YJDI - BACSU - GREMLIN Contacts

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YJDI - Putative Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YjdI

UniProt:	O31650	Sequences: MAKKMAKTNAVRLIEQQNISYEVLGYKTDGQPVDGISVAEKIGYSLKYVYKTLVAAAGTNHYYVFVVPVAEELDVKKAAKVTGEKKIEMIAMKELLAVTGYLRGGCSPIGMKKLFPTYIDASAETLDFIIVSAGKIGMQLKLAPQDLARSCDAAFAEIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	159 (148)
Sequences:	4385 (2961)
Seq/√Len:	243.4

ECOLI - YBAK YEAK
BACSU - YJDI YWHH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_F	141_K	3.180	1.00
56_A	94_E	2.554	1.00
61_H	116_P	2.547	1.00
146_D	149_R	2.526	1.00
15_E	21_Y	2.520	1.00
35_G	69_V	2.512	1.00
82_T	118_Y	2.492	1.00
148_A	155_F	2.365	1.00
95_L	106_C	2.290	1.00
57_A	84_E	2.193	1.00
124_E	155_F	2.152	1.00
143_A	146_D	2.087	1.00
36_I	40_E	2.054	1.00
81_V	156_A	2.032	1.00
77_K	157_E	2.001	1.00
65_F	78_A	1.923	1.00
91_A	94_E	1.918	1.00
121_A	157_E	1.854	1.00
22_E	141_K	1.849	1.00
62_Y	98_V	1.842	1.00
13_L	17_Q	1.837	1.00
114_L	152_D	1.808	1.00
130_I	141_K	1.759	1.00
17_Q	150_S	1.724	1.00
24_L	141_K	1.690	1.00
48_Y	126_L	1.675	1.00
55_A	78_A	1.615	1.00
47_K	126_L	1.574	1.00
45_S	48_Y	1.568	1.00
55_A	73_L	1.547	1.00
92_M	103_R	1.490	1.00
50_Y	66_V	1.468	1.00
63_Y	78_A	1.466	1.00
111_M	117_T	1.443	1.00
47_K	70_A	1.401	1.00
148_A	153_A	1.388	1.00
121_A	125_T	1.380	1.00
12_R	15_E	1.367	1.00
54_V	115_F	1.355	1.00
96_L	102_L	1.330	1.00
12_R	16_Q	1.317	1.00
81_V	154_A	1.282	1.00
57_A	61_H	1.281	1.00
145_Q	148_A	1.272	1.00
23_V	138_M	1.267	1.00
37_S	41_K	1.263	1.00
44_Y	130_I	1.256	1.00
124_E	145_Q	1.249	1.00
24_L	130_I	1.232	1.00
62_Y	115_F	1.226	1.00
58_G	84_E	1.217	1.00
74_D	77_K	1.216	1.00
119_I	148_A	1.216	1.00
76_K	80_K	1.203	1.00
118_Y	158_I	1.202	1.00
64_V	111_M	1.195	1.00
50_Y	123_A	1.193	1.00
48_Y	141_K	1.187	1.00
11_V	23_V	1.187	1.00
22_E	128_F	1.161	1.00
57_A	87_I	1.150	1.00
56_A	88_E	1.147	1.00
19_I	150_S	1.137	1.00
63_Y	82_T	1.136	1.00
123_A	155_F	1.123	1.00
9_N	112_K	1.113	1.00
11_V	15_E	1.108	1.00
37_S	40_E	1.104	1.00
62_Y	90_I	1.098	1.00
55_A	63_Y	1.091	1.00
118_Y	156_A	1.080	1.00
65_F	158_I	1.078	1.00
53_L	73_L	1.078	1.00
122_S	125_T	1.077	1.00
121_A	124_E	1.071	1.00
8_T	12_R	1.067	1.00
14_I	140_L	1.065	1.00
48_Y	128_F	1.054	1.00
94_E	98_V	1.032	1.00
90_I	98_V	1.022	1.00
40_E	46_L	1.012	1.00
116_P	154_A	1.012	1.00
29_D	37_S	1.011	1.00
53_L	89_M	1.010	1.00
56_A	62_Y	1.005	1.00
120_D	157_E	0.955	1.00
63_Y	84_E	0.949	1.00
84_E	87_I	0.944	1.00
131_V	142_L	0.942	1.00
94_E	97_A	0.939	1.00
36_I	46_L	0.936	1.00
71_E	122_S	0.931	1.00
98_V	115_F	0.920	1.00
123_A	129_I	0.915	1.00
29_D	32_P	0.912	1.00
77_K	80_K	0.895	1.00
54_V	95_L	0.888	1.00
56_A	60_N	0.884	1.00
135_K	138_M	0.882	1.00
119_I	123_A	0.875	0.99
96_L	103_R	0.875	0.99
26_Y	29_D	0.874	0.99
95_L	103_R	0.874	0.99
118_Y	154_A	0.867	0.99
34_D	37_S	0.867	0.99
102_L	136_I	0.866	0.99
42_I	130_I	0.863	0.99
133_A	139_Q	0.852	0.99
57_A	63_Y	0.847	0.99
126_L	129_I	0.846	0.99
133_A	140_L	0.843	0.99
27_K	41_K	0.835	0.99
145_Q	149_R	0.832	0.99
142_L	146_D	0.830	0.99
17_Q	149_R	0.827	0.99
40_E	43_G	0.826	0.99
44_Y	49_V	0.819	0.99
33_V	37_S	0.817	0.99
26_Y	137_G	0.801	0.99
25_G	138_M	0.791	0.99
124_E	148_A	0.784	0.99
28_T	37_S	0.777	0.99
29_D	33_V	0.775	0.99
127_D	143_A	0.774	0.99
119_I	153_A	0.767	0.99
108_P	147_L	0.762	0.99
46_L	70_A	0.761	0.99
50_Y	129_I	0.761	0.99
26_Y	42_I	0.760	0.99
35_G	46_L	0.758	0.98
13_L	16_Q	0.749	0.98
61_H	84_E	0.744	0.98
38_V	139_Q	0.744	0.98
20_S	146_D	0.744	0.98
9_N	12_R	0.738	0.98
42_I	139_Q	0.738	0.98
49_V	139_Q	0.737	0.98
109_I	151_C	0.736	0.98
14_I	21_Y	0.734	0.98
52_T	64_V	0.731	0.98
32_P	37_S	0.725	0.98
78_A	87_I	0.721	0.98
50_Y	122_S	0.719	0.98
109_I	147_L	0.715	0.98
124_E	144_P	0.714	0.98
93_K	96_L	0.712	0.98
119_I	155_F	0.711	0.98
88_E	91_A	0.708	0.98
63_Y	87_I	0.706	0.98
50_Y	126_L	0.693	0.97
57_A	82_T	0.691	0.97
36_I	70_A	0.676	0.97
54_V	90_I	0.675	0.97
60_N	84_E	0.671	0.97
131_V	147_L	0.670	0.97
11_V	21_Y	0.669	0.97
100_G	112_K	0.666	0.97
119_I	147_L	0.664	0.97
92_M	95_L	0.663	0.96
144_P	155_F	0.658	0.96
132_S	139_Q	0.657	0.96
19_I	146_D	0.657	0.96
66_V	119_I	0.651	0.96
145_Q	155_F	0.650	0.96
26_Y	32_P	0.648	0.96
29_D	34_D	0.646	0.96
55_A	65_F	0.643	0.96
98_V	113_K	0.639	0.96
44_Y	141_K	0.631	0.95
67_V	73_L	0.626	0.95
92_M	96_L	0.621	0.95
15_E	20_S	0.620	0.95
65_F	82_T	0.616	0.95
14_I	19_I	0.614	0.95
77_K	81_V	0.612	0.95
65_F	73_L	0.595	0.94
76_K	85_K	0.594	0.94
55_A	87_I	0.594	0.94
130_I	139_Q	0.585	0.93
19_I	22_E	0.584	0.93
57_A	60_N	0.584	0.93
48_Y	127_D	0.583	0.93
64_V	115_F	0.582	0.93
111_M	115_F	0.579	0.93
48_Y	130_I	0.572	0.92
35_G	39_A	0.571	0.92
65_F	118_Y	0.568	0.92
34_D	38_V	0.567	0.92
21_Y	146_D	0.562	0.92
10_A	140_L	0.561	0.92
54_V	99_T	0.560	0.92
54_V	106_C	0.556	0.91
53_L	67_V	0.555	0.91
71_E	120_D	0.554	0.91
110_G	115_F	0.551	0.91
16_Q	113_K	0.551	0.91
13_L	150_S	0.551	0.91
99_T	112_K	0.551	0.91
14_I	150_S	0.547	0.91
24_L	128_F	0.546	0.91
50_Y	67_V	0.543	0.90
68_P	71_E	0.541	0.90
56_A	91_A	0.540	0.90
67_V	158_I	0.538	0.90
55_A	89_M	0.534	0.90
20_S	143_A	0.532	0.89
66_V	131_V	0.526	0.89
50_Y	120_D	0.525	0.89
67_V	71_E	0.525	0.89
25_G	135_K	0.524	0.89
29_D	41_K	0.524	0.89
10_A	107_S	0.519	0.88
70_A	125_T	0.518	0.88
56_A	90_I	0.516	0.88
38_V	49_V	0.513	0.88
117_T	151_C	0.513	0.88
28_T	32_P	0.511	0.87
101_Y	107_S	0.509	0.87
51_K	101_Y	0.506	0.87
10_A	14_I	0.506	0.87
45_S	126_L	0.505	0.87
38_V	44_Y	0.500	0.86

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
2dxaA	1	0.9623	100	0.213	Contact Map
1dbuA	1	0.9245	100	0.215	Contact Map
3op6A	2	0.9434	100	0.22	Contact Map
2z0xA	1	0.9686	100	0.223	Contact Map
1vjfA	1	0.956	100	0.241	Contact Map
1wdvA	1	0.9371	100	0.244	Contact Map
1vkiA	2	0.9623	100	0.257	Contact Map
3memA	1	0.8553	100	0.377	Contact Map
2j3lA	2	0.9748	97.9	0.807	Contact Map
1s3cA	2	0.7736	48.8	0.919	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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