EB - PFAM28P - GREMLIN Contacts

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PFAM:	PF01683	Sequences: CPPGYVCVNGKCVPKVKLGESCSSDEQCTGGSVCVNGVCQCPPGYVAVNGKC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (49)
Sequences:	3090 (2691)
Seq/√Len:	384.4
META:	0.182

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_L	47_A	3.429	1.00
17_K	20_E	3.191	1.00
42_P	45_Y	3.021	1.00
16_V	20_E	2.851	1.00
24_S	27_Q	2.159	1.00
35_V	40_Q	2.007	1.00
4_G	15_K	1.919	1.00
33_V	42_P	1.669	1.00
13_V	27_Q	1.532	1.00
31_G	42_P	1.459	1.00
18_L	32_S	1.458	1.00
47_A	50_G	1.452	1.00
21_S	38_V	1.367	1.00
28_C	39_C	1.366	1.00
17_K	50_G	1.333	1.00
30_G	33_V	1.223	1.00
48_V	51_K	1.210	1.00
7_C	41_C	1.206	1.00
8_V	13_V	1.186	1.00
36_N	40_Q	1.117	1.00
16_V	27_Q	1.078	1.00
35_V	43_P	1.078	1.00
6_V	9_N	1.075	1.00
23_S	27_Q	1.061	1.00
29_T	32_S	1.039	1.00
19_G	47_A	0.998	1.00
15_K	30_G	0.970	1.00
15_K	29_T	0.899	1.00
26_E	31_G	0.814	1.00
23_S	26_E	0.799	1.00
5_Y	14_P	0.787	1.00
5_Y	41_C	0.781	1.00
19_G	34_C	0.750	1.00
24_S	37_G	0.749	1.00
49_N	52_C	0.742	1.00
43_P	47_A	0.739	1.00
23_S	44_G	0.738	1.00
18_L	29_T	0.722	1.00
14_P	20_E	0.719	1.00
37_G	40_Q	0.717	1.00
6_V	13_V	0.716	1.00
25_D	42_P	0.715	1.00
47_A	51_K	0.693	0.99
31_G	45_Y	0.693	0.99
30_G	47_A	0.684	0.99
21_S	26_E	0.680	0.99
24_S	51_K	0.677	0.99
21_S	37_G	0.653	0.99
5_Y	8_V	0.647	0.99
46_V	50_G	0.641	0.99
16_V	29_T	0.639	0.99
5_Y	23_S	0.634	0.99
40_Q	47_A	0.634	0.99
10_G	15_K	0.618	0.99
17_K	29_T	0.616	0.99
41_C	52_C	0.614	0.99
12_C	22_C	0.609	0.99
7_C	29_T	0.605	0.99
22_C	52_C	0.604	0.99
20_E	50_G	0.599	0.98
8_V	38_V	0.597	0.98
19_G	40_Q	0.581	0.98
23_S	51_K	0.567	0.98
6_V	26_E	0.562	0.98
19_G	38_V	0.559	0.98
11_K	42_P	0.559	0.98
22_C	41_C	0.555	0.97
22_C	28_C	0.543	0.97
48_V	52_C	0.535	0.97
14_P	23_S	0.526	0.97
13_V	37_G	0.521	0.96
6_V	15_K	0.515	0.96
9_N	49_N	0.502	0.96
15_K	27_Q	0.500	0.95

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
1z1yA	2	0.7885	67	0.614	Contact Map
4um9B	2	0.1538	63.4	0.623	Contact Map
3fbyA	3	0.7115	62.5	0.625	Contact Map
4nehB	1	0.9038	62	0.627	Contact Map
1yo8A	1	0.9231	60.9	0.629	Contact Map
2wg3C	1	0.2885	58.5	0.634	Contact Map
4bspA	1	0.7692	58.4	0.634	Contact Map
2mgpA	1	0.9615	57.2	0.636	Contact Map
4ufrB	1	1	57.2	0.636	Contact Map
4xlwB	2	0.8846	55.3	0.641	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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