PcfJ - PFAM28P - GREMLIN Contacts

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PcfJ - PcfJ-like protein

PFAM:	PF14284	Sequences: TWRDYLDMLEKLGKDLHNPKYLCPKDLKKAHDRLVKKYNAKKEKERAEEIKKKAKEDEKRFKELKKKYEFEDGGYIIRVPKSVEELIEEGKALHHCVGSNEYYDRVAKGESLILFLRKKDKPDEPFYTIEVSLDGKVVQCRGKCNKNPEYHEEIIKFVNKWAKLIRKRM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (162)
Sequences:	2684 (2182)
Seq/√Len:	171.4
META:	0.89

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
141_R	145_N	3.116	1.00
90_G	98_G	2.854	1.00
94_H	144_C	2.743	1.00
121_K	124_E	2.578	1.00
80_P	115_F	2.578	1.00
28_K	32_D	2.526	1.00
97_V	128_T	2.252	1.00
116_L	129_I	2.213	1.00
30_A	33_R	2.146	1.00
97_V	113_I	2.018	1.00
86_L	103_Y	1.986	1.00
92_A	125_P	1.983	1.00
130_E	139_Q	1.954	1.00
104_D	108_K	1.941	1.00
80_P	86_L	1.939	1.00
95_H	128_T	1.937	1.00
78_R	85_E	1.927	1.00
86_L	113_I	1.885	1.00
8_M	35_V	1.871	1.00
76_I	122_P	1.861	1.00
75_Y	126_F	1.859	1.00
94_H	143_K	1.773	1.00
26_D	29_K	1.712	1.00
45_E	49_E	1.699	1.00
111_S	130_E	1.667	1.00
72_D	160_K	1.646	1.00
41_K	45_E	1.629	1.00
93_L	143_K	1.625	1.00
105_R	110_E	1.598	1.00
44_K	48_E	1.546	1.00
81_K	85_E	1.544	1.00
8_M	32_D	1.533	1.00
89_E	128_T	1.506	1.00
12_L	38_Y	1.502	1.00
118_K	126_F	1.497	1.00
39_N	42_K	1.490	1.00
155_I	159_N	1.468	1.00
90_G	97_V	1.468	1.00
89_E	117_R	1.463	1.00
88_E	92_A	1.449	1.00
89_E	115_F	1.446	1.00
35_V	39_N	1.432	1.00
47_A	50_I	1.430	1.00
11_K	38_Y	1.427	1.00
76_I	119_K	1.425	1.00
8_M	34_L	1.395	1.00
46_R	49_E	1.378	1.00
142_G	146_K	1.377	1.00
89_E	95_H	1.371	1.00
84_E	88_E	1.367	1.00
78_R	81_K	1.352	1.00
39_N	91_K	1.342	1.00
77_I	114_L	1.326	1.00
74_G	119_K	1.308	1.00
38_Y	42_K	1.298	1.00
71_E	119_K	1.281	1.00
43_E	46_R	1.276	1.00
75_Y	116_L	1.260	1.00
48_E	52_K	1.247	1.00
143_K	146_K	1.224	1.00
118_K	121_K	1.208	1.00
161_W	165_I	1.208	1.00
32_D	35_V	1.205	1.00
131_V	162_A	1.194	1.00
8_M	11_K	1.191	1.00
89_E	97_V	1.191	1.00
129_I	140_C	1.180	1.00
5_Y	9_L	1.180	1.00
11_K	42_K	1.174	1.00
4_D	31_H	1.158	1.00
8_M	12_L	1.149	1.00
132_S	138_V	1.147	1.00
5_Y	30_A	1.136	1.00
9_L	21_Y	1.135	1.00
93_L	125_P	1.114	1.00
30_A	34_L	1.103	1.00
159_N	162_A	1.100	1.00
19_P	22_L	1.095	1.00
95_H	142_G	1.095	1.00
79_V	114_L	1.077	1.00
148_P	151_H	1.075	1.00
95_H	125_P	1.063	1.00
58_E	62_K	1.048	0.99
142_G	148_P	1.046	0.99
36_K	39_N	1.042	0.99
50_I	54_A	1.022	0.99
46_R	50_I	1.022	0.99
83_V	103_Y	1.011	0.99
87_I	98_G	0.998	0.99
106_V	112_L	0.996	0.99
8_M	38_Y	0.991	0.99
45_E	48_E	0.989	0.99
90_G	95_H	0.988	0.99
80_P	106_V	0.986	0.99
129_I	158_V	0.983	0.99
5_Y	34_L	0.978	0.99
127_Y	154_I	0.975	0.99
82_S	85_E	0.972	0.99
15_D	18_N	0.970	0.99
12_L	34_L	0.950	0.99
29_K	33_R	0.945	0.99
34_L	37_K	0.945	0.99
140_C	158_V	0.944	0.99
74_G	153_E	0.941	0.99
78_R	115_F	0.931	0.99
131_V	161_W	0.928	0.99
130_E	138_V	0.925	0.99
141_R	147_N	0.923	0.99
18_N	21_Y	0.922	0.99
9_L	14_K	0.915	0.99
2_W	27_L	0.914	0.99
11_K	41_K	0.914	0.99
116_L	127_Y	0.911	0.99
7_D	11_K	0.910	0.99
70_F	157_F	0.898	0.98
53_K	56_E	0.898	0.98
42_K	46_R	0.887	0.98
24_P	30_A	0.877	0.98
105_R	111_S	0.858	0.98
12_L	41_K	0.855	0.98
127_Y	140_C	0.838	0.97
74_G	118_K	0.832	0.97
77_I	157_F	0.827	0.97
48_E	51_K	0.820	0.97
86_L	106_V	0.817	0.97
118_K	123_D	0.815	0.97
38_Y	41_K	0.814	0.97
127_Y	142_G	0.804	0.97
33_R	37_K	0.802	0.97
86_L	93_L	0.791	0.96
87_I	91_K	0.788	0.96
58_E	61_F	0.785	0.96
80_P	85_E	0.779	0.96
114_L	131_V	0.766	0.96
116_L	154_I	0.762	0.96
157_F	161_W	0.762	0.96
70_F	77_I	0.758	0.95
85_E	88_E	0.757	0.95
156_K	160_K	0.754	0.95
105_R	130_E	0.754	0.95
126_F	154_I	0.751	0.95
117_R	122_P	0.750	0.95
14_K	37_K	0.745	0.95
141_R	146_K	0.743	0.95
57_D	61_F	0.742	0.95
93_L	144_C	0.742	0.95
47_A	51_K	0.738	0.95
95_H	141_R	0.727	0.94
96_C	102_Y	0.727	0.94
71_E	76_I	0.723	0.94
152_E	156_K	0.718	0.94
49_E	52_K	0.717	0.94
89_E	93_L	0.710	0.94
14_K	34_L	0.709	0.94
50_I	53_K	0.704	0.93
61_F	64_L	0.698	0.93
150_Y	153_E	0.696	0.93
156_K	159_N	0.693	0.93
158_V	162_A	0.689	0.93
60_R	64_L	0.682	0.92
127_Y	151_H	0.679	0.92
41_K	44_K	0.678	0.92
148_P	158_V	0.675	0.92
129_I	161_W	0.670	0.91
31_H	35_V	0.670	0.91
7_D	10_E	0.669	0.91
6_L	10_E	0.669	0.91
51_K	55_K	0.668	0.91
132_S	135_G	0.656	0.91
62_K	84_E	0.654	0.90
79_V	106_V	0.654	0.90
4_D	8_M	0.653	0.90
65_K	81_K	0.646	0.90
10_E	13_G	0.643	0.90
39_N	43_E	0.640	0.90
110_E	134_D	0.639	0.89
129_I	137_V	0.634	0.89
152_E	155_I	0.634	0.89
72_D	75_Y	0.634	0.89
2_W	16_L	0.630	0.89
106_V	113_I	0.630	0.89
103_Y	106_V	0.630	0.89
80_P	93_L	0.628	0.89
43_E	47_A	0.628	0.89
151_H	154_I	0.628	0.89
8_M	27_L	0.626	0.88
117_R	128_T	0.620	0.88
60_R	63_E	0.618	0.88
78_R	117_R	0.618	0.88
86_L	116_L	0.616	0.88
12_L	37_K	0.608	0.87
77_I	116_L	0.606	0.87
76_I	79_V	0.605	0.87
116_L	157_F	0.605	0.87
151_H	155_I	0.602	0.87
34_L	38_Y	0.600	0.86
49_E	53_K	0.595	0.86
155_I	158_V	0.594	0.86
115_F	122_P	0.591	0.86
83_V	86_L	0.590	0.85
111_S	138_V	0.590	0.85
88_E	125_P	0.589	0.85
140_C	148_P	0.583	0.85
127_Y	141_R	0.580	0.84
127_Y	148_P	0.580	0.84
110_E	132_S	0.579	0.84
138_V	141_R	0.578	0.84
6_L	16_L	0.575	0.84
43_E	87_I	0.574	0.84
154_I	161_W	0.565	0.83
132_S	136_K	0.556	0.82
27_L	30_A	0.555	0.82
115_F	128_T	0.552	0.81
140_C	154_I	0.545	0.81
136_K	162_A	0.539	0.80
26_D	30_A	0.539	0.80
72_D	157_F	0.538	0.80
14_K	21_Y	0.536	0.80
37_K	40_A	0.534	0.79
20_K	25_K	0.532	0.79
106_V	111_S	0.532	0.79
80_P	113_I	0.531	0.79
46_R	104_D	0.530	0.79
161_W	164_L	0.527	0.78
112_L	133_L	0.524	0.78
69_E	76_I	0.524	0.78
131_V	136_K	0.523	0.78
9_L	16_L	0.522	0.78
20_K	94_H	0.520	0.77
42_K	45_E	0.519	0.77
38_Y	45_E	0.517	0.77
57_D	60_R	0.516	0.77
127_Y	146_K	0.515	0.77
98_G	103_Y	0.515	0.77
95_H	145_N	0.514	0.77
9_L	15_D	0.514	0.77
40_A	43_E	0.509	0.76
142_G	154_I	0.509	0.76
53_K	112_L	0.508	0.76
69_E	79_V	0.505	0.75
14_K	18_N	0.505	0.75
148_P	152_E	0.503	0.75
2_W	79_V	0.500	0.75

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
3s1sA	1	0.3964	11.8	0.929	Contact Map
3doaA	1	0.4556	6.5	0.937	Contact Map
4ys0A	1	0.3254	4.6	0.941	Contact Map
2kw6A	2	0.3195	4.1	0.942	Contact Map
2yggA	1	0.1598	2.7	0.948	Contact Map
2m1lA	2	0.284	2.6	0.948	Contact Map
3ci9A	5	0.1302	2.6	0.948	Contact Map
2jrbA	1	0.3254	2.1	0.95	Contact Map
2qfaB	1	0.1302	1.9	0.951	Contact Map
4nkjA	3	0.2604	1.9	0.952	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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