YRVD - BACSU - GREMLIN Contacts

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YRVD - Uncharacterized protein YrvD

UniProt:	O32045	Sequences: MNKQWTIIFALIFTLIVAIFAVINVRSVEVDYLFGRSEWPLILVILGSVLMGALIVFSVGIFQVMKLKREIKTLRKENRTAIHKQEDTHLADQTDTQDASAMIEKKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	107 (95)
Sequences:	213 (169)
Seq/√Len:	17.3

BACSU - YRVD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_E	75_R	5.382	1.00
32_Y	35_G	3.885	1.00
71_I	74_L	3.281	0.99
18_A	46_L	2.992	0.99
23_I	33_L	2.858	0.98
44_V	48_S	2.825	0.98
11_L	14_T	2.224	0.92
14_T	63_Q	2.081	0.89
5_W	16_I	1.978	0.87
20_F	30_V	1.761	0.79
10_A	17_V	1.674	0.76
27_S	70_E	1.596	0.72
19_I	23_I	1.574	0.71
22_V	45_I	1.533	0.69
22_V	25_V	1.513	0.68
3_K	6_T	1.488	0.67
15_L	46_L	1.476	0.66
32_Y	51_M	1.473	0.66
47_G	56_V	1.470	0.66
32_Y	37_S	1.456	0.65
3_K	32_Y	1.424	0.63
53_A	60_G	1.403	0.62
8_I	57_F	1.379	0.60
23_I	42_I	1.363	0.60
57_F	65_M	1.337	0.58
77_E	82_I	1.327	0.57
15_L	22_V	1.307	0.56
44_V	49_V	1.294	0.55
3_K	59_V	1.276	0.54
17_V	49_V	1.260	0.53
6_T	62_F	1.251	0.53
32_Y	44_V	1.228	0.51
49_V	64_V	1.191	0.49
14_T	46_L	1.166	0.48
9_F	17_V	1.152	0.47
36_R	42_I	1.149	0.47
11_L	15_L	1.131	0.46
16_I	86_E	1.115	0.45
36_R	72_K	1.072	0.42
13_F	69_R	1.062	0.42
73_T	77_E	1.054	0.41
25_V	30_V	1.046	0.41
13_F	43_L	1.033	0.40
2_N	68_K	1.027	0.39
39_W	44_V	0.995	0.38
5_W	47_G	0.976	0.37
9_F	55_I	0.973	0.36
72_K	75_R	0.973	0.36
2_N	81_A	0.943	0.35
15_L	47_G	0.941	0.35
81_A	88_T	0.940	0.35
30_V	74_L	0.930	0.34
12_I	56_V	0.929	0.34
3_K	63_Q	0.915	0.33
16_I	79_R	0.904	0.33
39_W	64_V	0.897	0.32
6_T	56_V	0.881	0.31
5_W	37_S	0.870	0.31
33_L	37_S	0.856	0.30
25_V	50_L	0.856	0.30
77_E	81_A	0.853	0.30
83_H	87_D	0.850	0.30
6_T	18_A	0.837	0.29
54_L	94_T	0.830	0.29
33_L	66_K	0.819	0.28
76_K	94_T	0.819	0.28
79_R	87_D	0.813	0.28
19_I	38_E	0.811	0.28
17_V	55_I	0.807	0.28
26_R	68_K	0.806	0.28
37_S	51_M	0.793	0.27
34_F	50_L	0.790	0.27
84_K	87_D	0.790	0.27
27_S	79_R	0.780	0.26
90_L	95_D	0.779	0.26
20_F	23_I	0.776	0.26
65_M	68_K	0.772	0.26
12_I	42_I	0.759	0.25
5_W	39_W	0.755	0.25
16_I	35_G	0.755	0.25
48_S	76_K	0.753	0.25
35_G	49_V	0.733	0.24
86_E	90_L	0.716	0.24
30_V	50_L	0.712	0.23
72_K	92_D	0.710	0.23
23_I	29_E	0.708	0.23
76_K	84_K	0.703	0.23
60_G	67_L	0.696	0.23
84_K	88_T	0.693	0.23
2_N	63_Q	0.691	0.22
48_S	59_V	0.688	0.22
19_I	66_K	0.686	0.22
16_I	83_H	0.685	0.22
81_A	84_K	0.679	0.22
10_A	31_D	0.666	0.21
25_V	39_W	0.660	0.21
21_A	43_L	0.657	0.21
20_F	50_L	0.654	0.21
11_L	85_Q	0.652	0.21
71_I	83_H	0.648	0.21
17_V	90_L	0.647	0.21
75_R	80_T	0.645	0.21
45_I	49_V	0.635	0.20
7_I	14_T	0.629	0.20
17_V	61_I	0.626	0.20
4_Q	30_V	0.623	0.20
16_I	71_I	0.614	0.19
56_V	59_V	0.612	0.19
6_T	57_F	0.609	0.19
78_N	81_A	0.606	0.19
15_L	43_L	0.604	0.19
17_V	77_E	0.599	0.19
81_A	85_Q	0.596	0.19
37_S	44_V	0.595	0.19
82_I	88_T	0.590	0.19
6_T	58_S	0.587	0.18
53_A	84_K	0.583	0.18
16_I	76_K	0.577	0.18
25_V	42_I	0.576	0.18
53_A	69_R	0.573	0.18
35_G	70_E	0.561	0.17
89_H	92_D	0.559	0.17
87_D	91_A	0.557	0.17
8_I	13_F	0.552	0.17
82_I	86_E	0.551	0.17
15_L	56_V	0.549	0.17
17_V	72_K	0.548	0.17
8_I	18_A	0.543	0.17
63_Q	68_K	0.540	0.17
18_A	63_Q	0.539	0.17
3_K	66_K	0.533	0.17
22_V	67_L	0.533	0.17
21_A	45_I	0.531	0.16
50_L	62_F	0.529	0.16
38_E	83_H	0.528	0.16
2_N	71_I	0.527	0.16
16_I	42_I	0.522	0.16
7_I	57_F	0.515	0.16
27_S	38_E	0.514	0.16
23_I	35_G	0.510	0.16
26_R	38_E	0.504	0.16
19_I	76_K	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
4qinA	2	0.9533	55.3	0.903	Contact Map
3pjsK	4	0.9813	40.5	0.911	Contact Map
4etpA	1	0.4112	35.2	0.914	Contact Map
3rvyA	3	0.5794	34.5	0.915	Contact Map
4q4gX	1	0	30.5	0.917	Contact Map
4cgkA	3	0.271	25.9	0.92	Contact Map
4c7rA	3	0.8505	25.7	0.92	Contact Map
2mn6B	2	0.3738	24.3	0.921	Contact Map
2ksdA	1	0.6822	23.8	0.921	Contact Map
2j5uA	4	0.3551	21.6	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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