YUSI - BACSU - GREMLIN Contacts

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YUSI - Uncharacterized protein YusI

UniProt:	O32175	Sequences: MSLTFYWYPKCGTCRKAKKWLEEHGKEINEIHIAEQPPSKEELKALYEKSGLDLKKFFNTSGMKYRELNLKEKLYHMSEDEQLELLASDGMLIKRPLTTDGEKVTVGFKEDQFEENWA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	118 (110)
Sequences:	2519 (1822)
Seq/√Len:	173.7

ECOLI - YFFB ARSC YFGD
BACSU - YUSI MGSR SPX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_E	28_I	3.154	1.00
40_K	84_E	2.602	1.00
47_Y	83_L	2.543	1.00
34_A	91_M	2.285	1.00
5_F	18_K	2.234	1.00
98_T	113_F	2.219	1.00
7_W	30_E	2.218	1.00
100_D	103_K	2.147	1.00
40_K	44_K	2.022	1.00
9_P	32_H	1.969	1.00
44_K	83_L	1.810	1.00
32_H	35_E	1.779	1.00
63_M	67_E	1.616	1.00
64_K	89_D	1.610	1.00
39_S	42_E	1.595	1.00
20_W	108_F	1.590	1.00
78_S	81_E	1.502	1.00
45_A	49_K	1.467	1.00
43_L	87_A	1.410	1.00
4_T	29_N	1.410	1.00
64_K	68_L	1.402	1.00
20_W	24_H	1.388	1.00
99_T	104_V	1.381	1.00
6_Y	31_I	1.377	1.00
5_F	14_C	1.363	1.00
109_K	112_Q	1.350	1.00
62_G	91_M	1.347	1.00
9_P	35_E	1.333	1.00
14_C	33_I	1.310	1.00
18_K	22_E	1.308	1.00
55_K	60_T	1.306	1.00
48_E	79_E	1.305	1.00
63_M	66_R	1.301	1.00
52_L	57_F	1.298	1.00
47_Y	57_F	1.291	1.00
18_K	30_E	1.262	1.00
56_K	61_S	1.249	1.00
31_I	37_P	1.228	1.00
76_H	81_E	1.217	1.00
42_E	99_T	1.212	1.00
58_F	86_L	1.207	1.00
52_L	106_V	1.191	1.00
70_L	73_K	1.182	1.00
7_W	18_K	1.157	1.00
31_I	42_E	1.151	1.00
10_K	15_R	1.145	1.00
111_D	114_E	1.144	1.00
61_S	109_K	1.135	1.00
64_K	67_E	1.135	1.00
56_K	106_V	1.125	1.00
40_K	83_L	1.123	1.00
86_L	92_L	1.121	1.00
42_E	45_A	1.120	1.00
42_E	46_L	1.083	1.00
14_C	18_K	1.068	1.00
49_K	104_V	1.068	1.00
112_Q	115_E	1.066	1.00
9_P	18_K	1.062	1.00
105_T	113_F	1.037	0.99
53_D	56_K	1.027	0.99
79_E	83_L	1.023	0.99
54_L	82_Q	0.999	0.99
20_W	114_E	0.996	0.99
37_P	93_I	0.988	0.99
74_L	77_M	0.980	0.99
40_K	80_D	0.979	0.99
29_N	36_Q	0.976	0.99
47_Y	53_D	0.962	0.99
8_Y	14_C	0.950	0.99
111_D	115_E	0.947	0.99
86_L	93_I	0.945	0.99
44_K	48_E	0.937	0.99
19_K	23_E	0.930	0.99
46_L	97_L	0.918	0.99
47_Y	54_L	0.908	0.99
110_E	114_E	0.907	0.99
97_L	106_V	0.906	0.99
4_T	31_I	0.902	0.98
5_F	98_T	0.898	0.98
65_Y	92_L	0.879	0.98
44_K	79_E	0.877	0.98
98_T	105_T	0.876	0.98
69_N	73_K	0.876	0.98
53_D	82_Q	0.871	0.98
43_L	83_L	0.866	0.98
44_K	80_D	0.863	0.98
73_K	81_E	0.862	0.98
14_C	92_L	0.859	0.98
46_L	104_V	0.855	0.98
3_L	26_K	0.849	0.98
77_M	81_E	0.832	0.97
52_L	56_K	0.832	0.97
24_H	114_E	0.831	0.97
52_L	104_V	0.830	0.97
3_L	100_D	0.827	0.97
74_L	82_Q	0.823	0.97
15_R	19_K	0.821	0.97
47_Y	79_E	0.819	0.97
73_K	77_M	0.806	0.97
70_L	74_L	0.802	0.97
31_I	36_Q	0.792	0.97
17_A	21_L	0.790	0.97
79_E	82_Q	0.781	0.96
57_F	106_V	0.780	0.96
73_K	88_S	0.769	0.96
45_A	99_T	0.745	0.95
84_E	88_S	0.740	0.95
22_E	27_E	0.738	0.95
41_E	44_K	0.731	0.95
70_L	75_Y	0.731	0.95
35_E	62_G	0.727	0.95
31_I	38_P	0.727	0.95
33_I	97_L	0.707	0.94
19_K	22_E	0.707	0.94
105_T	112_Q	0.700	0.93
12_G	19_K	0.695	0.93
68_L	85_L	0.692	0.93
18_K	28_I	0.687	0.93
33_I	93_I	0.687	0.93
34_A	64_K	0.686	0.93
5_F	21_L	0.676	0.92
7_W	32_H	0.669	0.92
8_Y	91_M	0.668	0.92
58_F	90_G	0.666	0.92
9_P	14_C	0.662	0.91
38_P	87_A	0.662	0.91
40_K	87_A	0.661	0.91
62_G	67_E	0.658	0.91
65_Y	77_M	0.654	0.91
49_K	102_E	0.650	0.91
12_G	15_R	0.649	0.90
10_K	32_H	0.644	0.90
99_T	102_E	0.641	0.90
58_F	82_Q	0.641	0.90
77_M	82_Q	0.630	0.89
55_K	82_Q	0.624	0.89
64_K	91_M	0.621	0.88
38_P	42_E	0.617	0.88
15_R	18_K	0.615	0.88
5_F	30_E	0.614	0.88
77_M	85_L	0.609	0.87
82_Q	86_L	0.607	0.87
67_E	89_D	0.605	0.87
49_K	103_K	0.604	0.87
57_F	97_L	0.597	0.86
52_L	97_L	0.594	0.86
6_Y	42_E	0.585	0.85
17_A	113_F	0.585	0.85
105_T	109_K	0.582	0.85
8_Y	34_A	0.581	0.85
6_Y	37_P	0.569	0.84
54_L	79_E	0.553	0.82
43_L	93_I	0.552	0.82
17_A	108_F	0.549	0.82
45_A	48_E	0.542	0.81
33_I	38_P	0.536	0.80
49_K	100_D	0.533	0.80
81_E	84_E	0.531	0.79
46_L	99_T	0.531	0.79
59_N	66_R	0.530	0.79
65_Y	76_H	0.512	0.77
9_P	91_M	0.509	0.76
69_N	75_Y	0.507	0.76
20_W	110_E	0.501	0.75
65_Y	74_L	0.500	0.75

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
3fz4A	1	0.9915	100	0.264	Contact Map
3gkxA	2	0.9915	100	0.264	Contact Map
2kokA	1	0.9746	100	0.288	Contact Map
1z3eA	1	0.9831	100	0.296	Contact Map
1s3cA	2	0.9661	100	0.299	Contact Map
2mu0A	1	0.9746	100	0.305	Contact Map
3f0iA	1	0.9746	100	0.306	Contact Map
2m46A	1	0.9831	100	0.309	Contact Map
3rdwA	1	0.9576	100	0.309	Contact Map
1rw1A	1	0.9661	100	0.313	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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