YQKD - BACSU - GREMLIN Contacts

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YQKD - Uncharacterized protein YqkD

UniProt:	P54567	Sequences: MKKILLAIGALVTAVIAIGIVFSHMILFIKKKTDEDIIKRETDNGHDVFESFEQMEKTAFVIPSAYGYDIKGYHVAPHDTPNTIIICHGVTMNVLNSLKYMHLFLDLGWNVLIYDHRRHGQSGGKTTSYGFYEKDDLNKVVSLLKNKTNHRGLIGIHGESMGAVTALLYAGAHCSDGADFYIADCPFACFDEQLAYRLRAEYRLPSWPLLPIADFFLKLRGGYRAREVSPLAVIDKIEKPVLFIHSKDDDYIPVSSTERLYEKKRGPKALYIAENGEHAMSYTKNRHTYRKTVQEFLDNMNDSTE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (239)
Sequences:	17081 (12755)
Seq/√Len:	825.1

ECOLI - YFHR PLDB YCJY FRSA DLHH YJFP RUTD MHPC YBFF BIOH YGHX MENH PTRB
BACSU - YQKD CAH YBFK NAP YTMA YITV YTAP YBDG YUGF YISY YBAC YDJP PLBAC YCGS YFHM RSBQ EST YQJL YUXL YRAK YVAM MENH YCLE
HALSA - Q9HPY2 Q9HPT9 Q9HN07 Q9HHP4 Q9HS46 Q9HRJ0 Q9HP29
SULSO - PIP Q7LX61 Q97VD6 Q97YB2 Q97WG0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
155_G	180_F	4.022	1.00
117_R	136_D	3.408	1.00
170_A	181_Y	3.326	1.00
61_V	69_D	3.161	1.00
247_K	274_E	2.756	1.00
63_P	69_D	2.706	1.00
107_L	294_Q	2.636	1.00
271_Y	292_T	2.606	1.00
261_Y	268_K	2.600	1.00
74_H	110_N	2.437	1.00
254_V	272_I	2.345	1.00
269_A	292_T	2.340	1.00
60_F	72_G	2.319	1.00
65_A	139_K	2.294	1.00
247_K	272_I	2.186	1.00
166_A	181_Y	2.184	1.00
273_A	292_T	2.142	1.00
155_G	297_L	2.124	1.00
183_A	186_P	2.095	1.00
269_A	299_N	2.084	1.00
83_T	110_N	2.075	1.00
142_S	177_G	2.034	1.00
143_L	147_K	1.971	1.00
76_A	110_N	1.934	1.00
167_L	183_A	1.851	1.00
156_I	166_A	1.786	1.00
143_L	146_N	1.777	1.00
107_L	298_D	1.753	1.00
233_V	236_K	1.735	1.00
258_E	272_I	1.693	1.00
75_V	113_I	1.686	1.00
285_N	288_T	1.634	1.00
241_V	264_K	1.623	1.00
128_S	131_F	1.615	1.00
69_D	123_G	1.612	1.00
81_P	110_N	1.608	1.00
182_I	293_V	1.599	1.00
254_V	258_E	1.589	1.00
62_I	140_V	1.582	1.00
138_N	142_S	1.565	1.00
87_C	137_L	1.560	1.00
150_H	153_L	1.552	1.00
273_A	288_T	1.537	1.00
245_H	254_V	1.531	1.00
59_A	71_K	1.527	1.00
145_K	177_G	1.522	1.00
291_K	295_E	1.521	1.00
141_V	154_I	1.503	1.00
288_T	292_T	1.497	1.00
112_L	140_V	1.481	1.00
101_M	113_I	1.453	1.00
109_W	298_D	1.436	1.00
65_A	135_D	1.430	1.00
73_Y	94_V	1.418	1.00
221_G	224_R	1.411	1.00
292_T	295_E	1.396	1.00
88_H	119_H	1.389	1.00
103_L	107_L	1.381	1.00
138_N	169_Y	1.379	1.00
258_E	262_E	1.375	1.00
245_H	257_T	1.368	1.00
182_I	297_L	1.365	1.00
74_H	112_L	1.357	1.00
66_Y	117_R	1.355	1.00
60_F	143_L	1.346	1.00
135_D	172_A	1.330	1.00
61_V	71_K	1.329	1.00
247_K	254_V	1.324	1.00
71_K	121_Q	1.317	1.00
163_A	186_P	1.317	1.00
261_Y	270_L	1.316	1.00
86_I	157_H	1.296	1.00
104_F	157_H	1.296	1.00
114_Y	140_V	1.282	1.00
168_L	172_A	1.273	1.00
247_K	275_N	1.265	1.00
129_Y	133_E	1.260	1.00
259_R	263_K	1.252	1.00
242_L	271_Y	1.252	1.00
235_D	263_K	1.251	1.00
87_C	166_A	1.241	1.00
248_D	275_N	1.239	1.00
71_K	122_S	1.236	1.00
273_A	276_G	1.218	1.00
181_Y	241_V	1.214	1.00
128_S	132_Y	1.210	1.00
62_I	72_G	1.210	1.00
153_L	179_D	1.209	1.00
72_G	112_L	1.176	1.00
182_I	242_L	1.165	1.00
89_G	160_S	1.161	1.00
87_C	116_H	1.161	1.00
157_H	184_D	1.158	1.00
82_N	109_W	1.158	1.00
83_T	112_L	1.157	1.00
184_D	289_Y	1.152	1.00
128_S	133_E	1.151	1.00
244_I	289_Y	1.150	1.00
243_F	257_T	1.143	1.00
127_T	130_G	1.143	1.00
102_H	106_D	1.134	1.00
258_E	270_L	1.131	1.00
83_T	144_L	1.131	1.00
181_Y	239_K	1.127	1.00
100_Y	290_R	1.126	1.00
103_L	294_Q	1.122	1.00
159_E	185_C	1.119	1.00
289_Y	293_V	1.117	1.00
87_C	114_Y	1.114	1.00
244_I	273_A	1.108	1.00
243_F	260_L	1.106	1.00
82_N	153_L	1.100	1.00
159_E	184_D	1.094	1.00
257_T	270_L	1.089	1.00
84_I	109_W	1.079	1.00
170_A	239_K	1.068	1.00
91_T	160_S	1.067	1.00
72_G	140_V	1.066	1.00
185_C	249_D	1.061	1.00
226_R	232_A	1.060	1.00
140_V	144_L	1.057	1.00
103_L	290_R	1.047	1.00
168_L	171_G	1.046	1.00
138_N	174_C	1.044	1.00
223_Y	227_E	1.042	1.00
294_Q	298_D	1.041	1.00
276_G	285_N	1.041	1.00
112_L	144_L	1.032	1.00
171_G	233_V	1.030	1.00
244_I	271_Y	1.026	1.00
127_T	131_F	1.016	1.00
229_S	232_A	1.013	1.00
255_S	258_E	1.012	1.00
68_Y	123_G	1.009	1.00
105_L	111_V	1.000	1.00
138_N	172_A	0.986	1.00
71_K	94_V	0.979	1.00
94_V	113_I	0.968	1.00
115_D	120_G	0.968	1.00
183_A	243_F	0.965	1.00
139_K	142_S	0.965	1.00
224_R	227_E	0.964	1.00
167_L	186_P	0.961	1.00
222_G	226_R	0.956	1.00
168_L	233_V	0.955	1.00
142_S	146_N	0.949	1.00
92_M	96_N	0.947	1.00
145_K	148_T	0.940	1.00
85_I	141_V	0.939	1.00
88_H	116_H	0.934	1.00
68_Y	117_R	0.934	1.00
87_C	156_I	0.933	1.00
156_I	169_Y	0.922	1.00
137_L	169_Y	0.919	1.00
70_I	122_S	0.913	1.00
155_G	182_I	0.911	1.00
59_A	121_Q	0.908	1.00
116_H	165_T	0.908	1.00
90_V	161_M	0.907	1.00
129_Y	134_K	0.905	1.00
94_V	121_Q	0.899	1.00
71_K	115_D	0.893	1.00
103_L	106_D	0.891	1.00
295_E	299_N	0.890	1.00
155_G	179_D	0.886	1.00
135_D	139_K	0.881	1.00
75_V	105_L	0.878	1.00
180_F	297_L	0.878	1.00
287_H	291_K	0.871	1.00
271_Y	288_T	0.871	1.00
62_I	139_K	0.854	1.00
180_F	296_F	0.848	1.00
76_A	81_P	0.847	1.00
57_K	75_V	0.847	1.00
243_F	261_Y	0.845	1.00
64_S	68_Y	0.839	1.00
101_M	105_L	0.839	1.00
182_I	244_I	0.838	1.00
141_V	178_A	0.838	1.00
188_A	260_L	0.837	1.00
185_C	245_H	0.834	1.00
257_T	261_Y	0.830	1.00
264_K	268_K	0.822	1.00
205_P	208_P	0.817	1.00
75_V	101_M	0.817	1.00
220_R	224_R	0.815	1.00
130_G	133_E	0.812	1.00
231_L	234_I	0.809	1.00
185_C	280_M	0.807	1.00
250_D	277_E	0.799	1.00
57_K	73_Y	0.798	1.00
276_G	280_M	0.793	1.00
86_I	111_V	0.790	1.00
84_I	111_V	0.786	1.00
160_S	278_H	0.784	1.00
157_H	182_I	0.783	1.00
176_D	238_E	0.781	1.00
91_T	161_M	0.781	1.00
189_C	229_S	0.780	1.00
184_D	244_I	0.780	1.00
174_C	177_G	0.779	1.00
288_T	291_K	0.776	1.00
85_I	112_L	0.776	1.00
191_D	226_R	0.776	1.00
187_F	252_I	0.775	1.00
169_Y	174_C	0.775	1.00
64_S	139_K	0.767	1.00
245_H	272_I	0.767	1.00
171_G	237_I	0.753	1.00
145_K	151_R	0.752	1.00
64_S	117_R	0.751	1.00
59_A	73_Y	0.750	1.00
94_V	115_D	0.747	1.00
84_I	157_H	0.743	1.00
157_H	293_V	0.728	1.00
99_K	102_H	0.728	1.00
164_V	187_F	0.727	1.00
161_M	165_T	0.725	1.00
156_I	178_A	0.724	1.00
114_Y	137_L	0.721	1.00
172_A	233_V	0.720	1.00
243_F	264_K	0.720	1.00
160_S	249_D	0.715	1.00
232_A	235_D	0.711	1.00
58_T	147_K	0.705	1.00
170_A	237_I	0.703	1.00
132_Y	135_D	0.700	1.00
295_E	298_D	0.698	1.00
164_V	167_L	0.697	1.00
142_S	145_K	0.696	1.00
192_E	259_R	0.694	1.00
163_A	252_I	0.694	1.00
127_T	133_E	0.692	1.00
116_H	119_H	0.692	1.00
223_Y	226_R	0.690	1.00
127_T	132_Y	0.690	1.00
222_G	225_A	0.690	1.00
278_H	281_S	0.688	1.00
189_C	192_E	0.684	1.00
109_W	155_G	0.684	1.00
84_I	104_F	0.683	1.00
86_I	113_I	0.682	1.00
218_K	221_G	0.682	1.00
219_L	223_Y	0.681	1.00
62_I	114_Y	0.681	1.00
142_S	174_C	0.679	1.00
109_W	297_L	0.677	1.00
259_R	262_E	0.675	1.00
83_T	154_I	0.672	1.00
238_E	266_G	0.672	1.00
138_N	177_G	0.664	1.00
194_L	198_L	0.664	1.00
180_F	240_P	0.661	1.00
221_G	225_A	0.658	1.00
194_L	197_R	0.655	1.00
60_F	74_H	0.655	1.00
115_D	122_S	0.654	1.00
134_K	168_L	0.654	1.00
62_I	65_A	0.652	1.00
166_A	170_A	0.648	1.00
242_L	296_F	0.640	1.00
86_I	101_M	0.640	1.00
192_E	256_S	0.640	1.00
269_A	295_E	0.640	1.00
265_R	268_K	0.638	1.00
154_I	178_A	0.634	1.00
167_L	260_L	0.631	1.00
159_E	279_A	0.630	1.00
140_V	143_L	0.629	1.00
186_P	252_I	0.629	1.00
158_G	166_A	0.628	1.00
185_C	279_A	0.626	1.00
245_H	270_L	0.624	1.00
101_M	111_V	0.618	1.00
243_F	270_L	0.617	1.00
91_T	119_H	0.616	1.00
85_I	114_Y	0.615	1.00
144_L	147_K	0.614	1.00
186_P	245_H	0.614	1.00
60_F	63_P	0.613	1.00
152_G	179_D	0.611	1.00
193_Q	196_Y	0.608	1.00
134_K	165_T	0.606	1.00
62_I	143_L	0.604	1.00
269_A	296_F	0.603	1.00
131_F	134_K	0.601	1.00
218_K	222_G	0.600	1.00
230_P	233_V	0.599	1.00
160_S	279_A	0.598	1.00
167_L	188_A	0.597	1.00
83_T	109_W	0.597	1.00
116_H	161_M	0.597	1.00
84_I	297_L	0.595	1.00
129_Y	190_F	0.594	1.00
197_R	200_A	0.594	1.00
255_S	259_R	0.593	1.00
61_V	72_G	0.591	1.00
85_I	178_A	0.590	1.00
258_E	261_Y	0.589	1.00
234_I	263_K	0.589	1.00
163_A	183_A	0.584	1.00
267_P	299_N	0.583	1.00
199_R	203_R	0.582	1.00
86_I	104_F	0.582	1.00
64_S	70_I	0.582	1.00
189_C	259_R	0.580	1.00
220_R	225_A	0.579	1.00
176_D	239_K	0.574	1.00
225_A	228_V	0.573	1.00
141_V	177_G	0.572	1.00
80_T	110_N	0.572	1.00
237_I	264_K	0.569	1.00
187_F	190_F	0.567	1.00
135_D	138_N	0.561	1.00
134_K	172_A	0.559	1.00
234_I	264_K	0.559	1.00
97_S	100_Y	0.557	1.00
65_A	68_Y	0.556	1.00
175_S	178_A	0.555	1.00
141_V	169_Y	0.550	1.00
186_P	257_T	0.549	1.00
277_E	283_T	0.548	1.00
138_N	178_A	0.547	1.00
254_V	270_L	0.547	1.00
85_I	137_L	0.546	1.00
170_A	241_V	0.546	1.00
249_D	252_I	0.545	1.00
90_V	119_H	0.541	1.00
170_A	178_A	0.540	1.00
137_L	165_T	0.539	1.00
202_Y	208_P	0.538	1.00
220_R	223_Y	0.537	1.00
144_L	148_T	0.534	1.00
87_C	165_T	0.533	1.00
100_Y	157_H	0.532	1.00
98_L	102_H	0.524	1.00
220_R	226_R	0.522	1.00
184_D	280_M	0.520	1.00
82_N	155_G	0.520	1.00
188_A	256_S	0.519	1.00
78_H	81_P	0.514	1.00
218_K	225_A	0.513	1.00
195_A	198_L	0.511	1.00
82_N	152_G	0.511	1.00
161_M	164_V	0.510	1.00
64_S	67_G	0.510	1.00
269_A	272_I	0.509	1.00
75_V	111_V	0.509	1.00
157_H	297_L	0.509	1.00
116_H	137_L	0.509	1.00
148_T	151_R	0.508	1.00
245_H	252_I	0.507	1.00
73_Y	113_I	0.506	1.00
219_L	222_G	0.505	1.00
110_N	149_N	0.502	1.00
100_Y	159_E	0.502	1.00
58_T	74_H	0.501	1.00
86_I	97_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
2wtmA	2	0.7902	100	0.376	Contact Map
2hdwA	2	0.859	100	0.383	Contact Map
1k8qA	1	0.8754	100	0.392	Contact Map
3pe6A	1	0.8262	100	0.402	Contact Map
4ns4A	1	0.7902	100	0.404	Contact Map
2y6uA	2	0.859	100	0.412	Contact Map
1zoiA	3	0.7574	100	0.415	Contact Map
3fobA	3	0.7803	100	0.415	Contact Map
3fnbA	2	0.9049	100	0.422	Contact Map
1mtzA	1	0.777	100	0.422	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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