PCF - BACSU - GREMLIN Contacts

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PCF - Positive control factor

UniProt:	P39784	Sequences: MQDLLFEYKRTLKQTRIQYKPLAEADESVLSAEELKDKKIIRNMITDLEYVTEWLEKGRQPGIRRAIDRRDVYQRLMIKDPRIIESFSSAMMFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQRQQEEMNRSLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	169 (151)
Sequences:	125 (103)
Seq/√Len:	8.4

BACSU - PCF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_V	55_L	4.236	0.98
144_S	148_T	3.507	0.95
125_H	135_I	3.446	0.94
132_Y	143_K	2.958	0.88
131_S	143_K	2.815	0.85
5_L	52_T	2.737	0.84
126_K	154_S	2.702	0.83
71_D	76_L	2.589	0.80
51_V	145_T	2.513	0.78
67_I	70_R	2.509	0.78
120_E	138_L	2.369	0.73
71_D	74_Q	2.359	0.73
117_R	139_L	2.153	0.66
19_Y	55_L	2.091	0.63
158_Q	161_Q	1.962	0.58
124_L	130_F	1.853	0.54
44_M	47_D	1.839	0.53
74_Q	107_I	1.777	0.50
115_T	121_M	1.769	0.50
115_T	148_T	1.739	0.49
18_Q	41_I	1.702	0.47
12_L	49_E	1.686	0.47
52_T	131_S	1.684	0.46
11_T	15_T	1.668	0.46
142_K	145_T	1.653	0.45
37_D	60_Q	1.650	0.45
64_R	69_R	1.638	0.45
129_C	141_V	1.629	0.44
104_R	116_D	1.611	0.43
148_T	151_K	1.537	0.40
11_T	157_M	1.521	0.40
19_Y	150_I	1.506	0.39
102_E	109_E	1.465	0.38
11_T	48_L	1.465	0.38
50_Y	54_W	1.450	0.37
118_E	156_K	1.441	0.37
40_I	124_L	1.384	0.34
111_L	120_E	1.359	0.33
68_D	85_E	1.353	0.33
131_S	147_Q	1.329	0.32
128_E	139_L	1.306	0.31
4_L	8_Y	1.305	0.31
82_R	85_E	1.297	0.31
115_T	149_T	1.260	0.30
15_T	48_L	1.228	0.29
119_K	127_V	1.191	0.27
111_L	114_L	1.184	0.27
63_I	142_K	1.182	0.27
141_V	146_V	1.174	0.27
136_A	161_Q	1.173	0.27
147_Q	153_A	1.166	0.27
153_A	156_K	1.161	0.26
84_I	87_F	1.150	0.26
146_V	153_A	1.123	0.25
18_Q	161_Q	1.121	0.25
7_E	99_V	1.114	0.25
63_I	101_E	1.114	0.25
55_L	59_R	1.111	0.25
121_M	124_L	1.110	0.25
100_S	142_K	1.089	0.24
65_R	70_R	1.084	0.24
13_K	117_R	1.080	0.24
3_D	6_F	1.078	0.24
67_I	120_E	1.074	0.24
13_K	41_I	1.073	0.24
6_F	119_K	1.066	0.24
42_R	47_D	1.065	0.23
12_L	39_K	1.060	0.23
125_H	147_Q	1.048	0.23
59_R	73_Y	1.035	0.23
54_W	73_Y	1.032	0.22
9_K	49_E	1.031	0.22
69_R	110_A	1.016	0.22
16_R	19_Y	1.011	0.22
81_P	110_A	1.007	0.22
103_D	106_R	0.999	0.22
132_Y	150_I	0.982	0.21
84_I	108_R	0.977	0.21
71_D	75_R	0.973	0.21
65_R	71_D	0.968	0.21
144_S	151_K	0.967	0.21
91_M	134_R	0.962	0.21
69_R	81_P	0.954	0.20
16_R	37_D	0.951	0.20
41_I	123_L	0.938	0.20
13_K	55_L	0.929	0.20
72_V	143_K	0.925	0.20
70_R	74_Q	0.918	0.19
82_R	87_F	0.917	0.19
70_R	75_R	0.917	0.19
85_E	120_E	0.912	0.19
9_K	77_M	0.906	0.19
83_I	107_I	0.895	0.19
95_P	98_Q	0.895	0.19
42_R	103_D	0.893	0.19
96_D	150_I	0.892	0.19
123_L	142_K	0.887	0.19
132_Y	147_Q	0.876	0.18
107_I	113_L	0.869	0.18
68_D	125_H	0.861	0.18
42_R	63_I	0.860	0.18
113_L	160_Q	0.859	0.18
141_V	145_T	0.858	0.18
97_G	141_V	0.855	0.18
72_V	76_L	0.853	0.18
113_L	159_R	0.845	0.17
55_L	93_F	0.844	0.17
62_G	69_R	0.839	0.17
34_E	50_Y	0.836	0.17
2_Q	101_E	0.827	0.17
119_K	157_M	0.827	0.17
4_L	7_E	0.826	0.17
53_E	62_G	0.822	0.17
134_R	157_M	0.820	0.17
14_Q	144_S	0.812	0.17
67_I	74_Q	0.808	0.17
7_E	90_A	0.807	0.17
59_R	68_D	0.806	0.17
47_D	73_Y	0.804	0.17
20_K	37_D	0.797	0.16
149_T	159_R	0.795	0.16
9_K	48_L	0.790	0.16
44_M	66_A	0.789	0.16
83_I	150_I	0.789	0.16
58_G	121_M	0.783	0.16
19_Y	39_K	0.780	0.16
45_I	49_E	0.779	0.16
33_E	55_L	0.776	0.16
39_K	157_M	0.764	0.16
9_K	56_E	0.762	0.16
104_R	110_A	0.758	0.15
59_R	66_A	0.756	0.15
68_D	73_Y	0.754	0.15
126_K	147_Q	0.751	0.15
4_L	61_P	0.743	0.15
55_L	154_S	0.731	0.15
150_I	153_A	0.730	0.15
78_I	132_Y	0.727	0.15
54_W	59_R	0.725	0.15
143_K	147_Q	0.724	0.15
37_D	40_I	0.712	0.14
39_K	130_F	0.707	0.14
68_D	76_L	0.706	0.14
51_V	144_S	0.705	0.14
5_L	21_P	0.703	0.14
133_E	145_T	0.696	0.14
12_L	121_M	0.696	0.14
65_R	69_R	0.693	0.14
74_Q	138_L	0.693	0.14
53_E	110_A	0.687	0.14
15_T	41_I	0.686	0.14
55_L	157_M	0.686	0.14
10_R	46_T	0.684	0.14
121_M	153_A	0.682	0.14
66_A	85_E	0.677	0.14
147_Q	151_K	0.672	0.14
79_K	131_S	0.670	0.14
52_T	113_L	0.655	0.13
102_E	112_A	0.655	0.13
19_Y	111_L	0.654	0.13
63_I	141_V	0.647	0.13
66_A	135_I	0.641	0.13
13_K	43_N	0.638	0.13
107_I	133_E	0.636	0.13
81_P	85_E	0.631	0.13
115_T	138_L	0.627	0.13
89_S	145_T	0.626	0.13
18_Q	37_D	0.624	0.13
146_V	150_I	0.618	0.13
59_R	145_T	0.618	0.13
100_S	110_A	0.616	0.13
12_L	45_I	0.613	0.13
43_N	64_R	0.609	0.12
86_S	138_L	0.608	0.12
81_P	107_I	0.606	0.12
13_K	49_E	0.601	0.12
20_K	129_C	0.599	0.12
14_Q	20_K	0.594	0.12
58_G	134_R	0.593	0.12
8_Y	152_R	0.593	0.12
52_T	56_E	0.585	0.12
7_E	104_R	0.581	0.12
150_I	158_Q	0.581	0.12
116_D	157_M	0.580	0.12
64_R	122_F	0.577	0.12
33_E	43_N	0.576	0.12
121_M	149_T	0.576	0.12
144_S	147_Q	0.575	0.12
44_M	123_L	0.570	0.12
120_E	130_F	0.570	0.12
76_L	84_I	0.569	0.12
15_T	85_E	0.566	0.12
5_L	73_Y	0.563	0.12
125_H	131_S	0.559	0.12
45_I	54_W	0.554	0.12
12_L	16_R	0.553	0.11
42_R	101_E	0.551	0.11
84_I	88_S	0.551	0.11
18_Q	150_I	0.548	0.11
4_L	131_S	0.547	0.11
86_S	90_A	0.545	0.11
140_G	149_T	0.545	0.11
59_R	150_I	0.543	0.11
101_E	158_Q	0.542	0.11
57_K	64_R	0.541	0.11
48_L	87_F	0.539	0.11
94_E	155_L	0.539	0.11
12_L	113_L	0.538	0.11
87_F	114_L	0.537	0.11
60_Q	68_D	0.536	0.11
121_M	139_L	0.532	0.11
19_Y	38_K	0.532	0.11
118_E	153_A	0.530	0.11
115_T	119_K	0.527	0.11
74_Q	85_E	0.524	0.11
95_P	158_Q	0.520	0.11
17_I	99_V	0.517	0.11
43_N	47_D	0.516	0.11
106_R	110_A	0.516	0.11
65_R	143_K	0.515	0.11
2_Q	37_D	0.510	0.11
114_L	120_E	0.508	0.11
99_V	145_T	0.506	0.11
68_D	82_R	0.505	0.11
62_G	68_D	0.503	0.11
109_E	157_M	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
1xsvA	2	0.432	98.9	0.805	Contact Map
3hugA	3	0.4734	98.9	0.809	Contact Map
1ku3A	1	0.3373	98.8	0.811	Contact Map
2q1zA	1	0.858	98.8	0.811	Contact Map
2lfwA	1	0.858	98.8	0.813	Contact Map
4cxfA	1	0.787	98.8	0.814	Contact Map
4nqwA	1	0.7633	98.8	0.814	Contact Map
3t72q	1	0.432	98.8	0.814	Contact Map
2rnjA	1	0.355	98.8	0.815	Contact Map
1or7A	2	0.8935	98.8	0.815	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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