YJJV - ECOLI - GREMLIN Contacts

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YJJV - Uncharacterized deoxyribonuclease YjjV

UniProt:	P39408	Sequences: MICRFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQALERRPAKVVAVGEIGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDLPRTGVVHGFSGSLQQAERFVQLGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNVP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12598
Length:	259 (251)
Sequences:	7120 (4998)
Seq/√Len:	315.4

ECOLI - YJJV YCFH TATD
BACSU - YABD
SULSO - Q981A2 Q97ZA2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_Q	125_R	3.459	1.00
117_D	147_R	3.090	1.00
232_V	235_E	2.761	1.00
163_L	196_K	2.647	1.00
102_L	140_K	2.642	1.00
54_E	89_P	2.528	1.00
27_R	222_R	2.497	1.00
154_G	174_Y	2.291	1.00
120_L	130_V	2.262	1.00
250_N	254_T	2.200	1.00
146_K	168_R	2.161	1.00
191_R	232_V	2.102	1.00
231_A	241_A	2.090	1.00
113_Q	140_K	2.024	1.00
85_L	95_V	1.984	1.00
134_S	141_L	1.943	1.00
121_K	148_H	1.853	1.00
199_L	237_R	1.851	1.00
10_C	36_I	1.848	1.00
62_A	94_A	1.843	1.00
26_Q	30_Q	1.842	1.00
18_S	21_E	1.832	1.00
246_Q	250_N	1.831	1.00
199_L	247_A	1.822	1.00
239_E	244_I	1.817	1.00
194_I	233_L	1.787	1.00
102_L	109_F	1.766	1.00
29_A	58_P	1.755	1.00
117_D	148_H	1.749	1.00
139_D	143_M	1.741	1.00
230_F	241_A	1.738	1.00
20_D	220_P	1.737	1.00
62_A	131_I	1.719	1.00
53_A	61_A	1.710	1.00
146_K	172_L	1.676	1.00
35_K	60_Y	1.665	1.00
114_W	118_E	1.662	1.00
98_I	119_Q	1.661	1.00
163_L	167_E	1.661	1.00
199_L	239_E	1.657	1.00
158_G	179_G	1.651	1.00
61_A	92_V	1.644	1.00
47_A	80_Q	1.643	1.00
168_R	171_Q	1.627	1.00
8_T	252_T	1.627	1.00
35_K	253_Y	1.622	1.00
156_V	169_F	1.612	1.00
98_I	130_V	1.599	1.00
22_E	55_N	1.598	1.00
204_L	230_F	1.586	1.00
167_E	171_Q	1.542	1.00
118_E	121_K	1.530	1.00
82_Q	126_Y	1.510	1.00
134_S	138_H	1.501	1.00
178_V	194_I	1.490	1.00
113_Q	143_M	1.488	1.00
182_I	233_L	1.467	1.00
51_A	55_N	1.452	1.00
167_E	196_K	1.451	1.00
231_A	235_E	1.447	1.00
143_M	147_R	1.446	1.00
155_V	255_L	1.439	1.00
116_L	132_L	1.434	1.00
6_I	35_K	1.434	1.00
175_K	201_S	1.424	1.00
166_A	176_I	1.420	1.00
78_L	118_E	1.413	1.00
85_L	126_Y	1.396	1.00
188_S	192_D	1.388	1.00
175_K	254_T	1.386	1.00
192_D	195_A	1.383	1.00
227_A	231_A	1.370	1.00
162_S	165_Q	1.365	1.00
188_S	191_R	1.354	1.00
127_D	153_T	1.338	1.00
42_E	45_N	1.337	1.00
142_A	168_R	1.330	1.00
113_Q	117_D	1.327	1.00
80_Q	83_Q	1.326	1.00
13_D	45_N	1.324	1.00
6_I	37_I	1.311	1.00
116_L	141_L	1.291	1.00
249_L	253_Y	1.276	1.00
124_K	148_H	1.269	1.00
228_R	231_A	1.268	1.00
49_V	61_A	1.264	1.00
117_D	144_H	1.264	1.00
176_I	197_L	1.261	1.00
28_A	36_I	1.254	1.00
51_A	54_E	1.252	1.00
191_R	236_L	1.246	1.00
68_G	104_G	1.245	1.00
37_I	93_V	1.245	1.00
102_L	113_Q	1.236	1.00
6_I	249_L	1.231	1.00
40_A	46_F	1.225	1.00
216_F	228_R	1.223	1.00
5_F	245_A	1.217	1.00
243_E	246_Q	1.214	1.00
10_C	208_A	1.213	1.00
198_P	201_S	1.204	1.00
233_L	244_I	1.201	1.00
5_F	230_F	1.201	1.00
240_P	243_E	1.200	1.00
216_F	225_Q	1.193	1.00
178_V	202_L	1.180	1.00
249_L	252_T	1.180	1.00
203_L	255_L	1.178	1.00
108_Q	111_R	1.177	1.00
230_F	248_L	1.170	1.00
113_Q	144_H	1.169	1.00
43_A	46_F	1.165	1.00
109_F	113_Q	1.164	1.00
50_L	61_A	1.163	1.00
239_E	243_E	1.157	1.00
38_V	49_V	1.146	1.00
170_V	201_S	1.142	1.00
74_S	77_S	1.115	1.00
164_Q	167_E	1.115	1.00
39_P	131_I	1.111	1.00
248_L	252_T	1.106	1.00
23_A	27_R	1.082	1.00
194_I	237_R	1.081	1.00
20_D	23_A	1.074	1.00
232_V	236_L	1.072	1.00
22_E	26_Q	1.072	1.00
68_G	107_P	1.071	1.00
17_F	220_P	1.070	1.00
36_I	59_L	1.067	1.00
5_F	226_A	1.063	1.00
204_L	226_A	1.050	1.00
54_E	91_K	1.046	1.00
105_D	109_F	1.046	1.00
83_Q	86_E	1.045	1.00
70_L	115_L	1.043	1.00
216_F	219_Q	1.038	1.00
82_Q	86_E	1.036	1.00
139_D	165_Q	1.036	1.00
43_A	77_S	1.036	1.00
110_E	114_W	1.032	1.00
110_E	113_Q	1.031	1.00
221_N	225_Q	1.030	1.00
47_A	51_A	1.025	1.00
138_H	165_Q	1.019	1.00
121_K	125_R	1.016	1.00
139_D	168_R	1.011	1.00
6_I	252_T	1.006	1.00
38_V	59_L	0.989	1.00
163_L	193_V	0.988	1.00
175_K	255_L	0.985	1.00
161_G	165_Q	0.985	1.00
184_Y	212_P	0.981	1.00
192_D	196_K	0.979	1.00
204_L	233_L	0.976	1.00
69_M	72_K	0.975	1.00
27_R	224_E	0.966	1.00
111_R	114_W	0.963	1.00
185_P	214_N	0.962	1.00
50_L	89_P	0.958	1.00
50_L	63_L	0.950	1.00
154_G	255_L	0.946	1.00
82_Q	122_L	0.941	1.00
48_R	51_A	0.939	1.00
230_F	245_A	0.932	1.00
53_A	59_L	0.926	1.00
23_A	26_Q	0.925	1.00
73_H	78_L	0.925	1.00
182_I	194_I	0.916	1.00
178_V	197_L	0.914	1.00
222_R	225_Q	0.909	1.00
247_A	250_N	0.901	1.00
37_I	252_T	0.899	1.00
177_G	203_L	0.899	1.00
43_A	80_Q	0.896	1.00
47_A	84_A	0.896	1.00
244_I	248_L	0.888	1.00
12_F	223_P	0.887	1.00
230_F	244_I	0.884	1.00
204_L	248_L	0.881	1.00
8_T	203_L	0.878	1.00
22_E	56_Y	0.874	1.00
25_L	56_Y	0.868	1.00
245_A	249_L	0.866	1.00
86_E	126_Y	0.863	1.00
199_L	244_I	0.862	1.00
163_L	192_D	0.861	1.00
149_D	152_R	0.860	1.00
70_L	111_R	0.859	1.00
103_F	136_R	0.859	1.00
124_K	151_P	0.859	1.00
194_I	236_L	0.858	1.00
142_A	169_F	0.850	1.00
50_L	54_E	0.847	1.00
243_E	247_A	0.845	1.00
155_V	256_F	0.841	1.00
73_H	115_L	0.839	1.00
49_V	53_A	0.838	1.00
237_R	244_I	0.833	1.00
79_E	83_Q	0.832	1.00
132_L	156_V	0.830	1.00
170_V	198_P	0.826	1.00
134_S	161_G	0.826	1.00
227_A	241_A	0.825	1.00
79_E	82_Q	0.821	1.00
127_D	152_R	0.817	1.00
78_L	82_Q	0.815	1.00
109_F	140_K	0.813	1.00
120_L	124_K	0.808	1.00
17_F	20_D	0.808	1.00
77_S	80_Q	0.805	1.00
138_H	161_G	0.794	1.00
92_V	128_L	0.789	1.00
124_K	152_R	0.788	1.00
80_Q	84_A	0.785	1.00
39_P	62_A	0.783	1.00
41_T	45_N	0.782	1.00
132_L	141_L	0.778	1.00
65_L	73_H	0.773	1.00
63_L	92_V	0.769	0.99
68_G	106_D	0.768	0.99
140_K	143_M	0.766	0.99
230_F	234_C	0.765	0.99
241_A	245_A	0.764	0.99
75_D	118_E	0.763	0.99
122_L	126_Y	0.762	0.99
17_F	21_E	0.760	0.99
226_A	229_V	0.759	0.99
8_T	155_V	0.757	0.99
170_V	176_I	0.753	0.99
142_A	165_Q	0.753	0.99
138_H	169_F	0.747	0.99
195_A	236_L	0.744	0.99
25_L	36_I	0.744	0.99
233_L	237_R	0.744	0.99
5_F	227_A	0.741	0.99
150_L	153_T	0.740	0.99
31_A	227_A	0.740	0.99
34_G	249_L	0.736	0.99
124_K	149_D	0.728	0.99
242_D	246_Q	0.726	0.99
146_K	171_Q	0.721	0.99
13_D	48_R	0.721	0.99
73_H	77_S	0.720	0.99
153_T	257_N	0.717	0.99
27_R	30_Q	0.717	0.99
175_K	203_L	0.713	0.99
105_D	108_Q	0.710	0.99
250_N	253_Y	0.704	0.99
95_V	98_I	0.700	0.99
181_T	184_Y	0.699	0.99
5_F	249_L	0.697	0.99
37_I	62_A	0.697	0.99
202_L	244_I	0.696	0.99
144_H	147_R	0.692	0.99
46_F	84_A	0.692	0.99
45_N	49_V	0.692	0.99
26_Q	29_A	0.689	0.99
111_R	115_L	0.688	0.99
124_K	150_L	0.686	0.99
144_H	148_H	0.685	0.99
117_D	121_K	0.682	0.99
239_E	247_A	0.679	0.99
8_T	131_I	0.678	0.99
188_S	195_A	0.678	0.99
14_F	210_D	0.677	0.99
120_L	144_H	0.673	0.99
155_V	177_G	0.672	0.99
184_Y	215_G	0.669	0.99
60_Y	91_K	0.669	0.99
195_A	238_R	0.666	0.99
202_L	237_R	0.665	0.99
198_P	237_R	0.655	0.98
63_L	84_A	0.654	0.98
190_T	193_V	0.653	0.98
25_L	29_A	0.650	0.98
106_D	109_F	0.650	0.98
42_E	72_K	0.648	0.98
5_F	241_A	0.645	0.98
181_T	211_M	0.645	0.98
40_A	49_V	0.645	0.98
5_F	204_L	0.641	0.98
18_S	48_R	0.641	0.98
100_L	137_T	0.633	0.98
46_F	63_L	0.632	0.98
98_I	115_L	0.632	0.98
169_F	176_I	0.631	0.98
134_S	169_F	0.627	0.98
78_L	122_L	0.627	0.98
20_D	24_S	0.625	0.98
94_A	131_I	0.621	0.98
170_V	197_L	0.611	0.97
21_E	24_S	0.610	0.97
46_F	49_V	0.610	0.97
166_A	193_V	0.609	0.97
60_Y	93_V	0.609	0.97
120_L	148_H	0.607	0.97
166_A	170_V	0.606	0.97
212_P	225_Q	0.604	0.97
15_P	18_S	0.604	0.97
166_A	197_L	0.603	0.97
46_F	81_L	0.597	0.97
127_D	257_N	0.597	0.97
70_L	107_P	0.596	0.97
247_A	254_T	0.595	0.97
71_E	108_Q	0.592	0.97
127_D	151_P	0.588	0.97
159_F	165_Q	0.586	0.97
202_L	248_L	0.584	0.97
197_L	202_L	0.583	0.97
37_I	256_F	0.582	0.97
184_Y	218_G	0.577	0.96
181_T	190_T	0.576	0.96
138_H	142_A	0.576	0.96
203_L	252_T	0.575	0.96
46_F	61_A	0.574	0.96
237_R	247_A	0.572	0.96
83_Q	89_P	0.572	0.96
28_A	222_R	0.571	0.96
189_K	192_D	0.570	0.96
131_I	256_F	0.570	0.96
170_V	196_K	0.566	0.96
142_A	146_K	0.562	0.96
156_V	177_G	0.559	0.96
71_E	107_P	0.558	0.96
155_V	203_L	0.557	0.96
200_A	254_T	0.556	0.96
142_A	172_L	0.556	0.96
28_A	33_V	0.555	0.95
234_C	241_A	0.553	0.95
175_K	251_N	0.549	0.95
24_S	220_P	0.549	0.95
191_R	195_A	0.548	0.95
103_F	135_R	0.547	0.95
168_R	172_L	0.547	0.95
13_D	38_V	0.547	0.95
76_V	79_E	0.545	0.95
179_G	211_M	0.541	0.95
247_A	251_N	0.540	0.95
251_N	254_T	0.539	0.95
13_D	41_T	0.535	0.95
138_H	141_L	0.535	0.95
115_L	119_Q	0.534	0.94
28_A	32_G	0.531	0.94
182_I	190_T	0.531	0.94
132_L	154_G	0.530	0.94
71_E	111_R	0.530	0.94
190_T	194_I	0.529	0.94
159_F	169_F	0.527	0.94
6_I	253_Y	0.527	0.94
179_G	204_L	0.527	0.94
29_A	34_G	0.526	0.94
68_G	105_D	0.525	0.94
158_G	211_M	0.524	0.94
182_I	244_I	0.522	0.94
119_Q	123_A	0.521	0.94
122_L	125_R	0.520	0.94
200_A	247_A	0.513	0.93
121_K	124_K	0.511	0.93
25_L	59_L	0.511	0.93
242_D	245_A	0.511	0.93
8_T	177_G	0.510	0.93
178_V	181_T	0.508	0.93
31_A	224_E	0.507	0.93
21_E	220_P	0.507	0.93
41_T	69_M	0.506	0.93
16_P	220_P	0.506	0.93
225_Q	228_R	0.506	0.93
64_G	119_Q	0.506	0.93
75_D	114_W	0.505	0.93
93_V	252_T	0.505	0.93
85_L	92_V	0.504	0.93
9_H	131_I	0.504	0.93
25_L	58_P	0.503	0.93
123_A	130_V	0.502	0.92
154_G	176_I	0.502	0.92
52_L	59_L	0.500	0.92

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
3e2vA	1	0.973	100	0.191	Contact Map
3ipwA	1	0.9923	100	0.245	Contact Map
2xioA	1	0.9846	100	0.318	Contact Map
1j6oA	1	0.9923	100	0.334	Contact Map
3gg7A	1	0.9305	100	0.346	Contact Map
3rcmA	1	0.9846	100	0.373	Contact Map
1xwyA	1	0.9768	100	0.373	Contact Map
1zzmA	1	1	100	0.377	Contact Map
2y1hA	2	0.9768	100	0.387	Contact Map
2gzxA	1	0.9691	100	0.396	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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