YRDA - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YRDA - Protein YrdA

UniProt:	P0A9W9	Sequences: MSDVLRPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKSSYNPDGNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQGNQTQP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12838
Length:	184 (159)
Sequences:	5116 (3254)
Seq/√Len:	258.1

ECOLI - YRDA CAIE PAAY THGA WBBJ WCAF LPXA LPXD MAA YAIX GLMU WCAB
BACSU - YTOA DAPH EPSM MAA YVOF CYSE
HALSA - Q9HQ06 Q9HNN1 Q9HPT3
SULSO - Q980E1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_R	86_D	3.388	1.00
66_L	81_L	3.125	1.00
56_A	85_E	2.738	1.00
103_R	121_D	2.614	1.00
36_D	57_R	2.568	1.00
136_L	142_Y	2.550	1.00
35_D	56_A	2.533	1.00
16_G	35_D	2.438	1.00
86_D	103_R	2.402	1.00
117_I	135_R	2.389	1.00
125_G	143_L	2.387	1.00
34_A	56_A	2.372	1.00
101_G	120_D	2.358	1.00
120_D	138_S	2.285	1.00
79_N	115_G	2.255	1.00
121_D	139_G	2.133	1.00
102_N	120_D	2.001	1.00
85_E	102_N	1.994	1.00
32_R	53_Q	1.983	1.00
84_G	102_N	1.909	1.00
131_P	134_K	1.838	1.00
101_G	117_I	1.745	1.00
41_P	175_Y	1.742	1.00
37_V	85_E	1.715	1.00
14_Q	32_R	1.699	1.00
30_D	51_Y	1.665	1.00
119_E	138_S	1.659	1.00
95_L	98_C	1.646	1.00
11_L	30_D	1.642	1.00
82_T	99_T	1.599	1.00
99_T	117_I	1.586	1.00
18_R	36_D	1.585	1.00
154_S	157_E	1.558	1.00
122_V	140_Y	1.550	1.00
43_V	64_S	1.545	1.00
139_G	158_K	1.525	1.00
119_E	135_R	1.522	1.00
128_S	147_V	1.513	1.00
65_M	92_K	1.501	1.00
24_S	42_L	1.499	1.00
112_L	116_A	1.485	1.00
92_K	109_G	1.478	1.00
57_R	169_V	1.444	1.00
22_D	41_P	1.432	1.00
63_G	92_K	1.359	1.00
55_G	85_E	1.330	1.00
137_E	149_Q	1.330	1.00
143_L	150_I	1.329	1.00
33_L	39_I	1.281	1.00
60_I	64_S	1.281	1.00
124_I	130_V	1.268	1.00
140_Y	152_P	1.268	1.00
142_Y	149_Q	1.252	1.00
119_E	137_E	1.251	1.00
149_Q	152_P	1.247	1.00
64_S	93_V	1.246	1.00
137_E	140_Y	1.244	1.00
122_V	138_S	1.229	1.00
140_Y	149_Q	1.207	1.00
27_V	31_V	1.205	1.00
104_V	138_S	1.201	1.00
42_L	63_G	1.192	1.00
34_A	53_Q	1.187	1.00
167_N	172_K	1.167	1.00
151_R	157_E	1.160	1.00
18_R	35_D	1.147	1.00
15_I	19_V	1.135	1.00
33_L	37_V	1.133	1.00
124_I	136_L	1.127	1.00
53_Q	82_T	1.109	1.00
114_D	132_Q	1.105	1.00
32_R	51_Y	1.105	1.00
115_G	133_N	1.067	1.00
60_I	89_V	1.054	1.00
58_T	102_N	1.048	1.00
121_D	158_K	1.045	1.00
50_H	78_G	1.036	1.00
104_V	122_V	1.035	1.00
88_T	164_S	1.027	1.00
26_V	42_L	1.014	1.00
116_A	130_V	1.013	1.00
163_Y	166_N	1.011	1.00
58_T	87_V	0.989	1.00
100_I	106_V	0.971	1.00
106_V	112_L	0.958	1.00
94_M	108_M	0.952	1.00
171_W	174_E	0.951	1.00
45_I	52_V	0.943	1.00
17_Q	35_D	0.932	1.00
130_V	147_V	0.932	1.00
27_V	33_L	0.923	1.00
166_N	170_K	0.920	1.00
159_A	162_R	0.919	1.00
31_V	45_I	0.914	1.00
54_I	58_T	0.901	1.00
111_I	127_G	0.899	1.00
34_A	85_E	0.891	1.00
127_G	145_S	0.889	1.00
39_I	45_I	0.889	1.00
21_I	25_S	0.888	1.00
155_D	158_K	0.883	1.00
122_V	142_Y	0.882	1.00
24_S	41_P	0.881	1.00
94_M	109_G	0.877	1.00
100_I	104_V	0.870	1.00
50_H	80_P	0.864	1.00
129_L	145_S	0.857	1.00
36_D	173_D	0.850	0.99
81_L	95_L	0.846	0.99
142_Y	147_V	0.845	0.99
141_L	153_L	0.836	0.99
163_Y	167_N	0.835	0.99
106_V	124_I	0.832	0.99
161_L	164_S	0.824	0.99
104_V	120_D	0.823	0.99
122_V	136_L	0.816	0.99
44_V	63_G	0.806	0.99
69_T	114_D	0.804	0.99
16_G	19_V	0.795	0.99
55_G	82_T	0.790	0.99
84_G	101_G	0.786	0.99
139_G	155_D	0.778	0.99
49_V	68_V	0.777	0.99
124_I	142_Y	0.770	0.99
105_L	123_M	0.759	0.99
89_V	95_L	0.753	0.99
164_S	168_Y	0.753	0.99
121_D	162_R	0.752	0.99
37_V	58_T	0.745	0.99
84_G	99_T	0.742	0.99
128_S	145_S	0.740	0.99
45_I	54_I	0.735	0.98
58_T	83_I	0.733	0.98
111_I	129_L	0.721	0.98
51_Y	80_P	0.717	0.98
137_E	142_Y	0.715	0.98
139_G	152_P	0.705	0.98
60_I	66_L	0.703	0.98
153_L	157_E	0.702	0.98
42_L	92_K	0.701	0.98
51_Y	82_T	0.698	0.98
19_V	37_V	0.697	0.98
16_G	34_A	0.691	0.98
15_I	33_L	0.687	0.98
110_S	128_S	0.686	0.98
170_K	174_E	0.684	0.98
155_D	159_A	0.680	0.97
11_L	14_Q	0.679	0.97
170_K	173_D	0.675	0.97
103_R	162_R	0.673	0.97
50_H	79_N	0.673	0.97
36_D	56_A	0.672	0.97
113_L	126_A	0.672	0.97
109_G	127_G	0.671	0.97
55_G	58_T	0.669	0.97
87_V	100_I	0.668	0.97
58_T	85_E	0.668	0.97
106_V	110_S	0.667	0.97
18_R	176_L	0.666	0.97
101_G	122_V	0.664	0.97
101_G	104_V	0.663	0.97
169_V	172_K	0.663	0.97
101_G	119_E	0.662	0.97
98_C	116_A	0.660	0.97
162_R	166_N	0.658	0.97
87_V	102_N	0.656	0.97
166_N	169_V	0.654	0.97
97_G	114_D	0.654	0.97
172_K	176_L	0.652	0.97
61_Q	91_H	0.650	0.97
86_D	162_R	0.649	0.97
68_V	77_D	0.648	0.97
37_V	56_A	0.648	0.97
113_L	129_L	0.647	0.97
87_V	104_V	0.643	0.96
113_L	116_A	0.640	0.96
167_N	170_K	0.636	0.96
173_D	176_L	0.636	0.96
14_Q	30_D	0.633	0.96
103_R	120_D	0.633	0.96
167_N	171_W	0.631	0.96
124_I	147_V	0.623	0.96
57_R	85_E	0.623	0.96
83_I	87_V	0.622	0.96
159_A	163_Y	0.621	0.96
136_L	149_Q	0.615	0.95
37_V	54_I	0.614	0.95
26_V	44_V	0.613	0.95
101_G	138_S	0.613	0.95
91_H	108_M	0.605	0.95
68_V	79_N	0.605	0.95
87_V	120_D	0.589	0.94
31_V	47_G	0.587	0.94
79_N	97_G	0.585	0.94
86_D	169_V	0.585	0.94
30_D	53_Q	0.582	0.94
15_I	27_V	0.578	0.94
20_M	41_P	0.568	0.93
93_V	110_S	0.567	0.93
34_A	55_G	0.567	0.93
39_I	43_V	0.567	0.93
119_E	122_V	0.563	0.93
141_L	151_R	0.562	0.93
137_E	152_P	0.560	0.93
83_I	95_L	0.560	0.93
169_V	173_D	0.558	0.93
86_D	166_N	0.557	0.92
136_L	140_Y	0.551	0.92
110_S	124_I	0.551	0.92
116_A	134_K	0.550	0.92
64_S	92_K	0.549	0.92
59_N	88_T	0.541	0.91
98_C	114_D	0.541	0.91
96_H	114_D	0.539	0.91
66_L	83_I	0.538	0.91
95_L	100_I	0.536	0.91
160_G	163_Y	0.534	0.91
153_L	158_K	0.533	0.91
89_V	106_V	0.528	0.90
144_G	147_V	0.527	0.90
69_T	77_D	0.527	0.90
45_I	66_L	0.524	0.90
50_H	69_T	0.523	0.90
49_V	167_N	0.521	0.90
171_W	175_Y	0.519	0.90
49_V	69_T	0.519	0.90
67_H	96_H	0.518	0.90
33_L	54_I	0.517	0.89
36_D	172_K	0.516	0.89
94_M	111_I	0.514	0.89
19_V	33_L	0.509	0.89
121_D	138_S	0.506	0.88
164_S	167_N	0.506	0.88
38_G	172_K	0.506	0.88
83_I	89_V	0.503	0.88
131_P	147_V	0.502	0.88
116_A	135_R	0.502	0.88
55_G	102_N	0.500	0.88

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
3r3rA	3	0.9783	100	0.296	Contact Map
1xhdA	3	0.9348	100	0.328	Contact Map
3r1wA	3	0.9837	100	0.333	Contact Map
3ixcA	3	0.8967	100	0.334	Contact Map
1v3wA	3	0.9402	100	0.348	Contact Map
4n27A	3	0.9348	100	0.36	Contact Map
4mfgA	3	0.913	100	0.365	Contact Map
3c8vA	3	0.8804	100	0.393	Contact Map
3tv0A	3	0.7609	100	0.397	Contact Map
4r36A	3	0.9891	100	0.404	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.

Page generated in 0.0078 seconds.