YPJP - BACSU - GREMLIN Contacts

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YPJP - Uncharacterized protein YpjP

UniProt:	P54172	Sequences: MKLWMRKTLVVLFTIVTFGLVSPPAALMADKPSGQPSSLEQNDYTAFYDEHDLYDDESDDRRDPELLFQSYKEQLLDSAEDQSFLKFGSRIAPVIEDDYRKEILPKIENVISDYLATLQDDEAYQDVVISSMPSAGKTEKIFNVYNRTTGEDLLRFHVRRDHPPHDGYWFNFHYHTAEDGFQSHHELGSIYWDRNTPPNWMSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	203 (200)
Sequences:	124 (104)
Seq/√Len:	7.3

BACSU - YPJP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_K	155_R	3.866	0.96
106_K	109_N	3.767	0.95
94_V	107_I	3.491	0.92
24_P	27_L	3.486	0.92
97_D	102_E	3.260	0.89
136_G	160_R	2.662	0.77
99_Y	190_I	2.481	0.71
152_D	155_R	2.474	0.71
163_P	189_S	2.408	0.69
108_E	142_F	2.371	0.68
75_L	201_M	2.233	0.63
137_K	199_N	2.172	0.61
106_K	150_G	2.161	0.60
87_F	187_L	2.145	0.60
83_S	99_Y	2.145	0.60
126_D	147_R	2.116	0.58
39_L	185_H	2.079	0.57
146_N	149_T	2.002	0.54
16_V	194_R	1.920	0.51
136_G	170_F	1.837	0.48
130_S	143_N	1.809	0.46
17_T	23_P	1.760	0.45
14_T	27_L	1.759	0.45
18_F	83_S	1.695	0.42
71_Y	75_L	1.632	0.40
95_I	140_K	1.626	0.39
95_I	154_L	1.619	0.39
19_G	200_W	1.613	0.39
22_S	187_L	1.579	0.38
6_R	169_W	1.576	0.38
156_F	188_G	1.566	0.37
130_S	140_K	1.549	0.37
134_S	138_T	1.544	0.36
135_A	201_M	1.534	0.36
49_D	149_T	1.529	0.36
80_E	163_P	1.526	0.36
29_A	110_V	1.517	0.35
87_F	99_Y	1.512	0.35
8_T	154_L	1.512	0.35
7_K	10_V	1.502	0.35
143_N	163_P	1.497	0.35
24_P	110_V	1.484	0.34
60_D	180_G	1.481	0.34
4_W	7_K	1.459	0.33
21_V	187_L	1.441	0.33
13_F	76_L	1.441	0.33
94_V	182_Q	1.439	0.33
68_F	153_L	1.432	0.32
80_E	100_R	1.432	0.32
83_S	87_F	1.429	0.32
161_D	171_N	1.428	0.32
89_S	169_W	1.420	0.32
6_R	193_D	1.419	0.32
22_S	138_T	1.398	0.31
7_K	110_V	1.395	0.31
13_F	24_P	1.395	0.31
14_T	69_Q	1.392	0.31
143_N	152_D	1.389	0.31
21_V	87_F	1.388	0.31
12_L	15_I	1.362	0.30
36_P	67_L	1.337	0.29
32_P	135_A	1.336	0.29
21_V	163_P	1.317	0.29
160_R	170_F	1.287	0.28
193_D	196_T	1.285	0.28
140_K	171_N	1.273	0.27
93_P	138_T	1.264	0.27
91_I	170_F	1.257	0.27
89_S	130_S	1.246	0.26
6_R	160_R	1.241	0.26
143_N	155_R	1.231	0.26
42_N	101_K	1.211	0.25
76_L	114_Y	1.210	0.25
22_S	87_F	1.207	0.25
32_P	169_W	1.189	0.25
18_F	68_F	1.179	0.24
121_D	153_L	1.173	0.24
7_K	190_I	1.173	0.24
74_Q	162_H	1.167	0.24
11_V	180_G	1.162	0.24
155_R	188_G	1.154	0.24
78_S	110_V	1.151	0.24
87_F	143_N	1.134	0.23
137_K	163_P	1.123	0.23
107_I	142_F	1.119	0.23
90_R	108_E	1.111	0.22
13_F	25_A	1.105	0.22
110_V	190_I	1.095	0.22
161_D	170_F	1.078	0.22
178_E	182_Q	1.062	0.21
100_R	182_Q	1.059	0.21
108_E	196_T	1.056	0.21
50_E	144_V	1.053	0.21
83_S	142_F	1.044	0.21
166_D	169_W	1.041	0.21
15_I	189_S	1.037	0.21
83_S	161_D	1.028	0.20
130_S	155_R	1.026	0.20
19_G	23_P	1.014	0.20
5_M	34_G	1.013	0.20
20_L	113_D	1.012	0.20
79_A	105_P	1.002	0.20
9_L	125_Q	1.002	0.20
96_E	187_L	0.989	0.19
81_D	101_K	0.985	0.19
98_D	102_E	0.971	0.19
130_S	190_I	0.970	0.19
6_R	107_I	0.958	0.19
30_D	112_S	0.957	0.19
3_L	155_R	0.949	0.18
104_L	163_P	0.944	0.18
91_I	165_H	0.939	0.18
64_P	69_Q	0.932	0.18
23_P	200_W	0.924	0.18
62_R	65_E	0.919	0.18
101_K	147_R	0.912	0.18
87_F	154_L	0.909	0.17
94_V	181_F	0.908	0.17
115_L	119_Q	0.905	0.17
136_G	169_W	0.903	0.17
98_D	142_F	0.903	0.17
146_N	189_S	0.902	0.17
131_S	142_F	0.898	0.17
13_F	27_L	0.887	0.17
65_E	82_Q	0.884	0.17
188_G	195_N	0.884	0.17
3_L	165_H	0.883	0.17
14_T	92_A	0.882	0.17
121_D	177_A	0.876	0.17
7_K	12_L	0.876	0.17
130_S	150_G	0.873	0.17
99_Y	142_F	0.872	0.17
96_E	154_L	0.869	0.17
6_R	136_G	0.864	0.16
8_T	95_I	0.860	0.16
57_E	90_R	0.856	0.16
171_N	189_S	0.853	0.16
15_I	128_V	0.853	0.16
8_T	16_V	0.851	0.16
113_D	153_L	0.851	0.16
7_K	13_F	0.850	0.16
2_K	13_F	0.848	0.16
10_V	23_P	0.847	0.16
2_K	28_M	0.846	0.16
87_F	127_V	0.844	0.16
8_T	138_T	0.840	0.16
89_S	143_N	0.837	0.16
111_I	125_Q	0.830	0.16
107_I	133_P	0.830	0.16
135_A	165_H	0.828	0.16
13_F	28_M	0.827	0.16
87_F	95_I	0.821	0.16
100_R	130_S	0.817	0.15
66_L	153_L	0.811	0.15
24_P	111_I	0.809	0.15
130_S	134_S	0.804	0.15
114_Y	140_K	0.798	0.15
114_Y	176_T	0.795	0.15
124_Y	155_R	0.795	0.15
10_V	80_E	0.790	0.15
93_P	190_I	0.788	0.15
144_V	195_N	0.787	0.15
143_N	162_H	0.786	0.15
14_T	103_I	0.782	0.15
96_E	134_S	0.782	0.15
142_F	156_F	0.780	0.15
52_D	116_A	0.777	0.15
1_M	201_M	0.775	0.15
131_S	144_V	0.774	0.15
166_D	187_L	0.771	0.15
43_D	106_K	0.769	0.14
103_I	188_G	0.768	0.14
80_E	84_F	0.767	0.14
154_L	187_L	0.767	0.14
152_D	188_G	0.764	0.14
137_K	151_E	0.763	0.14
126_D	148_T	0.763	0.14
46_A	85_L	0.759	0.14
163_P	170_F	0.757	0.14
22_S	183_S	0.756	0.14
170_F	201_M	0.755	0.14
1_M	18_F	0.753	0.14
89_S	199_N	0.750	0.14
20_L	155_R	0.746	0.14
138_T	193_D	0.742	0.14
7_K	23_P	0.738	0.14
25_A	28_M	0.731	0.14
2_K	162_H	0.728	0.14
110_V	116_A	0.718	0.14
134_S	161_D	0.715	0.13
193_D	202_S	0.715	0.13
38_S	97_D	0.714	0.13
22_S	93_P	0.714	0.13
54_Y	72_K	0.713	0.13
91_I	117_T	0.711	0.13
24_P	29_A	0.710	0.13
7_K	166_D	0.710	0.13
30_D	40_E	0.710	0.13
37_S	73_E	0.710	0.13
138_T	202_S	0.709	0.13
80_E	182_Q	0.708	0.13
13_F	77_D	0.707	0.13
160_R	169_W	0.704	0.13
104_L	170_F	0.703	0.13
9_L	92_A	0.698	0.13
26_A	38_S	0.696	0.13
160_R	201_M	0.692	0.13
127_V	157_H	0.691	0.13
15_I	161_D	0.688	0.13
18_F	87_F	0.685	0.13
2_K	21_V	0.681	0.13
20_L	191_Y	0.680	0.13
114_Y	149_T	0.676	0.13
67_L	186_E	0.674	0.13
4_W	19_G	0.674	0.13
30_D	94_V	0.673	0.13
27_L	78_S	0.668	0.13
180_G	185_H	0.667	0.13
28_M	161_D	0.664	0.13
87_F	163_P	0.664	0.13
93_P	135_A	0.661	0.13
150_G	163_P	0.657	0.12
13_F	110_V	0.655	0.12
110_V	176_T	0.653	0.12
138_T	160_R	0.652	0.12
11_V	124_Y	0.650	0.12
107_I	156_F	0.650	0.12
146_N	151_E	0.642	0.12
109_N	134_S	0.640	0.12
21_V	80_E	0.639	0.12
104_L	160_R	0.638	0.12
111_I	154_L	0.634	0.12
110_V	138_T	0.633	0.12
62_R	149_T	0.629	0.12
54_Y	62_R	0.626	0.12
96_E	104_L	0.625	0.12
101_K	120_D	0.620	0.12
143_N	154_L	0.619	0.12
103_I	117_T	0.618	0.12
71_Y	119_Q	0.618	0.12
84_F	114_Y	0.606	0.12
160_R	193_D	0.601	0.12
65_E	69_Q	0.600	0.12
130_S	146_N	0.596	0.11
21_V	95_I	0.595	0.11
83_S	108_E	0.595	0.11
110_V	124_Y	0.591	0.11
129_I	140_K	0.591	0.11
9_L	34_G	0.589	0.11
87_F	190_I	0.588	0.11
74_Q	84_F	0.585	0.11
142_F	171_N	0.583	0.11
27_L	31_K	0.581	0.11
95_I	157_H	0.578	0.11
89_S	126_D	0.578	0.11
87_F	130_S	0.577	0.11
144_V	194_R	0.572	0.11
103_I	131_S	0.566	0.11
112_S	148_T	0.566	0.11
2_K	163_P	0.565	0.11
115_L	124_Y	0.564	0.11
130_S	189_S	0.563	0.11
98_D	108_E	0.562	0.11
46_A	92_A	0.561	0.11
57_E	67_L	0.559	0.11
68_F	151_E	0.558	0.11
93_P	154_L	0.556	0.11
113_D	163_P	0.555	0.11
39_L	146_N	0.554	0.11
98_D	131_S	0.554	0.11
33_S	177_A	0.550	0.11
21_V	154_L	0.547	0.11
71_Y	124_Y	0.545	0.11
111_I	143_N	0.542	0.11
153_L	183_S	0.540	0.11
83_S	98_D	0.536	0.11
31_K	160_R	0.533	0.10
100_R	160_R	0.531	0.10
19_G	160_R	0.529	0.10
105_P	191_Y	0.528	0.10
161_D	193_D	0.527	0.10
89_S	202_S	0.524	0.10
43_D	63_D	0.520	0.10
7_K	19_G	0.520	0.10
113_D	146_N	0.519	0.10
1_M	58_S	0.519	0.10
12_L	40_E	0.519	0.10
102_E	117_T	0.515	0.10
111_I	152_D	0.514	0.10
106_K	186_E	0.508	0.10
66_L	118_L	0.506	0.10
87_F	150_G	0.504	0.10
96_E	193_D	0.504	0.10
17_T	200_W	0.503	0.10
82_Q	141_I	0.502	0.10
169_W	199_N	0.502	0.10
2_K	166_D	0.502	0.10
4_W	200_W	0.501	0.10
95_I	163_P	0.500	0.10
95_I	114_Y	0.500	0.10

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
2wgoA	1	0.3744	9.3	0.972	Contact Map
1jqkA	3	0.3498	6.8	0.974	Contact Map
4pj0U	1	0.4138	6.5	0.974	Contact Map
1gnlA	1	0.3005	5.7	0.975	Contact Map
1m55A	1	0.532	5.1	0.975	Contact Map
1gntA	1	0.2956	4.4	0.976	Contact Map
3rvyA	3	0.1576	4.3	0.976	Contact Map
3layA	5	0.335	3.8	0.977	Contact Map
4udxX	2	0.3695	3.5	0.977	Contact Map
2lk9A	1	0.1182	3	0.978	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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