YRDC - BACSU - GREMLIN Contacts

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YRDC - Uncharacterized isochorismatase family protein YrdC

UniProt:	O07081	Sequences: MEEKKALIIVDVQKAFDDKKWGERNNVKAEENISKILELWREKGWTVIYIQHTSDKPHSLFHPKNEGFAIKEIVKPMDEEVIITKTVNSSFIGTNLEEFLKLNEITTVVITGLTTPHCVSTTTRMSGNLGFDTYLISDATAAFGMRDQNDTYYDAATIHNISLATLHDEFATILTTDQLINDFIKTH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	187 (161)
Sequences:	10080 (6938)
Seq/√Len:	546.8

ECOLI - RUTB YECD PNCA YCAC
BACSU - YRDC YDDQ YWOC YAAI PNCA
HALSA - Q9HQL7 Q9HMH5
SULSO - Q97VZ5 Q97YW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_E	101_K	3.456	1.00
51_Q	84_T	2.882	1.00
107_T	132_D	2.813	1.00
97_E	131_F	2.751	1.00
40_W	45_W	2.735	1.00
89_S	125_M	2.612	1.00
33_I	111_T	2.440	1.00
5_K	107_T	2.427	1.00
97_E	129_L	2.403	1.00
12_V	33_I	2.322	1.00
36_I	136_I	2.305	1.00
107_T	134_Y	2.287	1.00
110_I	123_T	2.221	1.00
15_A	67_G	2.034	1.00
95_N	99_F	1.986	1.00
4_K	106_T	1.982	1.00
126_S	133_T	1.948	1.00
120_S	124_R	1.926	1.00
83_I	99_F	1.907	1.00
90_S	122_T	1.869	1.00
32_N	139_A	1.864	1.00
166_L	171_A	1.864	1.00
14_K	66_E	1.841	1.00
6_A	105_I	1.840	1.00
48_I	99_F	1.813	1.00
39_L	43_K	1.797	1.00
32_N	35_K	1.771	1.00
41_R	80_E	1.665	1.00
14_K	72_E	1.636	1.00
5_K	109_V	1.595	1.00
17_D	71_K	1.573	1.00
137_S	173_I	1.547	1.00
109_V	136_I	1.545	1.00
81_V	99_F	1.524	1.00
40_W	109_V	1.518	1.00
9_I	37_L	1.516	1.00
66_E	69_A	1.512	1.00
50_I	90_S	1.504	1.00
137_S	175_T	1.463	1.00
25_N	28_K	1.427	1.00
46_T	103_N	1.418	1.00
34_S	38_E	1.414	1.00
9_I	111_T	1.410	1.00
115_T	140_T	1.397	1.00
108_V	126_S	1.389	1.00
116_P	142_A	1.381	1.00
63_P	84_T	1.372	1.00
119_V	135_L	1.345	1.00
53_T	68_F	1.328	1.00
99_F	103_N	1.307	1.00
34_S	73_I	1.303	1.00
110_I	122_T	1.302	1.00
125_M	129_L	1.282	1.00
8_I	110_I	1.280	1.00
9_I	12_V	1.263	1.00
98_E	102_L	1.256	1.00
135_L	140_T	1.255	1.00
29_A	33_I	1.252	1.00
145_M	160_N	1.239	1.00
101_K	131_F	1.224	1.00
10_V	118_C	1.218	1.00
38_E	42_E	1.202	1.00
53_T	84_T	1.196	1.00
51_Q	70_I	1.191	1.00
7_L	40_W	1.176	1.00
31_E	73_I	1.155	1.00
37_L	41_R	1.137	1.00
160_N	164_A	1.121	1.00
109_V	134_Y	1.099	1.00
36_I	139_A	1.093	1.00
14_K	69_A	1.084	1.00
37_L	49_Y	1.065	1.00
9_I	33_I	1.063	1.00
51_Q	82_I	1.041	1.00
32_N	138_D	1.035	1.00
99_F	102_L	1.026	1.00
121_T	124_R	1.026	1.00
157_T	160_N	1.024	1.00
123_T	135_L	1.009	1.00
159_H	163_L	1.001	1.00
62_H	65_N	0.998	1.00
115_T	163_L	0.983	1.00
35_K	39_L	0.978	1.00
5_K	45_W	0.974	1.00
108_V	133_T	0.971	1.00
70_I	82_I	0.971	1.00
100_L	131_F	0.961	1.00
39_L	42_E	0.958	1.00
95_N	98_E	0.948	1.00
77_M	80_E	0.947	1.00
115_T	142_A	0.930	1.00
120_S	162_S	0.914	1.00
115_T	159_H	0.908	1.00
6_A	48_I	0.905	1.00
53_T	63_P	0.904	1.00
29_A	141_A	0.903	1.00
49_Y	76_P	0.898	1.00
136_I	174_L	0.898	1.00
11_D	85_K	0.894	1.00
12_V	113_L	0.888	1.00
36_I	111_T	0.886	1.00
14_K	18_D	0.883	1.00
120_S	165_T	0.882	1.00
69_A	75_K	0.874	1.00
111_T	139_A	0.870	1.00
137_S	163_L	0.868	1.00
35_K	38_E	0.864	1.00
92_I	129_L	0.862	1.00
34_S	76_P	0.857	1.00
38_E	77_M	0.852	1.00
136_I	139_A	0.848	1.00
49_Y	70_I	0.847	1.00
87_V	130_G	0.838	1.00
87_V	93_G	0.838	1.00
6_A	100_L	0.838	1.00
55_D	63_P	0.833	1.00
8_I	96_L	0.827	1.00
91_F	126_S	0.820	1.00
90_S	96_L	0.818	1.00
76_P	80_E	0.817	1.00
30_E	34_S	0.814	1.00
123_T	166_L	0.807	1.00
144_G	157_T	0.797	1.00
46_T	105_I	0.795	1.00
33_I	139_A	0.795	1.00
37_L	47_V	0.790	1.00
142_A	159_H	0.790	1.00
134_Y	174_L	0.788	1.00
10_V	110_I	0.785	1.00
56_K	59_S	0.777	1.00
66_E	72_E	0.772	1.00
48_I	103_N	0.769	1.00
106_T	132_D	0.765	1.00
4_K	107_T	0.755	1.00
110_I	119_V	0.755	1.00
48_I	81_V	0.750	1.00
132_D	172_T	0.749	1.00
72_E	75_K	0.747	1.00
30_E	71_K	0.741	1.00
49_Y	79_E	0.738	1.00
157_T	161_I	0.736	1.00
38_E	75_K	0.732	1.00
16_F	118_C	0.731	1.00
14_K	71_K	0.726	1.00
125_M	128_N	0.725	1.00
41_R	77_M	0.724	1.00
31_E	35_K	0.722	1.00
163_L	173_I	0.722	1.00
81_V	103_N	0.720	1.00
113_L	141_A	0.714	1.00
28_K	31_E	0.709	1.00
76_P	82_I	0.707	1.00
31_E	34_S	0.707	1.00
34_S	75_K	0.705	1.00
46_T	99_F	0.705	1.00
110_I	133_T	0.702	1.00
29_A	113_L	0.702	1.00
49_Y	80_E	0.701	1.00
12_V	71_K	0.685	1.00
140_T	159_H	0.683	1.00
22_G	27_V	0.682	1.00
157_T	164_A	0.675	1.00
116_P	165_T	0.671	1.00
161_I	165_T	0.670	1.00
123_T	133_T	0.670	1.00
114_T	142_A	0.659	1.00
37_L	40_W	0.654	1.00
41_R	79_E	0.654	1.00
116_P	143_F	0.652	1.00
18_D	27_V	0.651	1.00
9_I	49_Y	0.651	1.00
162_S	165_T	0.645	1.00
26_N	113_L	0.644	1.00
158_I	162_S	0.644	1.00
24_R	141_A	0.642	1.00
4_K	104_E	0.641	1.00
158_I	161_I	0.641	1.00
7_L	36_I	0.635	1.00
158_I	164_A	0.635	1.00
71_K	74_V	0.634	1.00
36_I	109_V	0.633	1.00
17_D	30_E	0.630	1.00
51_Q	68_F	0.627	1.00
65_N	68_F	0.626	1.00
98_E	101_K	0.624	1.00
121_T	170_F	0.622	1.00
162_S	166_L	0.615	1.00
92_I	128_N	0.614	1.00
144_G	158_I	0.614	1.00
15_A	61_F	0.614	1.00
52_H	61_F	0.607	1.00
92_I	125_M	0.605	1.00
41_R	47_V	0.604	1.00
37_L	80_E	0.597	1.00
19_K	22_G	0.594	1.00
114_T	117_H	0.593	1.00
57_P	60_L	0.591	1.00
12_V	29_A	0.590	1.00
41_R	49_Y	0.588	1.00
7_L	111_T	0.588	1.00
48_I	83_I	0.586	1.00
89_S	128_N	0.582	0.99
55_D	86_T	0.580	0.99
40_W	46_T	0.574	0.99
88_N	122_T	0.572	0.99
159_H	162_S	0.572	0.99
13_Q	51_Q	0.572	0.99
49_Y	74_V	0.571	0.99
46_T	81_V	0.569	0.99
114_T	143_F	0.568	0.99
140_T	163_L	0.566	0.99
49_Y	82_I	0.566	0.99
7_L	37_L	0.563	0.99
164_A	168_D	0.559	0.99
109_V	138_D	0.559	0.99
119_V	140_T	0.556	0.99
133_T	136_I	0.554	0.99
58_H	61_F	0.552	0.99
36_I	40_W	0.549	0.99
24_R	28_K	0.547	0.99
30_E	74_V	0.546	0.99
88_N	128_N	0.543	0.99
64_K	69_A	0.541	0.99
51_Q	69_A	0.541	0.99
161_I	164_A	0.540	0.99
60_L	65_N	0.539	0.99
100_L	105_I	0.525	0.99
13_Q	50_I	0.523	0.99
18_D	66_E	0.522	0.99
137_S	167_H	0.520	0.99
28_K	32_N	0.519	0.99
134_Y	172_T	0.516	0.99
83_I	95_N	0.515	0.99
164_A	167_H	0.515	0.99
76_P	79_E	0.513	0.99
12_V	74_V	0.511	0.99
17_D	26_N	0.510	0.99
88_N	127_G	0.510	0.99
86_T	95_N	0.509	0.99
30_E	73_I	0.505	0.99
61_F	67_G	0.504	0.99
117_H	143_F	0.500	0.98

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
3mcwA	2	1	100	0.165	Contact Map
3oqpA	2	0.9893	100	0.174	Contact Map
4l07A	4	0.9412	100	0.175	Contact Map
3irvA	2	1	100	0.176	Contact Map
3lqyA	2	0.9519	100	0.18	Contact Map
1nbaA	4	0.9412	100	0.182	Contact Map
3ot4A	4	0.9251	100	0.183	Contact Map
3hb7A	3	0.9251	100	0.19	Contact Map
3hu5A	3	0.9198	100	0.194	Contact Map
2fq1A	2	0.9412	100	0.197	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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