USPD - ECOLI - GREMLIN Contacts

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USPD - Universal stress protein D

UniProt:	P0AAB8	Sequences: MAYKHIGVAISGNEEDALLVNKALELARHNDAHLTLIHIDDGLSELYPGIYFPATEDILQLLKNKSDNKLYKLTKNIQWPKTKLRIERGEMPETLLEIMQKEQCDLLVCGHHHSFINRLMPAYRGMINKMSADLLIVPFIDK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11877
Length:	142 (131)
Sequences:	20960 (17089)
Seq/√Len:	1493.1

ECOLI - USPD USPA USPC USPG USPF USPE
BACSU - YXIE NHAX
HALSA - Q9HRP5 Q9HMI9 Q9HPQ8 Q9HPF7 Q9HP90 Q9HMJ0 Q9HPP5 Q9HRD8 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_T	85_R	2.974	1.00
7_G	104_C	2.818	1.00
5_H	35_T	2.764	1.00
92_P	125_G	2.702	1.00
22_K	135_L	2.431	1.00
5_H	33_H	2.414	1.00
33_H	83_K	2.368	1.00
106_L	135_L	2.270	1.00
85_R	98_I	2.169	1.00
107_L	132_A	2.002	1.00
63_K	67_D	1.985	1.00
109_C	126_M	1.944	1.00
35_T	104_C	1.937	1.00
89_G	94_T	1.887	1.00
35_T	83_K	1.880	1.00
87_E	94_T	1.850	1.00
35_T	98_I	1.781	1.00
124_R	128_N	1.778	1.00
99_M	107_L	1.744	1.00
8_V	23_A	1.739	1.00
37_I	98_I	1.724	1.00
9_A	109_C	1.696	1.00
39_I	94_T	1.665	1.00
9_A	95_L	1.659	1.00
94_T	97_E	1.514	1.00
26_L	30_N	1.480	1.00
33_H	81_K	1.451	1.00
32_A	105_D	1.426	1.00
107_L	130_M	1.413	1.00
125_G	129_K	1.410	1.00
100_Q	131_S	1.403	1.00
67_D	71_Y	1.389	1.00
96_L	129_K	1.370	1.00
66_S	70_L	1.348	1.00
8_V	20_V	1.334	1.00
23_A	27_A	1.329	1.00
91_M	122_A	1.292	1.00
59_L	63_K	1.268	1.00
69_K	72_K	1.243	1.00
87_E	98_I	1.233	1.00
98_I	104_C	1.224	1.00
71_Y	75_K	1.216	1.00
99_M	131_S	1.216	1.00
21_N	73_L	1.209	1.00
107_L	126_M	1.187	1.00
62_L	66_S	1.179	1.00
71_Y	84_L	1.173	1.00
99_M	132_A	1.164	1.00
5_H	105_D	1.157	1.00
66_S	69_K	1.151	1.00
39_I	91_M	1.141	1.00
115_F	118_R	1.130	1.00
62_L	65_K	1.117	1.00
12_G	38_H	1.106	1.00
69_K	73_L	1.099	1.00
37_I	87_E	1.099	1.00
65_K	69_K	1.075	1.00
5_H	104_C	1.067	1.00
22_K	137_V	1.064	1.00
60_Q	64_N	1.054	1.00
130_M	134_L	1.049	1.00
64_N	68_N	1.042	1.00
118_R	124_R	1.035	1.00
40_D	88_R	1.029	1.00
38_H	66_S	1.016	1.00
109_C	123_Y	1.003	1.00
37_I	95_L	0.997	1.00
67_D	84_L	0.992	1.00
99_M	104_C	0.990	1.00
25_E	29_H	0.988	1.00
56_E	60_Q	0.987	1.00
74_T	77_I	0.985	1.00
127_I	136_I	0.984	1.00
73_L	77_I	0.978	1.00
16_D	19_L	0.975	1.00
113_H	117_N	0.964	1.00
73_L	76_N	0.952	1.00
22_K	26_L	0.949	1.00
20_V	36_L	0.945	1.00
96_L	99_M	0.942	1.00
65_K	68_N	0.921	1.00
23_A	108_V	0.920	1.00
71_Y	74_T	0.917	1.00
13_N	16_D	0.917	1.00
22_K	25_E	0.914	1.00
27_A	34_L	0.900	1.00
10_I	36_L	0.888	1.00
59_L	62_L	0.880	1.00
6_I	106_L	0.879	1.00
54_A	57_D	0.879	1.00
74_T	84_L	0.876	1.00
23_A	34_L	0.876	1.00
22_K	133_D	0.870	1.00
17_A	69_K	0.868	1.00
7_G	37_I	0.864	1.00
68_N	72_K	0.860	1.00
10_I	19_L	0.847	1.00
56_E	59_L	0.844	1.00
9_A	110_G	0.839	1.00
30_N	105_D	0.837	1.00
47_Y	50_I	0.824	1.00
96_L	130_M	0.818	1.00
96_L	126_M	0.811	1.00
40_D	86_I	0.810	1.00
7_G	98_I	0.809	1.00
77_I	80_P	0.808	1.00
72_K	75_K	0.804	1.00
72_K	76_N	0.803	1.00
123_Y	136_I	0.801	1.00
7_G	107_L	0.800	1.00
21_N	76_N	0.796	1.00
49_G	52_F	0.795	1.00
90_E	93_E	0.792	1.00
18_L	21_N	0.789	1.00
10_I	20_V	0.787	1.00
24_L	77_I	0.786	1.00
24_L	28_R	0.786	1.00
67_D	70_L	0.785	1.00
74_T	78_Q	0.783	1.00
17_A	21_N	0.783	1.00
92_P	122_A	0.782	1.00
10_I	17_A	0.775	1.00
8_V	19_L	0.774	1.00
20_V	24_L	0.765	1.00
8_V	34_L	0.759	1.00
108_V	135_L	0.756	1.00
94_T	98_I	0.746	1.00
109_C	136_I	0.745	1.00
36_L	70_L	0.737	1.00
63_K	66_S	0.733	1.00
26_L	29_H	0.731	1.00
36_L	82_T	0.708	1.00
24_L	80_P	0.706	1.00
58_I	62_L	0.706	1.00
37_I	94_T	0.702	1.00
60_Q	63_K	0.699	1.00
68_N	71_Y	0.698	1.00
27_A	30_N	0.695	1.00
6_I	108_V	0.692	1.00
55_T	59_L	0.689	1.00
61_L	64_N	0.686	1.00
61_L	65_K	0.684	1.00
95_L	126_M	0.678	1.00
108_V	137_V	0.673	1.00
25_E	28_R	0.668	1.00
17_A	73_L	0.663	1.00
103_Q	132_A	0.657	1.00
57_D	61_L	0.653	1.00
27_A	32_A	0.648	1.00
57_D	60_Q	0.643	1.00
119_L	123_Y	0.639	1.00
100_Q	132_A	0.637	1.00
58_I	61_L	0.636	1.00
70_L	74_T	0.617	1.00
92_P	96_L	0.616	1.00
13_N	112_H	0.614	1.00
26_L	108_V	0.613	1.00
64_N	67_D	0.610	1.00
23_A	32_A	0.608	1.00
39_I	89_G	0.607	1.00
66_S	77_I	0.605	1.00
92_P	129_K	0.605	1.00
10_I	16_D	0.604	1.00
15_E	18_L	0.598	1.00
25_E	77_I	0.597	1.00
53_P	57_D	0.594	1.00
55_T	58_I	0.594	1.00
96_L	125_G	0.592	1.00
6_I	27_A	0.591	1.00
126_M	134_L	0.589	1.00
92_P	126_M	0.586	1.00
82_T	85_R	0.583	1.00
43_L	46_L	0.583	1.00
112_H	115_F	0.579	1.00
112_H	119_L	0.576	1.00
111_H	123_Y	0.574	1.00
110_G	137_V	0.572	1.00
67_D	73_L	0.567	1.00
51_Y	54_A	0.566	1.00
74_T	79_W	0.563	1.00
127_I	134_L	0.560	1.00
28_R	80_P	0.560	1.00
19_L	108_V	0.550	1.00
21_N	77_I	0.543	1.00
53_P	56_E	0.541	1.00
11_S	16_D	0.541	1.00
28_R	77_I	0.539	1.00
14_E	17_A	0.537	1.00
89_G	97_E	0.537	1.00
20_V	73_L	0.536	1.00
93_E	97_E	0.534	1.00
75_K	78_Q	0.523	1.00
70_L	73_L	0.522	1.00
40_D	59_L	0.518	1.00
42_G	45_E	0.512	1.00
17_A	76_N	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	0.9859	99.9	0.17	Contact Map
3tnjA	2	0.9155	99.9	0.224	Contact Map
5ahwA	4	0.9859	99.9	0.226	Contact Map
2dumA	2	0.9648	99.9	0.231	Contact Map
3s3tA	4	0.9648	99.9	0.235	Contact Map
4wnyA	2	0.8803	99.8	0.248	Contact Map
3fg9A	3	0.9507	99.8	0.254	Contact Map
3fdxA	2	0.8521	99.8	0.255	Contact Map
1mjhA	2	0.9437	99.8	0.259	Contact Map
3mt0A	1	0.9085	99.8	0.262	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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