DUF2953 - PFAM28P - GREMLIN Contacts

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DUF2953 - Protein of unknown function (DUF2953)

PFAM:	PF11167	Sequences: TRIGLGDAADTGILYGALWALKGLLLGLLSRYFRLKKPDISVTPDFNEEVFEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (51)
Sequences:	2736 (2254)
Seq/√Len:	315.6
META:	0.793

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_Y	19_W	3.425	1.00
2_R	52_E	2.757	1.00
2_R	45_D	2.454	1.00
2_R	43_T	2.393	1.00
5_L	14_L	2.176	1.00
30_S	35_L	1.954	1.00
45_D	48_E	1.940	1.00
5_L	10_D	1.903	1.00
18_L	42_V	1.593	1.00
12_G	46_F	1.420	1.00
4_G	51_F	1.362	1.00
20_A	24_L	1.330	1.00
6_G	49_E	1.257	1.00
19_W	23_G	1.160	1.00
9_A	13_I	1.129	1.00
28_L	32_Y	1.124	1.00
24_L	27_G	1.105	1.00
11_T	44_P	1.103	1.00
20_A	23_G	1.083	1.00
17_A	20_A	1.044	1.00
3_I	18_L	1.038	1.00
8_A	47_N	1.034	1.00
13_I	17_A	1.033	1.00
9_A	12_G	1.010	1.00
5_L	11_T	0.996	1.00
19_W	38_P	0.990	1.00
3_I	15_Y	0.978	1.00
8_A	11_T	0.953	1.00
19_W	22_K	0.932	1.00
22_K	26_L	0.924	1.00
12_G	15_Y	0.892	1.00
22_K	42_V	0.884	1.00
6_G	10_D	0.876	1.00
9_A	16_G	0.868	1.00
45_D	50_V	0.868	1.00
28_L	31_R	0.866	1.00
13_I	16_G	0.862	1.00
27_G	30_S	0.851	1.00
23_G	27_G	0.848	1.00
16_G	19_W	0.833	1.00
16_G	20_A	0.820	1.00
26_L	30_S	0.818	1.00
48_E	52_E	0.807	1.00
10_D	14_L	0.787	1.00
14_L	17_A	0.786	1.00
3_I	11_T	0.783	1.00
38_P	41_S	0.772	0.99
26_L	40_I	0.768	0.99
2_R	48_E	0.751	0.99
22_K	25_L	0.750	0.99
22_K	40_I	0.748	0.99
49_E	52_E	0.747	0.99
2_R	50_V	0.735	0.99
27_G	31_R	0.735	0.99
31_R	34_R	0.727	0.99
26_L	43_T	0.722	0.99
7_D	12_G	0.689	0.99
22_K	38_P	0.664	0.98
30_S	33_F	0.659	0.98
32_Y	35_L	0.640	0.98
8_A	45_D	0.627	0.98
22_K	41_S	0.611	0.97
11_T	14_L	0.590	0.97
4_G	8_A	0.584	0.97
10_D	17_A	0.582	0.97
15_Y	44_P	0.571	0.96
15_Y	23_G	0.570	0.96
34_R	37_K	0.555	0.95
38_P	42_V	0.547	0.95
10_D	27_G	0.543	0.95
3_I	42_V	0.529	0.94
40_I	46_F	0.521	0.94
26_L	37_K	0.509	0.93
6_G	48_E	0.508	0.93
15_Y	42_V	0.500	0.92
15_Y	22_K	0.500	0.92

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
1z5hA	3	0.3962	10.7	0.813	Contact Map
4b8rA	1	0.434	7.8	0.825	Contact Map
1ua4A	1	0.4151	7.3	0.827	Contact Map
1l2lA	1	0.3396	5.1	0.839	Contact Map
4twkA	2	0.7358	5	0.84	Contact Map
2yd0A	1	0.6226	4.8	0.841	Contact Map
2wswA	3	1	4.6	0.842	Contact Map
3u9wA	1	0.6226	3.6	0.851	Contact Map
3bjqA	4	0.9057	3	0.856	Contact Map
1x8pA	1	0.3396	2.9	0.857	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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