YKTA - BACSU - GREMLIN Contacts

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YKTA - UPF0223 protein YktA

UniProt:	Q45497	Sequences: MEYQYPMNEDWTTEEAVDVIAFFQQVELAYEKGADREELLKAYRRFKEIVPGKAEEKKLCGEFEEQSTYSPYRTVKQARESDHAKIKM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	88 (85)
Sequences:	350 (281)
Seq/√Len:	30.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_K	80_E	3.647	1.00
47_K	56_E	3.065	1.00
26_V	39_L	2.513	0.99
18_D	45_R	2.488	0.99
73_R	76_K	2.314	0.99
60_C	71_P	2.172	0.98
25_Q	34_A	2.009	0.97
52_G	55_E	1.910	0.96
45_R	48_E	1.897	0.96
5_Y	67_S	1.803	0.95
31_E	69_Y	1.745	0.94
23_F	71_P	1.707	0.93
39_L	75_V	1.670	0.92
25_Q	42_A	1.617	0.91
3_Y	69_Y	1.529	0.88
39_L	74_T	1.526	0.88
40_L	78_A	1.508	0.88
22_F	71_P	1.440	0.85
3_Y	31_E	1.430	0.85
5_Y	69_Y	1.415	0.84
29_A	74_T	1.373	0.82
30_Y	74_T	1.365	0.82
55_E	58_K	1.357	0.82
23_F	59_L	1.347	0.81
35_D	38_E	1.345	0.81
45_R	49_I	1.331	0.80
70_S	73_R	1.329	0.80
7_M	66_Q	1.318	0.80
50_V	56_E	1.293	0.78
54_A	57_K	1.282	0.78
63_F	67_S	1.260	0.76
81_S	84_A	1.212	0.74
15_E	49_I	1.191	0.72
64_E	70_S	1.173	0.71
36_R	81_S	1.157	0.70
3_Y	63_F	1.155	0.70
63_F	69_Y	1.136	0.69
60_C	73_R	1.100	0.66
60_C	70_S	1.095	0.66
58_K	70_S	1.095	0.66
7_M	84_A	1.091	0.65
76_K	79_R	1.088	0.65
36_R	40_L	1.056	0.63
47_K	50_V	1.055	0.63
15_E	22_F	1.046	0.62
3_Y	27_E	1.045	0.62
29_A	34_A	1.026	0.61
21_A	24_Q	1.002	0.59
35_D	83_H	0.987	0.58
3_Y	67_S	0.976	0.57
28_L	32_K	0.949	0.55
5_Y	27_E	0.947	0.54
17_V	20_I	0.916	0.52
30_Y	63_F	0.910	0.51
48_E	51_P	0.905	0.51
5_Y	63_F	0.887	0.50
7_M	59_L	0.878	0.49
27_E	63_F	0.851	0.47
29_A	78_A	0.838	0.46
44_R	75_V	0.830	0.45
77_Q	80_E	0.820	0.44
32_K	85_K	0.816	0.44
11_W	19_V	0.812	0.44
26_V	57_K	0.812	0.44
17_V	24_Q	0.806	0.43
37_E	41_K	0.803	0.43
58_K	62_E	0.792	0.42
2_E	83_H	0.791	0.42
35_D	85_K	0.782	0.41
35_D	65_E	0.779	0.41
3_Y	8_N	0.764	0.40
18_D	48_E	0.760	0.40
15_E	52_G	0.755	0.39
9_E	16_A	0.750	0.39
51_P	54_A	0.735	0.38
64_E	67_S	0.732	0.37
30_Y	64_E	0.722	0.37
58_K	61_G	0.721	0.37
53_K	58_K	0.721	0.37
47_K	52_G	0.721	0.37
81_S	86_I	0.713	0.36
28_L	38_E	0.702	0.35
59_L	62_E	0.695	0.35
36_R	44_R	0.695	0.35
26_V	40_L	0.694	0.35
22_F	26_V	0.688	0.34
14_E	83_H	0.688	0.34
44_R	48_E	0.681	0.34
19_V	50_V	0.678	0.33
56_E	75_V	0.674	0.33
13_T	70_S	0.674	0.33
23_F	51_P	0.665	0.33
77_Q	81_S	0.664	0.32
2_E	34_A	0.662	0.32
11_W	70_S	0.654	0.32
41_K	82_D	0.645	0.31
5_Y	31_E	0.644	0.31
53_K	79_R	0.642	0.31
53_K	70_S	0.624	0.30
57_K	60_C	0.621	0.30
4_Q	7_M	0.619	0.29
39_L	42_A	0.615	0.29
18_D	49_I	0.612	0.29
10_D	42_A	0.609	0.29
3_Y	64_E	0.601	0.28
40_L	74_T	0.599	0.28
15_E	27_E	0.595	0.28
4_Q	58_K	0.569	0.26
10_D	20_I	0.567	0.26
19_V	47_K	0.565	0.26
48_E	86_I	0.564	0.26
44_R	77_Q	0.564	0.26
46_F	60_C	0.560	0.26
37_E	83_H	0.560	0.26
20_I	24_Q	0.556	0.25
29_A	33_G	0.553	0.25
55_E	60_C	0.551	0.25
28_L	80_E	0.550	0.25
3_Y	66_Q	0.547	0.25
32_K	77_Q	0.537	0.24
28_L	65_E	0.536	0.24
45_R	51_P	0.523	0.23
19_V	49_I	0.517	0.23
59_L	71_P	0.512	0.23
50_V	59_L	0.509	0.23
27_E	30_Y	0.506	0.22
18_D	33_G	0.504	0.22
25_Q	41_K	0.500	0.22

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
2oy9A	2	0.9659	100	0.023	Contact Map
2q07A	1	0.7386	19.9	0.925	Contact Map
4n5xA	1	0.8068	14.9	0.929	Contact Map
2opoA	2	0.8977	13.3	0.931	Contact Map
1c7vA	1	0.7614	9.5	0.935	Contact Map
2ox1A	2	0.75	9.5	0.935	Contact Map
4ociA	2	0.7727	6.5	0.94	Contact Map
1q80A	1	0.875	6.1	0.941	Contact Map
1ij5A	1	0.9091	5.9	0.941	Contact Map
3i5gC	1	0.8977	5.8	0.941	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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