YCCU - ECOLI - GREMLIN Contacts

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YCCU - Uncharacterized protein YccU

UniProt:	P75874	Sequences: MKETDIAGILTSTHTIALVGASDKPDRPSYRVMKYLLDQGYHVIPVSPKVAGKTLLGQKGYGTLADVPEKVDMVDVFRNSEAAWGVAQEAIAIGAKTLWMQLGVINEQAAVLARDAGLNVVMDRCPAIEIPRLGLAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13723
Length:	137 (127)
Sequences:	1842 (1250)
Seq/√Len:	110.9

ECOLI - YCCU
BACSU - YNET
HALSA - Q9HRP2
SULSO - Q97Z29

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_T	66_D	3.497	1.00
88_Q	112_L	2.916	1.00
42_H	58_Q	2.424	1.00
35_Y	130_I	2.387	1.00
15_T	42_H	2.327	1.00
37_L	58_Q	2.283	1.00
111_V	115_D	2.246	1.00
13_T	73_M	2.200	1.00
62_G	66_D	2.163	1.00
67_V	71_V	2.131	1.00
84_W	106_N	2.111	1.00
65_A	89_E	2.047	1.00
87_A	98_L	2.023	1.00
102_L	128_I	1.986	1.00
61_Y	68_P	1.834	1.00
21_A	33_M	1.827	1.00
23_D	50_V	1.806	1.00
42_H	69_E	1.800	1.00
65_A	92_A	1.794	1.00
7_A	11_T	1.778	1.00
34_K	38_D	1.758	1.00
8_G	12_S	1.719	1.00
110_A	122_M	1.704	1.00
9_I	97_T	1.669	1.00
83_A	100_M	1.637	1.00
129_E	132_R	1.594	1.00
70_K	96_K	1.552	1.00
15_T	69_E	1.544	1.00
44_I	69_E	1.512	1.00
64_L	93_I	1.486	1.00
46_V	67_V	1.452	1.00
87_A	109_A	1.438	1.00
124_R	129_E	1.421	1.00
54_T	59_K	1.399	1.00
50_V	55_L	1.393	1.00
24_K	27_R	1.365	1.00
105_I	123_D	1.326	1.00
84_W	112_L	1.309	0.99
55_L	60_G	1.280	0.99
82_A	85_G	1.271	0.99
71_V	93_I	1.269	0.99
76_V	98_L	1.231	0.99
91_I	116_A	1.229	0.99
13_T	97_T	1.229	0.99
110_A	120_V	1.217	0.99
39_Q	130_I	1.217	0.99
73_M	126_P	1.204	0.99
91_I	112_L	1.186	0.99
112_L	116_A	1.176	0.99
107_E	122_M	1.169	0.99
85_G	88_Q	1.152	0.99
73_M	97_T	1.146	0.99
76_V	100_M	1.136	0.99
15_T	44_I	1.134	0.98
97_T	119_N	1.129	0.98
13_T	72_D	1.117	0.98
31_R	127_A	1.112	0.98
18_L	43_V	1.111	0.98
37_L	56_L	1.109	0.98
111_V	114_R	1.098	0.98
113_A	118_L	1.076	0.98
87_A	113_A	1.074	0.98
28_P	31_R	1.063	0.98
91_I	118_L	1.058	0.98
16_I	73_M	1.049	0.97
79_N	82_A	1.046	0.97
16_I	126_P	1.028	0.97
110_A	114_R	1.023	0.97
18_L	33_M	1.001	0.97
8_G	119_N	0.987	0.96
102_L	129_E	0.982	0.96
28_P	32_V	0.978	0.96
22_S	29_S	0.975	0.96
127_A	131_P	0.967	0.96
98_L	113_A	0.965	0.96
30_Y	34_K	0.964	0.96
83_A	104_V	0.961	0.96
50_V	53_K	0.958	0.96
107_E	111_V	0.954	0.96
37_L	43_V	0.952	0.96
78_R	82_A	0.949	0.95
105_I	122_M	0.946	0.95
91_I	95_A	0.942	0.95
19_V	74_V	0.938	0.95
95_A	118_L	0.927	0.95
27_R	79_N	0.926	0.95
35_Y	127_A	0.904	0.94
63_T	89_E	0.904	0.94
75_D	126_P	0.899	0.94
84_W	88_Q	0.899	0.94
37_L	42_H	0.868	0.93
84_W	108_Q	0.867	0.93
77_F	101_Q	0.866	0.93
5_D	119_N	0.864	0.93
94_G	118_L	0.845	0.92
24_K	49_K	0.842	0.92
106_N	112_L	0.839	0.91
54_T	60_G	0.835	0.91
21_A	55_L	0.833	0.91
31_R	34_K	0.807	0.90
106_N	109_A	0.806	0.90
50_V	60_G	0.797	0.89
8_G	11_T	0.797	0.89
100_M	120_V	0.792	0.89
16_I	41_Y	0.773	0.88
47_S	50_V	0.754	0.86
53_K	59_K	0.751	0.86
53_K	62_G	0.751	0.86
9_I	121_V	0.740	0.85
90_A	118_L	0.737	0.85
19_V	90_A	0.733	0.85
49_K	53_K	0.725	0.84
23_D	49_K	0.724	0.84
88_Q	92_A	0.704	0.83
30_Y	56_L	0.698	0.82
83_A	106_N	0.692	0.81
36_L	126_P	0.686	0.81
90_A	98_L	0.684	0.81
29_S	33_M	0.684	0.81
96_K	119_N	0.679	0.80
61_Y	67_V	0.677	0.80
22_S	86_V	0.675	0.80
44_I	67_V	0.674	0.80
107_E	110_A	0.674	0.80
35_Y	39_Q	0.671	0.79
26_D	31_R	0.670	0.79
36_L	43_V	0.661	0.78
76_V	86_V	0.658	0.78
85_G	89_E	0.658	0.78
32_V	77_F	0.649	0.77
5_D	12_S	0.648	0.77
80_S	106_N	0.647	0.77
76_V	83_A	0.646	0.77
33_M	36_L	0.645	0.77
12_S	96_K	0.642	0.76
5_D	8_G	0.639	0.76
54_T	57_G	0.638	0.76
43_V	58_Q	0.635	0.76
45_P	60_G	0.634	0.75
21_A	43_V	0.633	0.75
33_M	43_V	0.631	0.75
91_I	94_G	0.627	0.75
4_T	7_A	0.620	0.74
27_R	104_V	0.615	0.73
6_I	124_R	0.610	0.73
19_V	86_V	0.602	0.72
102_L	127_A	0.602	0.72
4_T	8_G	0.600	0.71
23_D	30_Y	0.596	0.71
100_M	113_A	0.593	0.71
87_A	91_I	0.590	0.70
45_P	59_K	0.588	0.70
67_V	93_I	0.588	0.70
25_P	30_Y	0.586	0.70
90_A	95_A	0.578	0.69
23_D	55_L	0.571	0.68
32_V	101_Q	0.571	0.68
87_A	112_L	0.566	0.67
72_D	96_K	0.559	0.66
25_P	34_K	0.557	0.66
25_P	32_V	0.556	0.66
35_Y	131_P	0.556	0.66
33_M	56_L	0.554	0.65
90_A	94_G	0.552	0.65
6_I	121_V	0.552	0.65
21_A	32_V	0.551	0.65
102_L	105_I	0.549	0.65
31_R	131_P	0.547	0.64
23_D	29_S	0.544	0.64
75_D	101_Q	0.536	0.63
88_Q	91_I	0.536	0.63
47_S	60_G	0.535	0.63
21_A	37_L	0.533	0.62
80_S	104_V	0.531	0.62
18_L	21_A	0.530	0.62
58_Q	61_Y	0.528	0.62
31_R	35_Y	0.525	0.61
21_A	60_G	0.519	0.60
41_Y	47_S	0.516	0.60
13_T	126_P	0.515	0.60
115_D	118_L	0.515	0.60
10_L	41_Y	0.511	0.59
23_D	47_S	0.509	0.59
85_G	106_N	0.507	0.59
22_S	47_S	0.506	0.58
87_A	106_N	0.504	0.58
27_R	33_M	0.504	0.58
47_S	79_N	0.503	0.58
21_A	56_L	0.501	0.58
83_A	87_A	0.500	0.58

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
3ff4A	1	0.8832	99.9	0.502	Contact Map
2csuA	2	0.9416	99.9	0.544	Contact Map
2duwA	1	1	99.9	0.558	Contact Map
1iukA	1	0.9927	99.9	0.567	Contact Map
2d59A	1	0.9854	99.8	0.603	Contact Map
1y81A	1	0.8467	99.8	0.62	Contact Map
3pffA	2	0.9197	99.7	0.648	Contact Map
2fp4A	1	0.9781	99.6	0.677	Contact Map
2yv1A	1	0.9343	99.6	0.691	Contact Map
3mwdB	1	0.927	99.5	0.7	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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