TRUB - HALSA - GREMLIN Contacts

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TRUB - Probable tRNA pseudouridine synthase B

UniProt:	Q9HPA4	Sequences: MGIRPPPGERSPAAVLSFGVVNLDKPPGPSAHQVSAWIRDLVGVEKAAHAGTLDPKVTGCLPVLTGTATRIAPALLEGFKEYVAVLELHDDPPRILPDVIEAFTGEIYQKPPKKSAVARRLRTRTVYDLDVLDVDGRQVLLRIRCESGTYIRKLCHDIGRALGTNAHMGHLRRSATTPFDDTDLVTLHDLADAVAWLRDTDDTEPPDAPADALRAAVQPAERALTHLPRLTIADSAAHEVATGAPVYAPGVIDTTALPTPPADGALVACYTAGGTAVCLGRLVGDPDADAGVVVALERVLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	301 (241)
Sequences:	3006 (2153)
Seq/√Len:	138.7

ECOLI - TRUB
BACSU - TRUB
HALSA - TRUB
SULSO - TRUB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_Y	123_T	4.016	1.00
106_E	123_T	3.732	1.00
24_D	172_R	3.406	1.00
93_P	97_P	3.311	1.00
23_L	34_V	3.061	1.00
83_V	142_R	2.888	1.00
106_E	125_T	2.712	1.00
81_E	142_R	2.705	1.00
22_N	60_C	2.617	1.00
102_A	161_A	2.485	1.00
239_E	244_A	2.449	1.00
81_E	144_R	2.431	1.00
132_L	142_R	2.308	1.00
27_P	58_T	2.296	1.00
87_E	138_Q	2.282	1.00
92_P	95_I	2.268	1.00
38_I	47_A	2.219	1.00
87_E	169_G	2.172	1.00
99_V	158_I	2.145	1.00
128_D	144_R	2.115	1.00
86_L	155_C	2.084	1.00
130_D	142_R	2.031	1.00
113_K	119_R	1.987	1.00
91_D	160_R	1.984	1.00
117_V	122_R	1.979	1.00
88_L	139_V	1.945	1.00
100_I	131_V	1.919	1.00
86_L	141_L	1.906	1.00
83_V	140_L	1.890	1.00
58_T	172_R	1.889	1.00
95_I	98_D	1.873	1.00
38_I	63_V	1.870	1.00
44_V	65_T	1.869	1.00
110_K	121_L	1.844	1.00
100_I	129_L	1.835	1.00
155_C	168_M	1.834	1.00
103_F	161_A	1.812	1.00
143_I	154_L	1.804	1.00
85_V	140_L	1.790	1.00
159_G	166_A	1.782	1.00
233_A	236_A	1.762	1.00
84_A	141_L	1.730	1.00
86_L	139_V	1.724	1.00
64_L	72_A	1.714	1.00
50_A	64_L	1.710	1.00
85_V	138_Q	1.693	1.00
93_P	134_V	1.644	1.00
79_F	144_R	1.641	1.00
107_I	124_R	1.638	1.00
159_G	164_T	1.618	1.00
23_L	190_L	1.602	1.00
159_G	165_N	1.600	1.00
101_E	104_T	1.595	1.00
133_D	140_L	1.590	1.00
232_I	240_V	1.586	1.00
81_E	175_A	1.558	1.00
188_H	191_A	1.539	1.00
153_K	156_H	1.529	1.00
186_T	189_D	1.528	1.00
97_P	131_V	1.516	1.00
91_D	165_N	1.479	1.00
191_A	195_A	1.452	1.00
32_H	39_R	1.433	1.00
60_C	184_L	1.431	1.00
24_D	58_T	1.413	1.00
22_N	184_L	1.409	1.00
38_I	65_T	1.407	1.00
37_W	191_A	1.403	1.00
144_R	175_A	1.395	1.00
83_V	132_L	1.351	1.00
134_V	139_V	1.343	1.00
100_I	141_L	1.340	1.00
104_T	129_L	1.331	1.00
18_F	67_T	1.322	1.00
138_Q	169_G	1.317	1.00
27_P	56_K	1.312	1.00
212_A	215_A	1.308	1.00
181_D	184_L	1.301	1.00
218_Q	222_R	1.292	1.00
20_V	64_L	1.266	1.00
86_L	166_A	1.264	1.00
85_V	169_G	1.259	1.00
108_Y	121_L	1.257	1.00
37_W	40_D	1.255	1.00
84_A	168_M	1.255	1.00
87_E	90_D	1.251	1.00
97_P	104_T	1.250	1.00
72_A	76_L	1.238	1.00
131_V	139_V	1.218	1.00
128_D	142_R	1.203	1.00
50_A	72_A	1.166	0.99
81_E	174_S	1.161	0.99
85_V	170_H	1.158	0.99
44_V	47_A	1.148	0.99
103_F	157_D	1.146	0.99
67_T	70_R	1.138	0.99
99_V	102_A	1.135	0.99
99_V	161_A	1.131	0.99
127_Y	144_R	1.127	0.99
29_P	37_W	1.126	0.99
56_K	168_M	1.110	0.99
32_H	36_A	1.110	0.99
79_F	127_Y	1.106	0.99
156_H	160_R	1.105	0.99
143_I	151_I	1.102	0.99
221_E	270_Y	1.098	0.99
268_A	276_A	1.096	0.99
179_F	222_R	1.080	0.99
21_V	38_I	1.078	0.99
77_E	147_S	1.078	0.99
239_E	242_T	1.062	0.99
238_H	242_T	1.056	0.99
96_L	139_V	1.049	0.99
104_T	128_D	1.049	0.99
24_D	181_D	1.045	0.99
189_D	192_D	1.043	0.99
180_D	183_D	1.027	0.99
30_S	33_Q	1.025	0.99
172_R	181_D	1.023	0.99
57_V	117_V	1.022	0.99
26_P	188_H	1.021	0.99
94_R	98_D	1.017	0.99
126_V	154_L	1.009	0.98
193_A	216_A	1.009	0.98
125_T	146_E	1.005	0.98
27_P	170_H	0.994	0.98
119_R	153_K	0.991	0.98
175_A	180_D	0.977	0.98
108_Y	120_R	0.976	0.98
127_Y	146_E	0.972	0.98
185_V	216_A	0.963	0.98
93_P	133_D	0.961	0.98
90_D	167_H	0.956	0.98
113_K	153_K	0.956	0.98
21_V	42_V	0.956	0.98
185_V	190_L	0.953	0.98
60_C	181_D	0.949	0.98
129_L	141_L	0.947	0.98
78_G	177_T	0.943	0.98
42_V	65_T	0.941	0.98
47_A	65_T	0.933	0.97
70_R	73_P	0.909	0.97
38_I	190_L	0.901	0.97
145_C	149_T	0.894	0.97
86_L	168_M	0.894	0.97
41_L	191_A	0.894	0.97
194_V	213_L	0.889	0.97
84_A	155_C	0.885	0.96
129_L	154_L	0.883	0.96
232_I	236_A	0.879	0.96
88_L	162_L	0.876	0.96
33_Q	37_W	0.867	0.96
240_V	278_C	0.864	0.96
87_E	137_R	0.862	0.96
47_A	63_V	0.859	0.96
271_T	275_T	0.858	0.96
29_P	34_V	0.856	0.96
97_P	130_D	0.855	0.96
20_V	223_A	0.851	0.96
126_V	145_C	0.847	0.95
84_A	129_L	0.847	0.95
236_A	239_E	0.846	0.95
112_P	153_K	0.840	0.95
132_L	140_L	0.825	0.95
20_V	71_I	0.824	0.95
96_L	134_V	0.820	0.95
140_L	170_H	0.816	0.94
88_L	164_T	0.813	0.94
129_L	158_I	0.806	0.94
83_V	174_S	0.805	0.94
100_I	158_I	0.801	0.94
224_L	227_L	0.799	0.94
240_V	269_C	0.798	0.94
33_Q	40_D	0.797	0.94
32_H	35_S	0.790	0.93
232_I	237_A	0.790	0.93
157_D	160_R	0.785	0.93
131_V	134_V	0.782	0.93
185_V	189_D	0.781	0.93
21_V	65_T	0.779	0.93
219_P	222_R	0.779	0.93
91_D	156_H	0.771	0.93
42_V	190_L	0.771	0.93
104_T	107_I	0.769	0.93
91_D	164_T	0.768	0.93
73_P	76_L	0.762	0.92
228_P	265_A	0.762	0.92
222_R	225_T	0.760	0.92
98_D	101_E	0.756	0.92
274_G	278_C	0.751	0.92
38_I	42_V	0.750	0.92
142_R	174_S	0.749	0.92
24_D	186_T	0.747	0.91
193_A	212_A	0.745	0.91
129_L	143_I	0.744	0.91
35_S	47_A	0.744	0.91
73_P	77_E	0.732	0.91
159_G	162_L	0.731	0.91
85_V	139_V	0.730	0.91
22_N	58_T	0.727	0.90
100_I	104_T	0.727	0.90
62_P	176_T	0.724	0.90
94_R	97_P	0.724	0.90
22_N	181_D	0.723	0.90
235_S	239_E	0.721	0.90
154_L	158_I	0.719	0.90
236_A	244_A	0.719	0.90
271_T	277_V	0.719	0.90
57_V	176_T	0.709	0.89
40_D	43_G	0.702	0.89
139_V	158_I	0.701	0.89
76_L	117_V	0.700	0.89
87_E	167_H	0.697	0.88
29_P	187_L	0.697	0.88
103_F	154_L	0.696	0.88
41_L	186_T	0.695	0.88
135_D	140_L	0.694	0.88
36_A	40_D	0.692	0.88
75_L	78_G	0.688	0.88
119_R	156_H	0.687	0.88
35_S	65_T	0.687	0.88
37_W	41_L	0.684	0.87
88_L	166_A	0.683	0.87
237_A	272_A	0.682	0.87
65_T	217_V	0.681	0.87
58_T	170_H	0.679	0.87
194_V	212_A	0.678	0.87
97_P	101_E	0.676	0.87
267_V	270_Y	0.676	0.87
41_L	194_V	0.674	0.87
220_A	223_A	0.674	0.87
71_I	223_A	0.672	0.87
78_G	176_T	0.672	0.87
71_I	224_L	0.671	0.86
107_I	126_V	0.669	0.86
95_I	99_V	0.666	0.86
247_Y	250_G	0.666	0.86
270_Y	278_C	0.657	0.85
26_P	29_P	0.656	0.85
135_D	138_Q	0.655	0.85
84_A	170_H	0.655	0.85
41_L	190_L	0.647	0.84
183_D	218_Q	0.647	0.84
235_S	238_H	0.647	0.84
96_L	162_L	0.646	0.84
84_A	151_I	0.643	0.84
270_Y	276_A	0.643	0.84
179_F	223_A	0.641	0.84
213_L	216_A	0.639	0.84
252_I	255_T	0.633	0.83
22_N	183_D	0.631	0.83
120_R	124_R	0.628	0.83
229_R	268_A	0.628	0.83
112_P	224_L	0.627	0.83
118_A	121_L	0.621	0.82
91_D	167_H	0.621	0.82
22_N	172_R	0.620	0.82
113_K	118_A	0.620	0.82
134_V	137_R	0.620	0.82
111_P	121_L	0.620	0.82
241_A	275_T	0.619	0.82
175_A	178_P	0.617	0.81
29_P	40_D	0.614	0.81
20_V	168_M	0.612	0.81
64_L	147_S	0.612	0.81
274_G	277_V	0.610	0.81
111_P	119_R	0.606	0.80
231_T	271_T	0.605	0.80
126_V	149_T	0.605	0.80
93_P	131_V	0.603	0.80
21_V	190_L	0.603	0.80
43_G	194_V	0.603	0.80
239_E	250_G	0.602	0.80
38_I	41_L	0.602	0.80
110_K	119_R	0.602	0.80
99_V	103_F	0.601	0.80
126_V	143_I	0.599	0.80
240_V	277_V	0.599	0.80
100_I	139_V	0.599	0.80
229_R	274_G	0.597	0.79
224_L	276_A	0.596	0.79
50_A	76_L	0.596	0.79
86_L	167_H	0.596	0.79
17_S	65_T	0.595	0.79
236_A	246_V	0.594	0.79
271_T	274_G	0.592	0.79
234_D	273_G	0.590	0.79
52_T	168_M	0.589	0.78
155_C	159_G	0.588	0.78
230_L	236_A	0.587	0.78
216_A	219_P	0.583	0.78
60_C	176_T	0.583	0.78
114_K	124_R	0.581	0.78
107_I	125_T	0.581	0.78
21_V	216_A	0.580	0.77
110_K	113_K	0.579	0.77
76_L	79_F	0.578	0.77
264_G	269_C	0.575	0.77
109_Q	157_D	0.574	0.77
267_V	273_G	0.572	0.76
88_L	165_N	0.572	0.76
42_V	63_V	0.569	0.76
147_S	168_M	0.569	0.76
238_H	241_A	0.567	0.76
237_A	241_A	0.566	0.76
41_L	187_L	0.562	0.75
18_F	46_K	0.561	0.75
268_A	271_T	0.561	0.75
32_H	44_V	0.560	0.75
98_D	102_A	0.558	0.75
64_L	71_I	0.558	0.75
156_H	159_G	0.557	0.75
104_T	130_D	0.557	0.75
188_H	192_D	0.556	0.74
18_F	66_G	0.555	0.74
26_P	187_L	0.553	0.74
26_P	46_K	0.552	0.74
124_R	146_E	0.552	0.74
20_V	72_A	0.551	0.74
68_A	220_A	0.549	0.73
44_V	66_G	0.548	0.73
149_T	154_L	0.548	0.73
129_L	151_I	0.546	0.73
234_D	237_A	0.539	0.72
211_D	214_R	0.536	0.72
23_L	35_S	0.536	0.72
234_D	238_H	0.535	0.72
141_L	151_I	0.534	0.71
236_A	240_V	0.534	0.71
221_E	268_A	0.534	0.71
96_L	141_L	0.528	0.71
35_S	52_T	0.527	0.70
32_H	47_A	0.526	0.70
162_L	165_N	0.525	0.70
19_G	217_V	0.524	0.70
265_A	268_A	0.523	0.70
147_S	176_T	0.522	0.70
236_A	248_A	0.522	0.70
40_D	191_A	0.521	0.70
71_I	220_A	0.521	0.70
97_P	134_V	0.519	0.69
99_V	162_L	0.519	0.69
141_L	155_C	0.518	0.69
86_L	158_I	0.517	0.69
186_T	190_L	0.515	0.69
57_V	165_N	0.515	0.69
57_V	84_A	0.515	0.69
36_A	39_R	0.514	0.69
18_F	220_A	0.514	0.69
93_P	136_G	0.513	0.68
185_V	193_A	0.512	0.68
111_P	122_R	0.512	0.68
225_T	229_R	0.511	0.68
119_R	154_L	0.510	0.68
33_Q	47_A	0.509	0.68
237_A	271_T	0.508	0.68
50_A	75_L	0.507	0.68
98_D	192_D	0.504	0.67
124_R	149_T	0.503	0.67
37_W	187_L	0.503	0.67
72_A	177_T	0.500	0.66
26_P	186_T	0.500	0.66

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
3u28A	1	0.9502	100	0.198	Contact Map
2apoA	1	0.9302	100	0.206	Contact Map
2ausC	1	0.9269	100	0.211	Contact Map
1k8wA	1	0.8904	100	0.213	Contact Map
1r3eA	1	0.8704	100	0.216	Contact Map
1sgvA	1	0.8007	100	0.229	Contact Map
2v9kA	1	0.5714	100	0.717	Contact Map
1kskA	1	0.5781	99.8	0.806	Contact Map
4lgtA	1	0.6213	98.9	0.881	Contact Map
3dh3A	1	0.6047	98.7	0.891	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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