YNDL - BACSU - GREMLIN Contacts

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YNDL - UPF0714 protein YndL

UniProt:	O31815	Sequences: MKPAKVSLLRRLLHSLKHVDCNIAKRFPSTIKIVKLLMIFMVFTPISSIYAEDVYQNFEELKNNEDPSDYGVVTKETGSPVLVLAIHGGGIEGGTSEVARELSKEYSMYLFEGLKSAGNSVLHITSTHFDEPRALKMTGNHEYVISLHGYAEEDQQIEVGGTDRVRAADLVEKLQHAGFPAVLLNMDHPHAGVSPNNIANKSKTGLSIQIEMSTGFRKSLFGIFSLKSRAVTQNERFYEFTEVMFRFLKNSY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	252 (198)
Sequences:	167 (139)
Seq/√Len:	9.8

BACSU - YNDL YOQZ YMAC YJQB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_I	240_F	5.610	1.00
65_E	115_K	4.047	0.99
115_K	121_V	3.827	0.98
216_F	240_F	3.761	0.98
157_I	216_F	3.346	0.96
152_E	213_S	3.043	0.93
86_I	158_E	2.929	0.91
212_M	248_L	2.406	0.81
109_Y	129_F	2.398	0.80
229_R	234_N	2.364	0.79
115_K	124_I	2.275	0.77
85_A	95_T	2.248	0.76
113_G	119_N	2.248	0.76
109_Y	131_E	2.247	0.76
150_Y	213_S	2.221	0.75
231_V	234_N	2.198	0.74
84_L	138_T	2.155	0.72
58_F	124_I	2.076	0.69
163_D	204_T	1.993	0.66
128_H	195_P	1.954	0.65
82_L	144_V	1.952	0.64
174_L	179_F	1.951	0.64
86_I	99_A	1.928	0.63
144_V	202_S	1.919	0.63
59_E	124_I	1.895	0.62
86_I	187_D	1.883	0.62
85_A	99_A	1.880	0.61
60_E	64_N	1.848	0.60
162_T	207_S	1.829	0.59
186_M	244_M	1.828	0.59
109_Y	132_P	1.805	0.58
207_S	247_F	1.708	0.54
149_G	217_R	1.701	0.53
145_I	166_R	1.687	0.53
225_S	229_R	1.639	0.51
96_S	192_G	1.631	0.50
96_S	112_E	1.612	0.49
224_F	234_N	1.526	0.46
84_L	134_A	1.513	0.45
103_S	108_M	1.509	0.45
107_S	131_E	1.501	0.44
58_F	129_F	1.489	0.44
72_V	131_E	1.474	0.43
109_Y	174_L	1.461	0.43
90_G	117_A	1.420	0.41
74_T	210_I	1.396	0.40
101_E	241_T	1.393	0.40
94_G	97_E	1.375	0.39
199_A	207_S	1.369	0.39
134_A	198_I	1.369	0.39
71_G	126_S	1.367	0.38
86_I	146_S	1.359	0.38
70_Y	181_A	1.355	0.38
225_S	228_S	1.349	0.38
83_V	196_N	1.328	0.37
116_S	215_G	1.320	0.36
168_A	210_I	1.319	0.36
101_E	201_K	1.299	0.36
227_K	234_N	1.287	0.35
158_E	190_H	1.233	0.33
107_S	141_H	1.229	0.33
82_L	199_A	1.219	0.32
171_V	181_A	1.216	0.32
127_T	194_S	1.207	0.32
55_Y	179_F	1.204	0.32
108_M	124_I	1.204	0.32
60_E	86_I	1.189	0.31
181_A	212_M	1.188	0.31
65_E	70_Y	1.156	0.30
55_Y	94_G	1.153	0.30
94_G	157_I	1.150	0.30
70_Y	110_L	1.143	0.29
158_E	187_D	1.141	0.29
95_T	99_A	1.136	0.29
57_N	124_I	1.103	0.28
155_Q	236_R	1.101	0.28
90_G	118_G	1.099	0.28
67_P	96_S	1.090	0.27
150_Y	216_F	1.084	0.27
228_S	232_T	1.082	0.27
170_L	208_I	1.077	0.27
174_L	220_L	1.073	0.27
104_K	245_F	1.071	0.27
146_S	163_D	1.063	0.26
102_L	244_M	1.060	0.26
124_I	131_E	1.054	0.26
117_A	129_F	1.045	0.26
215_G	219_S	1.044	0.26
139_G	151_A	1.039	0.26
226_L	229_R	1.028	0.25
129_F	132_P	1.028	0.25
170_L	174_L	1.015	0.25
141_H	234_N	1.009	0.25
129_F	237_F	1.008	0.25
179_F	220_L	1.008	0.25
159_V	181_A	1.004	0.24
134_A	138_T	1.004	0.24
147_L	240_F	1.004	0.24
90_G	195_P	0.968	0.23
124_I	129_F	0.965	0.23
216_F	219_S	0.963	0.23
107_S	110_L	0.962	0.23
144_V	170_L	0.960	0.23
224_F	227_K	0.957	0.23
171_V	190_H	0.953	0.23
112_E	145_I	0.936	0.22
82_L	137_M	0.928	0.22
130_D	178_G	0.928	0.22
244_M	250_N	0.927	0.22
128_H	180_P	0.919	0.22
111_F	197_N	0.908	0.21
176_H	246_R	0.907	0.21
76_E	159_V	0.902	0.21
159_V	235_E	0.897	0.21
166_R	207_S	0.894	0.21
96_S	212_M	0.894	0.21
123_H	211_E	0.884	0.21
123_H	148_H	0.884	0.21
148_H	211_E	0.884	0.21
230_A	234_N	0.878	0.20
58_F	109_Y	0.874	0.20
212_M	227_K	0.872	0.20
88_G	94_G	0.868	0.20
128_H	182_V	0.867	0.20
167_A	247_F	0.863	0.20
114_L	188_H	0.860	0.20
62_K	115_K	0.858	0.20
135_L	213_S	0.857	0.20
95_T	137_M	0.854	0.20
71_G	113_G	0.847	0.20
85_A	103_S	0.847	0.20
98_V	147_L	0.844	0.19
170_L	240_F	0.844	0.19
156_Q	213_S	0.841	0.19
84_L	144_V	0.839	0.19
62_K	131_E	0.837	0.19
223_I	227_K	0.836	0.19
238_Y	241_T	0.828	0.19
113_G	141_H	0.826	0.19
124_I	145_I	0.824	0.19
88_G	192_G	0.822	0.19
124_I	179_F	0.822	0.19
185_N	223_I	0.815	0.19
147_L	170_L	0.815	0.19
156_Q	180_P	0.810	0.18
136_K	163_D	0.810	0.18
237_F	245_F	0.798	0.18
189_P	201_K	0.795	0.18
95_T	102_L	0.794	0.18
86_I	198_I	0.792	0.18
116_S	249_K	0.791	0.18
210_I	246_R	0.790	0.18
73_V	112_E	0.787	0.18
83_V	96_S	0.786	0.18
58_F	131_E	0.784	0.18
157_I	170_L	0.784	0.18
117_A	195_P	0.777	0.18
145_I	242_E	0.776	0.18
57_N	239_E	0.775	0.18
145_I	232_T	0.775	0.18
115_K	213_S	0.771	0.17
98_V	239_E	0.766	0.17
113_G	208_I	0.763	0.17
93_G	141_H	0.763	0.17
196_N	223_I	0.755	0.17
93_G	198_I	0.755	0.17
82_L	141_H	0.754	0.17
199_A	247_F	0.753	0.17
58_F	62_K	0.752	0.17
234_N	237_F	0.751	0.17
81_V	205_G	0.751	0.17
58_F	237_F	0.749	0.17
78_G	169_D	0.747	0.17
208_I	243_V	0.744	0.17
102_L	147_L	0.739	0.17
112_E	186_M	0.728	0.16
90_G	226_L	0.725	0.16
99_A	110_L	0.719	0.16
157_I	210_I	0.717	0.16
139_G	153_E	0.713	0.16
71_G	112_E	0.708	0.16
125_T	211_E	0.706	0.16
125_T	148_H	0.706	0.16
143_Y	206_L	0.705	0.16
74_T	145_I	0.705	0.16
70_Y	190_H	0.701	0.16
65_E	69_D	0.698	0.16
96_S	201_K	0.695	0.16
137_M	202_S	0.692	0.15
166_R	208_I	0.690	0.15
163_D	226_L	0.689	0.15
56_Q	60_E	0.689	0.15
230_A	233_Q	0.687	0.15
83_V	240_F	0.680	0.15
179_F	239_E	0.679	0.15
158_E	181_A	0.678	0.15
70_Y	208_I	0.672	0.15
119_N	220_L	0.670	0.15
85_A	102_L	0.668	0.15
243_V	247_F	0.667	0.15
121_V	124_I	0.667	0.15
100_R	104_K	0.667	0.15
54_V	121_V	0.660	0.15
98_V	220_L	0.660	0.15
59_E	229_R	0.652	0.15
59_E	131_E	0.650	0.15
219_S	225_S	0.649	0.14
129_F	242_E	0.647	0.14
68_S	220_L	0.646	0.14
55_Y	115_K	0.643	0.14
190_H	243_V	0.643	0.14
126_S	139_G	0.642	0.14
187_D	213_S	0.640	0.14
108_M	207_S	0.635	0.14
124_I	247_F	0.631	0.14
155_Q	213_S	0.629	0.14
192_G	209_Q	0.623	0.14
151_A	172_E	0.619	0.14
135_L	201_K	0.618	0.14
229_R	232_T	0.618	0.14
138_T	220_L	0.616	0.14
84_L	234_N	0.616	0.14
236_R	242_E	0.616	0.14
98_V	205_G	0.616	0.14
164_R	167_A	0.613	0.14
60_E	151_A	0.608	0.14
112_E	244_M	0.608	0.14
220_L	236_R	0.606	0.14
54_V	60_E	0.603	0.13
120_S	163_D	0.598	0.13
156_Q	216_F	0.590	0.13
52_E	205_G	0.588	0.13
220_L	228_S	0.588	0.13
137_M	214_T	0.588	0.13
99_A	240_F	0.587	0.13
109_Y	124_I	0.587	0.13
94_G	240_F	0.586	0.13
55_Y	112_E	0.586	0.13
75_K	174_L	0.585	0.13
95_T	111_F	0.582	0.13
58_F	208_I	0.581	0.13
177_A	246_R	0.580	0.13
63_N	144_V	0.580	0.13
103_S	228_S	0.579	0.13
75_K	241_T	0.576	0.13
235_E	239_E	0.575	0.13
53_D	61_L	0.575	0.13
181_A	187_D	0.573	0.13
167_A	171_V	0.570	0.13
93_G	162_T	0.568	0.13
162_T	247_F	0.565	0.13
114_L	248_L	0.565	0.13
117_A	121_V	0.565	0.13
60_E	242_E	0.564	0.13
186_M	218_K	0.563	0.13
166_R	181_A	0.555	0.12
57_N	242_E	0.554	0.12
99_A	131_E	0.552	0.12
83_V	219_S	0.550	0.12
162_T	230_A	0.549	0.12
202_S	245_F	0.549	0.12
127_T	244_M	0.543	0.12
74_T	191_A	0.542	0.12
80_P	176_H	0.542	0.12
97_E	125_T	0.541	0.12
53_D	82_L	0.540	0.12
57_N	98_V	0.537	0.12
158_E	237_F	0.535	0.12
103_S	201_K	0.531	0.12
189_P	218_K	0.531	0.12
102_L	146_S	0.530	0.12
116_S	178_G	0.529	0.12
136_K	246_R	0.528	0.12
100_R	247_F	0.523	0.12
97_E	229_R	0.521	0.12
138_T	192_G	0.520	0.12
219_S	248_L	0.517	0.12
159_V	199_A	0.516	0.12
174_L	208_I	0.515	0.12
62_K	109_Y	0.515	0.12
80_P	118_G	0.513	0.12
152_E	187_D	0.512	0.12
219_S	238_Y	0.509	0.12
54_V	236_R	0.508	0.12
101_E	237_F	0.507	0.12
65_E	107_S	0.506	0.12
127_T	178_G	0.506	0.12
90_G	202_S	0.504	0.12
59_E	192_G	0.503	0.11
108_M	197_N	0.502	0.11
138_T	144_V	0.502	0.11
100_R	202_S	0.501	0.11
119_N	221_F	0.501	0.11
162_T	180_P	0.501	0.11
75_K	201_K	0.501	0.11
152_E	215_G	0.500	0.11
56_Q	151_A	0.500	0.11

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
3a9lA	2	0.7857	100	0.294	Contact Map
2odfA	2	0.7222	93.5	0.943	Contact Map
2q7sA	1	0.6825	78.2	0.956	Contact Map
3czxA	2	0.623	64.7	0.96	Contact Map
3qayA	1	0.6071	55.8	0.962	Contact Map
1xovA	1	0.6111	33	0.967	Contact Map
4lq6A	1	0.631	29.5	0.968	Contact Map
1jwqA	1	0.5992	26.3	0.968	Contact Map
4rn7A	1	0.6071	23.6	0.969	Contact Map
1riiA	4	0.4563	20.4	0.97	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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