YVPB - BACSU - GREMLIN Contacts

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YVPB - Uncharacterized protein YvpB

UniProt:	O34735	Sequences: MKTLRTLCVLMILSGVIFFGLKIDAKDIDIPFLNSLKKVVSDSDTDSAANSKKELKGSAKPLDVILYNQMDAPRLYNGCEVTSLAMVLNYAGYDVTKNTLANQVATVPLTYSSGLKGDPNDGFVGDMANGPGLGVYHRPIYQLAKTYAGDKVSDLTGKSISAVYQQLEKGNPVWVITTANFTPVDNMQTWKTPNGTIEITYSEHSVAVTGYDDKYVYLNDPYGYKNRKTDRTSFEKAWKQMGSQAVVIQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	250 (206)
Sequences:	350 (276)
Seq/√Len:	19.2

BACSU - YVPB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_V	207_A	3.694	1.00
75_L	101_A	3.282	1.00
60_K	167_L	3.171	0.99
137_H	154_D	3.166	0.99
75_L	97_K	3.063	0.99
67_Y	85_A	2.755	0.98
82_T	97_K	2.640	0.98
175_V	234_F	2.579	0.97
76_Y	127_M	2.576	0.97
239_K	243_S	2.562	0.97
135_V	139_P	2.521	0.97
81_V	100_L	2.465	0.97
177_T	206_V	2.412	0.96
220_D	227_R	2.383	0.96
84_L	144_A	2.381	0.96
134_G	203_E	2.291	0.95
178_T	184_V	2.270	0.95
86_M	219_N	2.267	0.95
120_N	138_R	2.260	0.95
192_T	195_G	2.255	0.94
85_A	100_L	2.253	0.94
164_Y	167_L	2.208	0.94
164_Y	231_R	2.189	0.94
99_T	103_Q	2.144	0.93
208_V	216_V	2.109	0.92
160_I	235_E	2.056	0.91
97_K	101_A	2.049	0.91
218_L	229_T	2.049	0.91
174_W	205_S	2.042	0.91
135_V	140_I	2.019	0.90
105_A	142_Q	2.018	0.90
209_T	226_N	1.930	0.88
72_A	222_Y	1.898	0.87
145_K	152_V	1.888	0.87
73_P	97_K	1.869	0.86
63_D	225_K	1.837	0.85
91_A	248_I	1.834	0.85
87_V	207_A	1.826	0.85
235_E	239_K	1.789	0.84
137_H	244_Q	1.780	0.84
160_I	164_Y	1.770	0.83
75_L	82_T	1.728	0.82
191_K	196_T	1.717	0.81
74_R	97_K	1.705	0.81
140_I	174_W	1.622	0.77
87_V	247_V	1.598	0.76
77_N	199_I	1.511	0.72
207_A	213_D	1.491	0.71
82_T	100_L	1.463	0.69
118_D	194_N	1.462	0.69
168_E	211_Y	1.459	0.69
81_V	85_A	1.429	0.68
164_Y	235_E	1.391	0.65
76_Y	128_A	1.391	0.65
181_F	229_T	1.368	0.64
74_R	98_N	1.365	0.64
100_L	143_L	1.359	0.64
77_N	201_Y	1.339	0.62
96_T	99_T	1.335	0.62
97_K	100_L	1.334	0.62
91_A	148_A	1.313	0.61
156_T	197_I	1.309	0.61
111_Y	116_K	1.308	0.61
73_P	101_A	1.295	0.60
74_R	222_Y	1.292	0.60
141_Y	152_V	1.280	0.59
117_G	122_G	1.268	0.58
216_V	234_F	1.261	0.58
140_I	246_V	1.244	0.57
218_L	231_R	1.242	0.56
126_D	130_G	1.235	0.56
212_D	217_Y	1.214	0.55
77_N	178_T	1.204	0.54
118_D	155_L	1.202	0.54
57_G	168_E	1.198	0.54
81_V	143_L	1.191	0.53
166_Q	171_N	1.190	0.53
75_L	81_V	1.182	0.53
132_G	237_A	1.173	0.52
77_N	184_V	1.168	0.52
177_T	181_F	1.124	0.49
107_V	116_K	1.111	0.48
120_N	136_Y	1.097	0.47
89_N	154_D	1.096	0.47
43_S	47_S	1.093	0.47
176_I	199_I	1.074	0.46
178_T	187_M	1.073	0.46
179_A	224_Y	1.068	0.45
116_K	176_I	1.068	0.45
163_V	208_V	1.064	0.45
199_I	203_E	1.056	0.45
187_M	237_A	1.048	0.44
74_R	96_T	1.035	0.43
184_V	240_Q	1.031	0.43
81_V	97_K	1.028	0.43
180_N	184_V	1.028	0.43
42_D	46_D	1.027	0.43
81_V	101_A	1.019	0.42
140_I	205_S	1.015	0.42
85_A	97_K	1.014	0.42
135_V	143_L	1.009	0.42
87_V	248_I	1.003	0.41
135_V	205_S	0.992	0.41
86_M	207_A	0.991	0.41
62_L	90_Y	0.976	0.40
212_D	215_Y	0.973	0.40
238_W	247_V	0.960	0.39
155_L	245_A	0.950	0.38
205_S	227_R	0.949	0.38
73_P	132_G	0.947	0.38
145_K	149_G	0.931	0.37
136_Y	203_E	0.930	0.37
92_G	220_D	0.919	0.36
144_A	176_I	0.918	0.36
233_S	237_A	0.916	0.36
76_Y	202_S	0.915	0.36
177_T	234_F	0.915	0.36
137_H	141_Y	0.904	0.35
119_P	197_I	0.896	0.35
161_S	164_Y	0.886	0.34
85_A	89_N	0.875	0.34
197_I	232_T	0.864	0.33
98_N	222_Y	0.863	0.33
84_L	97_K	0.861	0.33
162_A	165_Q	0.846	0.32
163_V	236_K	0.843	0.32
79_C	204_H	0.837	0.32
104_V	135_V	0.830	0.31
69_Q	80_E	0.830	0.31
77_N	127_M	0.827	0.31
178_T	241_M	0.825	0.31
194_N	243_S	0.820	0.31
145_K	150_D	0.818	0.31
105_A	197_I	0.817	0.31
160_I	216_V	0.814	0.30
215_Y	228_K	0.807	0.30
121_D	145_K	0.804	0.30
82_T	101_A	0.802	0.30
44_D	51_S	0.801	0.30
169_K	173_V	0.792	0.29
120_N	194_N	0.785	0.29
45_T	49_A	0.784	0.29
136_Y	242_G	0.781	0.29
91_A	171_N	0.780	0.29
156_T	248_I	0.779	0.29
137_H	203_E	0.777	0.28
89_N	209_T	0.777	0.28
41_S	230_D	0.769	0.28
58_S	211_Y	0.761	0.28
118_D	191_K	0.755	0.27
180_N	220_D	0.754	0.27
68_N	222_Y	0.751	0.27
58_S	162_A	0.751	0.27
73_P	85_A	0.747	0.27
134_G	244_Q	0.746	0.27
40_V	48_A	0.744	0.27
94_D	150_D	0.744	0.27
122_G	143_L	0.743	0.27
163_V	235_E	0.741	0.27
122_G	135_V	0.740	0.27
107_V	122_G	0.736	0.26
76_Y	115_L	0.723	0.26
117_G	200_T	0.718	0.25
63_D	232_T	0.716	0.25
152_V	227_R	0.716	0.25
65_I	190_W	0.712	0.25
170_G	214_K	0.712	0.25
209_T	219_N	0.712	0.25
80_E	204_H	0.711	0.25
91_A	207_A	0.710	0.25
75_L	98_N	0.709	0.25
136_Y	184_V	0.709	0.25
128_A	178_T	0.708	0.25
199_I	205_S	0.708	0.25
66_L	225_K	0.708	0.25
99_T	112_S	0.706	0.25
132_G	203_E	0.694	0.24
44_D	48_A	0.683	0.24
232_T	243_S	0.683	0.24
141_Y	155_L	0.682	0.24
40_V	43_S	0.682	0.24
113_S	165_Q	0.681	0.24
207_A	247_V	0.681	0.24
182_T	218_L	0.681	0.24
163_V	173_V	0.678	0.24
214_K	236_K	0.678	0.24
133_L	174_W	0.677	0.24
181_F	237_A	0.675	0.23
157_G	173_V	0.671	0.23
84_L	147_Y	0.668	0.23
94_D	239_K	0.666	0.23
203_E	244_Q	0.662	0.23
62_L	214_K	0.661	0.23
139_P	143_L	0.661	0.23
85_A	132_G	0.659	0.23
181_F	206_V	0.659	0.23
41_S	50_N	0.652	0.22
192_T	200_T	0.652	0.22
74_R	85_A	0.651	0.22
53_K	89_N	0.649	0.22
144_A	152_V	0.649	0.22
96_T	120_N	0.646	0.22
75_L	84_L	0.645	0.22
42_D	51_S	0.645	0.22
124_V	190_W	0.641	0.22
119_P	203_E	0.641	0.22
68_N	72_A	0.637	0.22
154_D	245_A	0.636	0.22
49_A	52_K	0.634	0.22
40_V	50_N	0.634	0.22
142_Q	236_K	0.631	0.22
77_N	176_I	0.628	0.21
107_V	117_G	0.627	0.21
86_M	209_T	0.626	0.21
117_G	139_P	0.623	0.21
73_P	156_T	0.622	0.21
166_Q	218_L	0.620	0.21
57_G	159_S	0.620	0.21
95_V	139_P	0.620	0.21
56_K	62_L	0.619	0.21
157_G	236_K	0.619	0.21
109_L	222_Y	0.614	0.21
107_V	126_D	0.612	0.21
176_I	205_S	0.609	0.21
142_Q	145_K	0.606	0.20
141_Y	154_D	0.605	0.20
192_T	197_I	0.604	0.20
183_P	236_K	0.604	0.20
89_N	120_N	0.603	0.20
161_S	213_D	0.602	0.20
116_K	127_M	0.598	0.20
152_V	246_V	0.598	0.20
77_N	134_G	0.597	0.20
127_M	176_I	0.597	0.20
81_V	84_L	0.596	0.20
93_Y	105_A	0.595	0.20
76_Y	203_E	0.594	0.20
167_L	198_E	0.592	0.20
76_Y	201_Y	0.590	0.20
141_Y	167_L	0.590	0.20
73_P	234_F	0.586	0.20
91_A	151_K	0.586	0.20
134_G	140_I	0.585	0.20
74_R	82_T	0.583	0.20
147_Y	157_G	0.580	0.19
122_G	139_P	0.580	0.19
117_G	206_V	0.579	0.19
131_P	205_S	0.577	0.19
104_V	140_I	0.577	0.19
136_Y	147_Y	0.575	0.19
89_N	102_N	0.575	0.19
202_S	218_L	0.575	0.19
60_K	231_R	0.575	0.19
83_S	224_Y	0.573	0.19
165_Q	224_Y	0.573	0.19
231_R	235_E	0.573	0.19
57_G	60_K	0.572	0.19
177_T	216_V	0.571	0.19
47_S	50_N	0.569	0.19
104_V	127_M	0.569	0.19
169_K	243_S	0.566	0.19
167_L	173_V	0.562	0.19
105_A	220_D	0.562	0.19
134_G	241_M	0.559	0.19
207_A	248_I	0.558	0.19
137_H	207_A	0.556	0.18
164_Y	211_Y	0.555	0.18
118_D	124_V	0.554	0.18
42_D	49_A	0.552	0.18
63_D	219_N	0.551	0.18
65_I	86_M	0.551	0.18
165_Q	230_D	0.549	0.18
46_D	196_T	0.549	0.18
121_D	194_N	0.548	0.18
55_L	214_K	0.546	0.18
91_A	112_S	0.545	0.18
133_L	209_T	0.544	0.18
228_K	235_E	0.544	0.18
134_G	201_Y	0.542	0.18
56_K	163_V	0.541	0.18
117_G	143_L	0.541	0.18
49_A	55_L	0.539	0.18
109_L	193_P	0.537	0.18
40_V	169_K	0.537	0.18
187_M	200_T	0.536	0.18
68_N	98_N	0.532	0.18
154_D	207_A	0.531	0.18
121_D	196_T	0.530	0.18
141_Y	145_K	0.529	0.17
41_S	51_S	0.526	0.17
49_A	214_K	0.526	0.17
232_T	239_K	0.526	0.17
134_G	199_I	0.521	0.17
165_Q	169_K	0.521	0.17
67_Y	188_Q	0.519	0.17
47_S	53_K	0.518	0.17
178_T	218_L	0.518	0.17
76_Y	179_A	0.514	0.17
122_G	229_T	0.509	0.17
119_P	135_V	0.507	0.17
136_Y	241_M	0.506	0.17
97_K	216_V	0.505	0.17
45_T	52_K	0.504	0.17
90_Y	172_P	0.504	0.17
82_T	85_A	0.503	0.17
116_K	208_V	0.503	0.17
118_D	196_T	0.502	0.16
63_D	167_L	0.500	0.16
127_M	224_Y	0.500	0.16

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
3ervA	1	0.768	100	0.496	Contact Map
3k8uA	1	0.536	99.6	0.799	Contact Map
3zuaA	1	0.52	98.9	0.858	Contact Map
3b79A	1	0.484	98.8	0.864	Contact Map
4ry2A	2	0.516	98.6	0.874	Contact Map
1x9yA	1	0.824	98.2	0.889	Contact Map
1cv8A	2	0.616	98.1	0.889	Contact Map
2bu3A	1	0.7	97.8	0.898	Contact Map
4d8bA	1	0.756	97.8	0.899	Contact Map
1pxvA	2	0.648	97.2	0.908	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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