YBCO - ECOLI - GREMLIN Contacts

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YBCO - Uncharacterized protein YbcO

UniProt:	P68661	Sequences: MADLRKAARGRECQVRIPGVCNGNPETSVLAHIRLTGLCGTGTKPPDLIATIACSACHDEIDRRTHFVDAGYAKECALEGMARTQVIWLKEGVIKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13631
Length:	96 (92)
Sequences:	109 (75)
Seq/√Len:	7.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_A	53_A	3.749	0.96
11_R	91_E	2.776	0.82
60_E	65_T	2.391	0.71
17_I	76_C	2.383	0.71
52_I	88_W	2.380	0.71
7_A	52_I	2.334	0.69
31_A	50_A	2.258	0.66
52_I	93_V	2.185	0.64
4_L	88_W	2.168	0.63
60_E	63_R	2.120	0.61
22_N	55_S	1.972	0.55
28_S	52_I	1.967	0.55
20_V	68_V	1.895	0.52
69_D	72_Y	1.876	0.51
4_L	12_E	1.840	0.50
5_R	30_L	1.798	0.48
38_L	49_I	1.784	0.48
7_A	93_V	1.738	0.46
78_L	82_A	1.714	0.45
60_E	66_H	1.663	0.43
28_S	88_W	1.648	0.42
88_W	93_V	1.598	0.40
55_S	59_D	1.592	0.40
34_R	45_P	1.567	0.39
67_F	73_A	1.525	0.37
23_G	82_A	1.480	0.36
78_L	81_M	1.460	0.35
2_A	5_R	1.436	0.34
22_N	26_E	1.425	0.34
3_D	7_A	1.402	0.33
63_R	66_H	1.362	0.32
60_E	73_A	1.324	0.30
72_Y	76_C	1.314	0.30
63_R	68_V	1.202	0.26
25_P	28_S	1.167	0.25
24_N	65_T	1.096	0.23
33_I	81_M	1.082	0.23
17_I	24_N	1.082	0.23
63_R	73_A	1.060	0.22
30_L	50_A	1.047	0.22
15_V	53_A	1.038	0.21
20_V	30_L	1.035	0.21
50_A	71_G	1.030	0.21
87_I	94_I	0.976	0.20
11_R	93_V	0.972	0.20
66_H	73_A	0.948	0.19
2_A	6_K	0.934	0.19
34_R	37_G	0.880	0.17
79_E	83_R	0.879	0.17
33_I	82_A	0.869	0.17
13_C	21_C	0.868	0.17
12_E	92_G	0.866	0.17
31_A	66_H	0.855	0.17
15_V	80_G	0.848	0.17
39_C	73_A	0.846	0.17
48_L	89_L	0.843	0.17
68_V	90_K	0.836	0.16
39_C	43_T	0.829	0.16
59_D	64_R	0.826	0.16
11_R	77_A	0.818	0.16
87_I	93_V	0.804	0.16
36_T	49_I	0.793	0.16
61_I	81_M	0.793	0.16
10_G	24_N	0.785	0.15
20_V	69_D	0.780	0.15
49_I	74_K	0.773	0.15
10_G	23_G	0.773	0.15
11_R	52_I	0.767	0.15
2_A	61_I	0.764	0.15
41_T	45_P	0.764	0.15
15_V	31_A	0.762	0.15
17_I	61_I	0.749	0.15
54_C	57_C	0.748	0.15
60_E	69_D	0.743	0.14
27_T	54_C	0.738	0.14
57_C	62_D	0.723	0.14
75_E	80_G	0.718	0.14
67_F	71_G	0.717	0.14
17_I	38_L	0.716	0.14
27_T	59_D	0.710	0.14
18_P	41_T	0.705	0.14
60_E	67_F	0.705	0.14
4_L	94_I	0.700	0.14
4_L	52_I	0.699	0.14
63_R	72_Y	0.698	0.14
3_D	88_W	0.694	0.14
65_T	94_I	0.693	0.14
42_G	70_A	0.692	0.13
46_P	86_V	0.687	0.13
34_R	39_C	0.683	0.13
33_I	51_T	0.681	0.13
43_T	71_G	0.681	0.13
39_C	45_P	0.672	0.13
39_C	46_P	0.659	0.13
9_R	59_D	0.655	0.13
77_A	91_E	0.650	0.13
19_G	38_L	0.650	0.13
28_S	49_I	0.649	0.13
7_A	88_W	0.646	0.13
46_P	93_V	0.643	0.13
9_R	53_A	0.640	0.13
20_V	74_K	0.636	0.12
19_G	29_V	0.631	0.12
55_S	80_G	0.617	0.12
66_H	70_A	0.617	0.12
54_C	62_D	0.615	0.12
52_I	91_E	0.614	0.12
57_C	64_R	0.611	0.12
33_I	45_P	0.608	0.12
67_F	70_A	0.606	0.12
77_A	81_M	0.596	0.12
9_R	28_S	0.592	0.12
57_C	84_T	0.583	0.12
6_K	30_L	0.582	0.12
42_G	84_T	0.576	0.11
2_A	60_E	0.569	0.11
51_T	77_A	0.564	0.11
72_Y	75_E	0.563	0.11
13_C	16_R	0.558	0.11
6_K	11_R	0.553	0.11
18_P	69_D	0.551	0.11
71_G	78_L	0.550	0.11
33_I	77_A	0.545	0.11
67_F	75_E	0.545	0.11
7_A	46_P	0.542	0.11
7_A	38_L	0.541	0.11
34_R	79_E	0.540	0.11
26_E	55_S	0.538	0.11
37_G	79_E	0.537	0.11
33_I	78_L	0.531	0.11
9_R	68_V	0.530	0.11
41_T	48_L	0.529	0.11
19_G	39_C	0.524	0.11
69_D	73_A	0.520	0.11
22_N	27_T	0.518	0.11
41_T	94_I	0.506	0.10
12_E	70_A	0.504	0.10
6_K	52_I	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
3g27A	2	0.8438	100	0.289	Contact Map
3plwA	1	0.7812	25.5	0.937	Contact Map
1i8oA	2	0.5625	14.7	0.944	Contact Map
1gnlA	1	0.8229	13.5	0.945	Contact Map
1cchA	1	0.5417	11.3	0.947	Contact Map
1w2lA	1	0.5833	9.5	0.949	Contact Map
4rknA	4	0.9479	9	0.949	Contact Map
1gntA	1	0.8229	8.3	0.95	Contact Map
3ob4A	2	0.25	7.9	0.95	Contact Map
1qn2A	1	0.5729	7.2	0.951	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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