PSUK - ECOLI - GREMLIN Contacts

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PSUK - Pseudouridine kinase

UniProt:	P30235	Sequences: MREKDYVVIIGSANIDVAGYSHESLNYADSNPGKIKFTPGGVGRNIAQNLALLGNKAWLLSAVGSDFYGQSLLTQTNQSGVYVDKCLIVPGENTSSYLSLLDNTGEMLVAINDMNISNAITAEYLAQHGEFIQRAKVIVADCNISEEALAWILDNAANVPVFVDPVSAWKCVKVRDRLNQIHTLKPNRLEAETLSGIALSGREDVAKVAAWFHQHGLNRLVLSMGGDGVYYSDISGESGWSAPIKTNVINVTGAGDAMMAGLASCWVDGMPFAESVRFAQGCSSMALSCEYTNNPDLSIANVISLVENAECLN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11646
Length:	313 (280)
Sequences:	22656 (17030)
Seq/√Len:	1017.7

ECOLI - PSUK YEII RBSK YDJH YEGV SQUV K1PF PFKB KDGK FRLD HLDE INGK
BACSU - YDJE IOLC RBSK KDGK FRLD K1PF
HALSA - Q9HMJ3 Q9HP13 Q9HSM7
SULSO - Q981E2 KDGK Q97W01 Q980X6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_N	264_S	3.131	1.00
139_V	162_F	2.682	1.00
73_L	88_I	2.679	1.00
58_W	82_Y	2.552	1.00
224_M	230_Y	2.492	1.00
231_Y	276_V	2.489	1.00
8_V	135_A	2.434	1.00
265_C	270_M	2.372	1.00
271_P	274_E	2.369	1.00
229_V	258_M	2.255	1.00
70_Q	88_I	2.150	1.00
65_S	90_P	2.093	1.00
50_L	55_N	2.088	1.00
213_H	232_S	2.082	1.00
188_R	224_M	2.029	1.00
162_F	263_A	1.983	1.00
52_L	79_S	1.971	1.00
9_I	47_A	1.952	1.00
265_C	278_F	1.909	1.00
298_S	301_N	1.898	1.00
257_A	282_C	1.878	1.00
62_A	124_Y	1.875	1.00
137_V	160_P	1.873	1.00
160_P	182_H	1.841	1.00
48_Q	79_S	1.822	1.00
62_A	89_V	1.806	1.00
206_A	238_S	1.798	1.00
270_M	274_E	1.776	1.00
185_K	259_M	1.771	1.00
182_H	218_N	1.768	1.00
77_N	83_V	1.767	1.00
49_N	260_A	1.748	1.00
268_D	299_I	1.746	1.00
239_G	273_A	1.738	1.00
209_A	232_S	1.719	1.00
254_A	287_L	1.719	1.00
74_T	78_Q	1.691	1.00
229_V	280_Q	1.688	1.00
230_Y	240_W	1.685	1.00
283_S	287_L	1.661	1.00
73_L	77_N	1.657	1.00
137_V	162_F	1.655	1.00
75_Q	78_Q	1.653	1.00
183_T	219_R	1.649	1.00
273_A	277_R	1.648	1.00
262_L	275_S	1.620	1.00
154_D	180_Q	1.617	1.00
224_M	240_W	1.597	1.00
231_Y	239_G	1.595	1.00
289_C	301_N	1.574	1.00
261_G	282_C	1.555	1.00
7_V	50_L	1.554	1.00
150_A	154_D	1.554	1.00
221_V	262_L	1.547	1.00
211_W	215_H	1.541	1.00
219_R	233_D	1.514	1.00
50_L	264_S	1.511	1.00
244_I	281_G	1.507	1.00
250_N	291_Y	1.507	1.00
137_V	263_A	1.493	1.00
246_T	288_S	1.491	1.00
231_Y	272_F	1.482	1.00
224_M	227_D	1.478	1.00
13_A	61_S	1.474	1.00
65_S	70_Q	1.462	1.00
151_W	154_D	1.460	1.00
70_Q	74_T	1.456	1.00
164_D	223_S	1.444	1.00
211_W	214_Q	1.441	1.00
204_D	207_K	1.424	1.00
241_S	276_V	1.423	1.00
233_D	237_E	1.410	1.00
197_I	211_W	1.391	1.00
39_P	72_L	1.389	1.00
181_I	184_L	1.383	1.00
261_G	278_F	1.382	1.00
160_P	183_T	1.381	1.00
233_D	236_G	1.370	1.00
92_E	119_A	1.370	1.00
206_A	210_A	1.366	1.00
37_F	71_S	1.351	1.00
15_I	71_S	1.348	1.00
213_H	234_I	1.340	1.00
69_G	94_T	1.337	1.00
65_S	88_I	1.335	1.00
44_R	76_T	1.335	1.00
17_V	35_I	1.310	1.00
165_P	186_P	1.309	1.00
153_L	161_V	1.288	1.00
264_S	268_D	1.287	1.00
73_L	86_C	1.286	1.00
210_A	214_Q	1.279	1.00
56_K	82_Y	1.274	1.00
241_S	280_Q	1.252	1.00
133_Q	157_A	1.251	1.00
229_V	276_V	1.247	1.00
244_I	277_R	1.234	1.00
160_P	218_N	1.232	1.00
150_A	176_D	1.232	1.00
210_A	232_S	1.228	1.00
75_Q	79_S	1.226	1.00
132_I	135_A	1.224	1.00
146_E	149_L	1.223	1.00
262_L	266_W	1.213	1.00
219_R	262_L	1.212	1.00
39_P	75_Q	1.211	1.00
219_R	272_F	1.206	1.00
261_G	279_A	1.206	1.00
155_N	182_H	1.202	1.00
224_M	228_G	1.200	1.00
89_V	92_E	1.197	1.00
262_L	279_A	1.192	1.00
185_K	223_S	1.181	1.00
265_C	275_S	1.181	1.00
219_R	266_W	1.176	1.00
109_V	112_N	1.175	1.00
223_S	258_M	1.173	1.00
274_E	277_R	1.171	1.00
70_Q	73_L	1.170	1.00
71_S	74_T	1.170	1.00
121_T	124_Y	1.167	1.00
51_A	81_V	1.166	1.00
46_I	139_V	1.162	1.00
53_L	261_G	1.161	1.00
17_V	37_F	1.138	1.00
55_N	267_V	1.133	1.00
175_R	215_H	1.131	1.00
210_A	238_S	1.130	1.00
197_I	207_K	1.129	1.00
22_H	103_N	1.124	1.00
50_L	57_A	1.123	1.00
149_L	153_L	1.117	1.00
74_T	77_N	1.116	1.00
108_L	111_I	1.114	1.00
191_A	222_L	1.109	1.00
207_K	210_A	1.106	1.00
285_M	289_C	1.105	1.00
232_S	238_S	1.098	1.00
248_V	287_L	1.090	1.00
47_A	57_A	1.089	1.00
285_M	288_S	1.089	1.00
140_A	161_V	1.086	1.00
146_E	150_A	1.084	1.00
139_V	263_A	1.082	1.00
67_F	70_Q	1.076	1.00
244_I	280_Q	1.072	1.00
191_A	208_V	1.071	1.00
248_V	251_V	1.065	1.00
183_T	262_L	1.062	1.00
22_H	34_K	1.053	1.00
183_T	266_W	1.052	1.00
48_Q	52_L	1.046	1.00
244_I	284_S	1.040	1.00
265_C	268_D	1.036	1.00
13_A	72_L	1.034	1.00
58_W	131_F	1.031	1.00
138_I	159_V	1.030	1.00
246_T	287_L	1.029	1.00
219_R	231_Y	1.026	1.00
209_A	222_L	1.019	1.00
188_R	227_D	1.011	1.00
51_A	80_G	1.008	1.00
49_N	257_A	1.007	1.00
147_E	151_W	1.005	1.00
139_V	259_M	1.003	1.00
107_M	111_I	1.002	1.00
155_N	180_Q	1.001	1.00
243_P	280_Q	0.999	1.00
55_N	268_D	0.998	1.00
122_A	151_W	0.996	1.00
9_I	43_G	0.993	1.00
58_W	135_A	0.991	1.00
280_Q	283_S	0.981	1.00
20_Y	36_K	0.979	1.00
147_E	150_A	0.979	1.00
66_D	94_T	0.977	1.00
65_S	91_G	0.977	1.00
17_V	96_S	0.976	1.00
18_A	38_T	0.973	1.00
185_K	262_L	0.972	1.00
50_L	260_A	0.971	1.00
257_A	286_A	0.969	1.00
262_L	272_F	0.967	1.00
163_V	181_I	0.965	1.00
58_W	85_K	0.960	1.00
275_S	279_A	0.956	1.00
218_N	234_I	0.949	1.00
13_A	59_L	0.948	1.00
10_I	138_I	0.948	1.00
63_V	73_L	0.945	1.00
64_G	94_T	0.941	1.00
71_S	75_Q	0.941	1.00
63_V	69_G	0.936	1.00
264_S	299_I	0.933	1.00
234_I	237_E	0.931	1.00
13_A	44_R	0.926	1.00
277_R	281_G	0.923	1.00
17_V	68_Y	0.923	1.00
39_P	71_S	0.922	1.00
187_N	190_E	0.921	1.00
195_S	208_V	0.920	1.00
135_A	159_V	0.919	1.00
207_K	211_W	0.917	1.00
51_A	56_K	0.913	1.00
8_V	60_L	0.913	1.00
89_V	119_A	0.911	1.00
150_A	153_L	0.904	1.00
19_G	98_L	0.903	1.00
227_D	240_W	0.897	1.00
209_A	220_L	0.892	1.00
186_P	191_A	0.890	1.00
237_E	273_A	0.890	1.00
270_M	278_F	0.887	1.00
73_L	83_V	0.886	1.00
53_L	282_C	0.885	1.00
264_S	278_F	0.883	1.00
247_N	288_S	0.883	1.00
188_R	192_E	0.882	1.00
63_V	86_C	0.877	1.00
266_W	275_S	0.870	1.00
228_G	243_P	0.865	1.00
144_I	149_L	0.862	1.00
248_V	288_S	0.860	1.00
87_L	124_Y	0.858	1.00
63_V	88_I	0.857	1.00
83_V	86_C	0.849	1.00
62_A	87_L	0.848	1.00
23_E	26_N	0.846	1.00
249_I	290_E	0.843	1.00
106_E	109_V	0.843	1.00
72_L	94_T	0.833	1.00
271_P	275_S	0.830	1.00
126_A	151_W	0.822	1.00
44_R	293_N	0.819	1.00
257_A	261_G	0.818	1.00
164_D	185_K	0.813	1.00
46_I	259_M	0.802	1.00
128_H	131_F	0.797	1.00
178_L	181_I	0.796	1.00
258_M	280_Q	0.795	1.00
7_V	267_V	0.789	1.00
132_I	159_V	0.785	1.00
14_N	95_S	0.784	1.00
257_A	283_S	0.783	1.00
261_G	265_C	0.777	1.00
120_I	124_Y	0.774	1.00
8_V	58_W	0.770	1.00
213_H	233_D	0.770	1.00
280_Q	284_S	0.768	1.00
176_D	179_N	0.767	1.00
51_A	57_A	0.765	1.00
210_A	213_H	0.765	1.00
241_S	273_A	0.765	1.00
162_F	185_K	0.764	1.00
16_D	40_G	0.764	1.00
145_S	149_L	0.762	1.00
100_L	108_L	0.761	1.00
206_A	240_W	0.757	1.00
241_S	277_R	0.754	1.00
137_V	267_V	0.752	1.00
283_S	286_A	0.749	1.00
148_A	152_I	0.749	1.00
73_L	87_L	0.749	1.00
233_D	272_F	0.747	1.00
164_D	186_P	0.746	1.00
8_V	131_F	0.745	1.00
7_V	137_V	0.742	1.00
144_I	147_E	0.740	1.00
142_C	163_V	0.738	1.00
15_I	37_F	0.738	1.00
278_F	302_V	0.736	1.00
131_F	135_A	0.731	1.00
124_Y	127_Q	0.725	1.00
221_V	231_Y	0.724	1.00
149_L	152_I	0.722	1.00
47_A	59_L	0.719	1.00
15_I	68_Y	0.719	1.00
53_L	278_F	0.716	1.00
209_A	213_H	0.713	1.00
33_G	110_A	0.708	1.00
281_G	285_M	0.706	1.00
58_W	84_D	0.705	1.00
66_D	69_G	0.703	1.00
99_S	252_T	0.699	1.00
53_L	264_S	0.694	1.00
48_Q	293_N	0.690	1.00
258_M	276_V	0.689	1.00
108_L	112_N	0.688	1.00
239_G	276_V	0.686	1.00
117_S	120_I	0.685	1.00
209_A	238_S	0.682	1.00
278_F	299_I	0.680	1.00
162_F	183_T	0.679	1.00
230_Y	238_S	0.677	1.00
92_E	116_I	0.667	1.00
105_G	109_V	0.666	1.00
99_S	109_V	0.665	1.00
53_L	302_V	0.664	1.00
191_A	212_F	0.663	1.00
285_M	301_N	0.663	1.00
68_Y	96_S	0.662	1.00
145_S	148_A	0.657	1.00
25_L	31_N	0.654	1.00
258_M	283_S	0.651	1.00
75_Q	293_N	0.651	1.00
233_D	239_G	0.649	1.00
270_M	275_S	0.646	1.00
61_S	86_C	0.645	1.00
208_V	212_F	0.645	1.00
155_N	158_N	0.643	1.00
206_A	232_S	0.643	1.00
40_G	45_N	0.643	1.00
100_L	110_A	0.641	1.00
258_M	279_A	0.641	1.00
123_E	126_A	0.639	1.00
19_G	33_G	0.635	1.00
228_G	240_W	0.634	1.00
85_K	131_F	0.634	1.00
205_V	208_V	0.627	1.00
205_V	224_M	0.625	1.00
47_A	81_V	0.624	1.00
162_F	259_M	0.623	1.00
146_E	153_L	0.621	1.00
37_F	68_Y	0.620	1.00
140_A	153_L	0.617	1.00
226_G	245_K	0.616	1.00
67_F	71_S	0.616	1.00
206_A	230_Y	0.615	1.00
79_S	298_S	0.615	1.00
34_K	103_N	0.613	1.00
144_I	148_A	0.613	1.00
179_N	216_G	0.608	1.00
184_L	220_L	0.608	1.00
197_I	208_V	0.606	1.00
56_K	136_K	0.605	1.00
20_Y	103_N	0.605	1.00
19_G	35_I	0.605	1.00
137_V	183_T	0.604	1.00
42_V	166_V	0.602	1.00
153_L	180_Q	0.601	1.00
36_K	290_E	0.599	1.00
260_A	264_S	0.596	1.00
221_V	258_M	0.595	1.00
136_K	159_V	0.594	1.00
116_I	124_Y	0.593	1.00
206_A	209_A	0.591	1.00
252_T	292_T	0.591	1.00
213_H	217_L	0.586	1.00
276_V	280_Q	0.585	1.00
120_I	125_L	0.584	1.00
102_D	106_E	0.583	1.00
161_V	181_I	0.583	1.00
175_R	179_N	0.582	1.00
20_Y	290_E	0.581	1.00
42_V	143_N	0.581	1.00
185_K	221_V	0.581	1.00
53_L	260_A	0.577	1.00
105_G	111_I	0.576	1.00
233_D	238_S	0.575	1.00
44_R	59_L	0.572	1.00
269_G	275_S	0.572	1.00
7_V	55_N	0.569	1.00
102_D	108_L	0.569	1.00
229_V	241_S	0.566	1.00
179_N	215_H	0.561	1.00
217_L	220_L	0.561	1.00
50_L	263_A	0.560	1.00
285_M	302_V	0.560	1.00
95_S	117_S	0.559	1.00
12_S	143_N	0.559	1.00
197_I	204_D	0.554	1.00
67_F	74_T	0.554	1.00
122_A	126_A	0.549	1.00
246_T	284_S	0.549	1.00
46_I	263_A	0.548	1.00
140_A	149_L	0.547	1.00
164_D	256_D	0.546	1.00
70_Q	77_N	0.545	1.00
116_I	119_A	0.542	1.00
76_T	81_V	0.541	1.00
266_W	269_G	0.540	1.00
12_S	166_V	0.539	1.00
39_P	293_N	0.539	1.00
150_A	180_Q	0.538	1.00
192_E	197_I	0.537	1.00
189_L	193_T	0.537	1.00
225_G	251_V	0.535	1.00
51_A	79_S	0.535	1.00
56_K	267_V	0.533	1.00
45_N	292_T	0.532	1.00
46_I	260_A	0.530	1.00
191_A	205_V	0.530	1.00
241_S	244_I	0.529	1.00
191_A	232_S	0.528	1.00
9_I	50_L	0.527	1.00
272_F	276_V	0.527	1.00
223_S	256_D	0.527	1.00
17_V	98_L	0.523	1.00
282_C	302_V	0.523	1.00
137_V	266_W	0.521	1.00
176_D	180_Q	0.521	1.00
272_F	275_S	0.521	1.00
188_R	225_G	0.520	1.00
97_Y	111_I	0.520	1.00
136_K	160_P	0.519	1.00
13_A	76_T	0.519	1.00
9_I	57_A	0.518	1.00
131_F	134_R	0.517	1.00
274_E	278_F	0.517	1.00
168_A	171_C	0.516	1.00
216_G	220_L	0.511	1.00
97_Y	143_N	0.509	1.00
146_E	151_W	0.508	1.00
182_H	219_R	0.508	1.00
226_G	248_V	0.506	1.00
16_D	97_Y	0.503	1.00
106_E	112_N	0.502	1.00
265_C	269_G	0.501	1.00
106_E	111_I	0.500	1.00
46_I	50_L	0.500	1.00

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
1rkdA	2	0.9681	100	0.184	Contact Map
3kzhA	2	0.9904	100	0.19	Contact Map
2fv7A	2	0.9649	100	0.194	Contact Map
1vm7A	2	0.9457	100	0.197	Contact Map
2rbcA	2	0.9585	100	0.198	Contact Map
4xdaA	2	0.9681	100	0.205	Contact Map
3ry7A	2	0.9521	100	0.209	Contact Map
2nwhA	2	0.9617	100	0.215	Contact Map
3vasA	1	0.9489	100	0.22	Contact Map
2qcvA	3	0.9585	100	0.221	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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