DTD - ECOLI - GREMLIN Contacts

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DTD - D-aminoacyl-tRNA deacylase

UniProt:	P0A6M4	Sequences: MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11852
Length:	145 (144)
Sequences:	3497 (2390)
Seq/√Len:	199.1

ECOLI - DTD
BACSU - DTD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_L	142_W	2.660	1.00
10_R	132_S	2.589	1.00
43_N	112_R	2.533	1.00
110_V	122_T	2.370	1.00
15_V	20_T	2.305	1.00
39_E	108_Y	2.261	1.00
42_A	108_Y	2.212	1.00
27_L	54_I	2.159	1.00
112_R	115_Q	2.136	1.00
51_G	89_M	2.056	1.00
103_E	107_D	2.032	1.00
75_V	110_V	1.929	1.00
18_E	124_R	1.913	1.00
65_N	68_Q	1.906	1.00
20_T	124_R	1.865	1.00
10_R	134_V	1.828	1.00
21_G	121_Q	1.778	1.00
38_D	41_K	1.756	1.00
3_A	29_V	1.750	1.00
28_L	133_L	1.736	1.00
101_R	104_A	1.715	1.00
9_T	130_Q	1.712	1.00
8_V	28_L	1.693	1.00
62_M	139_V	1.691	1.00
73_V	113_C	1.690	1.00
34_E	82_A	1.683	1.00
11_A	28_L	1.623	1.00
12_S	132_S	1.622	1.00
75_V	109_F	1.601	1.00
13_V	131_V	1.555	1.00
47_E	51_G	1.548	1.00
46_C	113_C	1.515	1.00
14_T	132_S	1.497	1.00
61_K	93_F	1.413	1.00
57_D	63_N	1.409	1.00
27_L	66_V	1.387	1.00
3_A	31_L	1.367	1.00
14_T	19_V	1.365	1.00
19_V	22_E	1.359	1.00
3_A	49_V	1.338	1.00
43_N	108_Y	1.333	1.00
111_E	115_Q	1.329	1.00
35_K	95_K	1.323	1.00
72_S	119_N	1.319	1.00
30_L	133_L	1.310	1.00
2_I	144_Q	1.295	1.00
130_Q	134_V	1.285	1.00
66_V	71_G	1.272	1.00
130_Q	136_D	1.263	1.00
25_A	69_A	1.247	1.00
2_I	142_W	1.245	1.00
66_V	73_V	1.227	1.00
29_V	49_V	1.216	1.00
111_E	114_R	1.213	1.00
66_V	118_M	1.212	1.00
84_D	95_K	1.209	1.00
35_K	98_S	1.198	1.00
75_V	113_C	1.186	1.00
24_G	72_S	1.171	1.00
41_K	44_R	1.168	1.00
58_A	64_L	1.164	1.00
83_A	141_F	1.160	1.00
56_S	93_F	1.158	1.00
77_S	106_Y	1.147	1.00
85_T	143_L	1.142	1.00
35_K	97_A	1.129	1.00
107_D	111_E	1.126	1.00
9_T	134_V	1.124	1.00
2_I	82_A	1.122	1.00
47_E	116_Q	1.121	1.00
40_Q	43_N	1.119	1.00
108_Y	112_R	1.116	1.00
46_C	112_R	1.115	1.00
75_V	106_Y	1.110	1.00
51_G	67_Q	1.099	1.00
114_R	122_T	1.076	1.00
11_A	133_L	1.075	1.00
12_S	22_E	1.074	1.00
31_L	109_F	1.069	1.00
50_L	118_M	1.068	1.00
56_S	60_G	1.064	1.00
21_G	74_L	1.038	1.00
46_C	116_Q	1.033	1.00
39_E	43_N	1.031	1.00
42_A	105_L	1.013	1.00
49_V	109_F	1.011	1.00
97_A	101_R	1.007	1.00
103_E	124_R	1.002	1.00
34_E	95_K	0.988	1.00
6_Q	133_L	0.985	1.00
72_S	121_Q	0.972	0.99
39_E	104_A	0.972	0.99
9_T	136_D	0.971	0.99
67_Q	116_Q	0.958	0.99
42_A	112_R	0.950	0.99
56_S	61_K	0.947	0.99
36_D	101_R	0.930	0.99
29_V	75_V	0.927	0.99
47_E	89_M	0.926	0.99
100_D	103_E	0.910	0.99
50_L	113_C	0.904	0.99
33_V	42_A	0.901	0.99
98_S	101_R	0.896	0.99
35_K	101_R	0.893	0.99
14_T	130_Q	0.881	0.99
110_V	114_R	0.880	0.99
42_A	45_L	0.880	0.99
64_L	67_Q	0.869	0.99
3_A	45_L	0.844	0.99
101_R	105_L	0.842	0.99
31_L	75_V	0.838	0.98
50_L	73_V	0.838	0.98
32_G	82_A	0.837	0.98
28_L	76_V	0.835	0.98
128_D	136_D	0.835	0.98
64_L	68_Q	0.827	0.98
43_N	46_C	0.824	0.98
34_E	144_Q	0.817	0.98
108_Y	111_E	0.816	0.98
107_D	122_T	0.814	0.98
74_L	121_Q	0.813	0.98
33_V	97_A	0.812	0.98
50_L	116_Q	0.799	0.98
25_A	56_S	0.795	0.98
41_K	144_Q	0.794	0.98
112_R	116_Q	0.787	0.98
43_N	47_E	0.784	0.98
21_G	76_V	0.774	0.97
36_D	41_K	0.773	0.97
33_V	45_L	0.772	0.97
114_R	119_N	0.756	0.97
124_R	127_A	0.754	0.97
45_L	109_F	0.744	0.97
25_A	136_D	0.744	0.97
30_L	140_T	0.727	0.96
78_Q	81_L	0.717	0.96
42_A	46_C	0.715	0.96
131_V	135_N	0.713	0.96
39_E	112_R	0.700	0.95
82_A	144_Q	0.683	0.95
36_D	97_A	0.674	0.94
8_V	24_G	0.672	0.94
53_R	63_N	0.670	0.94
44_R	83_A	0.668	0.94
16_E	124_R	0.665	0.94
15_V	124_R	0.660	0.94
84_D	94_S	0.659	0.94
67_Q	70_G	0.655	0.93
53_R	90_R	0.654	0.93
109_F	113_C	0.651	0.93
13_V	20_T	0.647	0.93
52_Y	141_F	0.641	0.93
5_I	49_V	0.638	0.93
12_S	19_V	0.637	0.92
98_S	104_A	0.636	0.92
41_K	45_L	0.628	0.92
52_Y	85_T	0.627	0.92
55_F	71_G	0.627	0.92
84_D	92_S	0.626	0.92
45_L	143_L	0.626	0.92
7_R	139_V	0.625	0.92
113_C	120_T	0.625	0.92
44_R	47_E	0.623	0.92
29_V	73_V	0.615	0.91
9_T	25_A	0.615	0.91
66_V	69_A	0.613	0.91
16_E	19_V	0.612	0.91
42_A	109_F	0.612	0.91
16_E	127_A	0.611	0.91
4_L	30_L	0.610	0.91
23_I	121_Q	0.604	0.90
103_E	126_A	0.603	0.90
49_V	75_V	0.601	0.90
36_D	82_A	0.600	0.90
46_C	50_L	0.600	0.90
72_S	118_M	0.598	0.90
48_R	52_Y	0.582	0.89
97_A	102_A	0.580	0.89
130_Q	133_L	0.573	0.88
15_V	21_G	0.573	0.88
31_L	106_Y	0.572	0.88
10_R	130_Q	0.570	0.88
82_A	96_G	0.569	0.88
13_V	76_V	0.567	0.87
8_V	23_I	0.563	0.87
141_F	144_Q	0.559	0.87
106_Y	109_F	0.557	0.86
22_E	121_Q	0.554	0.86
7_R	136_D	0.553	0.86
38_D	42_A	0.551	0.86
47_E	112_R	0.547	0.86
102_A	125_F	0.545	0.85
64_L	69_A	0.543	0.85
52_Y	143_L	0.543	0.85
3_A	109_F	0.542	0.85
104_A	108_Y	0.538	0.85
92_S	95_K	0.537	0.84
63_N	92_S	0.536	0.84
5_I	143_L	0.534	0.84
44_R	48_R	0.529	0.84
40_Q	44_R	0.528	0.83
32_G	96_G	0.525	0.83
27_L	73_V	0.523	0.83
32_G	142_W	0.522	0.83
38_D	105_L	0.522	0.83
65_N	69_A	0.519	0.82
63_N	90_R	0.518	0.82
86_E	144_Q	0.515	0.82
99_P	126_A	0.511	0.81
27_L	93_F	0.504	0.81
28_L	134_V	0.504	0.81
93_F	99_P	0.502	0.80
60_G	64_L	0.501	0.80
12_S	134_V	0.501	0.80
15_V	127_A	0.500	0.80
70_G	118_M	0.500	0.80

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
1jkeA	5	1	100	0.025	Contact Map
2dboA	2	1	100	0.025	Contact Map
1j7gA	2	0.9931	100	0.032	Contact Map
2okvA	2	0.9931	100	0.045	Contact Map
4nbiA	2	1	100	0.046	Contact Map
1tc5A	2	0.9862	100	0.12	Contact Map
4rriA	2	0.8345	74.4	0.932	Contact Map
4rrfA	2	0.8345	71.5	0.933	Contact Map
4rrqA	2	0.8345	70	0.934	Contact Map
2g5xA	1	0.3586	41.4	0.945	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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