RARD - ECOLI - GREMLIN Contacts

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RARD - Protein RarD

UniProt:	P27844	Sequences: MDAKQTRQGVLLALAAYFIWGIAPAYFKLIYYVPADEILTHRVIWSFFFMVVLMSICRQWSYLKTLIQTPQKIFMLAVSAVLIGGNWLLFIWAVNNHHMLEASLGYFINPLVNIVLGMIFLGERFRRMQWLAVILAICGVLVQLWTFGSLPIIALGLAFSFAFYGLVRKKIAVEAQTGMLIETMWLLPVAAIYLFAIADSSTSHMGQNPMSLNLLLIAAGIVTTVPLLCFTAAATRLRLSTLGFFQYIGPTLMFLLAVTFYGEKPGADKMVTFAFIWVALAIFVMDAIYTQRRTSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11466
Length:	296 (268)
Sequences:	37124 (27769)
Seq/√Len:	1696.2

ECOLI - RARD YTFF YHBE YIJE YEDA YICL YDDG EAMA RHTA
BACSU - YOJE YCXC YVBV YBFH YDED YRDR YDFC YETK YWFM YXXF YCBK YYAM YDEK YOAV
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97X73 Q97UX3 Q97UE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_A	154_A	3.361	1.00
12_L	232_A	3.062	1.00
232_A	236_R	2.899	1.00
257_A	263_E	2.715	1.00
92_W	153_I	2.609	1.00
47_F	184_M	2.489	1.00
89_L	156_G	2.417	1.00
69_T	72_K	2.397	1.00
232_A	235_T	2.343	1.00
40_T	191_A	2.302	1.00
103_S	253_M	2.267	1.00
132_A	279_A	2.263	1.00
21_G	252_L	2.182	1.00
217_I	220_G	2.147	1.00
89_L	153_I	2.142	1.00
27_F	91_I	2.076	1.00
13_A	233_A	2.071	1.00
28_K	263_E	2.058	1.00
112_V	158_A	2.055	1.00
123_E	169_K	2.049	1.00
116_L	166_L	2.039	1.00
85_G	160_S	1.927	1.00
118_M	125_F	1.924	1.00
117_G	123_E	1.870	1.00
44_I	187_L	1.864	1.00
21_G	256_L	1.864	1.00
26_Y	218_A	1.845	1.00
126_R	129_Q	1.809	1.00
113_N	243_G	1.808	1.00
219_A	222_V	1.797	1.00
174_E	177_T	1.783	1.00
97_H	101_E	1.777	1.00
108_I	112_V	1.766	1.00
188_P	192_I	1.758	1.00
114_I	133_V	1.755	1.00
51_V	180_L	1.743	1.00
215_L	218_A	1.739	1.00
52_V	55_S	1.727	1.00
217_I	222_V	1.724	1.00
18_F	252_L	1.699	1.00
192_I	195_F	1.688	1.00
209_P	212_L	1.667	1.00
47_F	187_L	1.631	1.00
218_A	222_V	1.619	1.00
136_A	247_Y	1.616	1.00
92_W	96_N	1.614	1.00
89_L	160_S	1.604	1.00
238_R	241_T	1.585	1.00
266_G	269_K	1.584	1.00
281_A	285_M	1.574	1.00
112_V	162_A	1.539	1.00
51_V	55_S	1.535	1.00
210_M	214_L	1.513	1.00
102_A	154_A	1.503	1.00
132_A	283_F	1.501	1.00
70_P	74_F	1.486	1.00
53_L	57_C	1.484	1.00
168_R	231_T	1.451	1.00
12_L	229_C	1.437	1.00
112_V	159_F	1.419	1.00
267_A	271_V	1.414	1.00
74_F	78_V	1.410	1.00
211_S	214_L	1.402	1.00
208_N	212_L	1.389	1.00
16_A	233_A	1.382	1.00
142_V	275_F	1.358	1.00
117_G	121_L	1.355	1.00
132_A	282_I	1.346	1.00
46_S	183_T	1.338	1.00
75_M	167_V	1.337	1.00
252_L	256_L	1.320	1.00
78_V	167_V	1.313	1.00
25_A	256_L	1.311	1.00
49_F	224_T	1.306	1.00
99_M	257_A	1.306	1.00
98_H	101_E	1.304	1.00
116_L	120_F	1.303	1.00
71_Q	74_F	1.302	1.00
92_W	95_N	1.296	1.00
40_T	187_L	1.292	1.00
70_P	73_I	1.288	1.00
212_L	219_A	1.288	1.00
10_V	245_F	1.287	1.00
142_V	268_D	1.287	1.00
52_V	56_I	1.284	1.00
214_L	218_A	1.276	1.00
127_R	131_L	1.275	1.00
71_Q	75_M	1.269	1.00
48_F	52_V	1.268	1.00
34_P	37_E	1.261	1.00
215_L	219_A	1.257	1.00
28_K	31_Y	1.256	1.00
214_L	217_I	1.251	1.00
128_M	282_I	1.249	1.00
162_A	166_L	1.249	1.00
136_A	279_A	1.247	1.00
45_W	220_G	1.235	1.00
274_A	278_V	1.232	1.00
20_W	226_P	1.231	1.00
270_M	274_A	1.230	1.00
134_I	138_C	1.220	1.00
100_L	254_F	1.216	1.00
130_W	134_I	1.214	1.00
104_L	273_F	1.211	1.00
248_I	252_L	1.207	1.00
22_I	256_L	1.206	1.00
96_N	153_I	1.205	1.00
139_G	272_T	1.198	1.00
256_L	260_F	1.197	1.00
82_L	163_F	1.170	1.00
72_K	173_V	1.166	1.00
265_P	270_M	1.165	1.00
90_F	94_V	1.161	1.00
11_L	15_A	1.161	1.00
119_I	122_G	1.159	1.00
77_A	185_W	1.153	1.00
42_R	223_T	1.148	1.00
40_T	44_I	1.148	1.00
125_F	130_W	1.139	1.00
127_R	130_W	1.135	1.00
189_V	192_I	1.134	1.00
33_V	212_L	1.128	1.00
143_Q	272_T	1.128	1.00
210_M	213_N	1.111	1.00
16_A	229_C	1.097	1.00
94_V	102_A	1.096	1.00
47_F	180_L	1.092	1.00
121_L	166_L	1.091	1.00
97_H	154_A	1.087	1.00
193_Y	197_I	1.087	1.00
40_T	194_L	1.084	1.00
75_M	171_I	1.082	1.00
55_S	59_Q	1.077	1.00
116_L	163_F	1.075	1.00
84_G	189_V	1.073	1.00
36_D	193_Y	1.059	1.00
81_V	189_V	1.055	1.00
128_M	285_M	1.055	1.00
9_G	233_A	1.052	1.00
220_G	224_T	1.050	1.00
16_A	20_W	1.046	1.00
80_A	185_W	1.042	1.00
113_N	165_G	1.038	1.00
118_M	124_R	1.037	1.00
39_L	91_I	1.034	1.00
123_E	129_Q	1.034	1.00
82_L	160_S	1.032	1.00
217_I	221_I	1.031	1.00
9_G	236_R	1.024	1.00
116_L	162_A	1.024	1.00
105_G	158_A	1.022	1.00
128_M	286_D	1.021	1.00
82_L	167_V	1.014	1.00
32_Y	212_L	1.013	1.00
99_M	261_Y	1.012	1.00
15_A	229_C	1.011	1.00
27_F	94_V	1.011	1.00
36_D	88_L	1.009	1.00
84_G	190_A	1.004	1.00
139_G	276_I	0.993	1.00
113_N	239_L	0.983	1.00
169_K	238_R	0.977	1.00
211_S	215_L	0.976	1.00
19_I	229_C	0.975	1.00
20_W	230_F	0.971	1.00
43_V	186_L	0.969	1.00
35_A	39_L	0.968	1.00
148_G	151_P	0.965	1.00
74_F	77_A	0.964	1.00
234_A	242_L	0.963	1.00
55_S	58_R	0.952	1.00
59_Q	174_E	0.947	1.00
116_L	159_F	0.945	1.00
251_T	273_F	0.942	1.00
113_N	162_A	0.933	1.00
44_I	191_A	0.924	1.00
116_L	119_I	0.924	1.00
169_K	239_L	0.923	1.00
105_G	154_A	0.922	1.00
104_L	141_L	0.918	1.00
108_I	140_V	0.915	1.00
158_A	162_A	0.915	1.00
145_W	148_G	0.910	1.00
25_A	260_F	0.905	1.00
196_A	199_D	0.901	1.00
14_L	252_L	0.893	1.00
59_Q	62_Y	0.892	1.00
237_L	242_L	0.891	1.00
22_I	218_A	0.890	1.00
267_A	270_M	0.887	1.00
212_L	216_L	0.887	1.00
212_L	215_L	0.879	1.00
238_R	242_L	0.877	1.00
173_V	178_G	0.876	1.00
17_Y	248_I	0.876	1.00
83_I	164_Y	0.871	1.00
126_R	130_W	0.870	1.00
17_Y	252_L	0.865	1.00
99_M	263_E	0.865	1.00
29_L	215_L	0.865	1.00
114_I	125_F	0.863	1.00
213_N	217_I	0.861	1.00
73_I	185_W	0.861	1.00
234_A	238_R	0.861	1.00
41_H	45_W	0.858	1.00
75_M	79_S	0.856	1.00
49_F	52_V	0.849	1.00
75_M	170_K	0.845	1.00
51_V	184_M	0.845	1.00
17_Y	21_G	0.841	1.00
135_L	279_A	0.832	1.00
84_G	88_L	0.831	1.00
184_M	188_P	0.826	1.00
195_F	198_A	0.823	1.00
88_L	92_W	0.820	1.00
50_M	224_T	0.820	1.00
138_C	142_V	0.817	1.00
154_A	158_A	0.816	1.00
193_Y	196_A	0.816	1.00
76_L	173_V	0.813	1.00
39_L	190_A	0.812	1.00
138_C	275_F	0.810	1.00
25_A	257_A	0.806	1.00
258_V	265_P	0.804	1.00
192_I	196_A	0.791	1.00
124_R	128_M	0.791	1.00
38_I	219_A	0.788	1.00
37_E	194_L	0.784	1.00
180_L	184_M	0.781	1.00
86_N	160_S	0.780	1.00
97_H	102_A	0.778	1.00
237_L	241_T	0.774	1.00
13_A	245_F	0.772	1.00
209_P	213_N	0.770	1.00
218_A	221_I	0.770	1.00
163_F	167_V	0.770	1.00
140_V	144_L	0.769	1.00
145_W	150_L	0.768	1.00
142_V	271_V	0.766	1.00
73_I	77_A	0.766	1.00
254_F	273_F	0.764	1.00
69_T	73_I	0.763	1.00
271_V	275_F	0.762	1.00
56_I	59_Q	0.760	1.00
254_F	265_P	0.760	1.00
47_F	51_V	0.759	1.00
268_D	271_V	0.758	1.00
233_A	242_L	0.757	1.00
114_I	129_Q	0.757	1.00
111_L	136_A	0.754	1.00
115_V	119_I	0.753	1.00
181_I	185_W	0.749	1.00
258_V	264_K	0.748	1.00
124_R	127_R	0.745	1.00
10_V	241_T	0.741	1.00
131_L	135_L	0.740	1.00
24_P	90_F	0.740	1.00
225_V	229_C	0.736	1.00
147_F	151_P	0.735	1.00
86_N	164_Y	0.728	1.00
248_I	251_T	0.725	1.00
125_F	129_Q	0.722	1.00
212_L	220_G	0.721	1.00
113_N	166_L	0.718	1.00
54_M	180_L	0.717	1.00
185_W	189_V	0.717	1.00
37_E	41_H	0.709	1.00
30_I	212_L	0.706	1.00
24_P	103_S	0.706	1.00
147_F	150_L	0.703	1.00
85_G	89_L	0.703	1.00
273_F	277_W	0.703	1.00
194_L	198_A	0.695	1.00
83_I	227_L	0.692	1.00
195_F	199_D	0.691	1.00
80_A	84_G	0.687	1.00
186_L	190_A	0.687	1.00
173_V	177_T	0.684	1.00
185_W	188_P	0.684	1.00
30_I	38_I	0.678	1.00
25_A	99_M	0.678	1.00
118_M	122_G	0.677	1.00
123_E	240_S	0.674	1.00
33_V	37_E	0.674	1.00
44_I	48_F	0.671	1.00
278_V	282_I	0.671	1.00
161_F	165_G	0.667	1.00
244_F	283_F	0.662	1.00
204_H	207_Q	0.661	1.00
112_V	155_L	0.658	1.00
265_P	269_K	0.657	1.00
33_V	38_I	0.657	1.00
72_K	76_L	0.655	1.00
184_M	187_L	0.652	1.00
72_K	75_M	0.647	1.00
75_M	78_V	0.645	1.00
53_L	176_Q	0.644	1.00
54_M	58_R	0.642	1.00
205_M	208_N	0.641	1.00
13_A	237_L	0.639	1.00
32_Y	209_P	0.638	1.00
228_L	232_A	0.636	1.00
139_G	279_A	0.635	1.00
212_L	218_A	0.634	1.00
212_L	222_V	0.632	1.00
187_L	191_A	0.627	1.00
108_I	111_L	0.627	1.00
153_I	156_G	0.625	1.00
256_L	259_T	0.623	1.00
161_F	230_F	0.623	1.00
45_W	49_F	0.621	1.00
29_L	261_Y	0.620	1.00
266_G	270_M	0.617	1.00
177_T	181_I	0.616	1.00
76_L	178_G	0.614	1.00
114_I	118_M	0.610	1.00
257_A	261_Y	0.610	1.00
208_N	211_S	0.609	1.00
164_Y	168_R	0.607	1.00
34_P	198_A	0.605	1.00
57_C	174_E	0.602	1.00
104_L	144_L	0.601	1.00
197_I	200_S	0.601	1.00
83_I	182_E	0.598	1.00
146_T	149_S	0.595	1.00
105_G	155_L	0.594	1.00
208_N	213_N	0.594	1.00
115_V	133_V	0.593	1.00
110_P	247_Y	0.592	1.00
181_I	184_M	0.591	1.00
254_F	258_V	0.591	1.00
57_C	176_Q	0.588	1.00
9_G	237_L	0.587	1.00
135_L	282_I	0.587	1.00
53_L	56_I	0.586	1.00
152_I	156_G	0.585	1.00
179_M	231_T	0.583	1.00
129_Q	238_R	0.582	1.00
212_L	217_I	0.579	1.00
264_K	268_D	0.577	1.00
107_F	140_V	0.574	1.00
219_A	224_T	0.574	1.00
26_Y	215_L	0.573	1.00
255_L	258_V	0.573	1.00
164_Y	231_T	0.573	1.00
269_K	273_F	0.572	1.00
279_A	283_F	0.570	1.00
93_A	102_A	0.569	1.00
216_L	220_G	0.566	1.00
178_G	181_I	0.565	1.00
255_L	259_T	0.562	1.00
214_L	220_G	0.562	1.00
15_A	19_I	0.562	1.00
14_L	17_Y	0.561	1.00
126_R	286_D	0.560	1.00
259_T	262_G	0.559	1.00
84_G	193_Y	0.558	1.00
19_I	226_P	0.557	1.00
188_P	191_A	0.556	1.00
26_Y	217_I	0.556	1.00
69_T	74_F	0.553	1.00
165_G	230_F	0.552	1.00
159_F	163_F	0.551	1.00
83_I	186_L	0.551	1.00
246_Q	249_G	0.550	1.00
46_S	224_T	0.550	1.00
280_L	283_F	0.549	1.00
17_Y	249_G	0.546	1.00
90_F	102_A	0.545	1.00
121_L	169_K	0.545	1.00
23_A	91_I	0.544	1.00
77_A	81_V	0.543	1.00
121_L	170_K	0.542	1.00
22_I	217_I	0.541	1.00
108_I	136_A	0.540	1.00
79_S	168_R	0.538	1.00
207_Q	210_M	0.538	1.00
168_R	172_A	0.532	1.00
90_F	157_L	0.528	1.00
77_A	189_V	0.527	1.00
25_A	261_Y	0.526	1.00
73_I	181_I	0.525	1.00
48_F	51_V	0.523	1.00
108_I	158_A	0.523	1.00
13_A	230_F	0.520	1.00
158_A	161_F	0.516	1.00
107_F	158_A	0.516	1.00
37_E	198_A	0.514	1.00
93_A	97_H	0.514	1.00
209_P	214_L	0.514	1.00
62_Y	177_T	0.513	1.00
137_I	247_Y	0.513	1.00
39_L	88_L	0.513	1.00
258_V	270_M	0.510	1.00
91_I	95_N	0.509	1.00
264_K	269_K	0.506	1.00
34_P	197_I	0.506	1.00
120_F	163_F	0.506	1.00
233_A	237_L	0.503	1.00
111_L	133_V	0.500	1.00
215_L	220_G	0.500	1.00
36_D	190_A	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
2i68A	2	0.2601	98.9	0.747	Contact Map
3b5dA	2	0.3412	98.2	0.8	Contact Map
4he8J	1	0.5203	45.1	0.923	Contact Map
3wdoA	1	0.9324	19.1	0.936	Contact Map
2m20A	2	0.1182	13.2	0.941	Contact Map
2kluA	1	0.1453	12.7	0.941	Contact Map
2rddB	1	0.1081	12.7	0.941	Contact Map
4pypA	1	0.8277	10.9	0.943	Contact Map
4knfA	3	0.1351	10.6	0.943	Contact Map
4j05A	3	0.9189	10.5	0.943	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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