DUF2314 - PFAM28P - GREMLIN Contacts

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DUF2314 - Uncharacterized protein conserved in bacteria (DUF2314)

PFAM:	PF10077	Sequences: DPEMNAAIAKARATLPEFWAALAAPKRRIVPGEEGFAVKVPFTDGDGGGEGPEVEHMWLSDVEFDGGRFSGTLANEPRDVKGVKLGDRVTVPEDDISDWMYVDDGKLVGGYTIRVLRKRMPPEERAEFDKAWGLDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (121)
Sequences:	3190 (2490)
Seq/√Len:	226.4
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_H	97_S	4.523	1.00
110_G	113_I	2.742	1.00
59_L	71_G	2.322	1.00
68_R	90_T	2.310	1.00
117_R	129_D	2.224	1.00
42_F	57_M	2.198	1.00
41_P	54_V	2.122	1.00
9_A	13_A	2.064	1.00
3_E	118_K	2.018	1.00
8_I	97_S	1.906	1.00
92_P	95_D	1.867	1.00
70_S	90_T	1.855	1.00
3_E	119_R	1.809	1.00
57_M	73_L	1.774	1.00
42_F	89_V	1.765	1.00
122_P	126_A	1.737	1.00
76_E	85_L	1.697	1.00
19_W	69_F	1.673	1.00
10_K	13_A	1.648	1.00
117_R	125_R	1.562	1.00
19_W	23_A	1.536	1.00
14_T	111_Y	1.480	1.00
10_K	14_T	1.465	1.00
40_V	91_V	1.439	1.00
44_D	82_G	1.437	1.00
22_L	62_V	1.430	1.00
125_R	129_D	1.423	1.00
59_L	89_V	1.415	1.00
72_T	88_R	1.390	1.00
14_T	17_E	1.386	1.00
8_I	112_T	1.385	1.00
21_A	101_Y	1.374	1.00
63_E	70_S	1.373	1.00
100_M	107_L	1.372	1.00
70_S	88_R	1.370	1.00
16_P	93_E	1.347	1.00
115_V	119_R	1.336	1.00
33_E	36_F	1.329	1.00
126_A	130_K	1.323	1.00
60_S	74_A	1.320	1.00
4_M	8_I	1.311	1.00
84_K	87_D	1.288	1.00
107_L	110_G	1.279	1.00
100_M	110_G	1.254	1.00
18_F	36_F	1.250	1.00
23_A	64_F	1.235	1.00
44_D	80_V	1.227	1.00
43_T	54_V	1.216	1.00
2_P	5_N	1.214	1.00
19_W	93_E	1.206	1.00
6_A	9_A	1.196	1.00
5_N	8_I	1.166	1.00
61_D	72_T	1.161	1.00
65_D	70_S	1.151	1.00
7_A	115_V	1.140	1.00
15_L	96_I	1.131	1.00
73_L	83_V	1.125	1.00
1_D	119_R	1.107	1.00
4_M	112_T	1.096	1.00
39_K	75_N	1.076	1.00
15_L	38_V	1.071	1.00
6_A	10_K	1.068	1.00
37_A	74_A	1.066	1.00
126_A	129_D	1.044	1.00
7_A	112_T	1.029	1.00
73_L	89_V	1.019	1.00
44_D	47_G	1.010	1.00
64_F	69_F	0.999	1.00
121_P	124_E	0.989	1.00
25_P	33_E	0.982	1.00
122_P	125_R	0.976	1.00
33_E	103_D	0.974	1.00
3_E	115_V	0.965	1.00
44_D	81_K	0.952	1.00
101_Y	108_V	0.932	1.00
42_F	83_V	0.923	1.00
22_L	36_F	0.915	1.00
15_L	19_W	0.914	0.99
44_D	83_V	0.914	0.99
38_V	71_G	0.909	0.99
80_V	83_V	0.906	0.99
25_P	36_F	0.898	0.99
114_R	118_K	0.896	0.99
8_I	12_R	0.884	0.99
4_M	115_V	0.867	0.99
21_A	26_K	0.863	0.99
5_N	9_A	0.856	0.99
38_V	96_I	0.843	0.99
41_P	95_D	0.837	0.99
10_K	111_Y	0.833	0.99
26_K	32_G	0.827	0.99
127_E	130_K	0.822	0.99
21_A	36_F	0.818	0.99
63_E	88_R	0.814	0.99
39_K	56_H	0.811	0.99
26_K	33_E	0.810	0.99
20_A	24_A	0.805	0.99
25_P	32_G	0.801	0.99
15_L	93_E	0.798	0.99
4_M	97_S	0.798	0.99
59_L	73_L	0.789	0.99
57_M	75_N	0.788	0.99
40_V	95_D	0.781	0.98
123_E	127_E	0.776	0.98
83_V	87_D	0.770	0.98
40_V	59_L	0.765	0.98
17_E	21_A	0.755	0.98
99_W	111_Y	0.754	0.98
69_F	93_E	0.744	0.98
107_L	114_R	0.741	0.98
77_P	80_V	0.738	0.98
103_D	108_V	0.734	0.98
21_A	108_V	0.732	0.98
19_W	22_L	0.723	0.97
40_V	89_V	0.718	0.97
125_R	128_F	0.717	0.97
2_P	6_A	0.711	0.97
22_L	25_P	0.711	0.97
19_W	38_V	0.708	0.97
8_I	56_H	0.703	0.97
19_W	64_F	0.698	0.97
36_F	101_Y	0.696	0.97
17_E	20_A	0.693	0.97
68_R	92_P	0.685	0.96
37_A	60_S	0.685	0.96
18_F	99_W	0.683	0.96
36_F	108_V	0.682	0.96
22_L	61_D	0.678	0.96
74_A	85_L	0.672	0.96
45_G	81_K	0.671	0.96
55_E	75_N	0.670	0.96
42_F	73_L	0.670	0.96
39_K	112_T	0.669	0.96
35_G	101_Y	0.669	0.96
65_D	68_R	0.666	0.96
21_A	33_E	0.665	0.96
16_P	20_A	0.664	0.96
26_K	103_D	0.661	0.96
64_F	67_G	0.655	0.95
57_M	77_P	0.655	0.95
121_P	125_R	0.654	0.95
40_V	96_I	0.649	0.95
44_D	57_M	0.647	0.95
21_A	25_P	0.641	0.95
59_L	91_V	0.635	0.95
124_E	127_E	0.635	0.95
13_A	16_P	0.625	0.94
111_Y	114_R	0.623	0.94
55_E	77_P	0.599	0.93
57_M	79_D	0.592	0.92
41_P	97_S	0.592	0.92
17_E	101_Y	0.591	0.92
15_L	69_F	0.590	0.92
97_S	112_T	0.586	0.92
39_K	58_W	0.576	0.91
40_V	80_V	0.574	0.91
105_G	109_G	0.572	0.91
57_M	80_V	0.557	0.90
37_A	107_L	0.557	0.90
38_V	91_V	0.555	0.90
112_T	115_V	0.550	0.89
4_M	7_A	0.548	0.89
73_L	77_P	0.547	0.89
115_V	118_K	0.544	0.89
76_E	84_K	0.541	0.88
34_E	105_G	0.541	0.88
22_L	64_F	0.537	0.88
25_P	62_V	0.535	0.88
114_R	120_M	0.535	0.88
118_K	125_R	0.535	0.88
44_D	48_G	0.532	0.88
66_G	90_T	0.530	0.87
32_G	36_F	0.527	0.87
64_F	68_R	0.521	0.86
15_L	64_F	0.518	0.86
57_M	81_K	0.516	0.86
55_E	73_L	0.512	0.86
48_G	54_V	0.511	0.85
37_A	100_M	0.507	0.85
12_R	58_W	0.506	0.85
116_L	120_M	0.502	0.84
37_A	102_V	0.500	0.84

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
1c05A	1	0.8676	33.4	0.907	Contact Map
2vxaA	5	0.3015	23	0.914	Contact Map
3bbnD	1	0.8309	22.6	0.914	Contact Map
2ux9A	5	0.3162	21.2	0.915	Contact Map
2yizA	5	0.3088	20	0.916	Contact Map
2cc6A	5	0.3015	18.9	0.918	Contact Map
4tp8D	1	0.8382	16.7	0.919	Contact Map
3onrA	5	0.3382	15.9	0.92	Contact Map
4b2kA	5	0.3015	15.3	0.921	Contact Map
4b2hA	5	0.2868	14.7	0.922	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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