YEDK - ECOLI - GREMLIN Contacts

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YEDK - Putative SOS response-associated peptidase YedK

UniProt:	P76318	Sequences: MCGRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13278
Length:	222 (198)
Sequences:	3411 (2472)
Seq/√Len:	175.7

ECOLI - YEDK
BACSU - YOAM YOBE YOQW
HALSA - O51976 Q9HRI0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
100_A	128_M	4.230	1.00
44_V	145_F	4.180	1.00
81_A	148_V	4.144	1.00
46_L	59_V	4.046	1.00
131_I	146_L	3.801	1.00
97_I	172_A	3.314	1.00
18_L	127_F	3.283	1.00
102_G	117_F	2.663	1.00
168_S	171_A	2.648	1.00
114_Q	203_P	2.625	1.00
128_M	147_I	2.404	1.00
96_A	130_A	2.400	1.00
78_V	148_V	2.387	1.00
90_L	133_S	2.361	1.00
48_S	57_D	2.304	1.00
119_Y	200_S	2.154	1.00
119_Y	202_H	2.132	1.00
85_R	88_K	2.064	1.00
134_T	143_E	2.035	1.00
105_E	160_H	1.878	1.00
97_I	127_F	1.847	1.00
73_L	86_M	1.819	1.00
118_I	159_I	1.800	1.00
94_G	133_S	1.787	1.00
82_A	91_W	1.777	1.00
75_N	160_H	1.763	1.00
103_W	156_L	1.736	1.00
17_L	172_A	1.727	1.00
109_E	112_K	1.711	1.00
98_C	145_F	1.692	1.00
76_A	146_L	1.679	1.00
171_A	174_E	1.672	1.00
54_L	173_R	1.661	1.00
5_F	44_V	1.654	1.00
194_V	199_F	1.651	1.00
127_F	172_A	1.635	1.00
153_D	163_R	1.629	1.00
6_A	117_F	1.598	1.00
64_A	142_A	1.593	1.00
185_A	188_I	1.591	1.00
81_A	91_W	1.576	1.00
98_C	147_I	1.560	1.00
9_Q	101_D	1.524	1.00
10_T	13_D	1.523	1.00
46_L	145_F	1.508	1.00
118_I	156_L	1.503	1.00
186_S	190_A	1.496	1.00
38_V	44_V	1.495	1.00
126_I	199_F	1.459	1.00
120_R	124_Q	1.444	1.00
12_E	16_A	1.438	1.00
35_R	42_T	1.408	1.00
154_Q	157_V	1.387	1.00
136_F	141_E	1.371	1.00
48_S	55_H	1.360	1.00
7_Q	38_V	1.339	1.00
150_A	165_L	1.279	1.00
37_N	115_P	1.278	1.00
134_T	141_E	1.250	1.00
120_R	126_I	1.245	1.00
107_K	116_F	1.240	1.00
50_R	53_H	1.238	1.00
112_K	206_R	1.233	1.00
106_W	113_K	1.213	1.00
80_T	84_S	1.212	1.00
166_V	199_F	1.203	1.00
155_G	197_N	1.202	1.00
11_R	15_L	1.202	1.00
35_R	38_V	1.180	1.00
89_P	93_H	1.174	1.00
169_P	172_A	1.174	1.00
117_F	202_H	1.173	1.00
48_S	132_G	1.166	1.00
194_V	197_N	1.163	1.00
5_F	100_A	1.161	1.00
79_E	162_R	1.159	1.00
116_F	203_P	1.156	1.00
89_P	92_Q	1.152	1.00
45_L	56_L	1.141	1.00
98_C	130_A	1.139	1.00
167_L	171_A	1.132	1.00
94_G	132_G	1.131	1.00
196_A	199_F	1.117	1.00
118_I	201_W	1.109	1.00
64_A	144_G	1.105	1.00
129_A	165_L	1.101	1.00
46_L	96_A	1.096	1.00
97_I	167_L	1.082	1.00
80_T	87_F	1.050	1.00
59_V	143_E	1.048	1.00
136_F	140_D	1.040	0.99
90_L	94_G	1.028	0.99
155_G	199_F	1.019	0.99
64_A	73_L	1.017	0.99
75_N	105_E	1.017	0.99
185_A	190_A	1.015	0.99
126_I	172_A	1.013	0.99
151_A	161_D	1.009	0.99
3_G	74_I	1.007	0.99
121_A	200_S	1.002	0.99
20_E	56_L	1.001	0.99
120_R	168_S	0.993	0.99
96_A	132_G	0.987	0.99
41_G	71_P	0.982	0.99
21_D	53_H	0.981	0.99
9_Q	125_P	0.971	0.99
63_Y	144_G	0.965	0.99
177_R	180_I	0.965	0.99
150_A	153_D	0.957	0.99
62_G	74_I	0.957	0.99
150_A	163_R	0.956	0.99
103_W	153_D	0.951	0.99
154_Q	158_D	0.938	0.99
44_V	98_C	0.937	0.99
46_L	98_C	0.927	0.99
63_Y	133_S	0.925	0.99
108_K	113_K	0.906	0.99
41_G	60_F	0.904	0.99
73_L	87_F	0.901	0.99
4_R	106_W	0.900	0.99
4_R	37_N	0.897	0.98
108_K	111_D	0.881	0.98
8_S	101_D	0.877	0.98
155_G	201_W	0.876	0.98
39_A	42_T	0.869	0.98
155_G	158_D	0.857	0.98
5_F	45_L	0.855	0.98
37_N	106_W	0.849	0.98
57_D	143_E	0.847	0.98
47_L	54_L	0.840	0.98
78_V	150_A	0.840	0.98
174_E	177_R	0.830	0.98
103_W	158_D	0.828	0.97
81_A	131_I	0.825	0.97
108_K	112_K	0.811	0.97
20_E	23_E	0.802	0.97
109_E	114_Q	0.796	0.97
103_W	166_V	0.785	0.97
119_Y	123_G	0.783	0.96
120_R	199_F	0.782	0.96
173_R	177_R	0.778	0.96
7_Q	45_L	0.777	0.96
147_I	164_P	0.777	0.96
152_A	161_D	0.770	0.96
106_W	115_P	0.765	0.96
187_E	190_A	0.762	0.96
130_A	146_L	0.756	0.96
148_V	165_L	0.755	0.96
2_C	75_N	0.752	0.96
153_D	158_D	0.747	0.95
50_R	55_H	0.743	0.95
65_P	68_W	0.741	0.95
120_R	198_Q	0.738	0.95
61_W	95_R	0.737	0.95
126_I	166_V	0.733	0.95
9_Q	13_D	0.731	0.95
182_G	185_A	0.730	0.95
194_V	198_Q	0.729	0.95
77_R	105_E	0.729	0.95
76_A	87_F	0.729	0.95
152_A	155_G	0.721	0.94
66_G	133_S	0.719	0.94
13_D	16_A	0.719	0.94
63_Y	73_L	0.715	0.94
39_A	106_W	0.712	0.94
136_F	139_G	0.706	0.94
5_F	39_A	0.705	0.94
17_L	124_Q	0.705	0.94
84_S	87_F	0.702	0.94
61_W	164_P	0.699	0.93
44_V	61_W	0.694	0.93
89_P	133_S	0.688	0.93
9_Q	12_E	0.688	0.93
168_S	198_Q	0.687	0.93
3_G	40_P	0.687	0.93
36_Y	115_P	0.687	0.93
5_F	145_F	0.686	0.93
49_E	52_E	0.684	0.93
150_A	193_C	0.682	0.93
15_L	22_I	0.682	0.93
6_A	102_G	0.681	0.93
22_I	53_H	0.679	0.92
45_L	58_P	0.679	0.92
63_Y	86_M	0.678	0.92
5_F	38_V	0.675	0.92
178_Q	181_S	0.673	0.92
66_G	89_P	0.672	0.92
48_S	143_E	0.670	0.92
18_L	172_A	0.666	0.92
3_G	106_W	0.666	0.92
88_K	92_Q	0.664	0.92
105_E	162_R	0.656	0.91
5_F	99_F	0.654	0.91
93_H	133_S	0.653	0.91
130_A	147_I	0.653	0.91
137_E	140_D	0.649	0.91
49_E	54_L	0.648	0.91
107_K	110_G	0.648	0.91
180_I	186_S	0.648	0.91
100_A	147_I	0.647	0.91
73_L	146_L	0.646	0.90
80_T	83_T	0.645	0.90
2_C	160_H	0.645	0.90
120_R	125_P	0.642	0.90
2_C	105_E	0.641	0.90
37_N	102_G	0.640	0.90
151_A	157_V	0.635	0.90
151_A	154_Q	0.633	0.90
156_L	159_I	0.632	0.90
116_F	159_I	0.631	0.89
102_G	119_Y	0.630	0.89
39_A	115_P	0.627	0.89
124_Q	169_P	0.624	0.89
82_A	92_Q	0.623	0.89
36_Y	39_A	0.622	0.89
107_K	158_D	0.621	0.89
74_I	146_L	0.619	0.89
43_K	58_P	0.616	0.88
63_Y	71_P	0.615	0.88
112_K	197_N	0.614	0.88
195_P	198_Q	0.612	0.88
64_A	135_P	0.612	0.88
31_E	58_P	0.609	0.88
135_P	142_A	0.608	0.88
174_E	188_I	0.608	0.88
19_A	173_R	0.605	0.87
47_L	99_F	0.605	0.87
78_V	165_L	0.595	0.87
152_A	157_V	0.589	0.86
174_E	187_E	0.589	0.86
107_K	114_Q	0.586	0.86
101_D	117_F	0.585	0.86
65_P	69_D	0.582	0.85
15_L	20_E	0.581	0.85
133_S	144_G	0.579	0.85
12_E	21_D	0.577	0.85
67_W	70_K	0.577	0.85
9_Q	14_Y	0.572	0.84
40_P	74_I	0.572	0.84
203_P	206_R	0.566	0.84
121_A	198_Q	0.566	0.84
60_F	142_A	0.565	0.84
99_F	127_F	0.565	0.84
41_G	74_I	0.564	0.84
128_M	164_P	0.563	0.83
193_C	198_Q	0.563	0.83
7_Q	14_Y	0.560	0.83
153_D	196_A	0.558	0.83
120_R	123_G	0.555	0.83
59_V	145_F	0.554	0.82
98_C	128_M	0.554	0.82
18_L	47_L	0.553	0.82
103_W	164_P	0.551	0.82
107_K	113_K	0.551	0.82
104_F	162_R	0.549	0.82
76_A	131_I	0.548	0.82
104_F	204_V	0.546	0.82
153_D	193_C	0.545	0.81
151_A	170_E	0.542	0.81
32_P	45_L	0.542	0.81
14_Y	18_L	0.542	0.81
77_R	160_H	0.541	0.81
171_A	187_E	0.541	0.81
49_E	173_R	0.541	0.81
68_W	71_P	0.541	0.81
109_E	116_F	0.537	0.80
4_R	40_P	0.534	0.80
159_I	201_W	0.534	0.80
63_Y	90_L	0.533	0.80
180_I	185_A	0.529	0.79
181_S	187_E	0.527	0.79
17_L	169_P	0.526	0.79
45_L	145_F	0.526	0.79
5_F	98_C	0.522	0.79
95_R	178_Q	0.522	0.79
76_A	81_A	0.522	0.79
46_L	130_A	0.521	0.78
159_I	163_R	0.520	0.78
118_I	161_D	0.520	0.78
129_A	167_L	0.519	0.78
7_Q	10_T	0.516	0.78
104_F	115_P	0.515	0.78
101_D	125_P	0.514	0.78
6_A	101_D	0.513	0.77
11_R	31_E	0.513	0.77
108_K	161_D	0.510	0.77
3_G	41_G	0.510	0.77
116_F	201_W	0.507	0.77
65_P	144_G	0.505	0.76
79_E	151_A	0.505	0.76
16_A	21_D	0.504	0.76
64_A	70_K	0.503	0.76
118_I	150_A	0.503	0.76
139_G	142_A	0.502	0.76
103_W	199_F	0.502	0.76
193_C	199_F	0.500	0.76
32_P	58_P	0.500	0.76

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
2icuA	1	0.955	100	0.019	Contact Map
2bdvA	1	0.9279	100	0.051	Contact Map
2f20A	1	0.973	100	0.067	Contact Map
2aegA	1	0.9054	100	0.112	Contact Map
1zn6A	1	0.8694	100	0.15	Contact Map
2gs0B	1	0.0631	11.6	0.959	Contact Map
3bsuA	1	0.2207	8	0.961	Contact Map
2b3gB	2	0.1081	6.7	0.963	Contact Map
4a7kA	2	0.2387	4.3	0.966	Contact Map
3aj1A	5	0.6216	3.9	0.967	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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