DUF2313 - PFAM28P - GREMLIN Contacts

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DUF2313 - Uncharacterized protein conserved in bacteria (DUF2313)

PFAM:	PF10076	Sequences: QALLALLPPGYAWPRDPSELKALLEALAPELDRLDARADDLLDEAFPRTATELLPDWERVLGLPDDASKTLEERRARVLAKLRGRGGQTRAYFIELAAALGYGTITITEFRPFRAGRSRADPLEDWRYTWTVNFPTTVTRFRAGTSGAGENLRDWGNEVLECLIERIKPAHTIVIFAYT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	179 (162)
Sequences:	2955 (2419)
Seq/√Len:	190.0
META:	0.703

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_E	74_R	3.536	1.00
61_L	78_V	3.270	1.00
91_A	95_E	2.931	1.00
37_R	52_E	2.754	1.00
61_L	82_L	2.745	1.00
4_L	21_K	2.724	1.00
44_E	51_T	2.561	1.00
165_E	168_K	2.508	1.00
115_A	120_A	2.502	1.00
110_F	131_T	2.389	1.00
164_I	174_V	2.374	1.00
108_T	133_N	2.340	1.00
54_L	71_L	2.192	1.00
48_R	79_L	2.155	1.00
110_F	127_R	2.011	1.00
115_A	148_A	2.004	1.00
56_D	59_R	1.971	1.00
70_T	73_E	1.935	1.00
28_A	32_D	1.934	1.00
30_E	33_R	1.931	1.00
57_W	82_L	1.892	1.00
4_L	24_L	1.884	1.00
115_A	119_R	1.829	1.00
98_A	104_T	1.777	1.00
106_T	133_N	1.636	1.00
120_A	148_A	1.609	1.00
66_D	69_K	1.580	1.00
56_D	60_V	1.564	1.00
130_W	168_K	1.561	1.00
50_A	53_L	1.552	1.00
7_L	24_L	1.549	1.00
3_L	24_L	1.544	1.00
69_K	77_R	1.540	1.00
72_E	75_R	1.532	1.00
144_G	149_G	1.501	1.00
40_D	52_E	1.494	1.00
10_G	13_W	1.491	1.00
90_R	94_I	1.462	1.00
113_F	118_S	1.445	1.00
96_L	167_I	1.409	1.00
116_G	120_A	1.398	1.00
14_P	19_E	1.385	1.00
22_A	25_E	1.378	1.00
69_K	73_E	1.371	1.00
90_R	109_E	1.362	1.00
108_T	131_T	1.350	1.00
117_R	120_A	1.345	1.00
97_A	105_I	1.331	1.00
50_A	54_L	1.279	1.00
161_E	178_Y	1.268	1.00
54_L	75_R	1.262	1.00
3_L	31_L	1.255	1.00
94_I	106_T	1.244	1.00
113_F	117_R	1.236	1.00
148_A	152_L	1.232	1.00
116_G	144_G	1.200	1.00
116_G	149_G	1.199	1.00
105_I	132_V	1.189	1.00
64_P	162_C	1.184	1.00
168_K	172_T	1.179	1.00
44_E	52_E	1.172	1.00
130_W	174_V	1.144	1.00
161_E	165_E	1.143	1.00
161_E	176_F	1.141	1.00
115_A	123_L	1.139	1.00
9_P	13_W	1.128	1.00
106_T	135_P	1.110	1.00
110_F	129_T	1.095	1.00
27_L	31_L	1.095	1.00
40_D	51_T	1.083	1.00
7_L	20_L	1.075	1.00
130_W	172_T	1.072	1.00
93_F	130_W	1.070	1.00
144_G	148_A	1.061	1.00
84_G	92_Y	1.059	1.00
40_D	44_E	1.058	1.00
94_I	98_A	1.048	1.00
113_F	116_G	1.033	1.00
131_T	177_A	1.027	1.00
114_R	117_R	1.023	1.00
119_R	144_G	1.015	1.00
114_R	119_R	1.014	1.00
113_F	123_L	0.988	0.99
78_V	82_L	0.987	0.99
132_V	164_I	0.983	0.99
37_R	40_D	0.980	0.99
97_A	160_L	0.972	0.99
119_R	122_P	0.969	0.99
83_R	99_A	0.963	0.99
151_N	154_D	0.960	0.99
120_A	123_L	0.945	0.99
80_A	99_A	0.941	0.99
47_P	82_L	0.937	0.99
22_A	26_A	0.934	0.99
165_E	176_F	0.930	0.99
79_L	83_R	0.912	0.99
32_D	36_A	0.909	0.99
65_D	81_K	0.900	0.99
114_R	120_A	0.894	0.99
116_G	119_R	0.889	0.99
72_E	76_A	0.886	0.99
3_L	6_L	0.882	0.99
73_E	77_R	0.876	0.99
90_R	107_I	0.875	0.99
47_P	79_L	0.867	0.99
113_F	121_D	0.864	0.99
65_D	166_R	0.858	0.98
115_A	118_S	0.854	0.98
23_L	27_L	0.853	0.98
39_D	43_D	0.846	0.98
94_I	107_I	0.845	0.98
65_D	162_C	0.834	0.98
91_A	94_I	0.824	0.98
104_T	135_P	0.822	0.98
93_F	167_I	0.818	0.98
9_P	12_A	0.817	0.98
97_A	164_I	0.816	0.98
71_L	78_V	0.812	0.98
115_A	152_L	0.809	0.98
5_A	28_A	0.807	0.98
150_E	153_R	0.806	0.98
24_L	27_L	0.805	0.98
92_Y	96_L	0.802	0.98
98_A	105_I	0.801	0.98
129_T	175_I	0.801	0.98
86_G	92_Y	0.800	0.98
120_A	149_G	0.791	0.97
146_S	150_E	0.783	0.97
105_I	134_F	0.782	0.97
88_Q	92_Y	0.781	0.97
47_P	78_V	0.778	0.97
134_F	160_L	0.777	0.97
119_R	123_L	0.777	0.97
153_R	161_E	0.777	0.97
35_D	39_D	0.777	0.97
114_R	118_S	0.774	0.97
50_A	75_R	0.767	0.97
100_L	163_L	0.766	0.97
25_E	29_P	0.764	0.97
147_G	150_E	0.757	0.97
11_Y	20_L	0.756	0.97
118_S	121_D	0.756	0.97
51_T	75_R	0.754	0.97
14_P	21_K	0.750	0.96
110_F	126_W	0.741	0.96
133_N	177_A	0.740	0.96
46_F	49_T	0.736	0.96
88_Q	93_F	0.731	0.96
75_R	79_L	0.727	0.96
95_E	99_A	0.726	0.96
73_E	76_A	0.725	0.96
19_E	22_A	0.724	0.96
114_R	122_P	0.720	0.95
152_L	161_E	0.716	0.95
12_A	15_R	0.714	0.95
63_L	77_R	0.713	0.95
113_F	119_R	0.707	0.95
30_E	34_L	0.698	0.95
3_L	28_A	0.698	0.95
54_L	78_V	0.697	0.95
2_A	5_A	0.692	0.94
113_F	120_A	0.692	0.94
28_A	31_L	0.686	0.94
168_K	174_V	0.685	0.94
40_D	43_D	0.683	0.94
76_A	80_A	0.683	0.94
111_R	126_W	0.681	0.94
33_R	37_R	0.678	0.94
120_A	145_T	0.674	0.94
93_F	169_P	0.674	0.94
55_P	59_R	0.674	0.94
117_R	121_D	0.673	0.94
129_T	173_I	0.673	0.94
96_L	163_L	0.669	0.93
147_G	151_N	0.667	0.93
162_C	166_R	0.666	0.93
94_I	105_I	0.665	0.93
118_S	122_P	0.664	0.93
146_S	149_G	0.658	0.93
44_E	53_L	0.655	0.93
77_R	80_A	0.652	0.92
126_W	129_T	0.646	0.92
164_I	168_K	0.644	0.92
4_L	15_R	0.643	0.92
107_I	130_W	0.642	0.92
72_E	146_S	0.640	0.92
96_L	99_A	0.638	0.92
44_E	50_A	0.632	0.91
126_W	134_F	0.630	0.91
44_E	57_W	0.611	0.90
116_G	121_D	0.609	0.90
42_L	45_A	0.598	0.89
145_T	149_G	0.597	0.89
109_E	172_T	0.597	0.89
55_P	67_A	0.597	0.89
42_L	46_F	0.595	0.89
130_W	164_I	0.594	0.89
112_P	127_R	0.593	0.88
14_P	20_L	0.593	0.88
12_A	20_L	0.592	0.88
144_G	147_G	0.591	0.88
43_D	49_T	0.589	0.88
32_D	35_D	0.585	0.88
68_S	77_R	0.583	0.88
165_E	174_V	0.578	0.87
92_Y	95_E	0.577	0.87
75_R	78_V	0.569	0.86
81_K	166_R	0.565	0.86
112_P	115_A	0.565	0.86
131_T	175_I	0.560	0.85
163_L	167_I	0.560	0.85
50_A	78_V	0.556	0.85
4_L	28_A	0.551	0.85
111_R	127_R	0.550	0.84
144_G	150_E	0.546	0.84
47_P	50_A	0.543	0.84
11_Y	15_R	0.540	0.83
118_S	125_D	0.539	0.83
159_V	163_L	0.538	0.83
71_L	75_R	0.538	0.83
44_E	75_R	0.531	0.82
48_R	83_R	0.530	0.82
113_F	122_P	0.529	0.82
13_W	21_K	0.527	0.82
89_T	93_F	0.525	0.82
58_E	63_L	0.522	0.81
114_R	127_R	0.520	0.81
60_V	82_L	0.519	0.81
164_I	167_I	0.518	0.81
112_P	159_V	0.516	0.81
114_R	125_D	0.514	0.80
94_I	97_A	0.513	0.80
63_L	66_D	0.510	0.80
4_L	12_A	0.510	0.80
38_A	42_L	0.510	0.80
41_L	52_E	0.506	0.79
117_R	124_E	0.506	0.79
120_A	144_G	0.505	0.79
165_E	170_A	0.502	0.79
84_G	96_L	0.502	0.79
112_P	117_R	0.501	0.79
126_W	153_R	0.500	0.78
117_R	123_L	0.500	0.78

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
2nptA	1	0.324	11.1	0.927	Contact Map
3hzsA	3	0.5475	10.7	0.927	Contact Map
3vmtA	1	0.5531	9.3	0.93	Contact Map
2ycuA	1	0.3799	9.3	0.93	Contact Map
3smaA	2	0.3799	9	0.93	Contact Map
3ab3B	1	0.1844	8.7	0.93	Contact Map
3vlfB	1	0.4022	7.8	0.932	Contact Map
3ujpA	4	0.7374	7.2	0.933	Contact Map
1pq4A	1	0.7654	6.8	0.934	Contact Map
4utoA	1	0.7374	6.6	0.934	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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