PspC - PFAM28P - GREMLIN Contacts

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PspC - PspC domain

PFAM:	PF04024	Sequences: KRLYRSRDDRMIAGVCGGLAEYFGIDPTLVRLLFVLLTGILAYLILWIVIPEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (51)
Sequences:	52957 (30165)
Seq/√Len:	4223.9
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_A	47_W	3.982	1.00
16_C	34_F	2.293	1.00
16_C	30_V	2.177	1.00
7_R	52_E	2.093	1.00
6_S	9_D	2.018	1.00
6_S	21_E	1.859	1.00
6_S	17_G	1.812	1.00
46_L	50_I	1.807	1.00
23_F	30_V	1.748	1.00
9_D	17_G	1.591	1.00
3_L	50_I	1.552	1.00
26_D	29_L	1.551	1.00
34_F	38_T	1.530	1.00
25_I	30_V	1.432	1.00
8_D	11_M	1.363	1.00
10_R	17_G	1.296	1.00
9_D	27_P	1.282	1.00
45_I	49_V	1.268	1.00
19_L	30_V	1.192	1.00
10_R	52_E	1.182	1.00
20_A	27_P	1.153	1.00
34_F	39_G	1.149	1.00
17_G	27_P	1.141	1.00
29_L	33_L	1.114	1.00
5_R	52_E	1.062	1.00
5_R	13_A	1.033	1.00
28_T	32_L	1.000	1.00
18_G	22_Y	0.979	1.00
3_L	22_Y	0.973	1.00
6_S	10_R	0.951	1.00
17_G	21_E	0.912	1.00
34_F	46_L	0.911	1.00
7_R	10_R	0.905	1.00
5_R	47_W	0.886	1.00
20_A	30_V	0.848	1.00
4_Y	50_I	0.826	1.00
25_I	29_L	0.812	1.00
4_Y	21_E	0.787	1.00
15_V	50_I	0.783	1.00
19_L	23_F	0.779	1.00
9_D	21_E	0.766	1.00
35_V	38_T	0.755	1.00
15_V	47_W	0.749	1.00
15_V	46_L	0.746	1.00
20_A	25_I	0.746	1.00
42_A	46_L	0.716	1.00
2_R	22_Y	0.696	1.00
39_G	42_A	0.681	1.00
8_D	21_E	0.676	1.00
19_L	34_F	0.668	1.00
36_L	42_A	0.656	1.00
18_G	50_I	0.629	1.00
19_L	46_L	0.623	1.00
32_L	36_L	0.614	1.00
7_R	11_M	0.607	1.00
3_L	19_L	0.606	1.00
11_M	28_T	0.605	1.00
13_A	44_L	0.596	1.00
33_L	37_L	0.594	1.00
41_L	44_L	0.592	1.00
3_L	46_L	0.589	1.00
42_A	45_I	0.581	1.00
25_I	33_L	0.569	1.00
38_T	42_A	0.563	1.00
34_F	42_A	0.562	1.00
40_I	44_L	0.557	1.00
16_C	39_G	0.554	1.00
29_L	32_L	0.546	1.00
7_R	21_E	0.531	1.00
44_L	48_I	0.530	1.00
16_C	37_L	0.529	1.00
5_R	15_V	0.519	1.00
47_W	50_I	0.511	1.00
11_M	31_R	0.506	1.00
46_L	49_V	0.501	1.00
4_Y	22_Y	0.500	1.00

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
3czxA	2	0.5283	7.4	0.849	Contact Map
3l51B	1	0.9057	7	0.85	Contact Map
1jwqA	1	0.4906	5.9	0.855	Contact Map
4dw1A	3	0.3774	5.5	0.857	Contact Map
3ne8A	2	0.6226	5.2	0.86	Contact Map
4x0eA	1	0.0755	5.1	0.86	Contact Map
2xq2A	2	0.9434	4.2	0.865	Contact Map
4rsiB	1	0.9057	4.2	0.865	Contact Map
3nd0A	2	1	4	0.866	Contact Map
3m3pA	1	0.9623	4	0.867	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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