26_A	1.798	1.00
47_S	51_K	1.761	1.00
23_T	26_A	1.422	0.98
14_G	17_K	1.421	0.98
8_A	11_L	1.400	0.98
46_A	51_K	1.301	0.97
7_L	10_L	1.252	0.96
30_Q	33_V	1.247	0.96
36_A	41_Q	1.224	0.95
35_T	39_I	1.203	0.95
45_T	48_N	1.160	0.94
6_A	12_F	1.155	0.94
42_T	45_T	1.144	0.93
48_N	51_K	1.133	0.93
44_S	50_I	1.132	0.93
7_L	12_F	1.122	0.93
6_A	10_L	1.100	0.92
38_E	41_Q	1.092	0.92
4_I	15_Q	1.045	0.90
12_F	15_Q	1.043	0.90
5_L	15_Q	1.011	0.88
22_V	27_N	1.005	0.88
40_V	43_S	0.997	0.87
8_A	12_F	0.993	0.87
34_N	42_T	0.976	0.86
4_I	14_G	0.966	0.86
41_Q	44_S	0.886	0.80
2_I	7_L	0.882	0.80
4_I	11_L	0.879	0.80
20_W	30_Q	0.876	0.80
4_I	7_L	0.854	0.78
5_L	8_A	0.834	0.76
36_A	40_V	0.833	0.76
45_T	49_M	0.825	0.76
10_L	14_G	0.822	0.75
3_I	14_G	0.803	0.74
34_N	38_E	0.794	0.73
3_I	6_A	0.788	0.72
27_N	31_S	0.756	0.69
31_S	36_A	0.732	0.67
21_V	27_N	0.729	0.66
4_I	10_L	0.727	0.66
3_I	10_L	0.709	0.64
29_A	53_F	0.707	0.64
29_A	33_V	0.703	0.63
40_V	47_S	0.695	0.62
22_V	37_N	0.683	0.61
8_A	15_Q	0.651	0.57
31_S	35_T	0.646	0.57
10_L	15_Q	0.645	0.57
5_L	53_F	0.645	0.57
38_E	42_T	0.640	0.56
11_L	14_G	0.632	0.55
3_I	16_A	0.622	0.54
29_A	37_N	0.599	0.51
44_S	49_M	0.597	0.51
30_Q	38_E	0.589	0.50
47_S	50_I	0.581	0.49
30_Q	37_N	0.571	0.48
4_I	8_A	0.565	0.47
31_S	42_T	0.561	0.47
12_F	17_K	0.545	0.45
25_P	40_V	0.536	0.44
9_L	13_T	0.518	0.42
3_I	13_T	0.517	0.42
21_V	26_A	0.516	0.42
29_A	32_I	0.516	0.42
4_I	12_F	0.513	0.41
44_S	48_N	0.508	0.41
22_V	30_Q	0.507	0.41
11_L	15_Q	0.500	0.40

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
1r8iA	1	0.4528	67.4	0.781	Contact Map
1dbgA	1	0.5472	37.9	0.816	Contact Map
4o5jA	1	0.9811	6.5	0.872	Contact Map
2xfcB	3	0	2.8	0.892	Contact Map
2yewC	3	0.3396	2.8	0.893	Contact Map
4fczB	1	0.6226	2.8	0.893	Contact Map
3j0cB	3	0.3396	2.8	0.893	Contact Map
3j0fI	3	0.3396	2.7	0.893	Contact Map
4bgoA	1	0.6038	2.7	0.894	Contact Map
4pnbA	3	0.5283	2.6	0.894	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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