YODJ - BACSU - GREMLIN Contacts

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YODJ - Putative carboxypeptidase YodJ

UniProt:	O34866	Sequences: MKKSGKWFSLAAALSVTAIVGAGCSMSNGDAQKDTKTTAETKQTEQKTADSKKSNTQNSEFSLESQYFNDIKKVDGLETIQNPENILALVNKQYALPGNYEPSDLVIPDVEFSFEEKIQKRYIRKEAADALKTMFDAAKKEGYELAAVSGYRSYDRQKVIFDNEVSLKGERKAKEAVAYPGESEHQTGLAMDISSRSNGFELNEAFGSTADGKWVQDNAYKYGFIIRYPKNKEDITKYEYEPWHLRYVGKKAAKVIQDNDLTLEEYFEKVKKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	273 (234)
Sequences:	698 (638)
Seq/√Len:	41.7

BACSU - YODJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
218_N	221_K	9.851	1.00
226_I	245_L	5.400	1.00
161_F	174_K	4.555	1.00
220_Y	257_Q	3.736	1.00
252_A	256_I	3.673	1.00
154_Y	186_Q	3.541	1.00
225_I	256_I	3.242	1.00
164_E	177_V	3.192	1.00
158_K	162_D	3.170	1.00
133_T	250_K	3.050	1.00
170_E	174_K	3.017	1.00
255_V	259_N	2.931	1.00
137_A	222_Y	2.832	1.00
248_V	256_I	2.722	1.00
87_L	252_A	2.720	1.00
193_I	245_L	2.712	1.00
232_K	265_E	2.676	1.00
254_K	258_D	2.615	1.00
168_K	176_A	2.574	1.00
160_I	164_E	2.475	1.00
104_D	124_R	2.451	1.00
131_L	135_F	2.385	1.00
174_K	179_Y	2.319	1.00
147_A	191_M	2.231	1.00
206_F	209_T	2.225	1.00
89_L	94_Y	2.210	1.00
134_M	245_L	2.130	0.99
150_G	191_M	1.989	0.99
172_K	175_E	1.949	0.99
143_Y	211_D	1.942	0.99
123_I	127_A	1.910	0.99
215_V	245_L	1.880	0.99
164_E	176_A	1.870	0.98
148_V	194_S	1.829	0.98
161_F	170_E	1.810	0.98
165_V	173_A	1.764	0.98
220_Y	254_K	1.758	0.98
128_A	132_K	1.741	0.98
123_I	150_G	1.693	0.97
250_K	254_K	1.654	0.97
235_I	262_T	1.652	0.97
79_T	82_N	1.651	0.97
108_P	132_K	1.645	0.97
137_A	141_E	1.627	0.96
95_A	182_E	1.565	0.95
185_H	241_E	1.495	0.94
164_E	168_K	1.488	0.94
164_E	173_A	1.464	0.93
134_M	193_I	1.461	0.93
207_G	212_G	1.439	0.93
127_A	130_A	1.414	0.92
176_A	266_Y	1.399	0.92
212_G	216_Q	1.359	0.91
178_A	238_Y	1.358	0.91
200_F	205_A	1.330	0.90
107_I	122_Y	1.312	0.89
92_K	238_Y	1.296	0.88
107_I	121_R	1.285	0.88
235_I	265_E	1.285	0.88
192_D	244_H	1.274	0.87
121_R	150_G	1.271	0.87
176_A	239_E	1.270	0.87
134_M	226_I	1.254	0.87
229_P	262_T	1.243	0.86
161_F	165_V	1.242	0.86
241_E	244_H	1.231	0.86
185_H	192_D	1.213	0.85
256_I	261_L	1.199	0.84
149_S	185_H	1.198	0.84
152_R	157_Q	1.197	0.84
162_D	166_S	1.197	0.84
106_V	125_K	1.193	0.84
185_H	244_H	1.190	0.84
248_V	259_N	1.178	0.83
219_A	257_Q	1.177	0.83
195_S	211_D	1.164	0.82
87_L	256_I	1.163	0.82
123_I	128_A	1.161	0.82
152_R	183_S	1.116	0.79
175_E	239_E	1.085	0.77
160_I	168_K	1.074	0.77
119_Q	122_Y	1.072	0.77
175_E	233_E	1.061	0.76
252_A	255_V	1.047	0.75
252_A	267_F	1.046	0.75
208_S	212_G	1.040	0.74
179_Y	182_E	1.039	0.74
125_K	129_D	1.039	0.74
212_G	240_Y	1.032	0.74
38_T	46_Q	1.031	0.74
261_L	266_Y	1.017	0.73
227_R	264_E	1.015	0.73
228_Y	242_P	1.012	0.72
169_G	173_A	1.011	0.72
87_L	267_F	1.010	0.72
226_I	242_P	1.008	0.72
169_G	238_Y	1.004	0.72
104_D	125_K	1.003	0.72
83_P	97_P	0.996	0.71
248_V	263_L	0.996	0.71
261_L	269_K	0.994	0.71
214_W	218_N	0.993	0.71
145_L	206_F	0.971	0.69
130_A	133_T	0.970	0.69
252_A	261_L	0.956	0.68
147_A	150_G	0.956	0.68
85_N	124_R	0.952	0.68
177_V	238_Y	0.951	0.67
216_Q	245_L	0.951	0.67
161_F	179_Y	0.929	0.66
152_R	241_E	0.925	0.65
56_T	67_Y	0.912	0.64
32_Q	40_E	0.907	0.64
220_Y	228_Y	0.906	0.64
63_L	67_Y	0.905	0.64
43_Q	48_T	0.896	0.63
207_G	230_K	0.894	0.63
90_V	187_T	0.893	0.63
164_E	175_E	0.892	0.62
39_A	49_A	0.889	0.62
207_G	226_I	0.889	0.62
89_L	267_F	0.889	0.62
39_A	43_Q	0.887	0.62
152_R	185_H	0.884	0.62
149_S	152_R	0.883	0.62
192_D	241_E	0.875	0.61
132_K	136_D	0.875	0.61
66_Q	70_D	0.874	0.61
193_I	226_I	0.873	0.61
32_Q	35_T	0.854	0.59
198_N	205_A	0.849	0.59
80_I	88_A	0.849	0.59
183_S	241_E	0.846	0.58
80_I	267_F	0.836	0.57
157_Q	241_E	0.835	0.57
40_E	43_Q	0.825	0.56
198_N	203_N	0.821	0.56
124_R	127_A	0.821	0.56
144_E	196_R	0.819	0.56
40_E	47_K	0.814	0.55
256_I	267_F	0.808	0.55
173_A	180_P	0.799	0.54
154_Y	169_G	0.794	0.54
256_I	259_N	0.789	0.53
128_A	147_A	0.789	0.53
102_P	124_R	0.788	0.53
96_L	187_T	0.788	0.53
209_T	212_G	0.787	0.53
184_E	244_H	0.787	0.53
60_E	65_S	0.786	0.53
168_K	172_K	0.783	0.53
108_P	119_Q	0.777	0.52
90_V	183_S	0.777	0.52
254_K	257_Q	0.776	0.52
100_Y	154_Y	0.773	0.52
202_L	212_G	0.773	0.52
121_R	226_I	0.768	0.51
105_L	124_R	0.763	0.51
200_F	203_N	0.761	0.50
63_L	71_I	0.755	0.50
139_K	210_A	0.752	0.50
91_N	227_R	0.750	0.49
36_K	39_A	0.743	0.49
101_E	151_Y	0.741	0.49
162_D	213_K	0.737	0.48
35_T	38_T	0.729	0.47
94_Y	222_Y	0.729	0.47
227_R	236_T	0.729	0.47
135_F	145_L	0.728	0.47
107_I	117_K	0.727	0.47
157_Q	181_G	0.727	0.47
90_V	242_P	0.722	0.47
61_F	64_E	0.721	0.47
96_L	100_Y	0.721	0.47
91_N	184_E	0.716	0.46
31_A	34_D	0.715	0.46
165_V	189_L	0.713	0.46
85_N	126_E	0.711	0.46
149_S	241_E	0.709	0.46
87_L	251_K	0.708	0.46
184_E	189_L	0.707	0.45
178_A	186_Q	0.695	0.44
32_Q	36_K	0.692	0.44
126_E	169_G	0.691	0.44
173_A	179_Y	0.691	0.44
35_T	47_K	0.691	0.44
132_K	135_F	0.691	0.44
126_E	130_A	0.690	0.44
102_P	186_Q	0.686	0.43
56_T	66_Q	0.683	0.43
76_G	81_Q	0.683	0.43
102_P	105_L	0.682	0.43
257_Q	261_L	0.681	0.43
106_V	128_A	0.679	0.43
143_Y	242_P	0.677	0.43
147_A	156_R	0.677	0.43
256_I	263_L	0.676	0.43
53_K	58_N	0.674	0.42
126_E	129_D	0.672	0.42
177_V	228_Y	0.672	0.42
96_L	228_Y	0.669	0.42
81_Q	151_Y	0.669	0.42
172_K	208_S	0.667	0.42
93_Q	237_K	0.667	0.42
55_N	66_Q	0.663	0.41
131_L	191_M	0.663	0.41
31_A	36_K	0.661	0.41
86_I	124_R	0.661	0.41
85_N	127_A	0.658	0.41
146_A	200_F	0.658	0.41
45_E	62_S	0.656	0.41
42_K	45_E	0.655	0.41
146_A	194_S	0.653	0.40
136_D	140_K	0.652	0.40
180_P	241_E	0.651	0.40
138_A	145_L	0.650	0.40
163_N	266_Y	0.650	0.40
68_F	71_I	0.650	0.40
207_G	240_Y	0.649	0.40
134_M	161_F	0.648	0.40
108_P	147_A	0.648	0.40
56_T	60_E	0.645	0.40
88_A	162_D	0.644	0.40
226_I	240_Y	0.643	0.40
121_R	191_M	0.641	0.39
116_E	121_R	0.641	0.39
38_T	45_E	0.641	0.39
137_A	143_Y	0.639	0.39
54_S	62_S	0.638	0.39
229_P	232_K	0.638	0.39
33_K	213_K	0.637	0.39
202_L	266_Y	0.634	0.39
40_E	49_A	0.634	0.39
140_K	158_K	0.634	0.39
134_M	137_A	0.634	0.39
65_S	234_D	0.632	0.39
168_K	239_E	0.628	0.38
42_K	55_N	0.625	0.38
149_S	192_D	0.625	0.38
225_I	267_F	0.622	0.38
39_A	45_E	0.621	0.38
163_N	166_S	0.619	0.37
205_A	208_S	0.619	0.37
87_L	263_L	0.618	0.37
150_G	168_K	0.614	0.37
177_V	219_A	0.614	0.37
238_Y	262_T	0.614	0.37
35_T	41_T	0.614	0.37
54_S	58_N	0.612	0.37
127_A	191_M	0.611	0.37
86_I	105_L	0.610	0.37
38_T	48_T	0.610	0.37
85_N	169_G	0.610	0.37
69_N	99_N	0.609	0.37
220_Y	258_D	0.609	0.37
98_G	154_Y	0.608	0.36
108_P	121_R	0.604	0.36
35_T	45_E	0.603	0.36
107_I	118_I	0.599	0.36
36_K	42_K	0.598	0.36
34_D	40_E	0.596	0.35
107_I	226_I	0.596	0.35
39_A	52_K	0.595	0.35
35_T	40_E	0.591	0.35
255_V	260_D	0.590	0.35
35_T	39_A	0.587	0.35
37_T	46_Q	0.585	0.35
216_Q	231_N	0.585	0.35
185_H	190_A	0.583	0.34
149_S	177_V	0.583	0.34
83_P	86_I	0.582	0.34
169_G	186_Q	0.582	0.34
160_I	167_L	0.579	0.34
34_D	42_K	0.578	0.34
28_N	32_Q	0.578	0.34
185_H	243_W	0.577	0.34
103_S	129_D	0.577	0.34
40_E	46_Q	0.576	0.34
57_Q	65_S	0.576	0.34
178_A	241_E	0.573	0.34
88_A	100_Y	0.573	0.34
135_F	193_I	0.572	0.33
34_D	47_K	0.572	0.33
100_Y	105_L	0.572	0.33
152_R	243_W	0.569	0.33
263_L	268_E	0.568	0.33
33_K	39_A	0.567	0.33
105_L	128_A	0.566	0.33
62_S	166_S	0.564	0.33
224_F	228_Y	0.564	0.33
33_K	53_K	0.564	0.33
140_K	217_D	0.564	0.33
174_K	186_Q	0.563	0.33
118_I	173_A	0.560	0.32
29_G	38_T	0.556	0.32
250_K	253_A	0.555	0.32
134_M	214_W	0.553	0.32
37_T	48_T	0.553	0.32
221_K	254_K	0.553	0.32
192_D	243_W	0.552	0.32
92_K	186_Q	0.550	0.32
156_R	190_A	0.549	0.32
102_P	178_A	0.547	0.31
96_L	102_P	0.547	0.31
215_V	226_I	0.545	0.31
189_L	244_H	0.545	0.31
56_T	61_F	0.544	0.31
56_T	62_S	0.542	0.31
218_N	222_Y	0.541	0.31
51_S	59_S	0.539	0.31
225_I	261_L	0.539	0.31
143_Y	233_E	0.539	0.31
183_S	243_W	0.537	0.31
169_G	178_A	0.536	0.30
133_T	162_D	0.534	0.30
225_I	228_Y	0.532	0.30
30_D	41_T	0.531	0.30
31_A	40_E	0.530	0.30
61_F	69_N	0.530	0.30
89_L	252_A	0.528	0.30
59_S	65_S	0.527	0.30
54_S	59_S	0.527	0.30
157_Q	183_S	0.525	0.30
126_E	190_A	0.525	0.30
31_A	39_A	0.524	0.30
144_E	267_F	0.523	0.29
238_Y	241_E	0.522	0.29
215_V	256_I	0.521	0.29
30_D	34_D	0.520	0.29
30_D	33_K	0.519	0.29
55_N	65_S	0.519	0.29
84_E	256_I	0.517	0.29
66_Q	69_N	0.516	0.29
158_K	180_P	0.516	0.29
47_K	55_N	0.512	0.29
229_P	240_Y	0.511	0.29
29_G	32_Q	0.509	0.28
31_A	37_T	0.508	0.28
31_A	47_K	0.507	0.28
177_V	186_Q	0.507	0.28
37_T	42_K	0.506	0.28
64_E	71_I	0.506	0.28
135_F	206_F	0.506	0.28
205_A	239_E	0.506	0.28
108_P	135_F	0.505	0.28
138_A	195_S	0.505	0.28
147_A	198_N	0.505	0.28
130_A	206_F	0.503	0.28
101_E	104_D	0.502	0.28
118_I	156_R	0.501	0.28
45_E	48_T	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
4ox3A	1	0.7839	100	0.321	Contact Map
4mphA	2	0.674	100	0.341	Contact Map
4muqA	1	0.7179	100	0.364	Contact Map
4murA	2	0.6703	100	0.371	Contact Map
4nt9B	3	0.663	100	0.377	Contact Map
1r44A	1	0.6557	100	0.665	Contact Map
2vo9A	1	0.5165	99.8	0.761	Contact Map
2mxzA	1	0.4615	99.3	0.84	Contact Map
2ibgE	1	0.5165	96.7	0.92	Contact Map
3n1gB	1	0.5421	95.2	0.929	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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