PcfK - PFAM28P - GREMLIN Contacts

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PcfK - PcfK-like protein

PFAM:	PF14058	Sequences: KTTENFKETIKEYLDERAEEDELFAEKYAKPNKNIDDCITYILNEVQKQAKSGCNGFTDDEVYGWAVHYYDEDDIEVGKPINCKVVVNHTVELTEEEKAEARKKAIKKYQEEELAKLKKKKKKPKKKKKEEEGQLSLFDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (134)
Sequences:	1168 (897)
Seq/√Len:	77.5
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_K	15_D	3.939	1.00
7_K	36_D	2.876	1.00
27_K	30_K	2.853	1.00
15_D	28_Y	2.592	1.00
30_K	73_D	2.561	1.00
45_E	65_W	2.548	1.00
45_E	48_K	2.431	1.00
57_F	65_W	2.339	1.00
27_K	71_D	2.312	1.00
68_H	72_E	2.245	1.00
100_E	104_K	2.161	1.00
34_N	37_D	2.092	1.00
16_E	19_E	2.081	1.00
68_H	71_D	2.080	1.00
38_C	70_Y	2.050	1.00
46_V	65_W	2.031	1.00
42_I	66_A	1.972	1.00
11_K	28_Y	1.971	1.00
46_V	57_F	1.867	1.00
17_R	67_V	1.857	1.00
25_A	29_A	1.812	1.00
113_E	116_K	1.792	1.00
72_E	75_I	1.768	1.00
57_F	62_V	1.600	1.00
16_E	20_E	1.590	1.00
38_C	66_A	1.587	1.00
58_T	62_V	1.558	0.99
34_N	69_Y	1.553	0.99
67_V	71_D	1.492	0.99
17_R	20_E	1.477	0.99
64_G	68_H	1.470	0.99
76_E	79_K	1.458	0.99
37_D	40_T	1.415	0.99
38_C	42_I	1.351	0.98
113_E	117_L	1.310	0.98
40_T	44_N	1.287	0.98
24_F	28_Y	1.286	0.98
114_L	118_K	1.279	0.98
26_E	29_A	1.262	0.98
6_F	56_G	1.245	0.97
85_V	88_N	1.237	0.97
61_E	65_W	1.233	0.97
27_K	73_D	1.226	0.97
52_S	55_N	1.222	0.97
44_N	78_G	1.214	0.97
95_E	98_K	1.210	0.97
103_K	107_K	1.202	0.97
52_S	57_F	1.189	0.96
22_E	26_E	1.184	0.96
58_T	61_E	1.179	0.96
35_I	70_Y	1.171	0.96
12_E	16_E	1.162	0.96
33_K	69_Y	1.159	0.96
17_R	71_D	1.128	0.95
101_A	105_A	1.127	0.95
40_T	78_G	1.116	0.95
46_V	52_S	1.105	0.95
13_Y	17_R	1.101	0.94
104_K	108_K	1.101	0.94
8_E	11_K	1.095	0.94
12_E	15_D	1.086	0.94
119_K	122_K	1.075	0.94
33_K	38_C	1.068	0.94
94_T	97_E	1.068	0.94
114_L	117_L	1.061	0.93
107_K	111_E	1.058	0.93
106_I	109_Y	1.055	0.93
7_K	39_I	1.039	0.93
32_N	73_D	1.037	0.93
93_L	97_E	1.032	0.92
56_G	88_N	1.032	0.92
54_C	57_F	1.022	0.92
37_D	44_N	1.021	0.92
109_Y	114_L	1.008	0.91
8_E	12_E	0.987	0.91
111_E	114_L	0.985	0.90
5_N	8_E	0.981	0.90
112_E	117_L	0.981	0.90
115_A	118_K	0.974	0.90
109_Y	113_E	0.972	0.90
122_K	125_K	0.964	0.90
32_N	74_D	0.948	0.89
2_T	5_N	0.944	0.89
106_I	113_E	0.938	0.88
45_E	68_H	0.937	0.88
109_Y	118_K	0.934	0.88
131_E	135_L	0.933	0.88
102_R	110_Q	0.901	0.86
9_T	63_Y	0.900	0.86
59_D	63_Y	0.899	0.86
94_T	105_A	0.884	0.85
112_E	116_K	0.884	0.85
17_R	23_L	0.881	0.85
4_E	8_E	0.879	0.85
133_G	136_S	0.874	0.84
95_E	99_A	0.869	0.84
4_E	7_K	0.864	0.84
23_L	27_K	0.861	0.83
110_Q	114_L	0.861	0.83
110_Q	120_K	0.860	0.83
100_E	105_A	0.844	0.82
101_A	106_I	0.836	0.82
37_D	77_V	0.834	0.81
113_E	118_K	0.830	0.81
37_D	78_G	0.812	0.80
101_A	104_K	0.787	0.78
105_A	112_E	0.765	0.76
40_T	77_V	0.763	0.75
84_K	87_V	0.753	0.74
71_D	75_I	0.751	0.74
111_E	115_A	0.751	0.74
112_E	115_A	0.743	0.73
106_I	117_L	0.731	0.72
64_G	71_D	0.727	0.72
27_K	67_V	0.723	0.71
129_K	132_E	0.722	0.71
63_Y	66_A	0.721	0.71
93_L	105_A	0.718	0.71
10_I	137_L	0.715	0.71
126_K	129_K	0.709	0.70
18_A	28_Y	0.699	0.69
127_K	135_L	0.699	0.69
58_T	65_W	0.699	0.69
93_L	101_A	0.697	0.69
100_E	103_K	0.696	0.68
81_I	84_K	0.696	0.68
40_T	53_G	0.695	0.68
127_K	130_E	0.693	0.68
118_K	121_K	0.689	0.68
132_E	135_L	0.688	0.68
110_Q	117_L	0.678	0.66
24_F	38_C	0.676	0.66
95_E	105_A	0.669	0.65
115_A	119_K	0.661	0.64
64_G	72_E	0.656	0.64
103_K	106_I	0.649	0.63
99_A	111_E	0.648	0.63
104_K	107_K	0.643	0.62
107_K	110_Q	0.641	0.62
110_Q	115_A	0.629	0.61
106_I	110_Q	0.628	0.61
99_A	115_A	0.620	0.60
57_F	61_E	0.618	0.59
38_C	69_Y	0.618	0.59
18_A	24_F	0.617	0.59
109_Y	121_K	0.616	0.59
5_N	58_T	0.614	0.59
91_V	95_E	0.612	0.59
103_K	120_K	0.612	0.59
44_N	47_Q	0.610	0.58
70_Y	73_D	0.603	0.57
46_V	62_V	0.600	0.57
108_K	111_E	0.599	0.57
13_Y	67_V	0.598	0.57
97_E	109_Y	0.597	0.57
32_N	37_D	0.595	0.56
13_Y	41_Y	0.595	0.56
101_A	109_Y	0.591	0.56
47_Q	59_D	0.588	0.56
102_R	107_K	0.581	0.55
108_K	114_L	0.579	0.54
98_K	109_Y	0.579	0.54
3_T	6_F	0.576	0.54
130_E	135_L	0.573	0.54
17_R	27_K	0.562	0.52
126_K	133_G	0.555	0.51
30_K	68_H	0.554	0.51
105_A	109_Y	0.551	0.51
38_C	75_I	0.550	0.51
15_D	25_A	0.544	0.50
117_L	121_K	0.542	0.50
25_A	38_C	0.539	0.49
91_V	97_E	0.538	0.49
46_V	86_V	0.537	0.49
46_V	61_E	0.535	0.49
80_P	99_A	0.535	0.49
6_F	39_I	0.534	0.49
6_F	14_L	0.534	0.49
99_A	102_R	0.532	0.48
84_K	130_E	0.532	0.48
129_K	133_G	0.530	0.48
131_E	134_Q	0.528	0.48
102_R	106_I	0.525	0.48
12_E	22_E	0.524	0.47
106_I	118_K	0.523	0.47
97_E	105_A	0.522	0.47
94_T	102_R	0.521	0.47
80_P	83_C	0.521	0.47
36_D	39_I	0.519	0.47
7_K	35_I	0.519	0.47
30_K	34_N	0.517	0.47
114_L	119_K	0.512	0.46
43_L	62_V	0.511	0.46
27_K	32_N	0.510	0.46
109_Y	117_L	0.509	0.46
5_N	12_E	0.504	0.45
86_V	90_T	0.503	0.45
9_T	88_N	0.502	0.45
93_L	100_E	0.501	0.44
18_A	29_A	0.500	0.44
91_V	104_K	0.500	0.44

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
4x8qA	1	0.3714	10	0.924	Contact Map
3l9tA	1	0.3643	8.7	0.927	Contact Map
3jxyA	1	0.3929	8.1	0.927	Contact Map
3zljC	2	0	5.6	0.933	Contact Map
4f9kA	2	0.3857	4.6	0.935	Contact Map
2kygA	2	0.3571	4.6	0.935	Contact Map
3al0B	1	0.5	4.3	0.936	Contact Map
2od6A	2	0.3071	3.2	0.94	Contact Map
3h0lB	1	0.1071	3.2	0.94	Contact Map
1v9dA	3	0.6929	3.2	0.94	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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