YQED - BACSU - GREMLIN Contacts

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YQED - Uncharacterized protein YqeD

UniProt:	P54449	Sequences: MLKKVIGILVIIAIISVGFFQKEAWLDAIKAGGMFSVLFSMLLIAADVFFPIVPFALIAALNGAVFGTANGIWITLTGSMLGTILLFFLARYSFRDWARKKVQAYPAIQSYEASFNKNAFTAVLLGRLIPVIPSLVMNVICGLSQVRWHVFFFASLIGKIPNIVVVTIAGANFTSNKLLSISIYGTYILIIMLVIYKKFPHLLKVPKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	208 (175)
Sequences:	9623 (7079)
Seq/√Len:	535.1

ECOLI - YDJZ YDJX YQJA DEDA YGHB YABI YOHD
BACSU - YQED YHJE YTXB YKOX YNGC YBFM
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_I	148_W	3.974	1.00
72_I	164_V	2.935	1.00
147_R	150_V	2.722	1.00
67_G	70_N	2.445	1.00
120_F	154_A	2.372	1.00
84_I	152_F	2.368	1.00
80_M	156_L	2.364	1.00
95_R	112_E	2.364	1.00
195_I	199_F	2.359	1.00
120_F	150_V	2.214	1.00
124_L	157_I	2.107	1.00
40_S	62_N	2.079	1.00
181_I	185_G	1.995	1.00
45_A	85_L	1.967	1.00
67_G	71_G	1.886	1.00
76_L	160_I	1.886	1.00
118_N	121_T	1.868	1.00
109_Q	113_A	1.793	1.00
194_V	198_K	1.749	1.00
112_E	116_N	1.728	1.00
41_M	74_I	1.666	1.00
94_F	97_W	1.640	1.00
68_T	72_I	1.636	1.00
88_F	92_Y	1.609	1.00
176_N	180_S	1.589	1.00
148_W	152_F	1.585	1.00
75_T	163_I	1.564	1.00
176_N	179_L	1.547	1.00
72_I	167_T	1.545	1.00
168_I	172_N	1.539	1.00
90_A	143_L	1.520	1.00
63_G	170_G	1.519	1.00
91_R	145_Q	1.518	1.00
41_M	78_G	1.507	1.00
88_F	148_W	1.507	1.00
196_Y	200_P	1.502	1.00
183_I	187_Y	1.497	1.00
41_M	77_T	1.428	1.00
180_S	184_Y	1.428	1.00
68_T	168_I	1.427	1.00
80_M	152_F	1.423	1.00
190_I	193_L	1.402	1.00
37_V	74_I	1.367	1.00
83_T	155_S	1.361	1.00
196_Y	199_F	1.359	1.00
149_H	153_F	1.359	1.00
184_Y	188_I	1.348	1.00
103_Q	107_A	1.346	1.00
26_L	30_K	1.344	1.00
29_I	36_S	1.336	1.00
193_L	197_K	1.332	1.00
69_A	72_I	1.328	1.00
41_M	45_A	1.327	1.00
198_K	201_H	1.321	1.00
62_N	71_G	1.313	1.00
70_N	74_I	1.311	1.00
59_A	75_T	1.301	1.00
178_L	181_I	1.301	1.00
36_S	66_F	1.293	1.00
75_T	167_T	1.289	1.00
84_I	88_F	1.281	1.00
69_A	73_W	1.278	1.00
177_K	180_S	1.272	1.00
45_A	81_L	1.262	1.00
190_I	194_V	1.245	1.00
90_A	142_G	1.214	1.00
27_D	30_K	1.213	1.00
70_N	73_W	1.197	1.00
107_A	110_S	1.184	1.00
123_V	154_A	1.178	1.00
76_L	156_L	1.171	1.00
71_G	167_T	1.158	1.00
27_D	31_A	1.154	1.00
189_L	193_L	1.134	1.00
95_R	99_R	1.130	1.00
74_I	78_G	1.125	1.00
109_Q	112_E	1.123	1.00
198_K	202_L	1.119	1.00
121_T	125_L	1.113	1.00
161_P	164_V	1.112	1.00
128_L	161_P	1.109	1.00
112_E	145_Q	1.108	1.00
177_K	181_I	1.092	1.00
197_K	201_H	1.089	1.00
37_V	70_N	1.087	1.00
40_S	75_T	1.083	1.00
191_I	195_I	1.081	1.00
72_I	76_L	1.075	1.00
126_G	137_M	1.065	1.00
123_V	146_V	1.059	1.00
127_R	155_S	1.057	1.00
179_L	182_S	1.029	1.00
114_S	122_A	1.028	1.00
192_M	196_Y	1.020	1.00
112_E	144_S	1.011	1.00
63_G	167_T	1.011	1.00
59_A	167_T	1.006	1.00
163_I	167_T	0.996	1.00
66_F	71_G	0.982	1.00
44_I	48_V	0.982	1.00
149_H	152_F	0.976	1.00
56_A	166_V	0.971	1.00
44_I	59_A	0.969	1.00
115_F	141_C	0.965	1.00
73_W	77_T	0.959	1.00
41_M	81_L	0.957	1.00
152_F	156_L	0.952	1.00
186_T	190_I	0.950	1.00
199_F	202_L	0.950	1.00
155_S	159_K	0.946	1.00
59_A	63_G	0.944	1.00
44_I	47_D	0.940	1.00
178_L	182_S	0.935	1.00
92_Y	96_D	0.930	1.00
86_L	139_V	0.930	1.00
72_I	168_I	0.923	1.00
62_N	75_T	0.923	1.00
194_V	197_K	0.914	1.00
157_I	160_I	0.905	1.00
150_V	154_A	0.889	1.00
181_I	184_Y	0.883	1.00
61_L	64_A	0.878	1.00
68_T	167_T	0.874	1.00
35_F	39_F	0.872	1.00
32_G	39_F	0.870	1.00
134_S	159_K	0.861	1.00
124_L	154_A	0.861	1.00
73_W	76_L	0.858	1.00
99_R	104_A	0.857	1.00
69_A	168_I	0.851	1.00
120_F	153_F	0.846	1.00
37_V	67_G	0.839	1.00
104_A	109_Q	0.836	1.00
28_A	32_G	0.836	1.00
195_I	198_K	0.824	1.00
103_Q	106_P	0.818	1.00
138_N	155_S	0.818	1.00
134_S	162_N	0.817	1.00
180_S	183_I	0.816	1.00
79_S	159_K	0.815	1.00
61_L	65_V	0.814	1.00
179_L	183_I	0.812	1.00
187_Y	190_I	0.808	1.00
193_L	196_Y	0.802	1.00
113_A	117_K	0.800	1.00
164_V	168_I	0.796	1.00
101_K	104_A	0.794	1.00
62_N	66_F	0.794	1.00
76_L	80_M	0.794	1.00
76_L	163_I	0.793	1.00
46_A	51_P	0.782	1.00
150_V	153_F	0.781	1.00
127_R	138_N	0.778	1.00
83_T	138_N	0.774	1.00
185_G	189_L	0.768	1.00
113_A	116_N	0.766	1.00
44_I	58_I	0.765	1.00
153_F	157_I	0.761	1.00
124_L	161_P	0.758	1.00
83_T	127_R	0.754	1.00
182_S	185_G	0.753	1.00
38_L	42_L	0.750	1.00
106_P	110_S	0.749	1.00
81_L	85_L	0.748	1.00
87_F	151_F	0.746	1.00
97_W	101_K	0.745	1.00
63_G	71_G	0.742	1.00
56_A	134_S	0.734	1.00
159_K	162_N	0.733	1.00
59_A	79_S	0.727	1.00
45_A	78_G	0.725	1.00
125_L	129_I	0.724	1.00
45_A	48_V	0.722	1.00
98_A	108_I	0.721	1.00
34_M	38_L	0.719	1.00
188_I	192_M	0.711	1.00
86_L	135_L	0.710	1.00
176_N	181_I	0.705	1.00
57_L	61_L	0.700	1.00
53_V	135_L	0.699	1.00
47_D	82_G	0.693	1.00
137_M	141_C	0.692	1.00
98_A	102_V	0.692	1.00
51_P	86_L	0.692	1.00
47_D	135_L	0.690	1.00
80_M	159_K	0.689	1.00
169_A	173_F	0.688	1.00
114_S	117_K	0.687	1.00
74_I	77_T	0.687	1.00
177_K	188_I	0.687	1.00
95_R	98_A	0.675	1.00
154_A	158_G	0.673	1.00
44_I	78_G	0.671	1.00
182_S	186_T	0.671	1.00
37_V	41_M	0.662	1.00
185_G	200_P	0.661	1.00
50_F	86_L	0.660	1.00
47_D	55_F	0.660	1.00
87_F	148_W	0.658	1.00
169_A	172_N	0.655	1.00
165_V	169_A	0.651	1.00
187_Y	191_I	0.649	1.00
59_A	163_I	0.647	1.00
197_K	200_P	0.646	1.00
88_F	91_R	0.645	1.00
82_G	86_L	0.644	1.00
124_L	158_G	0.638	1.00
90_A	139_V	0.638	1.00
126_G	141_C	0.630	1.00
188_I	191_I	0.626	1.00
76_L	159_K	0.626	1.00
89_L	93_S	0.623	1.00
68_T	164_V	0.617	1.00
87_F	91_R	0.612	1.00
176_N	193_L	0.611	1.00
93_S	96_D	0.609	1.00
97_W	100_K	0.607	1.00
171_A	174_T	0.598	1.00
83_T	151_F	0.591	1.00
99_R	109_Q	0.591	1.00
184_Y	187_Y	0.584	0.99
176_N	183_I	0.576	0.99
110_S	114_S	0.573	0.99
111_Y	144_S	0.572	0.99
120_F	124_L	0.566	0.99
60_A	64_A	0.562	0.99
153_F	156_L	0.561	0.99
115_F	119_A	0.558	0.99
47_D	58_I	0.558	0.99
179_L	190_I	0.557	0.99
52_I	135_L	0.554	0.99
126_G	132_I	0.554	0.99
80_M	155_S	0.550	0.99
160_I	164_V	0.545	0.99
165_V	168_I	0.545	0.99
52_I	55_F	0.545	0.99
64_A	174_T	0.543	0.99
156_L	160_I	0.542	0.99
77_T	80_M	0.540	0.99
129_I	132_I	0.538	0.99
42_L	45_A	0.538	0.99
185_G	188_I	0.538	0.99
171_A	175_S	0.537	0.99
83_T	148_W	0.535	0.99
28_A	31_A	0.533	0.99
162_N	166_V	0.530	0.99
119_A	146_V	0.529	0.99
178_L	190_I	0.528	0.99
177_K	182_S	0.528	0.99
108_I	112_E	0.526	0.99
32_G	36_S	0.526	0.99
78_G	82_G	0.521	0.99
46_A	50_F	0.520	0.99
56_A	60_A	0.519	0.99
120_F	146_V	0.518	0.99
95_R	145_Q	0.518	0.99
96_D	99_R	0.511	0.99
72_I	160_I	0.508	0.99
84_I	155_S	0.508	0.99
99_R	112_E	0.504	0.98
44_I	55_F	0.502	0.98
110_S	113_A	0.500	0.98

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
4huqS	1	0.7308	36.9	0.92	Contact Map
2l2tA	2	0.1971	34.3	0.921	Contact Map
3ne5A	3	0.8846	31.3	0.923	Contact Map
2rddB	1	0.1538	26	0.926	Contact Map
3rlbA	1	0.7837	21.3	0.929	Contact Map
2m20A	2	0.1538	21.1	0.929	Contact Map
4dx5A	3	0.851	20.9	0.929	Contact Map
4dveA	3	0.7548	19.2	0.93	Contact Map
4a82A	2	0.8365	17.5	0.932	Contact Map
4x5mA	2	0.4375	17.4	0.932	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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