YFKD - BACSU - GREMLIN Contacts

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YFKD - Uncharacterized protein YfkD

UniProt:	O34579	Sequences: MMKKLFHSTLIVLLFFSFFGVQPIHAKKQFKVPNSVASISKENTYPNASQDQPMLQPSKLAKELLDHSEVKIENPHLIKMLNESNISGTPLAVGYRATIFLGKWALGYESNETVANWEYKKINTNRADNRGGKETAEMHYAQEQQYRVKGGLTAKVPNAEDVKSMMMQKAMKKTNLPLAFETVIGAGTKRDQIYKVAPKKIGYLHAYAPAVNEKGKVTYGEVYLVLKGNKRKLVVKNVTSQGIGAWIPVQDHVTFGFQLSSLPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	264 (248)
Sequences:	101 (75)
Seq/√Len:	4.7

BACSU - YFKD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_Y	226_L	4.704	0.95
61_A	148_V	4.104	0.90
122_I	253_V	3.549	0.81
32_V	100_F	3.290	0.76
25_H	179_A	3.284	0.76
54_M	80_M	2.909	0.66
157_P	219_Y	2.780	0.62
38_S	80_M	2.666	0.59
69_E	249_V	2.621	0.57
40_S	88_G	2.374	0.49
98_T	200_K	2.313	0.47
156_V	254_T	2.229	0.45
107_G	233_L	2.145	0.42
93_V	235_V	2.105	0.41
67_H	231_R	1.969	0.37
98_T	225_V	1.947	0.36
121_K	124_T	1.942	0.36
46_P	212_N	1.940	0.36
136_A	207_Y	1.914	0.35
38_S	68_S	1.904	0.35
124_T	143_E	1.842	0.33
156_V	164_S	1.834	0.33
134_E	148_V	1.821	0.33
88_G	98_T	1.811	0.32
179_A	183_V	1.807	0.32
156_V	184_I	1.807	0.32
115_A	200_K	1.802	0.32
115_A	141_A	1.769	0.31
133_K	198_P	1.748	0.31
93_V	238_V	1.734	0.30
90_P	229_N	1.726	0.30
38_S	168_Q	1.722	0.30
70_V	172_K	1.719	0.30
135_T	249_V	1.719	0.30
94_G	228_G	1.668	0.29
212_N	242_G	1.668	0.29
109_E	133_K	1.626	0.28
97_A	130_R	1.622	0.27
79_K	151_G	1.614	0.27
105_A	209_P	1.567	0.26
200_K	208_A	1.564	0.26
90_P	240_S	1.542	0.25
73_E	169_K	1.537	0.25
133_K	199_K	1.535	0.25
76_H	86_I	1.526	0.25
51_D	214_K	1.524	0.25
107_G	167_M	1.491	0.24
76_H	156_V	1.489	0.24
50_Q	53_P	1.473	0.24
160_E	175_N	1.459	0.24
37_A	190_R	1.456	0.23
40_S	196_V	1.454	0.23
90_P	159_A	1.444	0.23
46_P	112_E	1.427	0.23
154_A	180_F	1.421	0.23
35_S	128_D	1.421	0.23
89_T	229_N	1.412	0.22
95_Y	229_N	1.410	0.22
90_P	201_I	1.406	0.22
90_P	208_A	1.401	0.22
159_A	196_V	1.400	0.22
25_H	184_I	1.392	0.22
234_V	240_S	1.383	0.22
154_A	157_P	1.378	0.22
133_K	256_G	1.376	0.22
159_A	234_V	1.373	0.22
93_V	181_E	1.370	0.22
233_L	259_L	1.363	0.21
55_L	180_F	1.363	0.21
98_T	208_A	1.352	0.21
29_Q	127_A	1.351	0.21
17_S	100_F	1.348	0.21
13_L	93_V	1.343	0.21
51_D	212_N	1.337	0.21
81_L	107_G	1.318	0.20
68_S	115_A	1.314	0.20
111_N	183_V	1.312	0.20
42_E	165_M	1.311	0.20
55_L	151_G	1.306	0.20
127_A	136_A	1.282	0.20
120_K	256_G	1.260	0.19
156_V	192_Q	1.258	0.19
136_A	141_A	1.255	0.19
14_L	21_V	1.250	0.19
55_L	154_A	1.244	0.19
88_G	231_R	1.243	0.19
34_N	208_A	1.221	0.19
109_E	184_I	1.220	0.19
97_A	128_D	1.210	0.18
63_E	200_K	1.209	0.18
86_I	173_K	1.206	0.18
84_S	98_T	1.205	0.18
84_S	259_L	1.197	0.18
51_D	242_G	1.190	0.18
168_Q	171_M	1.184	0.18
13_L	27_K	1.182	0.18
38_S	109_E	1.179	0.18
115_A	139_H	1.175	0.18
90_P	95_Y	1.175	0.18
153_T	244_G	1.172	0.18
50_Q	55_L	1.171	0.18
46_P	242_G	1.168	0.18
34_N	84_S	1.166	0.18
12_V	16_F	1.157	0.17
138_M	200_K	1.149	0.17
42_E	65_L	1.126	0.17
136_A	257_F	1.124	0.17
49_S	164_S	1.120	0.17
206_A	226_L	1.111	0.17
165_M	190_R	1.109	0.17
53_P	128_D	1.102	0.16
109_E	198_P	1.099	0.16
105_A	231_R	1.090	0.16
105_A	238_V	1.084	0.16
120_K	155_K	1.083	0.16
24_I	253_V	1.081	0.16
84_S	157_P	1.071	0.16
217_V	230_K	1.064	0.16
130_R	157_P	1.063	0.16
26_A	93_V	1.059	0.16
68_S	258_Q	1.052	0.16
212_N	231_R	1.051	0.16
76_H	103_K	1.045	0.15
115_A	225_V	1.042	0.15
90_P	96_R	1.037	0.15
98_T	231_R	1.034	0.15
36_V	119_Y	1.032	0.15
84_S	196_V	1.031	0.15
20_G	172_K	1.025	0.15
160_E	206_A	1.025	0.15
141_A	200_K	1.021	0.15
92_A	229_N	1.018	0.15
101_L	130_R	1.017	0.15
68_S	107_G	1.011	0.15
232_K	253_V	1.011	0.15
56_Q	97_A	1.008	0.15
124_T	154_A	1.006	0.15
65_L	122_I	1.001	0.15
53_P	130_R	0.992	0.15
129_N	178_L	0.988	0.15
88_G	95_Y	0.982	0.14
57_P	221_E	0.981	0.14
65_L	105_A	0.971	0.14
158_N	238_V	0.971	0.14
60_L	86_I	0.971	0.14
68_S	233_L	0.968	0.14
35_S	97_A	0.968	0.14
92_A	95_Y	0.966	0.14
114_V	254_T	0.959	0.14
56_Q	240_S	0.956	0.14
59_K	66_D	0.933	0.14
81_L	122_I	0.933	0.14
183_V	233_L	0.931	0.14
96_R	127_A	0.930	0.14
124_T	230_K	0.928	0.14
62_K	66_D	0.927	0.14
18_F	24_I	0.927	0.14
12_V	96_R	0.922	0.13
195_K	203_Y	0.920	0.13
58_S	221_E	0.916	0.13
17_S	149_K	0.916	0.13
167_M	197_A	0.916	0.13
89_T	103_K	0.915	0.13
94_G	227_K	0.908	0.13
30_F	168_Q	0.906	0.13
90_P	234_V	0.904	0.13
115_A	136_A	0.904	0.13
13_L	26_A	0.893	0.13
56_Q	162_V	0.887	0.13
64_L	251_D	0.887	0.13
147_R	253_V	0.887	0.13
204_L	239_T	0.883	0.13
98_T	192_Q	0.879	0.13
50_Q	203_Y	0.878	0.13
38_S	71_K	0.875	0.13
46_P	51_D	0.871	0.13
88_G	105_A	0.868	0.13
35_S	130_R	0.867	0.13
99_I	202_G	0.864	0.13
138_M	191_D	0.861	0.13
163_K	209_P	0.857	0.13
63_E	127_A	0.854	0.13
100_F	238_V	0.850	0.12
183_V	191_D	0.846	0.12
115_A	211_V	0.845	0.12
91_L	141_A	0.843	0.12
32_V	80_M	0.840	0.12
13_L	148_V	0.839	0.12
32_V	158_N	0.837	0.12
93_V	169_K	0.837	0.12
81_L	200_K	0.827	0.12
34_N	107_G	0.827	0.12
122_I	186_A	0.820	0.12
63_E	235_V	0.817	0.12
80_M	168_Q	0.814	0.12
69_E	205_H	0.811	0.12
157_P	230_K	0.807	0.12
85_N	134_E	0.807	0.12
95_Y	103_K	0.805	0.12
81_L	93_V	0.804	0.12
111_N	259_L	0.804	0.12
111_N	201_I	0.804	0.12
52_Q	172_K	0.802	0.12
241_Q	252_H	0.802	0.12
101_L	110_S	0.792	0.12
22_Q	26_A	0.791	0.12
98_T	240_S	0.790	0.12
31_K	198_P	0.787	0.12
39_I	184_I	0.784	0.12
135_T	172_K	0.783	0.12
122_I	191_D	0.780	0.12
120_K	254_T	0.780	0.12
145_Q	195_K	0.778	0.12
54_M	81_L	0.771	0.11
137_E	256_G	0.769	0.11
118_E	212_N	0.763	0.11
73_E	145_Q	0.762	0.11
145_Q	216_K	0.762	0.11
121_K	219_Y	0.760	0.11
48_A	199_K	0.759	0.11
67_H	93_V	0.759	0.11
21_V	24_I	0.759	0.11
137_E	258_Q	0.755	0.11
158_N	183_V	0.753	0.11
65_L	253_V	0.753	0.11
161_D	173_K	0.753	0.11
95_Y	225_V	0.747	0.11
137_E	217_V	0.747	0.11
199_K	216_K	0.741	0.11
53_P	97_A	0.738	0.11
68_S	81_L	0.737	0.11
89_T	192_Q	0.736	0.11
61_A	85_N	0.734	0.11
66_D	235_V	0.732	0.11
53_P	154_A	0.732	0.11
214_K	251_D	0.729	0.11
92_A	231_R	0.725	0.11
48_A	205_H	0.725	0.11
101_L	162_V	0.722	0.11
16_F	138_M	0.721	0.11
45_Y	112_E	0.719	0.11
76_H	211_V	0.714	0.11
148_V	183_V	0.703	0.11
67_H	76_H	0.700	0.11
156_V	242_G	0.700	0.11
38_S	167_M	0.695	0.10
15_F	231_R	0.694	0.10
162_V	166_M	0.693	0.10
41_K	182_T	0.690	0.10
33_P	237_N	0.681	0.10
62_K	134_E	0.679	0.10
16_F	211_V	0.675	0.10
16_F	30_F	0.674	0.10
132_G	166_M	0.670	0.10
91_L	255_F	0.670	0.10
24_I	184_I	0.665	0.10
208_A	234_V	0.664	0.10
23_P	28_K	0.663	0.10
141_A	155_K	0.658	0.10
15_F	257_F	0.656	0.10
137_E	233_L	0.656	0.10
45_Y	55_L	0.652	0.10
29_Q	65_L	0.651	0.10
54_M	172_K	0.650	0.10
146_Y	178_L	0.649	0.10
17_S	137_E	0.647	0.10
85_N	235_V	0.646	0.10
69_E	137_E	0.644	0.10
66_D	233_L	0.644	0.10
54_M	70_V	0.643	0.10
91_L	154_A	0.642	0.10
167_M	231_R	0.640	0.10
90_P	235_V	0.639	0.10
71_K	91_L	0.637	0.10
57_P	166_M	0.636	0.10
34_N	256_G	0.636	0.10
223_Y	238_V	0.631	0.10
208_A	255_F	0.624	0.10
86_I	93_V	0.624	0.10
32_V	127_A	0.624	0.10
160_E	179_A	0.623	0.10
170_A	187_G	0.620	0.10
37_A	254_T	0.618	0.10
58_S	242_G	0.618	0.10
93_V	259_L	0.613	0.10
85_N	156_V	0.612	0.10
55_L	68_S	0.610	0.10
124_T	257_F	0.608	0.09
78_I	173_K	0.608	0.09
37_A	59_K	0.606	0.09
31_K	66_D	0.605	0.09
93_V	197_A	0.604	0.09
25_H	127_A	0.603	0.09
40_S	209_P	0.601	0.09
135_T	259_L	0.597	0.09
139_H	193_I	0.597	0.09
28_K	109_E	0.594	0.09
38_S	195_K	0.593	0.09
137_E	224_L	0.592	0.09
65_L	99_I	0.591	0.09
143_E	165_M	0.591	0.09
61_A	232_K	0.591	0.09
211_V	233_L	0.591	0.09
27_K	32_V	0.587	0.09
40_S	115_A	0.583	0.09
87_S	199_K	0.582	0.09
25_H	196_V	0.582	0.09
26_A	168_Q	0.580	0.09
20_G	65_L	0.578	0.09
169_K	172_K	0.575	0.09
36_V	177_P	0.575	0.09
133_K	144_Q	0.573	0.09
144_Q	205_H	0.572	0.09
48_A	73_E	0.572	0.09
79_K	103_K	0.572	0.09
68_S	151_G	0.569	0.09
118_E	173_K	0.565	0.09
42_E	157_P	0.565	0.09
112_E	208_A	0.564	0.09
36_V	95_Y	0.563	0.09
86_I	179_A	0.560	0.09
58_S	204_L	0.558	0.09
90_P	219_Y	0.558	0.09
97_A	219_Y	0.558	0.09
90_P	107_G	0.556	0.09
200_K	234_V	0.554	0.09
167_M	233_L	0.552	0.09
190_R	199_K	0.552	0.09
18_F	26_A	0.551	0.09
135_T	143_E	0.551	0.09
85_N	255_F	0.549	0.09
161_D	183_V	0.549	0.09
12_V	20_G	0.548	0.09
186_A	229_N	0.548	0.09
87_S	115_A	0.546	0.09
76_H	164_S	0.545	0.09
84_S	114_V	0.545	0.09
186_A	200_K	0.545	0.09
67_H	130_R	0.544	0.09
41_K	242_G	0.544	0.09
79_K	89_T	0.540	0.09
115_A	219_Y	0.536	0.09
181_E	233_L	0.536	0.09
42_E	138_M	0.533	0.09
226_L	231_R	0.531	0.09
13_L	28_K	0.531	0.09
85_N	119_Y	0.530	0.09
41_K	250_Q	0.529	0.09
70_V	160_E	0.526	0.09
144_Q	229_N	0.526	0.09
137_E	193_I	0.524	0.09
136_A	154_A	0.522	0.09
129_N	247_I	0.521	0.09
109_E	195_K	0.520	0.09
66_D	114_V	0.519	0.09
79_K	190_R	0.518	0.09
37_A	259_L	0.516	0.09
93_V	229_N	0.516	0.09
151_G	187_G	0.515	0.09
23_P	158_N	0.515	0.09
32_V	96_R	0.513	0.09
98_T	234_V	0.513	0.09
109_E	253_V	0.508	0.08
45_Y	50_Q	0.507	0.08
100_F	164_S	0.507	0.08
154_A	171_M	0.507	0.08
98_T	206_A	0.504	0.08
120_K	197_A	0.503	0.08
94_G	231_R	0.502	0.08
145_Q	224_L	0.502	0.08
170_A	180_F	0.501	0.08
91_L	196_V	0.500	0.08

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
4n91A	2	0.7273	27.6	0.976	Contact Map
4ng7A	1	0.7008	14.7	0.979	Contact Map
4n6dA	1	0.7311	12.2	0.98	Contact Map
4nf0A	2	0.7273	11.7	0.98	Contact Map
4nhbA	2	0.7311	9.8	0.981	Contact Map
4p47A	1	0.7576	9.4	0.981	Contact Map
4mx6A	1	0.7462	8.7	0.981	Contact Map
4o8mA	4	0.7273	7.1	0.982	Contact Map
4n6kA	1	0.7311	6.9	0.982	Contact Map
4xfeA	1	0.7273	6.7	0.982	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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