YaaC - PFAM28P - GREMLIN Contacts

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YaaC - YaaC-like Protein

PFAM:	PF14175	Sequences: QVLTFDSWEYVQLWLKRCYKKLAIEDAEKKSYENCYRFLYYLEQAREFYEAAENAPLSSKPLLLYYGFLNLAKALLLTKDPDYPESTSVLAHGVSTRKRKKQGYSFLEDEVKIQKNGLFPELSEYLFHVKPLEGEKYSLKDLLSNIPEIHRAYLTYTGKKELFIPLEIIRFRDKGTKELWFPAEILDDYHMTPERFLEYLEKDVIRSKKRFKWTEENIETSEEDLLLNLLKELHPLLRKPLLYINGYGRLYLPLRPDKLLRLPELLIHYLLMYNLSMIARYEPEWWGELLKHLDSKDYWLISEFLSISPRQFPYLIASE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	319 (303)
Sequences:	791 (732)
Seq/√Len:	42.0
META:	0.645

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_L	267_I	7.446	1.00
52_A	64_L	4.053	1.00
44_Q	61_P	3.678	1.00
46_R	50_E	3.620	1.00
44_Q	62_L	3.428	1.00
106_F	109_D	3.392	1.00
142_L	271_L	3.057	1.00
273_Y	277_M	2.886	1.00
72_A	122_L	2.784	1.00
62_L	279_A	2.655	1.00
272_M	312_F	2.623	1.00
94_V	270_L	2.566	1.00
304_F	308_S	2.509	1.00
4_T	10_Y	2.508	1.00
45_A	71_L	2.506	1.00
49_Y	68_F	2.426	1.00
65_Y	69_L	2.399	1.00
140_K	159_K	2.226	1.00
65_Y	303_E	2.164	1.00
13_L	17_R	2.118	0.99
272_M	304_F	2.083	0.99
53_E	310_R	2.015	0.99
264_E	311_Q	1.996	0.99
4_T	11_V	1.991	0.99
49_Y	304_F	1.978	0.99
48_F	299_W	1.972	0.99
121_E	124_E	1.942	0.99
192_T	196_F	1.937	0.99
43_E	47_E	1.929	0.99
153_Y	300_L	1.920	0.99
191_M	195_R	1.862	0.98
124_E	130_K	1.851	0.98
285_W	289_L	1.829	0.98
6_D	46_R	1.825	0.98
65_Y	70_N	1.781	0.98
67_G	286_W	1.780	0.98
67_G	313_P	1.769	0.98
65_Y	283_P	1.744	0.98
50_E	54_N	1.743	0.98
8_W	36_Y	1.742	0.98
13_L	16_K	1.733	0.98
55_A	59_S	1.722	0.97
11_V	17_R	1.716	0.97
303_E	311_Q	1.692	0.97
143_L	304_F	1.680	0.97
311_Q	314_Y	1.658	0.97
100_K	109_D	1.651	0.97
7_S	317_A	1.645	0.97
65_Y	276_S	1.630	0.96
310_R	314_Y	1.612	0.96
126_L	265_L	1.593	0.96
151_R	163_F	1.591	0.96
9_E	21_K	1.591	0.96
69_L	118_L	1.576	0.96
4_T	8_W	1.574	0.96
142_L	264_E	1.572	0.96
173_D	176_T	1.569	0.96
94_V	119_F	1.559	0.95
150_H	311_Q	1.549	0.95
128_H	131_P	1.548	0.95
60_K	309_P	1.547	0.95
56_P	59_S	1.543	0.95
65_Y	268_H	1.531	0.95
47_E	59_S	1.524	0.95
45_A	49_Y	1.520	0.95
49_Y	269_Y	1.515	0.95
65_Y	285_W	1.510	0.95
50_E	53_E	1.504	0.94
105_S	109_D	1.498	0.94
68_F	272_M	1.493	0.94
71_L	273_Y	1.478	0.94
4_T	13_L	1.474	0.94
152_A	303_E	1.449	0.93
43_E	56_P	1.434	0.93
8_W	11_V	1.427	0.93
68_F	309_P	1.403	0.92
143_L	267_I	1.398	0.92
8_W	14_W	1.378	0.91
250_L	254_L	1.377	0.91
73_K	117_G	1.375	0.91
55_A	63_L	1.366	0.91
70_N	293_L	1.361	0.91
150_H	163_F	1.356	0.91
195_R	199_Y	1.355	0.91
145_N	298_Y	1.353	0.91
13_L	23_A	1.352	0.90
122_L	312_F	1.348	0.90
193_P	196_F	1.347	0.90
263_P	266_L	1.347	0.90
4_T	9_E	1.347	0.90
226_L	238_R	1.341	0.90
251_Y	254_L	1.327	0.90
119_F	266_L	1.321	0.89
303_E	314_Y	1.321	0.89
139_L	271_L	1.320	0.89
10_Y	13_L	1.317	0.89
75_L	316_I	1.314	0.89
275_L	301_I	1.306	0.89
71_L	276_S	1.298	0.89
148_E	268_H	1.286	0.88
63_L	67_G	1.286	0.88
276_S	308_S	1.272	0.88
117_G	196_F	1.247	0.87
52_A	63_L	1.239	0.86
106_F	110_E	1.234	0.86
68_F	307_I	1.228	0.86
151_R	161_E	1.224	0.85
148_E	311_Q	1.222	0.85
193_P	197_L	1.218	0.85
310_R	317_A	1.217	0.85
9_E	16_K	1.214	0.85
95_S	112_K	1.206	0.85
66_Y	93_G	1.201	0.84
93_G	280_R	1.197	0.84
51_A	56_P	1.189	0.84
45_A	304_F	1.186	0.84
44_Q	139_L	1.168	0.83
5_F	8_W	1.165	0.82
77_L	273_Y	1.160	0.82
127_F	130_K	1.132	0.81
77_L	282_E	1.126	0.80
277_M	286_W	1.124	0.80
90_L	139_L	1.121	0.80
225_L	228_N	1.117	0.80
10_Y	18_C	1.114	0.80
66_Y	92_H	1.109	0.79
92_H	280_R	1.108	0.79
93_G	281_Y	1.101	0.79
279_A	287_G	1.100	0.79
12_Q	19_Y	1.098	0.79
242_L	278_I	1.093	0.78
141_D	306_S	1.093	0.78
165_P	269_Y	1.090	0.78
48_F	59_S	1.079	0.77
192_T	197_L	1.077	0.77
59_S	299_W	1.067	0.77
251_Y	260_L	1.065	0.76
44_Q	75_L	1.062	0.76
150_H	303_E	1.059	0.76
44_Q	51_A	1.056	0.76
191_M	200_L	1.054	0.76
84_P	282_E	1.035	0.74
274_N	277_M	1.022	0.73
70_N	286_W	1.017	0.73
92_H	281_Y	1.008	0.72
80_D	121_E	1.007	0.72
195_R	198_E	1.007	0.72
55_A	276_S	1.007	0.72
107_L	117_G	0.996	0.71
10_Y	16_K	0.991	0.71
200_L	203_D	0.987	0.71
139_L	274_N	0.983	0.70
66_Y	280_R	0.979	0.70
295_S	302_S	0.974	0.70
74_A	269_Y	0.973	0.70
11_V	16_K	0.972	0.70
194_E	199_Y	0.971	0.69
11_V	14_W	0.970	0.69
12_Q	17_R	0.967	0.69
230_L	234_H	0.960	0.69
61_P	75_L	0.959	0.68
146_I	261_R	0.958	0.68
150_H	251_Y	0.949	0.68
73_K	311_Q	0.946	0.67
272_M	299_W	0.945	0.67
242_L	245_N	0.939	0.67
290_L	294_D	0.937	0.67
253_P	279_A	0.936	0.67
309_P	313_P	0.936	0.67
75_L	94_V	0.932	0.66
45_A	128_H	0.929	0.66
64_L	146_I	0.926	0.66
45_A	192_T	0.924	0.66
44_Q	278_I	0.924	0.66
15_L	19_Y	0.922	0.65
303_E	312_F	0.917	0.65
61_P	275_L	0.913	0.65
65_Y	277_M	0.913	0.65
280_R	283_P	0.909	0.64
43_E	58_S	0.909	0.64
145_N	314_Y	0.908	0.64
196_F	200_L	0.905	0.64
67_G	70_N	0.905	0.64
55_A	244_I	0.903	0.64
64_L	139_L	0.899	0.63
47_E	56_P	0.898	0.63
193_P	200_L	0.894	0.63
214_T	217_N	0.893	0.63
211_F	216_E	0.893	0.63
17_R	22_L	0.892	0.63
57_L	278_I	0.887	0.62
181_F	247_Y	0.885	0.62
11_V	62_L	0.883	0.62
153_Y	159_K	0.881	0.62
59_S	62_L	0.881	0.62
64_L	68_F	0.881	0.62
274_N	282_E	0.879	0.62
66_Y	281_Y	0.879	0.62
104_Y	114_Q	0.878	0.62
272_M	305_L	0.877	0.61
91_A	114_Q	0.874	0.61
196_F	232_E	0.873	0.61
9_E	14_W	0.872	0.61
70_N	283_P	0.868	0.61
8_W	12_Q	0.867	0.61
191_M	196_F	0.858	0.60
23_A	38_F	0.855	0.59
11_V	39_L	0.855	0.59
166_L	183_A	0.851	0.59
60_K	306_S	0.841	0.58
7_S	11_V	0.838	0.58
262_L	301_I	0.832	0.57
6_D	39_L	0.825	0.57
12_Q	39_L	0.825	0.57
182_P	282_E	0.820	0.56
6_D	19_Y	0.820	0.56
13_L	21_K	0.819	0.56
14_W	18_C	0.819	0.56
236_L	262_L	0.817	0.56
94_V	113_I	0.814	0.56
73_K	274_N	0.812	0.56
44_Q	49_Y	0.805	0.55
14_W	23_A	0.805	0.55
206_R	213_W	0.804	0.55
296_K	309_P	0.804	0.55
67_G	235_P	0.803	0.55
9_E	12_Q	0.802	0.55
111_V	168_I	0.801	0.55
145_N	150_H	0.801	0.55
14_W	22_L	0.799	0.54
94_V	289_L	0.798	0.54
250_L	253_P	0.795	0.54
164_I	205_I	0.794	0.54
4_T	7_S	0.794	0.54
67_G	109_D	0.787	0.53
14_W	17_R	0.787	0.53
303_E	309_P	0.785	0.53
143_L	307_I	0.784	0.53
303_E	307_I	0.782	0.53
65_Y	311_Q	0.781	0.53
99_R	195_R	0.777	0.52
150_H	161_E	0.773	0.52
194_E	202_K	0.771	0.52
286_W	313_P	0.770	0.52
194_E	198_E	0.770	0.52
73_K	269_Y	0.770	0.52
73_K	309_P	0.769	0.52
70_N	303_E	0.769	0.52
72_A	118_L	0.766	0.51
226_L	229_L	0.764	0.51
109_D	118_L	0.762	0.51
13_L	20_K	0.761	0.51
101_K	109_D	0.755	0.50
72_A	84_P	0.753	0.50
137_Y	152_A	0.750	0.50
115_K	134_G	0.748	0.50
11_V	15_L	0.747	0.49
107_L	110_E	0.747	0.49
20_K	23_A	0.744	0.49
69_L	73_K	0.743	0.49
68_F	304_F	0.741	0.49
14_W	95_S	0.741	0.49
69_L	277_M	0.740	0.49
75_L	79_K	0.735	0.48
166_L	218_I	0.733	0.48
152_A	299_W	0.733	0.48
10_Y	15_L	0.730	0.48
170_R	227_L	0.730	0.48
49_Y	67_G	0.728	0.48
274_N	283_P	0.723	0.47
69_L	286_W	0.722	0.47
44_Q	274_N	0.718	0.47
166_L	246_G	0.717	0.47
112_K	135_E	0.716	0.47
80_D	115_K	0.714	0.46
48_F	303_E	0.711	0.46
299_W	314_Y	0.711	0.46
114_Q	117_G	0.710	0.46
297_D	300_L	0.706	0.46
117_G	301_I	0.703	0.45
58_S	64_L	0.701	0.45
291_K	313_P	0.699	0.45
70_N	312_F	0.699	0.45
41_Y	305_L	0.695	0.45
181_F	205_I	0.695	0.45
151_R	303_E	0.693	0.44
6_D	11_V	0.690	0.44
77_L	84_P	0.685	0.44
111_V	196_F	0.685	0.44
76_L	308_S	0.684	0.44
69_L	152_A	0.684	0.44
264_E	268_H	0.684	0.44
178_E	198_E	0.683	0.43
95_S	114_Q	0.682	0.43
4_T	16_K	0.681	0.43
154_L	300_L	0.676	0.43
198_E	202_K	0.675	0.43
48_F	63_L	0.673	0.43
65_Y	273_Y	0.672	0.42
114_Q	120_P	0.672	0.42
60_K	87_T	0.671	0.42
84_P	100_K	0.671	0.42
37_R	41_Y	0.668	0.42
49_Y	56_P	0.667	0.42
233_L	240_P	0.665	0.42
144_S	252_L	0.662	0.42
300_L	304_F	0.660	0.41
47_E	58_S	0.659	0.41
64_L	309_P	0.659	0.41
5_F	19_Y	0.655	0.41
184_E	276_S	0.655	0.41
8_W	48_F	0.652	0.41
239_K	258_K	0.650	0.40
106_F	114_Q	0.648	0.40
274_N	286_W	0.647	0.40
68_F	73_K	0.644	0.40
227_L	230_L	0.643	0.40
289_L	299_W	0.638	0.39
138_S	141_D	0.638	0.39
104_Y	110_E	0.638	0.39
51_A	263_P	0.635	0.39
49_Y	185_I	0.632	0.39
45_A	186_L	0.631	0.39
279_A	291_K	0.630	0.39
62_L	312_F	0.629	0.39
106_F	301_I	0.629	0.39
83_Y	97_R	0.628	0.38
13_L	22_L	0.627	0.38
145_N	163_F	0.626	0.38
77_L	83_Y	0.621	0.38
65_Y	286_W	0.621	0.38
286_W	311_Q	0.620	0.38
185_I	188_D	0.620	0.38
61_P	90_L	0.616	0.37
44_Q	70_N	0.615	0.37
148_E	313_P	0.615	0.37
206_R	209_K	0.615	0.37
138_S	152_A	0.614	0.37
16_K	21_K	0.609	0.37
63_L	273_Y	0.607	0.37
83_Y	118_L	0.605	0.36
10_Y	22_L	0.602	0.36
254_L	266_L	0.602	0.36
314_Y	317_A	0.601	0.36
148_E	308_S	0.598	0.36
84_P	104_Y	0.598	0.36
8_W	70_N	0.597	0.36
49_Y	268_H	0.596	0.36
73_K	90_L	0.596	0.36
192_T	198_E	0.596	0.36
8_W	51_A	0.595	0.36
185_I	250_L	0.594	0.36
283_P	304_F	0.593	0.35
70_N	287_G	0.593	0.35
117_G	286_W	0.592	0.35
73_K	277_M	0.588	0.35
153_Y	156_Y	0.588	0.35
43_E	123_S	0.586	0.35
12_Q	253_P	0.585	0.35
56_P	243_Y	0.584	0.35
60_K	83_Y	0.583	0.35
282_E	305_L	0.582	0.34
89_V	272_M	0.582	0.34
156_Y	315_L	0.582	0.34
77_L	148_E	0.581	0.34
232_E	265_L	0.581	0.34
69_L	273_Y	0.577	0.34
269_Y	277_M	0.577	0.34
205_I	223_E	0.576	0.34
61_P	286_W	0.576	0.34
262_L	295_S	0.574	0.34
149_I	164_I	0.570	0.33
262_L	315_L	0.569	0.33
80_D	85_E	0.569	0.33
90_L	118_L	0.568	0.33
52_A	288_E	0.568	0.33
74_A	148_E	0.567	0.33
145_N	299_W	0.566	0.33
16_K	23_A	0.566	0.33
77_L	90_L	0.565	0.33
58_S	279_A	0.564	0.33
100_K	117_G	0.563	0.33
118_L	272_M	0.562	0.33
196_F	222_E	0.562	0.33
145_N	279_A	0.561	0.33
18_C	21_K	0.561	0.33
6_D	10_Y	0.559	0.33
167_E	231_K	0.557	0.32
14_W	298_Y	0.556	0.32
41_Y	85_E	0.555	0.32
67_G	277_M	0.554	0.32
178_E	212_K	0.554	0.32
213_W	236_L	0.553	0.32
303_E	313_P	0.553	0.32
272_M	308_S	0.553	0.32
62_L	119_F	0.551	0.32
48_F	131_P	0.550	0.32
211_F	300_L	0.550	0.32
54_N	257_D	0.549	0.32
108_E	210_R	0.549	0.32
192_T	195_R	0.548	0.32
70_N	292_H	0.547	0.32
21_K	231_K	0.544	0.31
16_K	22_L	0.543	0.31
226_L	276_S	0.542	0.31
244_I	300_L	0.541	0.31
146_I	307_I	0.540	0.31
165_P	300_L	0.537	0.31
18_C	124_E	0.537	0.31
252_L	276_S	0.536	0.31
38_F	81_P	0.535	0.31
21_K	217_N	0.534	0.31
38_F	41_Y	0.534	0.31
112_K	130_K	0.533	0.30
55_A	315_L	0.533	0.30
20_K	214_T	0.533	0.30
149_I	300_L	0.533	0.30
110_E	117_G	0.530	0.30
69_L	312_F	0.530	0.30
220_T	231_K	0.530	0.30
149_I	304_F	0.529	0.30
43_E	46_R	0.526	0.30
160_K	248_G	0.526	0.30
147_P	308_S	0.525	0.30
10_Y	14_W	0.524	0.30
11_V	246_G	0.524	0.30
112_K	136_K	0.524	0.30
64_L	152_A	0.523	0.30
139_L	301_I	0.523	0.30
63_L	290_L	0.519	0.29
164_I	184_E	0.519	0.29
16_K	20_K	0.519	0.29
12_Q	16_K	0.518	0.29
6_D	22_L	0.516	0.29
311_Q	315_L	0.516	0.29
238_R	243_Y	0.516	0.29
76_L	118_L	0.514	0.29
149_I	260_L	0.514	0.29
108_E	212_K	0.512	0.29
64_L	113_I	0.512	0.29
45_A	48_F	0.512	0.29
197_L	215_E	0.509	0.29
273_Y	276_S	0.507	0.28
98_K	112_K	0.506	0.28
104_Y	109_D	0.506	0.28
305_L	312_F	0.506	0.28
237_L	242_L	0.505	0.28
57_L	146_I	0.504	0.28
119_F	123_S	0.504	0.28
97_R	282_E	0.504	0.28
71_L	313_P	0.503	0.28
116_N	190_H	0.502	0.28
90_L	96_T	0.501	0.28
289_L	304_F	0.500	0.28

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
2hsbA	2	0.373	8.2	0.963	Contact Map
1ufbA	3	0.3636	5.4	0.966	Contact Map
1wolA	1	0.3699	4.6	0.967	Contact Map
4lrvA	5	0.1442	3.6	0.969	Contact Map
4nqfA	2	0.4389	3.5	0.969	Contact Map
2h7bA	1	0.163	3.2	0.969	Contact Map
1bajA	2	0.1129	3.1	0.97	Contact Map
3o10A	2	0.4075	2.7	0.97	Contact Map
1o3uA	2	0.3574	2.3	0.972	Contact Map
2ld7B	1	0.2351	1.9	0.973	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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