T0878_316_358 - CASP12 - GREMLIN Contacts

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T0878_316_358 - T0878 316-358

ID:	23	Sequences: GTIAFQDPKLWKALCETDLIIPPPGKTDAQARAMIRKTHEPAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	43 (40)
Sequences:	11 (8)
Seq/√Len:	1.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_P	28_D	2.361	0.17
13_A	21_I	2.160	0.15
16_E	34_M	2.113	0.15
35_I	39_H	1.937	0.13
7_D	21_I	1.884	0.13
27_T	30_Q	1.855	0.13
17_T	37_K	1.831	0.13
29_A	32_R	1.682	0.12
18_D	37_K	1.674	0.12
20_I	26_K	1.455	0.10
7_D	13_A	1.396	0.10
9_K	12_K	1.380	0.10
37_K	40_E	1.340	0.09
26_K	33_A	1.245	0.09
26_K	34_M	1.168	0.09
27_T	36_R	1.118	0.08
9_K	40_E	1.108	0.08
4_A	23_P	1.050	0.08
4_A	25_G	1.050	0.08
10_L	23_P	1.050	0.08
10_L	25_G	1.050	0.08
4_A	10_L	1.050	0.08
29_A	33_A	1.037	0.08
2_T	11_W	1.016	0.08
2_T	6_Q	1.016	0.08
6_Q	11_W	1.016	0.08
2_T	5_F	0.967	0.08
5_F	11_W	0.967	0.08
5_F	38_T	0.919	0.07
28_D	32_R	0.904	0.07
18_D	36_R	0.900	0.07
11_W	14_L	0.814	0.07
2_T	14_L	0.814	0.07
6_Q	14_L	0.814	0.07
36_R	40_E	0.811	0.07
33_A	37_K	0.766	0.07
17_T	36_R	0.688	0.06
6_Q	38_T	0.687	0.06
2_T	38_T	0.687	0.06
11_W	38_T	0.687	0.06
28_D	33_A	0.685	0.06
21_I	32_R	0.684	0.06
12_K	26_K	0.656	0.06
16_E	26_K	0.618	0.06
12_K	33_A	0.603	0.06
8_P	37_K	0.601	0.06
13_A	18_D	0.601	0.06
8_P	13_A	0.594	0.06
19_L	25_G	0.575	0.06
4_A	19_L	0.575	0.06
10_L	19_L	0.575	0.06
19_L	23_P	0.575	0.06
16_E	36_R	0.570	0.06
18_D	40_E	0.544	0.06
26_K	32_R	0.535	0.06
20_I	28_D	0.530	0.06
3_I	35_I	0.509	0.06
30_Q	36_R	0.503	0.06
12_K	40_E	0.502	0.06
12_K	36_R	0.500	0.06

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
1cq3_A	1	0.8372	19.2	0.85	Contact Map
1odh_A	1	0.6744	9.1	0.87	Contact Map
2nw8_A	1	0.3953	8.2	0.873	Contact Map
3vk5_A	1	0.3488	5.6	0.882	Contact Map
1x6v_B	1	0.9535	5	0.885	Contact Map
2vga_A	1	0.8372	4.9	0.886	Contact Map
1vky_A	1	0.9302	4.7	0.886	Contact Map
4njc_A	1	1	4.4	0.888	Contact Map
3pt1_A	1	0.9302	4	0.89	Contact Map
3ddd_A	1	0.5116	3.7	0.892	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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