YDBC - BACSU - GREMLIN Contacts

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YDBC - Uncharacterized protein YdbC

UniProt:	P96598	Sequences: MLIKKMICEVDAANAEAFAKAQSQWEALSHISGFIKQAGGWRKTIDEPLTAEIISVWENREAYDHFMENEHDSIYEENDQKAVILSIEVTVYEEDKPFVHDLLHNPDIRYEPNWTVLKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (90)
Sequences:	180 (89)
Seq/√Len:	9.3

BACSU - YDBC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_M	53_I	2.515	0.82
4_K	66_F	2.467	0.80
40_G	80_Q	2.202	0.72
44_T	79_D	2.171	0.71
67_M	71_H	2.015	0.65
4_K	89_V	1.942	0.62
41_W	66_F	1.854	0.58
10_V	55_S	1.841	0.58
6_M	66_F	1.794	0.55
40_G	84_I	1.789	0.55
4_K	51_A	1.763	0.54
12_A	16_E	1.704	0.52
40_G	71_H	1.703	0.51
66_F	89_V	1.702	0.51
8_C	87_I	1.692	0.51
51_A	66_F	1.676	0.50
66_F	71_H	1.672	0.50
40_G	66_F	1.551	0.45
72_D	80_Q	1.534	0.44
4_K	41_W	1.494	0.42
6_M	51_A	1.494	0.42
34_F	66_F	1.438	0.40
69_N	88_E	1.422	0.39
16_E	61_E	1.418	0.39
19_A	41_W	1.401	0.38
32_S	93_E	1.360	0.37
21_A	75_Y	1.350	0.36
4_K	63_Y	1.307	0.34
16_E	81_K	1.296	0.34
4_K	80_Q	1.289	0.34
4_K	71_H	1.284	0.34
23_S	82_A	1.269	0.33
7_I	55_S	1.262	0.33
60_R	64_D	1.260	0.33
54_I	77_E	1.248	0.32
63_Y	66_F	1.232	0.32
41_W	71_H	1.208	0.31
66_F	80_Q	1.176	0.29
54_I	90_T	1.158	0.29
51_A	72_D	1.154	0.29
51_A	80_Q	1.143	0.28
74_I	89_V	1.140	0.28
4_K	67_M	1.138	0.28
4_K	40_G	1.134	0.28
68_E	73_S	1.121	0.27
31_I	73_S	1.089	0.26
4_K	72_D	1.084	0.26
78_N	92_Y	1.082	0.26
9_E	86_S	1.076	0.26
4_K	34_F	1.073	0.26
2_L	60_R	1.071	0.26
42_R	92_Y	1.065	0.25
8_C	71_H	1.041	0.25
17_A	31_I	1.033	0.24
40_G	67_M	1.011	0.24
2_L	31_I	0.990	0.23
44_T	47_E	0.977	0.23
71_H	80_Q	0.974	0.23
13_A	16_E	0.956	0.22
29_S	82_A	0.953	0.22
51_A	67_M	0.933	0.21
2_L	91_V	0.933	0.21
8_C	58_E	0.918	0.21
66_F	83_V	0.917	0.21
5_K	52_E	0.897	0.20
41_W	51_A	0.888	0.20
9_E	43_K	0.871	0.20
59_N	70_E	0.846	0.19
41_W	67_M	0.839	0.19
56_V	59_N	0.836	0.19
13_A	64_D	0.829	0.18
4_K	84_I	0.828	0.18
80_Q	84_I	0.825	0.18
6_M	41_W	0.819	0.18
75_Y	84_I	0.797	0.18
34_F	40_G	0.792	0.17
63_Y	91_V	0.779	0.17
80_Q	83_V	0.777	0.17
60_R	93_E	0.776	0.17
30_H	35_I	0.774	0.17
35_I	93_E	0.767	0.17
2_L	48_P	0.764	0.17
73_S	93_E	0.763	0.17
66_F	72_D	0.760	0.17
49_L	68_E	0.752	0.16
51_A	71_H	0.739	0.16
66_F	84_I	0.736	0.16
28_L	34_F	0.734	0.16
51_A	55_S	0.728	0.16
58_E	73_S	0.706	0.15
52_E	91_V	0.702	0.15
2_L	28_L	0.701	0.15
3_I	35_I	0.680	0.15
34_F	51_A	0.679	0.15
40_G	72_D	0.670	0.15
29_S	93_E	0.667	0.14
5_K	76_E	0.647	0.14
33_G	39_G	0.645	0.14
31_I	44_T	0.644	0.14
14_N	28_L	0.642	0.14
3_I	74_I	0.631	0.14
4_K	53_I	0.625	0.14
42_R	74_I	0.625	0.14
23_S	76_E	0.624	0.14
52_E	95_D	0.623	0.14
12_A	43_K	0.613	0.13
36_K	67_M	0.609	0.13
63_Y	80_Q	0.608	0.13
67_M	91_V	0.606	0.13
43_K	52_E	0.603	0.13
51_A	63_Y	0.599	0.13
34_F	71_H	0.597	0.13
3_I	7_I	0.596	0.13
16_E	47_E	0.579	0.13
16_E	20_K	0.578	0.13
4_K	83_V	0.573	0.13
2_L	49_L	0.560	0.12
15_A	69_N	0.557	0.12
70_E	79_D	0.556	0.12
2_L	42_R	0.551	0.12
73_S	76_E	0.549	0.12
67_M	72_D	0.537	0.12
32_S	44_T	0.537	0.12
61_E	68_E	0.536	0.12
43_K	86_S	0.532	0.12
26_E	29_S	0.532	0.12
41_W	80_Q	0.529	0.12
34_F	41_W	0.525	0.12
53_I	75_Y	0.516	0.11
76_E	82_A	0.513	0.11
53_I	74_I	0.510	0.11
48_P	77_E	0.507	0.11
48_P	81_K	0.504	0.11
70_E	86_S	0.500	0.11
40_G	51_A	0.500	0.11

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
1tz0A	3	0.8487	97.6	0.813	Contact Map
2gffA	2	0.8235	97.6	0.815	Contact Map
1sqeA	2	0.8067	97.6	0.815	Contact Map
2rilA	2	0.7311	97.5	0.816	Contact Map
2zdoA	2	0.8235	97.5	0.817	Contact Map
4zosA	2	0.7899	97.5	0.817	Contact Map
3e8oA	2	0.8403	97.4	0.819	Contact Map
2fb0A	2	0.7563	97.4	0.819	Contact Map
3f44A	1	0.8235	97.4	0.82	Contact Map
3hx9A	2	0.8403	97.4	0.82	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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