UvsY - PFAM28P - GREMLIN Contacts

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UvsY - Recombination, repair and ssDNA binding protein UvsY

PFAM:	PF11056	Sequences: MWEKDSKIDDTELDEESLKIPQLHAKYLKILSTEKLLLKKAEFDYKKLKKEKWEYYTGKADPEVYKEKILKKDDIDKYLDADEDLIKLELKIEYQEEKVDYLESILKQINNRTFQIKNAIEWRKFTSGM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (127)
Sequences:	3398 (2138)
Seq/√Len:	189.7
META:	0.985

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_K	121_E	3.530	1.00
121_E	124_K	3.249	1.00
107_K	110_N	2.750	1.00
16_E	19_K	2.702	1.00
62_P	66_K	2.543	1.00
52_K	84_D	2.268	1.00
101_Y	105_I	2.254	1.00
34_E	95_Q	2.038	1.00
40_K	44_D	2.019	1.00
42_E	96_E	2.001	1.00
123_R	126_T	1.971	1.00
3_E	29_K	1.966	1.00
61_D	64_V	1.934	1.00
51_E	68_K	1.742	1.00
47_K	83_E	1.721	1.00
18_L	119_A	1.700	1.00
79_L	85_L	1.666	1.00
45_Y	85_L	1.623	1.00
14_D	123_R	1.604	1.00
64_V	68_K	1.579	1.00
19_K	22_Q	1.579	1.00
54_E	78_Y	1.571	1.00
46_K	80_D	1.553	1.00
2_W	6_S	1.550	1.00
103_E	107_K	1.548	1.00
83_E	87_K	1.542	1.00
118_N	121_E	1.526	1.00
45_Y	88_L	1.523	1.00
62_P	65_Y	1.510	1.00
34_E	98_K	1.479	1.00
111_N	114_F	1.435	1.00
7_K	22_Q	1.407	1.00
60_A	65_Y	1.407	1.00
76_D	80_D	1.397	1.00
38_L	92_I	1.370	1.00
1_M	30_I	1.370	1.00
117_K	124_K	1.357	1.00
13_L	119_A	1.337	1.00
64_V	67_E	1.336	1.00
100_D	103_E	1.313	1.00
45_Y	89_E	1.304	1.00
38_L	96_E	1.299	1.00
12_E	15_E	1.296	1.00
48_L	52_K	1.261	1.00
69_I	72_K	1.261	1.00
50_K	54_E	1.235	1.00
65_Y	68_K	1.214	1.00
57_T	75_I	1.200	1.00
36_L	94_Y	1.184	1.00
41_A	88_L	1.176	1.00
39_K	93_E	1.175	1.00
17_S	118_N	1.175	1.00
51_E	60_A	1.165	1.00
35_K	97_E	1.137	1.00
2_W	105_I	1.120	1.00
41_A	91_K	1.100	1.00
71_K	74_D	1.096	1.00
31_L	103_E	1.076	1.00
60_A	64_V	1.073	1.00
50_K	81_A	1.069	1.00
95_Q	98_K	1.063	1.00
41_A	95_Q	1.062	1.00
100_D	104_S	1.059	1.00
89_E	93_E	1.052	1.00
29_K	33_T	1.052	1.00
52_K	85_L	1.048	1.00
47_K	51_E	1.036	1.00
43_F	90_L	1.014	1.00
30_I	102_L	1.007	1.00
53_W	59_K	1.007	1.00
63_E	67_E	0.997	0.99
4_K	7_K	0.990	0.99
96_E	100_D	0.989	0.99
93_E	96_E	0.986	0.99
25_A	29_K	0.982	0.99
45_Y	49_K	0.982	0.99
15_E	19_K	0.979	0.99
10_D	123_R	0.978	0.99
28_L	101_Y	0.966	0.99
48_L	88_L	0.965	0.99
16_E	112_R	0.955	0.99
44_D	47_K	0.947	0.99
107_K	111_N	0.943	0.99
34_E	99_V	0.939	0.99
54_E	59_K	0.930	0.99
123_R	127_S	0.929	0.99
42_E	46_K	0.919	0.99
44_D	91_K	0.905	0.99
17_S	119_A	0.904	0.99
70_L	74_D	0.892	0.99
36_L	97_E	0.892	0.99
36_L	40_K	0.872	0.99
20_I	112_R	0.861	0.98
37_L	40_K	0.855	0.98
5_D	26_K	0.854	0.98
52_K	82_D	0.850	0.98
84_D	87_K	0.846	0.98
9_D	12_E	0.844	0.98
35_K	39_K	0.839	0.98
46_K	89_E	0.839	0.98
35_K	100_D	0.838	0.98
108_Q	115_Q	0.826	0.98
49_K	77_K	0.823	0.98
113_T	117_K	0.823	0.98
63_E	66_K	0.822	0.98
5_D	27_Y	0.812	0.98
55_Y	58_G	0.799	0.98
38_L	95_Q	0.795	0.97
13_L	116_I	0.783	0.97
114_F	117_K	0.782	0.97
55_Y	60_A	0.775	0.97
43_F	86_I	0.767	0.97
10_D	15_E	0.762	0.97
38_L	99_V	0.725	0.96
122_W	126_T	0.721	0.95
87_K	90_L	0.720	0.95
27_Y	102_L	0.715	0.95
43_F	93_E	0.712	0.95
40_K	90_L	0.712	0.95
28_L	106_L	0.711	0.95
94_Y	98_K	0.707	0.95
125_F	128_G	0.689	0.94
74_D	77_K	0.679	0.94
60_A	68_K	0.678	0.94
111_N	115_Q	0.674	0.94
41_A	44_D	0.674	0.94
37_L	87_K	0.670	0.93
53_W	57_T	0.667	0.93
24_H	27_Y	0.666	0.93
39_K	42_E	0.662	0.93
17_S	116_I	0.661	0.93
69_I	74_D	0.659	0.93
10_D	14_D	0.651	0.92
31_L	35_K	0.647	0.92
56_Y	82_D	0.645	0.92
53_W	77_K	0.639	0.92
32_S	97_E	0.636	0.91
7_K	10_D	0.634	0.91
14_D	122_W	0.632	0.91
114_F	124_K	0.629	0.91
119_A	123_R	0.615	0.90
14_D	119_A	0.613	0.90
15_E	18_L	0.610	0.90
48_L	85_L	0.608	0.90
49_K	76_D	0.604	0.89
34_E	41_A	0.601	0.89
1_M	4_K	0.600	0.89
50_K	77_K	0.600	0.89
34_E	38_L	0.600	0.89
3_E	7_K	0.596	0.89
51_E	64_V	0.590	0.88
49_K	80_D	0.585	0.88
34_E	102_L	0.585	0.88
104_S	110_N	0.584	0.88
9_D	16_E	0.576	0.87
116_I	120_I	0.571	0.86
62_P	68_K	0.569	0.86
95_Q	99_V	0.566	0.86
39_K	90_L	0.566	0.86
91_K	94_Y	0.564	0.86
2_W	24_H	0.564	0.86
75_I	79_L	0.562	0.86
52_K	79_L	0.559	0.85
113_T	121_E	0.559	0.85
49_K	85_L	0.555	0.85
97_E	100_D	0.554	0.85
104_S	107_K	0.552	0.85
43_F	89_E	0.551	0.85
21_P	115_Q	0.548	0.84
38_L	42_E	0.546	0.84
48_L	84_D	0.546	0.84
27_Y	30_I	0.542	0.84
8_I	16_E	0.539	0.83
28_L	32_S	0.537	0.83
110_N	114_F	0.536	0.83
36_L	39_K	0.535	0.83
107_K	114_F	0.527	0.82
47_K	86_I	0.526	0.82
52_K	68_K	0.524	0.81
31_L	99_V	0.523	0.81
34_E	37_L	0.521	0.81
86_I	90_L	0.519	0.81
98_K	102_L	0.515	0.80
88_L	92_I	0.510	0.80
3_E	25_A	0.506	0.79
37_L	95_Q	0.503	0.79
56_Y	79_L	0.502	0.79
41_A	92_I	0.502	0.79
37_L	41_A	0.502	0.79
33_T	37_L	0.500	0.78

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
4r3zA	1	0.3721	4.3	0.927	Contact Map
3jsrA	1	0.6744	3.3	0.93	Contact Map
3ov9A	3	0.3721	3	0.932	Contact Map
4n78F	1	0.6047	2.6	0.934	Contact Map
1z96A	1	0.2248	2.6	0.934	Contact Map
3mnfA	4	0.2791	2.6	0.934	Contact Map
2gw6A	2	0.4264	2.5	0.934	Contact Map
2o3lA	1	0.6357	2.4	0.935	Contact Map
3b2eE	1	0.5349	2.4	0.935	Contact Map
2rklA	2	0.3411	2.4	0.935	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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