YVDC - BACSU - GREMLIN Contacts

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YVDC - Uncharacterized protein YvdC

UniProt:	O32263	Sequences: MQLADAEKWMKEFYEKRGWTEYGPFIRVGFLMEEAGELARAVRAYEIGRDRPDEKESSRAEQKQELIEEMGDVIGNIAILADMYGVSLEDVMKAHQEKLTKRFEHA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	106 (104)
Sequences:	113 (80)
Seq/√Len:	7.9

BACSU - YVDC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_R	66_L	3.556	0.94
6_A	75_G	2.343	0.70
39_A	65_E	2.314	0.69
71_G	95_H	2.308	0.69
20_T	75_G	2.206	0.65
17_R	50_D	1.963	0.55
28_V	80_L	1.948	0.55
53_D	76_N	1.946	0.55
53_D	71_G	1.803	0.49
53_D	95_H	1.771	0.48
6_A	82_D	1.761	0.47
51_R	71_G	1.630	0.42
62_Q	103_F	1.600	0.41
51_R	76_N	1.570	0.40
17_R	99_L	1.569	0.40
13_F	24_P	1.553	0.39
6_A	78_A	1.543	0.39
51_R	95_H	1.524	0.38
6_A	20_T	1.519	0.38
8_K	85_G	1.505	0.37
71_G	76_N	1.502	0.37
44_A	66_L	1.498	0.37
76_N	95_H	1.468	0.36
32_M	80_L	1.397	0.33
51_R	91_V	1.353	0.32
8_K	101_K	1.349	0.31
6_A	51_R	1.318	0.30
12_E	77_I	1.296	0.30
2_Q	86_V	1.287	0.29
10_M	51_R	1.286	0.29
45_Y	66_L	1.269	0.29
20_T	65_E	1.263	0.28
13_F	42_V	1.261	0.28
55_K	61_E	1.235	0.28
6_A	71_G	1.216	0.27
13_F	80_L	1.208	0.27
93_K	97_E	1.206	0.27
28_V	93_K	1.205	0.27
7_E	38_L	1.191	0.26
45_Y	58_S	1.191	0.26
6_A	95_H	1.185	0.26
45_Y	70_M	1.177	0.26
61_E	97_E	1.169	0.25
55_K	101_K	1.154	0.25
8_K	90_D	1.149	0.25
29_G	35_A	1.135	0.24
12_E	58_S	1.128	0.24
23_G	51_R	1.099	0.23
12_E	60_A	1.097	0.23
10_M	95_H	1.090	0.23
6_A	24_P	1.071	0.23
60_A	85_G	1.063	0.22
20_T	78_A	1.058	0.22
26_I	80_L	1.055	0.22
23_G	83_M	1.041	0.22
35_A	92_M	1.039	0.22
71_G	96_Q	1.038	0.22
42_V	80_L	1.033	0.21
38_L	66_L	1.018	0.21
40_R	45_Y	1.017	0.21
35_A	42_V	1.007	0.21
38_L	86_V	1.007	0.21
28_V	63_K	0.997	0.21
20_T	82_D	0.997	0.21
39_A	104_E	0.993	0.20
13_F	103_F	0.989	0.20
53_D	96_Q	0.987	0.20
23_G	67_I	0.985	0.20
75_G	78_A	0.979	0.20
49_R	54_E	0.967	0.20
8_K	60_A	0.965	0.20
71_G	91_V	0.956	0.19
91_V	95_H	0.953	0.19
59_R	103_F	0.947	0.19
81_A	87_S	0.945	0.19
38_L	79_I	0.940	0.19
23_G	38_L	0.931	0.19
71_G	88_L	0.926	0.19
29_G	75_G	0.916	0.18
24_P	80_L	0.909	0.18
30_F	50_D	0.893	0.18
50_D	99_L	0.889	0.18
78_A	82_D	0.884	0.18
22_Y	50_D	0.875	0.17
6_A	91_V	0.864	0.17
38_L	45_Y	0.861	0.17
5_D	101_K	0.850	0.17
7_E	103_F	0.849	0.17
20_T	79_I	0.846	0.17
88_L	95_H	0.846	0.17
6_A	53_D	0.834	0.17
15_E	78_A	0.831	0.16
79_I	83_M	0.821	0.16
57_S	67_I	0.797	0.16
15_E	97_E	0.793	0.16
29_G	63_K	0.783	0.15
71_G	81_A	0.778	0.15
78_A	91_V	0.776	0.15
28_V	40_R	0.768	0.15
6_A	10_M	0.764	0.15
53_D	91_V	0.743	0.15
25_F	51_R	0.739	0.15
32_M	59_R	0.728	0.14
44_A	74_I	0.727	0.14
13_F	22_Y	0.726	0.14
65_E	75_G	0.726	0.14
40_R	65_E	0.725	0.14
51_R	96_Q	0.723	0.14
55_K	97_E	0.719	0.14
22_Y	80_L	0.703	0.14
18_G	22_Y	0.698	0.14
81_A	96_Q	0.694	0.14
35_A	91_V	0.688	0.14
31_L	70_M	0.686	0.13
57_S	97_E	0.678	0.13
41_A	81_A	0.670	0.13
53_D	81_A	0.669	0.13
16_K	100_T	0.656	0.13
38_L	83_M	0.653	0.13
88_L	92_M	0.650	0.13
20_T	32_M	0.646	0.13
27_R	50_D	0.636	0.13
90_D	104_E	0.627	0.12
86_V	90_D	0.618	0.12
45_Y	83_M	0.608	0.12
12_E	61_E	0.607	0.12
22_Y	35_A	0.605	0.12
14_Y	102_R	0.597	0.12
14_Y	52_P	0.597	0.12
29_G	42_V	0.597	0.12
52_P	102_R	0.597	0.12
21_E	74_I	0.595	0.12
67_I	91_V	0.595	0.12
40_R	89_E	0.580	0.12
11_K	63_K	0.577	0.12
18_G	77_I	0.572	0.11
2_Q	5_D	0.571	0.11
28_V	39_A	0.565	0.11
21_E	39_A	0.560	0.11
57_S	63_K	0.559	0.11
79_I	82_D	0.559	0.11
56_E	85_G	0.549	0.11
44_A	62_Q	0.548	0.11
6_A	76_N	0.543	0.11
55_K	63_K	0.543	0.11
4_A	60_A	0.534	0.11
18_G	21_E	0.529	0.11
26_I	79_I	0.528	0.11
42_V	59_R	0.526	0.11
59_R	100_T	0.523	0.11
8_K	61_E	0.520	0.11
65_E	78_A	0.517	0.11
76_N	88_L	0.511	0.10
22_Y	26_I	0.508	0.10
40_R	44_A	0.507	0.10
67_I	90_D	0.500	0.10

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
4qgpA	4	0.9528	99.7	0.657	Contact Map
2a3qA	3	0.9717	99.7	0.661	Contact Map
2gtaA	4	0.9151	99.7	0.665	Contact Map
2q5zA	4	0.8868	99.6	0.694	Contact Map
4dk2A	2	0.7453	99.5	0.709	Contact Map
2oieA	3	0.8962	99.5	0.714	Contact Map
2q73A	4	0.8585	99.4	0.724	Contact Map
1vmgA	4	0.7642	99.2	0.759	Contact Map
2yxhA	2	0.8396	99	0.777	Contact Map
3craA	2	0.8019	98.9	0.784	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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