USPA - ECOLI - GREMLIN Contacts

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USPA - Universal stress protein A

UniProt:	P0AED0	Sequences: MAYKHILIAVDLSPESKVLVEKAVSMARPYNAKVSLIHVDVNYSDLYTGLIDVNLGDMQKRISEETHHALTELSTNAGYPITETLSGSGDLGQVLVDAIKKYDMDLVVCGHHQDFWSKLMSSARQLINTVHVDMLIVPLRDEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11390
Length:	144 (130)
Sequences:	20793 (17136)
Seq/√Len:	1502.9

ECOLI - USPA USPD USPC USPE USPG USPF
BACSU - NHAX YXIE
HALSA - Q9HMI9 Q9HMJ0 Q9HRP5 Q9HP90 Q9HPP5 Q9HPQ8 Q9HRD8 Q9HPF7 Q9HHX5 Q9HHY0 Q9HNX9 Q9HHV8 Q9HMU1
SULSO - Q97X90 Q97V57 Q7LXW4 Q97U40

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_S	85_L	2.966	1.00
7_L	104_M	2.826	1.00
5_H	35_S	2.754	1.00
92_G	125_Q	2.738	1.00
22_K	135_L	2.417	1.00
33_K	83_E	2.262	1.00
5_H	33_K	2.254	1.00
106_L	135_L	2.180	1.00
85_L	98_A	2.075	1.00
107_V	132_V	2.042	1.00
35_S	104_M	1.989	1.00
109_C	126_L	1.896	1.00
87_G	94_V	1.884	1.00
35_S	98_A	1.878	1.00
111_H	138_P	1.870	1.00
37_I	98_A	1.829	1.00
124_R	128_N	1.777	1.00
63_S	67_H	1.770	1.00
99_I	107_V	1.739	1.00
35_S	83_E	1.726	1.00
39_V	94_V	1.712	1.00
9_A	95_L	1.704	1.00
8_I	23_A	1.676	1.00
89_G	94_V	1.665	1.00
9_A	109_C	1.538	1.00
32_A	105_D	1.490	1.00
94_V	97_D	1.489	1.00
26_M	30_Y	1.480	1.00
69_A	72_E	1.424	1.00
96_V	129_T	1.421	1.00
33_K	81_I	1.414	1.00
66_T	70_L	1.392	1.00
107_V	130_V	1.389	1.00
59_Q	63_S	1.346	1.00
100_K	131_H	1.322	1.00
67_H	71_T	1.321	1.00
8_I	20_V	1.298	1.00
125_Q	129_T	1.281	1.00
91_L	122_S	1.261	1.00
87_G	98_A	1.235	1.00
5_H	105_D	1.221	1.00
23_A	27_A	1.201	1.00
66_T	69_A	1.195	1.00
98_A	104_M	1.168	1.00
69_A	73_L	1.164	1.00
99_I	131_H	1.159	1.00
21_E	73_L	1.156	1.00
65_E	69_A	1.138	1.00
107_V	126_L	1.135	1.00
99_I	132_V	1.126	1.00
62_I	66_T	1.122	1.00
71_T	75_T	1.118	1.00
62_I	65_E	1.106	1.00
5_H	104_M	1.086	1.00
37_I	87_G	1.077	1.00
111_H	136_I	1.055	1.00
51_I	54_N	1.051	1.00
39_V	91_L	1.036	1.00
74_S	78_G	1.025	1.00
12_L	38_H	1.022	1.00
22_K	137_V	1.021	1.00
65_E	68_H	1.014	1.00
113_Q	117_S	1.013	1.00
115_F	118_K	1.007	1.00
96_V	99_I	1.003	1.00
64_E	68_H	0.990	1.00
99_I	104_M	0.988	1.00
67_H	84_T	0.984	1.00
38_H	66_T	0.983	1.00
22_K	26_M	0.981	1.00
40_D	88_S	0.973	1.00
130_V	134_M	0.970	1.00
63_S	66_T	0.968	1.00
56_G	60_K	0.964	1.00
71_T	84_T	0.964	1.00
23_A	108_V	0.957	1.00
20_V	36_L	0.955	1.00
127_I	136_I	0.954	1.00
60_K	64_E	0.949	1.00
109_C	123_A	0.944	1.00
74_S	77_A	0.930	1.00
118_K	124_R	0.928	1.00
111_H	123_A	0.918	1.00
13_S	16_S	0.915	1.00
25_S	29_P	0.908	1.00
74_S	84_T	0.889	1.00
71_T	74_S	0.884	1.00
72_E	76_N	0.879	1.00
21_E	76_N	0.879	1.00
37_I	95_L	0.878	1.00
23_A	34_V	0.874	1.00
6_I	106_L	0.860	1.00
22_K	25_S	0.854	1.00
73_L	77_A	0.838	1.00
74_S	79_Y	0.838	1.00
10_V	17_K	0.836	1.00
96_V	130_V	0.832	1.00
58_M	62_I	0.832	1.00
7_L	37_I	0.829	1.00
73_L	76_N	0.826	1.00
16_S	19_L	0.821	1.00
27_A	34_V	0.820	1.00
15_E	139_L	0.815	1.00
7_L	98_A	0.814	1.00
30_Y	105_D	0.813	1.00
67_H	70_L	0.809	1.00
54_N	57_D	0.807	1.00
22_K	133_D	0.805	1.00
40_D	86_S	0.797	1.00
17_K	69_A	0.794	1.00
90_D	93_Q	0.794	1.00
108_V	135_L	0.793	1.00
10_V	36_L	0.791	1.00
17_K	21_E	0.790	1.00
77_A	80_P	0.788	1.00
24_V	28_R	0.776	1.00
92_G	122_S	0.775	1.00
72_E	75_T	0.773	1.00
56_G	59_Q	0.771	1.00
10_V	20_V	0.762	1.00
94_V	98_A	0.754	1.00
9_A	110_G	0.745	1.00
96_V	126_L	0.742	1.00
7_L	107_V	0.737	1.00
18_V	21_E	0.734	1.00
123_A	136_I	0.731	1.00
68_H	72_E	0.727	1.00
24_V	80_P	0.726	1.00
24_V	77_A	0.723	1.00
100_K	132_V	0.719	1.00
58_M	61_R	0.719	1.00
59_Q	62_I	0.718	1.00
52_D	55_L	0.716	1.00
70_L	74_S	0.713	1.00
108_V	137_V	0.709	1.00
17_K	73_L	0.704	1.00
40_D	59_Q	0.703	1.00
109_C	136_I	0.696	1.00
60_K	63_S	0.696	1.00
10_V	19_L	0.695	1.00
27_A	30_Y	0.693	1.00
57_D	60_K	0.686	1.00
47_Y	51_I	0.681	1.00
8_I	19_L	0.676	1.00
8_I	34_V	0.670	1.00
26_M	29_P	0.669	1.00
37_I	94_V	0.668	1.00
20_V	24_V	0.668	1.00
15_E	18_V	0.664	1.00
64_E	67_H	0.662	1.00
61_R	65_E	0.662	1.00
23_A	32_A	0.662	1.00
70_L	73_L	0.660	1.00
6_I	108_V	0.657	1.00
82_T	85_L	0.655	1.00
10_V	16_S	0.654	1.00
6_I	27_A	0.653	1.00
55_L	59_Q	0.649	1.00
26_M	108_V	0.648	1.00
25_S	28_R	0.648	1.00
68_H	71_T	0.648	1.00
55_L	58_M	0.644	1.00
18_V	139_L	0.644	1.00
95_L	126_L	0.644	1.00
27_A	32_A	0.644	1.00
119_L	123_A	0.637	1.00
103_D	132_V	0.630	1.00
36_L	82_T	0.617	1.00
61_R	64_E	0.616	1.00
36_L	70_L	0.610	1.00
92_G	129_T	0.603	1.00
67_H	73_L	0.601	1.00
25_S	77_A	0.599	1.00
28_R	77_A	0.597	1.00
51_I	55_L	0.596	1.00
43_Y	46_L	0.585	1.00
28_R	80_P	0.582	1.00
76_N	79_Y	0.577	1.00
57_D	61_R	0.574	1.00
92_G	126_L	0.569	1.00
96_V	125_Q	0.568	1.00
126_L	134_M	0.567	1.00
85_L	88_S	0.566	1.00
92_G	96_V	0.565	1.00
89_G	97_D	0.559	1.00
75_T	78_G	0.557	1.00
112_H	123_A	0.549	1.00
11_D	16_S	0.543	1.00
93_Q	97_D	0.542	1.00
47_Y	52_D	0.528	1.00
5_H	32_A	0.516	1.00
110_G	137_V	0.512	1.00
69_A	74_S	0.510	1.00
53_V	57_D	0.501	1.00
18_V	22_K	0.500	1.00

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
1jmvA	4	0.9722	99.9	0.172	Contact Map
3tnjA	2	0.9028	99.9	0.204	Contact Map
2dumA	2	0.9653	99.9	0.224	Contact Map
5ahwA	4	0.9722	99.9	0.229	Contact Map
4wnyA	2	0.8681	99.9	0.236	Contact Map
3s3tA	4	0.9514	99.8	0.239	Contact Map
1mjhA	2	0.9375	99.8	0.244	Contact Map
3fg9A	3	0.9375	99.8	0.245	Contact Map
3fdxA	2	0.8403	99.8	0.246	Contact Map
2z08A	4	0.8333	99.8	0.259	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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