YQKF - BACSU - GREMLIN Contacts

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YQKF - Uncharacterized oxidoreductase YqkF

UniProt:	P54569	Sequences: MRKRKLGTSDLDISEVGLGCMSLGTEKNKALSILDEAIELGINYLDTADLYDRGRNEEIVGDAIQNRRHDIILATKAGNRWDDGSEGWYWDPSKAYIKEAVKKSLTRLKTDYIDLYQLHGGTIEDNIDETIEAFEELKQEGVIRYYGISSIRPNVIKEYVKKSNIVSIMMQFSLFDRRPEEWLPLLEEHQISVVARGPVAKGLLTEKPLDQASESMKQNGYLSYSFEELTNARKAMEEVAPDLSMTEKSLQYLLAQPAVASVITGASKIEQLRENIQAANARRLTEEEIKALQSHTKQDIYKAHRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	306 (260)
Sequences:	32345 (20463)
Seq/√Len:	1269.1

ECOLI - YAJO YDJG GPR TAS YDHF YEAE YDBC DKGA DKGB
BACSU - YQKF GS69 IOLS YCCK YRPG YCSN YTBE GR
HALSA - Q9HNN3 Q9HPH9 Q9HQU7 Q9HSE6 Q9HS02 Q9HQT1
SULSO - Q97UG6 Q97ZZ1 Q97UV9 Q97UJ7 Q97V56 Q97U17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_E	273_R	3.208	1.00
102_K	142_V	2.929	1.00
65_Q	109_K	2.824	1.00
27_K	62_D	2.768	1.00
285_T	288_E	2.647	1.00
31_L	66_N	2.535	1.00
98_K	136_E	2.485	1.00
101_V	137_L	2.428	1.00
5_K	12_D	2.409	1.00
36_E	40_L	2.342	1.00
98_K	140_E	2.332	1.00
135_E	139_Q	2.133	1.00
31_L	62_D	2.079	1.00
103_K	107_R	2.050	1.00
255_A	289_I	2.048	1.00
112_Y	144_R	2.030	1.00
237_E	241_P	1.993	1.00
185_L	189_H	1.991	1.00
136_E	140_E	1.989	1.00
269_I	273_R	1.983	1.00
286_E	290_K	1.949	1.00
67_R	70_D	1.934	1.00
36_E	269_I	1.904	1.00
186_L	193_V	1.904	1.00
94_K	136_E	1.856	1.00
17_G	44_Y	1.844	1.00
40_L	273_R	1.796	1.00
157_K	161_K	1.753	1.00
243_L	281_A	1.726	1.00
256_Q	293_Q	1.725	1.00
117_Q	167_S	1.685	1.00
58_E	107_R	1.681	1.00
26_E	29_K	1.673	1.00
136_E	139_Q	1.670	1.00
94_K	98_K	1.670	1.00
31_L	35_D	1.661	1.00
235_A	238_E	1.641	1.00
244_S	274_E	1.641	1.00
36_E	39_E	1.638	1.00
157_K	185_L	1.632	1.00
40_L	276_I	1.631	1.00
73_L	110_T	1.624	1.00
98_K	102_K	1.620	1.00
133_A	136_E	1.619	1.00
37_A	42_I	1.615	1.00
277_Q	280_N	1.605	1.00
290_K	294_S	1.605	1.00
77_A	116_Y	1.603	1.00
238_E	291_A	1.603	1.00
35_D	66_N	1.601	1.00
75_T	113_I	1.600	1.00
31_L	63_A	1.588	1.00
192_S	261_S	1.581	1.00
251_Q	281_A	1.566	1.00
77_A	97_I	1.557	1.00
75_T	104_S	1.549	1.00
181_E	184_P	1.546	1.00
101_V	116_Y	1.523	1.00
27_K	31_L	1.506	1.00
20_C	45_L	1.496	1.00
99_E	103_K	1.487	1.00
74_A	117_Q	1.480	1.00
11_L	145_Y	1.471	1.00
152_R	155_V	1.470	1.00
38_I	71_I	1.453	1.00
29_K	32_S	1.448	1.00
55_R	58_E	1.446	1.00
49_D	100_A	1.438	1.00
243_L	247_E	1.412	1.00
102_K	106_T	1.409	1.00
187_E	257_P	1.408	1.00
34_L	63_A	1.408	1.00
160_V	189_H	1.397	1.00
184_P	188_E	1.396	1.00
273_R	277_Q	1.364	1.00
243_L	248_K	1.362	1.00
117_Q	194_V	1.360	1.00
251_Q	255_A	1.335	1.00
113_I	143_I	1.330	1.00
170_M	193_V	1.320	1.00
32_S	36_E	1.318	1.00
291_A	294_S	1.312	1.00
35_D	39_E	1.312	1.00
160_V	185_L	1.307	1.00
11_L	72_I	1.296	1.00
235_A	291_A	1.295	1.00
94_K	132_E	1.289	1.00
145_Y	166_V	1.287	1.00
103_K	106_T	1.280	1.00
128_D	162_K	1.268	1.00
137_L	143_I	1.262	1.00
143_I	146_Y	1.260	1.00
183_L	187_E	1.243	1.00
98_K	133_A	1.238	1.00
61_G	109_K	1.231	1.00
94_K	133_A	1.222	1.00
62_D	109_K	1.218	1.00
72_I	115_L	1.218	1.00
108_L	113_I	1.214	1.00
244_S	247_E	1.212	1.00
266_A	272_L	1.205	1.00
68_R	110_T	1.204	1.00
239_V	248_K	1.204	1.00
266_A	271_Q	1.198	1.00
28_N	32_S	1.198	1.00
153_P	185_L	1.190	1.00
96_Y	99_E	1.186	1.00
115_L	167_S	1.168	1.00
58_E	62_D	1.167	1.00
135_E	138_K	1.164	1.00
172_F	256_Q	1.155	1.00
138_K	166_V	1.144	1.00
57_E	104_S	1.144	1.00
129_E	132_E	1.139	1.00
95_A	99_E	1.138	1.00
234_K	238_E	1.137	1.00
237_E	245_M	1.131	1.00
270_E	273_R	1.128	1.00
157_K	189_H	1.127	1.00
68_R	112_Y	1.127	1.00
157_K	188_E	1.123	1.00
44_Y	194_V	1.123	1.00
93_S	96_Y	1.119	1.00
121_G	155_V	1.118	1.00
44_Y	74_A	1.110	1.00
134_F	146_Y	1.102	1.00
102_K	140_E	1.091	1.00
45_L	60_V	1.089	1.00
171_Q	176_D	1.087	1.00
253_L	262_V	1.086	1.00
101_V	113_I	1.085	1.00
174_L	292_L	1.084	1.00
9_S	145_Y	1.075	1.00
27_K	59_I	1.070	1.00
118_L	134_F	1.069	1.00
20_C	60_V	1.069	1.00
234_K	237_E	1.066	1.00
177_R	296_T	1.064	1.00
43_N	72_I	1.061	1.00
158_E	162_K	1.060	1.00
236_M	245_M	1.057	1.00
175_F	233_R	1.052	1.00
32_S	269_I	1.049	1.00
92_P	118_L	1.040	1.00
35_D	63_A	1.040	1.00
247_E	277_Q	1.034	1.00
33_I	272_L	1.026	1.00
5_K	10_D	1.018	1.00
8_T	166_V	1.018	1.00
137_L	142_V	1.016	1.00
254_L	278_A	0.994	1.00
14_S	43_N	0.992	1.00
148_I	165_I	0.985	1.00
179_P	193_V	0.983	1.00
174_L	249_S	0.978	1.00
62_D	66_N	0.975	1.00
184_P	187_E	0.970	1.00
132_E	136_E	0.968	1.00
153_P	157_K	0.962	1.00
114_D	144_R	0.958	1.00
15_E	254_L	0.958	1.00
64_I	71_I	0.957	1.00
14_S	42_I	0.954	1.00
272_L	276_I	0.940	1.00
194_V	261_S	0.940	1.00
167_S	194_V	0.940	1.00
57_E	107_R	0.936	1.00
9_S	166_V	0.936	1.00
98_K	101_V	0.934	1.00
274_E	277_Q	0.932	1.00
247_E	274_E	0.931	1.00
135_E	163_S	0.926	1.00
137_L	140_E	0.926	1.00
49_D	81_W	0.923	1.00
15_E	279_A	0.919	1.00
238_E	241_P	0.918	1.00
99_E	102_K	0.910	1.00
32_S	35_D	0.907	1.00
133_A	137_L	0.904	1.00
128_D	158_E	0.904	1.00
187_E	259_V	0.899	1.00
268_K	271_Q	0.893	1.00
34_L	45_L	0.891	1.00
38_I	67_R	0.891	1.00
177_R	180_E	0.889	1.00
270_E	274_E	0.889	1.00
290_K	293_Q	0.888	1.00
168_I	186_L	0.883	1.00
255_A	283_R	0.883	1.00
158_E	161_K	0.874	1.00
94_K	129_E	0.873	1.00
287_E	290_K	0.869	1.00
146_Y	165_I	0.868	1.00
58_E	106_T	0.864	1.00
98_K	137_L	0.860	1.00
49_D	96_Y	0.859	1.00
74_A	194_V	0.857	1.00
135_E	146_Y	0.855	1.00
185_L	188_E	0.855	1.00
132_E	135_E	0.853	1.00
256_Q	289_I	0.849	1.00
148_I	156_I	0.848	1.00
74_A	115_L	0.847	1.00
156_I	191_I	0.832	1.00
9_S	138_K	0.832	1.00
250_L	278_A	0.829	1.00
18_L	37_A	0.821	1.00
49_D	107_R	0.816	1.00
287_E	291_A	0.806	1.00
177_R	293_Q	0.803	1.00
249_S	253_L	0.800	1.00
49_D	103_K	0.783	1.00
183_L	193_V	0.781	1.00
36_E	272_L	0.781	1.00
172_F	183_L	0.775	1.00
28_N	31_L	0.774	1.00
227_E	231_N	0.774	1.00
255_A	286_E	0.773	1.00
160_V	164_N	0.768	1.00
40_L	277_Q	0.766	1.00
105_L	110_T	0.761	1.00
105_L	142_V	0.758	1.00
150_S	196_R	0.756	1.00
153_P	182_W	0.755	1.00
20_C	56_N	0.755	1.00
18_L	23_L	0.751	1.00
195_A	198_P	0.747	1.00
198_P	264_T	0.744	1.00
30_A	59_I	0.738	1.00
35_D	67_R	0.735	1.00
252_Y	293_Q	0.733	1.00
120_G	150_S	0.733	1.00
235_A	295_H	0.730	1.00
38_I	45_L	0.729	1.00
47_T	60_V	0.728	1.00
182_W	186_L	0.727	1.00
75_T	116_Y	0.724	1.00
179_P	184_P	0.723	1.00
267_S	271_Q	0.721	1.00
183_L	256_Q	0.721	1.00
16_V	254_L	0.720	1.00
101_V	142_V	0.716	1.00
243_L	277_Q	0.715	1.00
27_K	55_R	0.714	1.00
131_I	159_Y	0.710	1.00
230_T	234_K	0.710	1.00
284_L	288_E	0.709	1.00
246_T	274_E	0.708	1.00
243_L	280_N	0.706	1.00
17_G	264_T	0.705	1.00
131_I	146_Y	0.702	1.00
42_I	276_I	0.702	1.00
100_A	103_K	0.700	1.00
195_A	262_V	0.700	1.00
239_V	288_E	0.698	1.00
131_I	163_S	0.697	1.00
33_I	269_I	0.696	1.00
97_I	130_T	0.696	1.00
251_Q	278_A	0.695	1.00
97_I	137_L	0.695	1.00
248_K	288_E	0.686	1.00
117_Q	147_G	0.686	1.00
231_N	234_K	0.685	1.00
131_I	165_I	0.685	1.00
172_F	253_L	0.685	1.00
69_H	112_Y	0.676	1.00
130_T	133_A	0.674	1.00
148_I	151_I	0.673	1.00
186_L	191_I	0.669	1.00
67_R	71_I	0.668	1.00
153_P	181_E	0.667	1.00
34_L	38_I	0.665	1.00
43_N	70_D	0.663	1.00
233_R	237_E	0.662	1.00
192_S	260_A	0.660	1.00
11_L	144_R	0.657	1.00
253_L	260_A	0.656	1.00
104_S	116_Y	0.656	1.00
50_L	78_G	0.656	1.00
40_L	272_L	0.653	1.00
127_I	162_K	0.653	1.00
243_L	251_Q	0.653	1.00
240_A	248_K	0.647	1.00
13_I	261_S	0.645	1.00
248_K	284_L	0.644	1.00
23_L	33_I	0.643	1.00
172_F	193_V	0.641	1.00
284_L	289_I	0.640	1.00
240_A	245_M	0.640	1.00
77_A	92_P	0.639	1.00
155_V	158_E	0.639	1.00
160_V	163_S	0.638	1.00
157_K	160_V	0.638	1.00
288_E	291_A	0.638	1.00
127_I	130_T	0.636	1.00
138_K	145_Y	0.634	1.00
148_I	168_I	0.633	1.00
38_I	43_N	0.632	1.00
17_G	261_S	0.631	1.00
134_F	138_K	0.628	1.00
8_T	164_N	0.625	1.00
97_I	133_A	0.624	1.00
198_P	253_L	0.622	1.00
29_K	269_I	0.620	1.00
138_K	143_I	0.620	1.00
22_S	201_K	0.620	1.00
271_Q	274_E	0.619	1.00
55_R	59_I	0.618	1.00
105_L	113_I	0.618	1.00
239_V	291_A	0.616	1.00
113_I	116_Y	0.614	1.00
248_K	292_L	0.611	1.00
93_S	130_T	0.610	1.00
38_I	70_D	0.610	1.00
236_M	292_L	0.609	1.00
179_P	183_L	0.609	1.00
236_M	249_S	0.607	1.00
248_K	281_A	0.604	1.00
39_E	269_I	0.603	1.00
172_F	180_E	0.599	1.00
98_K	142_V	0.599	1.00
34_L	60_V	0.596	1.00
231_N	235_A	0.593	1.00
92_P	130_T	0.591	1.00
8_T	190_Q	0.591	1.00
33_I	266_A	0.590	1.00
81_W	96_Y	0.586	1.00
101_V	105_L	0.586	1.00
23_L	30_A	0.585	1.00
122_T	125_D	0.583	1.00
172_F	260_A	0.581	1.00
105_L	112_Y	0.579	1.00
26_E	30_A	0.577	1.00
197_G	201_K	0.576	1.00
128_D	132_E	0.576	1.00
46_D	169_M	0.575	1.00
254_L	262_V	0.571	1.00
118_L	130_T	0.569	1.00
247_E	281_A	0.567	1.00
148_I	159_Y	0.566	1.00
256_Q	260_A	0.565	1.00
154_N	157_K	0.565	1.00
6_L	192_S	0.564	1.00
160_V	191_I	0.562	1.00
21_M	197_G	0.560	1.00
116_Y	134_F	0.557	1.00
18_L	33_I	0.556	1.00
60_V	63_A	0.556	1.00
116_Y	143_I	0.553	1.00
239_V	295_H	0.552	1.00
175_F	203_L	0.552	1.00
195_A	259_V	0.551	1.00
47_T	56_N	0.550	1.00
25_T	29_K	0.550	1.00
251_Q	283_R	0.548	1.00
38_I	63_A	0.543	1.00
127_I	158_E	0.540	1.00
49_D	78_G	0.537	1.00
17_G	263_I	0.536	1.00
105_L	111_D	0.535	1.00
203_L	233_R	0.534	1.00
25_T	30_A	0.530	1.00
13_I	44_Y	0.530	1.00
127_I	155_V	0.529	1.00
94_K	97_I	0.526	1.00
16_V	279_A	0.525	1.00
64_I	67_R	0.523	1.00
58_E	109_K	0.523	1.00
76_K	119_H	0.522	1.00
230_T	233_R	0.519	1.00
101_V	133_A	0.519	1.00
138_K	164_N	0.517	1.00
77_A	100_A	0.515	1.00
176_D	179_P	0.515	1.00
174_L	252_Y	0.515	1.00
154_N	158_E	0.514	1.00
138_K	146_Y	0.514	1.00
62_D	65_Q	0.513	1.00
79_N	120_G	0.511	1.00
44_Y	72_I	0.510	1.00
174_L	296_T	0.509	1.00
121_G	151_I	0.508	1.00
266_A	275_N	0.507	1.00
195_A	253_L	0.506	1.00
23_L	265_G	0.506	1.00
45_L	64_I	0.506	1.00
24_G	56_N	0.505	1.00
50_L	79_N	0.503	1.00
269_I	272_L	0.501	1.00
147_G	167_S	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
1pyfA	1	0.9641	100	0.103	Contact Map
3v0sA	1	0.8725	100	0.108	Contact Map
1ynpA	1	0.9673	100	0.109	Contact Map
1pz1A	1	0.9902	100	0.113	Contact Map
3n2tA	1	0.9935	100	0.118	Contact Map
4xk2A	5	0.9542	100	0.119	Contact Map
3eauA	3	0.9771	100	0.122	Contact Map
3lutA	3	0.9706	100	0.123	Contact Map
3erpA	6	0.9248	100	0.129	Contact Map
3n6qA	5	0.9314	100	0.134	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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