SBP - BACSU - GREMLIN Contacts

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SBP - Small basic protein

UniProt:	P28265	Sequences: MWLPVLGLVLGIAIGLMTNLTIPSEYSNYLSLAVLAALDTLIGGIRAHLQGTYDEMVFVSGFFFNIILAISLAFLGVHLGVDLYLAGIFAFGVRLFQNIAVIRRNLLTKWTLSKKNKKNVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	121 (106)
Sequences:	361 (166)
Seq/√Len:	16.1

BACSU - SBP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_D	99_I	2.770	0.97
3_L	106_L	2.519	0.95
63_F	100_A	2.433	0.94
44_G	47_A	2.244	0.91
46_R	50_Q	2.162	0.89
14_I	18_T	2.091	0.88
86_A	89_F	2.036	0.86
85_L	88_I	2.030	0.86
28_N	82_D	2.030	0.86
29_Y	86_A	1.924	0.83
31_S	84_Y	1.922	0.83
20_L	79_L	1.858	0.80
39_D	94_R	1.817	0.79
75_L	105_N	1.748	0.76
70_I	100_A	1.723	0.75
38_L	102_I	1.707	0.74
87_G	91_F	1.683	0.73
40_T	78_H	1.628	0.71
60_S	64_F	1.616	0.70
70_I	80_G	1.609	0.70
38_L	42_I	1.602	0.69
86_A	93_V	1.587	0.69
8_L	23_P	1.575	0.68
4_P	7_G	1.544	0.66
75_L	95_L	1.541	0.66
59_V	105_N	1.528	0.66
34_V	99_I	1.511	0.65
26_Y	84_Y	1.478	0.63
22_I	85_L	1.457	0.62
44_G	54_D	1.447	0.61
37_A	54_D	1.399	0.59
80_G	92_G	1.374	0.57
12_I	107_L	1.365	0.57
80_G	83_L	1.337	0.55
18_T	77_V	1.335	0.55
94_R	103_R	1.288	0.52
15_G	47_A	1.280	0.52
32_L	57_V	1.274	0.51
13_A	52_T	1.270	0.51
6_L	86_A	1.268	0.51
18_T	71_S	1.215	0.48
10_L	21_T	1.189	0.46
72_L	86_A	1.186	0.46
64_F	99_I	1.179	0.46
7_G	100_A	1.163	0.45
90_A	93_V	1.150	0.44
45_I	95_L	1.131	0.43
61_G	91_F	1.127	0.43
13_A	17_M	1.127	0.43
40_T	57_V	1.116	0.42
88_I	93_V	1.094	0.41
5_V	47_A	1.078	0.40
30_L	74_F	1.075	0.40
61_G	87_G	1.075	0.40
5_V	12_I	1.069	0.40
13_A	47_A	1.068	0.40
6_L	10_L	1.067	0.39
5_V	48_H	1.039	0.38
11_G	96_F	1.022	0.37
44_G	56_M	1.000	0.36
100_A	104_R	0.980	0.35
40_T	82_D	0.978	0.35
34_V	81_V	0.976	0.35
29_Y	88_I	0.953	0.33
66_I	78_H	0.940	0.33
77_V	82_D	0.935	0.32
34_V	68_L	0.927	0.32
49_L	55_E	0.892	0.30
46_R	49_L	0.891	0.30
5_V	106_L	0.890	0.30
53_Y	87_G	0.890	0.30
60_S	91_F	0.884	0.30
22_I	49_L	0.871	0.29
35_L	71_S	0.870	0.29
74_F	82_D	0.861	0.29
29_Y	89_F	0.860	0.29
9_V	13_A	0.860	0.29
39_D	103_R	0.842	0.28
56_M	59_V	0.838	0.28
43_G	103_R	0.834	0.27
93_V	99_I	0.832	0.27
54_D	107_L	0.831	0.27
3_L	57_V	0.830	0.27
34_V	97_Q	0.830	0.27
9_V	57_V	0.829	0.27
4_P	24_S	0.814	0.27
9_V	77_V	0.805	0.26
91_F	103_R	0.795	0.26
40_T	64_F	0.788	0.25
85_L	93_V	0.786	0.25
73_A	86_A	0.780	0.25
73_A	90_A	0.773	0.25
7_G	96_F	0.767	0.24
7_G	11_G	0.754	0.24
52_T	105_N	0.736	0.23
37_A	85_L	0.732	0.23
44_G	48_H	0.729	0.23
16_L	57_V	0.715	0.22
3_L	90_A	0.714	0.22
36_A	62_F	0.711	0.22
5_V	101_V	0.702	0.22
3_L	105_N	0.702	0.22
9_V	24_S	0.695	0.22
21_T	85_L	0.693	0.21
34_V	75_L	0.688	0.21
22_I	30_L	0.685	0.21
38_L	53_Y	0.684	0.21
60_S	87_G	0.677	0.21
33_A	42_I	0.676	0.21
12_I	83_L	0.672	0.21
14_I	21_T	0.670	0.21
19_N	78_H	0.666	0.20
34_V	93_V	0.664	0.20
29_Y	37_A	0.663	0.20
40_T	99_I	0.661	0.20
50_Q	95_L	0.656	0.20
41_L	74_F	0.652	0.20
35_L	95_L	0.649	0.20
45_I	67_I	0.648	0.20
34_V	108_T	0.647	0.20
17_M	26_Y	0.644	0.20
33_A	41_L	0.643	0.20
28_N	59_V	0.642	0.20
10_L	23_P	0.642	0.20
82_D	85_L	0.634	0.19
10_L	48_H	0.622	0.19
30_L	44_G	0.619	0.19
6_L	108_T	0.614	0.18
14_I	71_S	0.614	0.18
5_V	51_G	0.603	0.18
37_A	89_F	0.589	0.18
19_N	26_Y	0.584	0.17
32_L	40_T	0.582	0.17
73_A	93_V	0.581	0.17
34_V	51_G	0.578	0.17
46_R	95_L	0.577	0.17
49_L	102_I	0.575	0.17
35_L	40_T	0.562	0.17
10_L	51_G	0.562	0.17
45_I	51_G	0.554	0.16
26_Y	91_F	0.549	0.16
90_A	97_Q	0.541	0.16
40_T	77_V	0.536	0.16
34_V	45_I	0.527	0.16
35_L	73_A	0.526	0.16
61_G	84_Y	0.521	0.15
51_G	78_H	0.517	0.15
32_L	37_A	0.514	0.15
26_Y	87_G	0.514	0.15
42_I	107_L	0.513	0.15
30_L	88_I	0.513	0.15
60_S	104_R	0.512	0.15
73_A	83_L	0.510	0.15
82_D	93_V	0.510	0.15
52_T	83_L	0.509	0.15
57_V	67_I	0.507	0.15
47_A	71_S	0.506	0.15
48_H	81_V	0.503	0.15
26_Y	56_M	0.500	0.15

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
4eneA	2	0.8347	19.2	0.94	Contact Map
4umwA	1	0.9008	9.5	0.948	Contact Map
3j08A	2	0.9917	9.2	0.948	Contact Map
3j09A	2	0.9752	8.5	0.949	Contact Map
3nd0A	2	0.8099	6.1	0.952	Contact Map
4r23A	1	0.0248	6	0.952	Contact Map
4gb32	4	0.4215	5.5	0.953	Contact Map
4rr3G	1	0.405	5.5	0.953	Contact Map
3w4tA	1	0.9174	5.5	0.953	Contact Map
1ncqB	4	0.4298	5.2	0.954	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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