CTD - PFAM28P - GREMLIN Contacts

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CTD - Spt5 C-terminal nonapeptide repeat binding Spt4

PFAM:	PF12815	Sequences: GSRTPAYGAASGSRTPAWGADGSRTPAYGGGGSRTPAWNAGSRTPAYGAAGSRTPAYSGAWDGSRTPAYGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (65)
Sequences:	601 (499)
Seq/√Len:	61.9
META:	0.469

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_G	48_G	1.813	1.00
13_S	33_S	1.686	0.99
37_A	56_A	1.661	0.99
28_Y	47_Y	1.594	0.99
19_G	48_G	1.527	0.98
52_S	64_S	1.521	0.98
32_G	51_G	1.513	0.98
23_S	42_S	1.477	0.98
8_G	29_G	1.475	0.98
9_A	20_A	1.461	0.98
34_R	53_R	1.446	0.98
23_S	33_S	1.437	0.98
33_S	52_S	1.427	0.98
9_A	30_G	1.395	0.97
13_S	52_S	1.390	0.97
38_W	57_Y	1.388	0.97
14_R	34_R	1.365	0.97
33_S	42_S	1.350	0.97
19_G	29_G	1.328	0.96
13_S	42_S	1.327	0.96
18_W	38_W	1.325	0.96
8_G	19_G	1.299	0.96
12_G	41_G	1.297	0.96
13_S	23_S	1.273	0.95
20_A	30_G	1.260	0.95
41_G	51_G	1.230	0.94
21_D	31_G	1.225	0.94
42_S	52_S	1.220	0.94
22_G	41_G	1.218	0.94
8_G	48_G	1.197	0.93
24_R	43_R	1.182	0.93
12_G	51_G	1.147	0.92
48_G	58_S	1.143	0.92
34_R	43_R	1.143	0.92
12_G	32_G	1.137	0.92
27_A	46_A	1.133	0.91
17_A	37_A	1.117	0.91
37_A	46_A	1.106	0.90
18_W	28_Y	1.094	0.90
42_S	64_S	1.067	0.89
18_W	47_Y	1.064	0.89
22_G	32_G	1.038	0.87
7_Y	18_W	1.034	0.87
12_G	22_G	1.027	0.87
14_R	43_R	1.016	0.86
43_R	65_R	0.992	0.85
6_A	17_A	0.991	0.85
28_Y	38_W	0.987	0.85
24_R	53_R	0.984	0.84
28_Y	57_Y	0.983	0.84
7_Y	38_W	0.961	0.83
53_R	65_R	0.958	0.83
11_S	50_A	0.956	0.83
38_W	47_Y	0.933	0.81
46_A	56_A	0.919	0.80
23_S	52_S	0.901	0.79
20_A	59_G	0.884	0.77
29_G	58_S	0.869	0.76
18_W	57_Y	0.865	0.76
24_R	34_R	0.858	0.75
14_R	53_R	0.855	0.75
35_T	54_T	0.848	0.74
7_Y	28_Y	0.843	0.74
43_R	53_R	0.825	0.72
17_A	46_A	0.818	0.72
40_A	50_A	0.815	0.72
27_A	37_A	0.801	0.70
22_G	51_G	0.794	0.70
17_A	27_A	0.790	0.69
47_Y	57_Y	0.789	0.69
32_G	41_G	0.780	0.68
3_R	24_R	0.765	0.67
21_D	40_A	0.750	0.65
6_A	27_A	0.711	0.61
19_G	58_S	0.705	0.60
15_T	44_T	0.685	0.58
31_G	50_A	0.677	0.57
30_G	59_G	0.658	0.55
3_R	34_R	0.643	0.53
25_T	44_T	0.641	0.53
31_G	40_A	0.627	0.52
21_D	50_A	0.624	0.51
7_Y	47_Y	0.606	0.49
30_G	49_A	0.602	0.49
30_G	39_N	0.596	0.48
13_S	64_S	0.587	0.47
15_T	54_T	0.586	0.47
14_R	24_R	0.580	0.46
51_G	63_G	0.569	0.45
39_N	49_A	0.567	0.45
33_S	64_S	0.563	0.44
6_A	56_A	0.561	0.44
17_A	56_A	0.554	0.43
4_T	15_T	0.532	0.41
56_A	68_A	0.520	0.40
11_S	21_D	0.520	0.40
40_A	60_A	0.502	0.38
25_T	54_T	0.500	0.37

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
1mjtA	2	0.338	1.8	0.889	Contact Map
4j7oA	1	0.6056	1	0.905	Contact Map
4fvyA	2	0.4789	0.8	0.909	Contact Map
2whxA	1	0.9296	0.7	0.912	Contact Map
2k3uB	1	0.0986	0.7	0.913	Contact Map
4e84A	2	0.0845	0.7	0.915	Contact Map
3ig5A	1	0.9155	0.7	0.915	Contact Map
1d0cA	2	0.3803	0.5	0.921	Contact Map
2brqC	2	0.1831	0.5	0.921	Contact Map
2vutI	1	0.2254	0.5	0.923	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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