PTH - BACSU - GREMLIN Contacts

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PTH - Peptidyl-tRNA hydrolase

UniProt:	P37470	Sequences: MLVIAGLGNPGKNYENTRHNVGFMVIDQLAKEWNIELNQNKFNGLYGTGFVSGKKVLLVKPLTYMNLSGECLRPLMDYYDVDNEDLTVIYDDLDLPTGKIRLRTKGSAGGHNGIKSLIQHLGTSEFDRIRIGIGRPVNGMKVVDYVLGSFTKEEAPEIEEAVDKSVKACEASLSKPFLEVMNEFNAKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	188 (184)
Sequences:	4096 (2803)
Seq/√Len:	206.6

ECOLI - PTH
BACSU - PTH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_R	77_D	3.325	1.00
118_I	126_F	3.118	1.00
76_M	86_L	2.797	1.00
90_Y	114_I	2.704	1.00
27_D	60_K	2.642	1.00
2_L	85_D	2.596	1.00
17_T	149_S	2.467	1.00
48_T	55_K	2.440	1.00
72_L	117_L	2.417	1.00
67_L	70_E	2.363	1.00
93_L	133_I	2.322	1.00
44_G	59_V	2.306	1.00
59_V	75_L	2.274	1.00
112_N	115_K	2.185	1.00
43_N	70_E	2.109	1.00
44_G	71_C	2.081	1.00
35_I	47_G	2.063	1.00
28_Q	31_K	2.012	1.00
35_I	49_G	1.979	1.00
93_L	142_V	1.964	1.00
5_A	72_L	1.854	1.00
26_I	58_L	1.836	1.00
12_K	15_E	1.767	1.00
32_E	167_K	1.751	1.00
116_S	120_H	1.729	1.00
16_N	24_M	1.694	1.00
108_A	115_K	1.691	1.00
32_E	170_E	1.610	1.00
45_L	62_L	1.608	1.00
30_A	58_L	1.606	1.00
171_A	180_V	1.603	1.00
108_A	118_I	1.576	1.00
28_Q	163_D	1.566	1.00
26_I	37_L	1.562	1.00
87_T	129_I	1.523	1.00
59_V	71_C	1.506	1.00
37_L	47_G	1.504	1.00
76_M	121_L	1.439	1.00
88_V	117_L	1.425	1.00
73_R	120_H	1.412	1.00
21_V	131_I	1.399	1.00
175_K	179_E	1.381	1.00
176_P	180_V	1.373	1.00
63_T	71_C	1.364	1.00
176_P	179_E	1.362	1.00
23_F	60_K	1.352	1.00
104_T	178_L	1.352	1.00
127_D	177_F	1.338	1.00
33_W	170_E	1.333	1.00
171_A	184_F	1.328	1.00
67_L	116_S	1.311	1.00
28_Q	32_E	1.310	1.00
83_N	123_T	1.306	1.00
97_T	161_A	1.299	1.00
143_V	148_G	1.276	1.00
171_A	175_K	1.276	1.00
155_A	159_E	1.274	1.00
25_V	162_V	1.235	1.00
114_I	126_F	1.235	1.00
82_D	85_D	1.230	1.00
137_V	140_M	1.229	1.00
116_S	119_Q	1.226	1.00
87_T	172_S	1.221	1.00
179_E	183_E	1.218	1.00
152_K	156_P	1.213	1.00
70_E	120_H	1.204	1.00
25_V	89_I	1.186	1.00
28_Q	166_V	1.185	1.00
24_M	155_A	1.179	1.00
157_E	160_E	1.177	1.00
97_T	134_G	1.173	1.00
135_R	142_V	1.161	1.00
104_T	127_D	1.147	1.00
33_W	49_G	1.139	1.00
102_L	177_F	1.137	1.00
175_K	183_E	1.136	1.00
30_A	37_L	1.133	1.00
3_V	81_V	1.132	1.00
131_I	161_A	1.126	1.00
10_P	62_L	1.125	1.00
7_L	65_M	1.125	1.00
151_T	154_E	1.112	1.00
18_R	154_E	1.108	1.00
16_N	155_A	1.087	1.00
140_M	144_D	1.085	1.00
25_V	165_S	1.081	1.00
89_I	169_C	1.071	1.00
94_D	130_R	1.069	1.00
43_N	74_P	1.067	1.00
25_V	131_I	1.065	1.00
141_K	144_D	1.060	1.00
32_E	166_V	1.051	1.00
30_A	47_G	1.041	1.00
3_V	59_V	1.039	1.00
29_L	169_C	1.034	1.00
37_L	60_K	1.029	1.00
24_M	150_F	1.018	1.00
76_M	81_V	1.013	1.00
33_W	51_V	1.013	1.00
4_I	89_I	1.005	1.00
102_L	129_I	1.004	1.00
28_Q	162_V	1.001	1.00
96_P	99_K	0.992	1.00
97_T	157_E	0.984	1.00
50_F	55_K	0.980	1.00
158_I	162_V	0.978	1.00
94_D	135_R	0.976	1.00
51_V	56_V	0.968	1.00
87_T	169_C	0.965	1.00
156_P	159_E	0.965	1.00
171_A	176_P	0.962	1.00
105_K	125_E	0.949	0.99
30_A	35_I	0.931	0.99
108_A	124_S	0.926	0.99
136_P	142_V	0.923	0.99
160_E	163_D	0.922	0.99
168_A	184_F	0.914	0.99
87_T	127_D	0.912	0.99
160_E	164_K	0.911	0.99
179_E	182_N	0.905	0.99
153_E	156_P	0.900	0.99
29_L	33_W	0.899	0.99
28_Q	159_E	0.899	0.99
24_M	162_V	0.895	0.99
97_T	158_I	0.894	0.99
52_S	174_S	0.892	0.99
92_D	109_G	0.891	0.99
156_P	160_E	0.889	0.99
56_V	173_L	0.885	0.99
65_M	111_H	0.884	0.99
44_G	62_L	0.876	0.99
23_F	61_P	0.876	0.99
21_V	24_M	0.870	0.99
115_K	119_Q	0.867	0.99
18_R	148_G	0.865	0.99
23_F	62_L	0.857	0.99
42_F	78_Y	0.856	0.99
32_E	163_D	0.851	0.99
25_V	169_C	0.848	0.99
5_A	86_L	0.839	0.99
164_K	167_K	0.839	0.99
161_A	165_S	0.838	0.99
16_N	149_S	0.832	0.99
95_L	99_K	0.830	0.99
70_E	116_S	0.825	0.98
74_P	77_D	0.821	0.98
129_I	172_S	0.818	0.98
170_E	174_S	0.816	0.98
37_L	46_Y	0.813	0.98
171_A	183_E	0.811	0.98
167_K	170_E	0.802	0.98
23_F	27_D	0.790	0.98
169_C	173_L	0.787	0.98
4_I	169_C	0.785	0.98
6_G	26_I	0.779	0.98
3_V	75_L	0.778	0.98
154_E	157_E	0.776	0.98
92_D	130_R	0.775	0.98
21_V	158_I	0.772	0.98
90_Y	94_D	0.771	0.98
2_L	54_K	0.770	0.98
168_A	180_V	0.768	0.98
93_L	135_R	0.755	0.97
46_Y	75_L	0.752	0.97
118_I	124_S	0.751	0.97
39_Q	48_T	0.743	0.97
171_A	174_S	0.740	0.97
103_R	106_G	0.730	0.97
42_F	74_P	0.730	0.97
97_T	150_F	0.728	0.97
45_L	60_K	0.725	0.97
90_Y	130_R	0.724	0.97
14_Y	17_T	0.722	0.97
2_L	82_D	0.722	0.97
77_D	120_H	0.722	0.97
89_I	131_I	0.720	0.96
150_F	158_I	0.713	0.96
86_L	121_L	0.708	0.96
163_D	167_K	0.708	0.96
41_K	46_Y	0.706	0.96
152_K	155_A	0.706	0.96
110_G	114_I	0.705	0.96
95_L	130_R	0.705	0.96
84_E	125_E	0.702	0.96
51_V	54_K	0.702	0.96
106_G	128_R	0.701	0.96
72_L	86_L	0.699	0.96
57_L	75_L	0.697	0.96
84_E	104_T	0.696	0.96
134_G	145_Y	0.691	0.96
52_S	170_E	0.688	0.95
102_L	168_A	0.688	0.95
37_L	45_L	0.683	0.95
159_E	163_D	0.681	0.95
166_V	170_E	0.676	0.95
110_G	118_I	0.674	0.95
95_L	101_R	0.674	0.95
106_G	114_I	0.669	0.95
42_F	59_V	0.668	0.95
166_V	169_C	0.668	0.95
108_A	114_I	0.667	0.95
46_Y	57_L	0.665	0.95
24_M	158_I	0.661	0.94
140_M	145_Y	0.648	0.94
5_A	59_V	0.644	0.94
50_F	53_G	0.641	0.93
49_G	56_V	0.638	0.93
133_I	146_V	0.636	0.93
129_I	169_C	0.634	0.93
172_S	180_V	0.627	0.93
4_I	87_T	0.620	0.92
100_I	161_A	0.620	0.92
102_L	127_D	0.618	0.92
3_V	76_M	0.617	0.92
46_Y	79_Y	0.616	0.92
162_V	166_V	0.614	0.92
8_G	23_F	0.613	0.92
11_G	64_Y	0.612	0.92
180_V	184_F	0.612	0.92
38_N	47_G	0.608	0.91
21_V	150_F	0.603	0.91
92_D	95_L	0.601	0.91
97_T	159_E	0.600	0.91
100_I	184_F	0.599	0.91
103_R	107_S	0.597	0.91
178_L	182_N	0.597	0.91
2_L	87_T	0.596	0.91
83_N	121_L	0.595	0.91
137_V	145_Y	0.594	0.90
129_I	165_S	0.593	0.90
119_Q	122_G	0.593	0.90
24_M	149_S	0.588	0.90
76_M	83_N	0.587	0.90
30_A	36_E	0.587	0.90
51_V	173_L	0.586	0.90
89_I	165_S	0.575	0.89
182_N	185_N	0.573	0.89
111_H	116_S	0.571	0.89
94_D	142_V	0.569	0.89
25_V	166_V	0.563	0.88
100_I	164_K	0.561	0.88
160_E	167_K	0.558	0.88
48_T	57_L	0.557	0.87
164_K	183_E	0.556	0.87
13_N	149_S	0.555	0.87
108_A	116_S	0.554	0.87
112_N	126_F	0.554	0.87
67_L	120_H	0.552	0.87
109_G	130_R	0.549	0.87
90_Y	105_K	0.543	0.86
93_L	136_P	0.542	0.86
131_I	165_S	0.541	0.86
114_I	130_R	0.541	0.86
57_L	79_Y	0.540	0.86
26_I	60_K	0.539	0.86
18_R	149_S	0.538	0.86
41_K	78_Y	0.538	0.86
90_Y	103_R	0.537	0.86
111_H	114_I	0.536	0.85
4_I	26_I	0.533	0.85
6_G	22_G	0.533	0.85
64_Y	67_L	0.531	0.85
104_T	177_F	0.528	0.85
100_I	129_I	0.527	0.84
11_G	15_E	0.526	0.84
42_F	79_Y	0.523	0.84
100_I	185_N	0.517	0.83
158_I	161_A	0.514	0.83
97_T	154_E	0.514	0.83
77_D	80_D	0.509	0.82
117_L	121_L	0.509	0.82
51_V	170_E	0.508	0.82
30_A	49_G	0.504	0.82
81_V	85_D	0.502	0.82
149_S	155_A	0.502	0.82
93_L	143_V	0.500	0.81

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
2pthA	1	1	100	0.01	Contact Map
2mjlA	1	1	100	0.011	Contact Map
4qt4A	1	0.9894	100	0.011	Contact Map
2z2iA	1	0.9309	100	0.011	Contact Map
4qajA	1	1	100	0.014	Contact Map
1rybA	1	0.9734	100	0.015	Contact Map
4lwrA	1	0.9947	100	0.017	Contact Map
3v2iA	1	0.9574	100	0.017	Contact Map
3neaA	1	0.9787	100	0.02	Contact Map
1cfzA	1	0.7766	48.8	0.946	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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