YAJD - ECOLI - GREMLIN Contacts

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YAJD - Uncharacterized protein YajD

UniProt:	P0AAQ2	Sequences: MAIIPKNYARLESGYREKALKIYPWVCGRCSREFVYSNLRELTVHHIDHDHTNNPEDGSNWELLCLYCHDHEHSKYTEADQYGTTVIAGEDAQKDVGEAKYNPFADLKAMMNKKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11097
Length:	115 (90)
Sequences:	766 (651)
Seq/√Len:	68.7

ECOLI - YAJD INSA1 INSA5 INSA6 INSA7 INSA2 INSA3 INSA4 SPRT
HALSA - F2Z681 Q9HSS9 O51967 Q9HR14
SULSO - Q97ZR7 RNP4 Q97XN0 Q97ZR5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_Y	19_A	6.314	1.00
57_D	60_N	3.599	1.00
60_N	73_H	3.476	1.00
57_D	73_H	2.716	1.00
27_C	30_C	2.417	1.00
34_F	64_L	2.285	1.00
19_A	24_P	2.235	1.00
70_D	73_H	1.980	1.00
64_L	73_H	1.931	1.00
50_D	54_N	1.910	1.00
36_Y	41_E	1.888	1.00
32_R	64_L	1.829	1.00
27_C	45_H	1.716	1.00
20_L	24_P	1.675	0.99
26_V	33_E	1.586	0.99
60_N	64_L	1.543	0.99
30_C	45_H	1.491	0.99
37_S	43_T	1.459	0.99
94_K	97_G	1.391	0.98
47_I	52_T	1.389	0.98
46_H	74_S	1.311	0.97
33_E	63_L	1.298	0.97
27_C	57_D	1.282	0.97
34_F	62_E	1.280	0.97
17_E	24_P	1.252	0.96
15_Y	21_K	1.243	0.96
15_Y	24_P	1.243	0.96
37_S	67_Y	1.230	0.96
44_V	66_L	1.219	0.96
88_A	93_Q	1.208	0.95
32_R	62_E	1.200	0.95
44_V	47_I	1.181	0.95
96_V	99_A	1.143	0.94
73_H	77_T	1.107	0.93
30_C	49_H	1.104	0.93
19_A	23_Y	1.097	0.92
70_D	77_T	1.075	0.92
97_G	100_K	1.069	0.91
67_Y	71_H	1.062	0.91
21_K	35_V	1.048	0.90
26_V	34_F	1.045	0.90
84_T	87_I	1.041	0.90
16_R	29_R	1.023	0.89
26_V	31_S	0.957	0.86
29_R	37_S	0.956	0.86
94_K	100_K	0.947	0.85
35_V	41_E	0.934	0.85
42_L	45_H	0.917	0.83
80_D	85_T	0.914	0.83
26_V	56_E	0.912	0.83
100_K	104_F	0.901	0.82
96_V	102_N	0.881	0.81
37_S	44_V	0.879	0.81
31_S	61_W	0.864	0.80
89_G	92_A	0.840	0.78
88_A	92_A	0.833	0.77
43_T	75_K	0.832	0.77
96_V	104_F	0.829	0.77
21_K	36_Y	0.822	0.76
100_K	103_P	0.819	0.76
55_P	67_Y	0.819	0.76
47_I	50_D	0.818	0.76
16_R	61_W	0.816	0.76
80_D	98_E	0.803	0.74
88_A	96_V	0.800	0.74
94_K	99_A	0.791	0.73
48_D	56_E	0.790	0.73
91_D	95_D	0.786	0.73
27_C	49_H	0.785	0.73
16_R	46_H	0.777	0.72
66_L	70_D	0.773	0.72
16_R	76_Y	0.767	0.71
14_G	17_E	0.766	0.71
92_A	96_V	0.750	0.69
37_S	65_C	0.744	0.69
28_G	58_G	0.741	0.68
14_G	44_V	0.740	0.68
30_C	57_D	0.739	0.68
95_D	99_A	0.731	0.67
92_A	98_E	0.730	0.67
29_R	46_H	0.721	0.66
93_Q	99_A	0.721	0.66
89_G	102_N	0.717	0.66
90_E	95_D	0.697	0.64
23_Y	53_N	0.696	0.64
82_Y	91_D	0.686	0.62
84_T	88_A	0.681	0.62
45_H	73_H	0.681	0.62
90_E	93_Q	0.673	0.61
98_E	103_P	0.669	0.60
55_P	65_C	0.663	0.60
14_G	18_K	0.661	0.60
98_E	101_Y	0.656	0.59
47_I	51_H	0.655	0.59
17_E	22_I	0.654	0.59
45_H	49_H	0.647	0.58
56_E	63_L	0.644	0.58
45_H	60_N	0.638	0.57
62_E	75_K	0.636	0.57
83_G	86_V	0.627	0.56
51_H	55_P	0.627	0.56
89_G	96_V	0.620	0.55
53_N	65_C	0.617	0.54
43_T	56_E	0.611	0.54
14_G	40_R	0.604	0.53
20_L	23_Y	0.602	0.53
60_N	70_D	0.602	0.53
81_Q	101_Y	0.591	0.51
19_A	25_W	0.585	0.51
83_G	88_A	0.580	0.50
17_E	47_I	0.578	0.50
94_K	103_P	0.573	0.49
54_N	66_L	0.569	0.49
15_Y	18_K	0.567	0.48
90_E	94_K	0.563	0.48
66_L	69_H	0.563	0.48
21_K	51_H	0.562	0.48
43_T	46_H	0.557	0.47
41_E	46_H	0.556	0.47
45_H	57_D	0.555	0.47
33_E	69_H	0.548	0.46
99_A	104_F	0.534	0.44
90_E	96_V	0.533	0.44
14_G	36_Y	0.530	0.44
43_T	71_H	0.525	0.43
88_A	98_E	0.519	0.43
94_K	102_N	0.518	0.43
80_D	88_A	0.518	0.43
69_H	75_K	0.517	0.42
16_R	74_S	0.515	0.42
82_Y	101_Y	0.514	0.42
84_T	103_P	0.513	0.42
44_V	50_D	0.510	0.42
92_A	97_G	0.507	0.41
86_V	92_A	0.500	0.40

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
2i13A	1	0.6522	99.5	0.376	Contact Map
3w5kB	1	0.687	99.4	0.398	Contact Map
1x6hA	1	0.713	99.4	0.4	Contact Map
2ee8A	1	0.7391	99.4	0.403	Contact Map
2lv2A	1	0.7043	99.4	0.403	Contact Map
4x9jA	1	0.6696	99.4	0.408	Contact Map
2dmdA	1	0.7304	99.4	0.41	Contact Map
2n25A	1	0.2	99.4	0.41	Contact Map
1x6eA	1	0.6261	99.4	0.418	Contact Map
2kmkA	1	0.6696	99.4	0.418	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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