SSPF - BACSU - GREMLIN Contacts

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SSPF - Protein SspF

UniProt:	P37549	Sequences: MGRRRGVMSDEFKYELAKDLGFYDTVKNGGWGEIRARDAGNMVKRAIEIAEQQMAQNQNNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	61 (57)
Sequences:	187 (78)
Seq/√Len:	10.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_I	39_A	2.799	0.91
47_I	51_E	2.595	0.87
45_R	49_I	2.559	0.86
22_F	39_A	2.238	0.77
16_L	49_I	2.023	0.70
22_F	34_I	1.965	0.67
29_G	33_E	1.813	0.61
16_L	42_M	1.720	0.56
10_D	14_Y	1.679	0.55
8_M	13_K	1.597	0.51
5_R	25_T	1.567	0.49
8_M	42_M	1.505	0.46
2_G	55_A	1.457	0.44
42_M	49_I	1.435	0.43
52_Q	56_Q	1.352	0.39
16_L	45_R	1.346	0.39
19_D	56_Q	1.346	0.39
23_Y	31_W	1.293	0.37
18_K	31_W	1.279	0.36
48_E	52_Q	1.249	0.35
4_R	24_D	1.213	0.33
15_E	26_V	1.196	0.33
36_A	48_E	1.190	0.32
39_A	45_R	1.134	0.30
4_R	44_K	1.130	0.30
18_K	23_Y	1.110	0.29
22_F	42_M	1.107	0.29
15_E	31_W	1.107	0.29
47_I	53_Q	1.058	0.27
4_R	29_G	1.006	0.25
14_Y	53_Q	1.002	0.25
36_A	39_A	0.984	0.25
15_E	18_K	0.976	0.24
34_I	45_R	0.970	0.24
32_G	37_R	0.966	0.24
13_K	32_G	0.934	0.23
4_R	41_N	0.924	0.23
3_R	6_G	0.923	0.23
10_D	56_Q	0.899	0.22
10_D	55_A	0.898	0.22
38_D	42_M	0.896	0.22
2_G	56_Q	0.896	0.22
22_F	33_E	0.885	0.21
33_E	38_D	0.878	0.21
35_R	39_A	0.871	0.21
19_D	54_M	0.855	0.20
26_V	31_W	0.834	0.20
33_E	37_R	0.818	0.19
11_E	37_R	0.808	0.19
2_G	37_R	0.789	0.19
5_R	48_E	0.776	0.18
22_F	45_R	0.769	0.18
1_M	6_G	0.749	0.17
14_Y	19_D	0.709	0.16
28_N	41_N	0.699	0.16
12_F	43_V	0.688	0.16
11_E	14_Y	0.687	0.16
18_K	50_A	0.677	0.16
37_R	54_M	0.676	0.16
12_F	16_L	0.671	0.15
38_D	48_E	0.668	0.15
5_R	51_E	0.647	0.15
18_K	26_V	0.646	0.15
27_K	39_A	0.638	0.15
23_Y	27_K	0.627	0.14
27_K	34_I	0.625	0.14
14_Y	23_Y	0.619	0.14
16_L	54_M	0.600	0.14
6_G	27_K	0.587	0.14
34_I	42_M	0.583	0.13
7_V	11_E	0.581	0.13
12_F	52_Q	0.572	0.13
42_M	45_R	0.569	0.13
19_D	45_R	0.560	0.13
31_W	48_E	0.555	0.13
43_V	47_I	0.554	0.13
22_F	35_R	0.542	0.13
10_D	31_W	0.539	0.12
22_F	36_A	0.535	0.12
24_D	54_M	0.527	0.12
29_G	35_R	0.519	0.12
48_E	56_Q	0.515	0.12
48_E	54_M	0.508	0.12
13_K	38_D	0.504	0.12
3_R	15_E	0.503	0.12
4_R	28_N	0.500	0.12

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
2z3xA	3	0.7869	99	0.623	Contact Map
3dnfA	2	0.5574	35.6	0.894	Contact Map
4h4dA	1	0.541	15.7	0.91	Contact Map
4n7bA	1	0.5738	13.1	0.913	Contact Map
4d10E	1	0.3607	7.5	0.922	Contact Map
4plpA	2	1	7.3	0.923	Contact Map
2fk5A	4	0.8197	7	0.924	Contact Map
2e1vA	1	0.3115	6.4	0.925	Contact Map
1k0wA	3	0.8361	6.3	0.925	Contact Map
3te6A	1	0.8525	6	0.926	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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